Last release

MarkDown.md

@@ -5,7 +5,7 @@ author: P.Y. Barriat
 description: Markdown and applications
 backgroundImage: url('assets/back.png')
 _backgroundImage: url('assets/garde.png')
-footer: 02/06/2023 | Markdown and applications | PY Barriat
+footer: 14/06/2023 | Markdown and applications | PY Barriat
 _footer: ""
 paginate: true
 _paginate: false
@@ -17,10 +17,10 @@ Markdown and applications<!--fit-->
 
 https://gogs.elic.ucl.ac.be/pbarriat/learning-markdown
 
-![h:280](assets/logo.png)
+![h:250](assets/logo.png)
 
 **Pierre-Yves Barriat**
-ELIC Training Sessions `June 13th, 2023`
+ELIC Training Sessions `June 14th, 2023`
 
 ---
 
@@ -310,14 +310,43 @@ Now you can take a look of the Markdown code of these **current slides** !
 
 # Markdown for a paper ?
 
-https://jaantollander.com/post/scientific-writing-with-markdown/
+## Scientific manuscript for submision
 
-https://curvenote.com/blog/writing-a-scientific-paper-faster-myst-markdown
+```bash
+pandoc -d article.yaml
+```
+
+Here, we use a `yaml` file to write all the pandoc options (passed with `-d`)
+
+## Scientific manuscript
+
+```bash
+pandoc -d article_nice.yaml
+```
+ 
+---
+
+# Conclusion
+
+* You can learn Markdown very quickly
+
+* Markdown is directly human-readable so it's easy to share with people who don't have Markdown processor installed
+
+* Installing a Markdown processor is easy
+
+* Markdown is easily convertible to HTML
+  > best choice for documents to be published both on the web and as printed text
+
+* You can create high-quality scientific documents
+
+---
 
-https://github.com/MartinHeroux/pandoc_article_template
+* Markdown is also good for quick note taking
+  > you can effortlessly apply text formattings to, e.g., highlight parts in your notes or to create formatted lists
 
-https://phd.row1.ca/phd
+* The layout can be controlled by settings within the raw documents or you simply keep the default settings
 
-https://github.com/MartinHeroux/latex-paper-template
+* The design of your document guarantees a consistent and uniform layout 
+  > font types and sizes of text and headings, tables and directories, footnotes, page numbering, line spacing and borders, etc
 
-https://github.com/MartinHeroux/markdown-latex-template
+* The file formats for writing the raw content in both languages (`*.md`, `*.tex`) are designated as **open format**

example/Makefile

@@ -1,103 +0,0 @@
-# References to main files
-TEX_FILE_MASTER     = tex_templates/manuscript.tex
-TEX_FILE_SI         = tex_templates/manuscript-si.tex
-TEX_FILE_PANDOC     = tex_templates/manuscript-pd.tex
-ARTICLE_FILE        = manuscript.md
-TEX_META_FILE       = tex_templates/metadata.tex
-PANDOC_META_FILE    = tex_templates/metadata-pd.yaml
-
-# Programs used
-TEX_ENGINE 	        = xelatex
-TEX                 = latexmk -$(TEX_ENGINE) -interaction=nonstopmode -file-line-error -pdf
-PYTHON 	            = python3
-
-# Paths to templates
-CUSTOM_REFERENCE_PATH   = tex_templates
-TEMPLATE_FILE_HTML      = html_templates/template.html
-TEMPLATE_STYLE_HTML     = html_templates/template.css
-DOCX_REFERENCE_FILE     = docx_templates/template.docx
-TEMPLATE_FILE_LATEX     = tex_templates/manuscript-pd.tex
-CLASS_FILE_LATEX        = tex_templates/pi-article
-PANDOC_SCHOLAR_PATH     = assets/pandoc-scholar
-
-# Options for pandoc-scholar
-PANDOC_READER_OPTIONS   = --data-dir=assets
-PANDOC_READER_OPTIONS  += --defaults=assets/base
-
-PANDOC_LATEX_OPTIONS    = --pdf-engine=$(TEX_ENGINE)
-PANDOC_LATEX_OPTIONS   += --variable=documentclass:$(CLASS_FILE_LATEX)
-PANDOC_LATEX_OPTIONS   += --natbib
-PANDOC_LATEX_OPTIONS   += --citeproc
-
-# PANDOC_HTML_OPTIONS     = --toc --self-contained
-PANDOC_HTML_OPTIONS     = --toc
-PANDOC_EPUB_OPTIONS     = --toc
-
-# Filter for converting chemical formulas
-PANDOC_DOCX_OPTIONS	   := --lua-filter=./assets/pd-chem-filter.lua $(PANDOC_WRITER_OPTIONS)
-
-OUTFILE_PREFIX          = index
-DEFAULT_EXTENSIONS     ?= html doc
-
-include $(PANDOC_SCHOLAR_PATH)/Makefile
-
-# Must be prepended to the options, as has to come before citeproc
-# PANDOC_WRITER_OPTIONS := --filter=pandoc-xnos $(PANDOC_WRITER_OPTIONS)
-PANDOC_WRITER_OPTIONS := --filter=pandoc-crossref $(PANDOC_WRITER_OPTIONS)
-PANDOC_WRITER_OPTIONS += --lua-filter=./assets/pd-image-filter.lua
-PANDOC_WRITER_OPTIONS += --csl=$(CUSTOM_REFERENCE_PATH)/ieee.csl
-
-# Building with latexmk
-.PHONY: build
-build: $(TEX_FILE_SI) $(TEX_FILE_MASTER)
-	$(TEX) $(TEX_FILE_SI)
-	$(TEX) $(TEX_FILE_MASTER)
-
-# Converting all svgs to png using inkscape
-SVGS = $(wildcard figs/*.svg)
-
-.PHONY: svg2fig
-svg2fig: $(SVGS)
-	$(PYTHON) ./scripts/inkscape-convert.py $(SVGS)
-
-# Making a pandoc markdown file
-.PHONY: tex2md
-tex2md:
-	$(PYTHON) ./assets/pd-meta.py --tex $(TEX_META_FILE) --yaml $(PANDOC_META_FILE)
-	pandoc -s $(TEX_FILE_PANDOC) -o $(ARTICLE_FILE) \
-	--from latex --to markdown+smart+grid_tables \
-	--metadata-file $(PANDOC_META_FILE) \
-	--lua-filter=./assets/pd-image-filter.lua \
-	--lua-filter=./assets/pd-chem-filter.lua \
-	--lua-filter=./assets/pd-ref-filter.lua \
-	--default-image-extension=".png" \
-	--verbose --columns=100 \
-	--citeproc
-
-# Making a diff of the manuscript with latexdiff
-.PHONY: diff
-diff:
-	git latexdiff HEAD -- --main $(TEX_FILE_MASTER) \
-	--no-view --latexmk --ignore-makefile \
-	--packages=amsmath,hyperref,siunitx,cleveref,mhchem \
-	--exclude-safecmd=pubSI -o manuscript-diff.pdf --verbose
-
-# Custom make commands for pandoc-scholar
-tex:	$(addprefix $(OUTFILE_PREFIX).,latex)
-pdf:	$(addprefix $(OUTFILE_PREFIX).,pdf)
-docx:	$(addprefix $(OUTFILE_PREFIX).,docx)
-html:	$(addprefix $(OUTFILE_PREFIX).,html)
-epub:	$(addprefix $(OUTFILE_PREFIX).,epub)
-
-# Submission scripts
-.PHONY: submit-condense
-submit-condense:
-	$(PYTHON) ./assets/submit-condense.py
-
-.PHONY: submit-zip
-submit-zip:
-	$(PYTHON) ./assets/submit-zip.py
-
-.PHONY: submit-clean
-submit-clean:
-	$(PYTHON) ./assets/submit-clean.py --dir ./condensed

example/article.yaml

@@ -28,5 +28,6 @@ variables:
 # headers, separated by one space.
 # Example: # Abstract {.unnumbered}
 
-# number-sections: true
-...
+number-sections: true
+
+# etc

example/assets/base.yaml

@@ -1,7 +0,0 @@
-verbosity: INFO
-
-# none, references, or javascript
-email-obfuscation: references
-
-# accept, reject, or all
-track-changes: all

example/assets/bibliography.bib

@@ -0,0 +1,45 @@
+
+@online{macfarlane:pandoc,
+  author = {John MacFarlane},
+  title = {About pandoc},
+  url = {http://johnmacfarlane.net/pandoc/},
+  urldate = {2015-02-03},
+}
+
+@online{macfarlane:pandocreadme,
+  author = {John MacFarlane},
+  title = {Pandoc User’s Guide},
+  url = {http://johnmacfarlane.net/pandoc/README.html},
+  urldate = {2015-02-03},
+}
+
+@online{ wiki:latexerrors,
+  author = {Wikibooks},
+  title = {LaTeX/Errors and Warnings --- Wikibooks The Free Textbook Project},
+  year = 2014,
+  url = {http://en.wikibooks.org/w/index.php?title=LaTeX/Errors_and_Warnings&oldid=2739496},
+  note = {Online; accessed 3-February-2015}
+}
+
+@online{ wiki:lorem,
+  author = {Wikisource},
+  title = {Lorem ipsum --- Wikisource},
+  year = 2013,
+  url = {http://la.wikisource.org/w/index.php?title=Lorem_ipsum&oldid=61677},
+  note = {[Online; accessed 3-februarii-2015]},
+}
+
+@online{wiki:kitten,
+  author  = {Wikimedia Commons, André Karwath},
+  title   = {Six weeks old cat},
+  year    = 2005,
+  urlseen = {2015-02-03},
+  url     = {http://commons.wikimedia.org/w/index.php?title=File:Six_weeks_old_cat_%28aka%29.jpg&oldid=141863103},
+}
+
+@online{ctan:listings,
+  author = {Brooks Moses, Jobst Hoffmann},
+  title = {listings – Typeset source code listings using LaTeX},
+  url = {http://www.ctan.org/pkg/listings},
+  urldate = {2015-02-03},
+}

example/assets/citation.csl

@@ -0,0 +1,161 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+  <info>
+    <title>ACM SIG Proceedings ("et al." for 15+ authors)</title>
+    <id>http://www.zotero.org/styles/acm-sig-proceedings-long-author-list</id>
+    <link href="http://www.zotero.org/styles/acm-sig-proceedings-long-author-list" rel="self"/>
+    <link href="http://www.acm.org/sigs/publications/proceedings-templates" rel="documentation"/>
+    <author>
+      <name>Naeem Esfahani</name>
+      <email>nesfaha2@gmu.edu</email>
+      <uri>http://mason.gmu.edu/~nesfaha2/</uri>
+    </author>
+    <contributor>
+      <name>Chris Horn</name>
+      <email>chris.horn@securedecisions.com</email>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <category field="engineering"/>
+    <updated>2013-08-29T05:27:03+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <macro name="author">
+    <choose>
+      <if type="webpage">
+        <text variable="title" suffix=":"/>
+      </if>
+      <else>
+        <names variable="author">
+          <name name-as-sort-order="all" and="text" sort-separator=", " initialize-with="." delimiter-precedes-last="never" delimiter=", "/>
+          <label form="short" prefix=" " suffix="." strip-periods="true"/>
+          <substitute>
+            <names variable="editor"/>
+            <names variable="translator"/>
+          </substitute>
+        </names>
+      </else>
+    </choose>
+  </macro>
+  <macro name="editor">
+    <names variable="editor">
+      <name initialize-with="." delimiter=", " and="text"/>
+      <label form="short" prefix=", "/>
+    </names>
+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
+    <layout prefix="[" suffix="]" delimiter=", ">
+      <text variable="citation-number"/>
+    </layout>
+  </citation>
+  <bibliography entry-spacing="0" second-field-align="flush" et-al-min="15" et-al-use-first="1">
+    <sort>
+      <key macro="author"/>
+      <key variable="title"/>
+    </sort>
+    <layout suffix=".">
+      <text variable="citation-number" prefix="[" suffix="] "/>
+      <text macro="author" suffix=" "/>
+      <date variable="issued" suffix=". ">
+        <date-part name="year"/>
+      </date>
+      <choose>
+        <if type="paper-conference">
+          <group delimiter=". ">
+            <text variable="title"/>
+            <group delimiter=" ">
+              <text variable="container-title" font-style="italic"/>
+              <group delimiter=", ">
+                <group delimiter=", " prefix="(" suffix=")">
+                  <text variable="publisher-place"/>
+                  <date variable="issued">
+                    <date-part name="month" form="short" suffix=" "/>
+                    <date-part name="year"/>
+                  </date>
+                </group>
+                <text variable="page"/>
+              </group>
+            </group>
+          </group>
+        </if>
+        <else-if type="article-journal">
+          <group delimiter=". ">
+            <text variable="title"/>
+            <text variable="container-title" font-style="italic"/>
+            <group delimiter=", ">
+              <text variable="volume"/>
+              <group delimiter=" ">
+                <text variable="issue"/>
+                <date variable="issued" prefix="(" suffix=")">
+                  <date-part name="month" form="short" suffix=" "/>
+                  <date-part name="year"/>
+                </date>
+              </group>
+              <text variable="page"/>
+            </group>
+          </group>
+        </else-if>
+        <else-if type="patent">
+          <group delimiter=". ">
+            <text variable="title"/>
+            <text variable="number"/>
+            <date variable="issued">
+              <date-part name="month" form="short" suffix=" "/>
+              <date-part name="day" suffix=", "/>
+              <date-part name="year"/>
+            </date>
+          </group>
+        </else-if>
+        <else-if type="thesis">
+          <group delimiter=". ">
+            <text variable="title" font-style="italic"/>
+            <text variable="archive_location" prefix="Doctoral Thesis #"/>
+            <text variable="publisher"/>
+          </group>
+        </else-if>
+        <else-if type="report">
+          <group delimiter=". ">
+            <text variable="title" font-style="italic"/>
+            <text variable="number" prefix="Technical Report #"/>
+            <text variable="publisher"/>
+          </group>
+        </else-if>
+        <else-if type="webpage">
+          <group delimiter=". ">
+            <text variable="URL" font-style="italic"/>
+            <date variable="accessed" prefix="Accessed: ">
+              <date-part name="year" suffix="-"/>
+              <date-part name="month" form="numeric-leading-zeros" suffix="-"/>
+              <date-part name="day" form="numeric-leading-zeros"/>
+            </date>
+          </group>
+        </else-if>
+        <else-if type="chapter paper-conference" match="any">
+          <group delimiter=". ">
+            <text variable="title"/>
+            <text variable="container-title" font-style="italic"/>
+            <text macro="editor"/>
+            <text variable="publisher"/>
+            <text variable="page"/>
+          </group>
+        </else-if>
+        <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
+          <group delimiter=". ">
+            <text variable="title" font-style="italic"/>
+            <text variable="publisher"/>
+          </group>
+        </else-if>
+        <else>
+          <group delimiter=". ">
+            <text variable="title"/>
+            <text variable="container-title" font-style="italic"/>
+            <text variable="publisher"/>
+          </group>
+        </else>
+      </choose>
+    </layout>
+  </bibliography>
+</style>

example/assets/inkscape-convert.py

@@ -1,62 +0,0 @@
-import os
-import pathlib
-import sys
-import subprocess
-
-inkscape = None
-
-if os.name == 'nt':
-    # Possible paths to check for the installation
-    inkscapePaths = [
-        r"C:\Program Files\Inkscape\bin\inkscape.exe",
-        r"C:\Program Files\Inkscape\inkscape.exe",
-        r"C:\Program Files (x86)\Inkscape\bin\inkscape.exe",
-        r"C:\Program Files (x86)\Inkscape\inkscape.exe",
-    ]
-    for path in inkscapePaths:
-        if pathlib.Path(path).exists():
-            inkscape = path
-    if not inkscape:
-        print("Can't find Inkscape installation, aborting.")
-        sys.exit()
-
-elif os.name == 'posix':
-    inkscape = 'inkscape'
-
-print("Conversion started")
-
-for f in sys.argv[1:]:
-    fullpath = pathlib.Path(f)
-    if fullpath.exists() and fullpath.suffix == '.svg':
-        print(f"Converting {fullpath} to PNG")
-        p = subprocess.run([
-            inkscape,
-            "--export-background-opacity=1",
-            "--export-type=png",
-            "--export-dpi=400",
-            f"--export-filename={fullpath.with_suffix('.png')}",
-            fullpath,
-        ],
-                           stdin=subprocess.PIPE,
-                           stdout=subprocess.PIPE,
-                           stderr=subprocess.STDOUT,
-                           universal_newlines=True)
-
-        print(f"Converting {fullpath} to PDF")
-        subprocess.run([
-            inkscape,
-            "-T",
-            "--export-background-opacity=1",
-            "--export-type=pdf",
-            "--export-dpi=400",
-            f"--export-filename={fullpath.with_suffix('.pdf')}",
-            fullpath,
-        ],
-                       stdin=subprocess.PIPE,
-                       stdout=subprocess.PIPE,
-                       stderr=subprocess.STDOUT,
-                       universal_newlines=True)
-    else:
-        print(f"Path {f} does not exist")
-
-print("Complete")

example/assets/master.bib

@@ -0,0 +1,9 @@
+@Book{xie2013ddrk,
+  Title                    = {Dynamic Documents with R and knitr},
+  Author                   = {Yihui Xie},
+  Publisher                = {Boca Raton, FL: CRC Press},
+  Year                     = {2013},
+
+  Owner                    = {steve},
+  Timestamp                = {2015.09.13}
+}

example/assets/pandoc-scholar/.github/FUNDING.yml

@@ -1 +0,0 @@
-github: tarleb

example/assets/pandoc-scholar/.github/workflows/ci.yml

@@ -1,48 +0,0 @@
-name: CI
-
-on:
-  pull_request:
-    paths-ignore:
-      - README.md
-      - ChangeLog.md
-      - LICENSE
-  push:
-    paths-ignore:
-      - README.md
-      - ChangeLog.md
-      - LICENSE
-
-jobs:
-  docker:
-    runs-on: ubuntu-18.04
-    strategy:
-      fail-fast: true
-      matrix:
-        distro:
-          - ubuntu
-          - alpine
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Create Docker image
-        run: |
-          docker build \
-              --tag pandocscholar/${{ matrix.distro }}:dev \
-              --file docker/${{ matrix.distro }}.Dockerfile \
-              .
-
-      - name: Run Docker on example
-        run: |
-          docker run --rm \
-                 --user "$(id -u):$(id -g)" \
-                 --volume "$(pwd)/example:/data" \
-                 pandocscholar/${{ matrix.distro }}:dev
-
-      - name: Login to Docker Hub
-        run: >-
-          echo "${{ secrets.DOCKER_HUB_TOKEN }}" |
-            docker login -u ${{ secrets.DOCKER_HUB_USERNAME }} --password-stdin
-
-      - name: Push dev image
-        run: docker push pandocscholar/${{ matrix.distro }}:dev

example/assets/pandoc-scholar/.github/workflows/release-docker.yml

@@ -1,59 +0,0 @@
-name: Manual Docker release
-
-on:
-  workflow_dispatch:
-    inputs:
-      tag:
-        name: tag name
-        required: true
-        default: latest
-        description: Tag under which the images should be published.
-      is-latest:
-        name: "is latest?"
-        required: true
-        default: false
-        description: Whether the build is also the latest version.
-
-jobs:
-  docker:
-    name: Docker release
-    runs-on: ubuntu-18.04
-    strategy:
-      fail-fast: false
-      matrix:
-        distro:
-          - ubuntu
-          - alpine
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Create Docker image
-        run: |
-          docker build \
-              --tag pandocscholar/${{ matrix.distro }}:latest \
-              --file docker/${{ matrix.distro }}.Dockerfile \
-              .
-
-      - name: Run Docker on example
-        run: |
-          docker run --rm \
-                 --user "$(id -u):$(id -g)" \
-                 --volume "$(pwd)/example:/data" \
-                 pandocscholar/${{ matrix.distro }}:latest
-
-      - name: Login to Docker Hub
-        run: >-
-          echo "${{ secrets.DOCKER_HUB_TOKEN }}" |
-            docker login -u ${{ secrets.DOCKER_HUB_USERNAME }} --password-stdin
-
-      - name: Push image as latest
-        if: github.event.inputs.is-latest != false
-        run: docker push pandocscholar/${{ matrix.distro }}:latest
-
-      - name: Push image as tag
-        run: |
-          docker tag \
-              pandocscholar/${{ matrix.distro }}:latest \
-              pandocscholar/${{ matrix.distro }}:${{ github.event.inputs.tag }}
-          docker push pandocscholar/${{ matrix.distro }}:${{ github.event.inputs.tag }}

example/assets/pandoc-scholar/.github/workflows/release.yml

@@ -1,96 +0,0 @@
-name: Release
-
-on:
-  push:
-    tags:
-      - v*
-
-jobs:
-  release:
-    name: Release Artifacts
-    runs-on: ubuntu-18.04
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Build collection
-        run: make archives
-
-      - name: Create release
-        id: create_release
-        uses: actions/create-release@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          tag_name: ${{ github.ref }}
-          release_name: pandoc-scholar ${{ github.ref }}
-          draft: false
-          prerelease: false
-
-      - name: Add zip archive to release
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }}
-          asset_path: ./dist/pandoc-scholar.zip
-          asset_name: pandoc-scholar.zip
-          asset_content_type: application/zip
-
-      - name: Add tar archive to release
-        uses: actions/upload-release-asset@v1
-        env:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
-        with:
-          upload_url: ${{ steps.create_release.outputs.upload_url }}
-          asset_path: ./dist/pandoc-scholar.tar.gz
-          asset_name: pandoc-scholar.tar.gz
-          asset_content_type: application/x-gtar
-
-  docker:
-    name: Docker release
-    runs-on: ubuntu-18.04
-    strategy:
-      fail-fast: false
-      matrix:
-        distro:
-          - ubuntu
-          - alpine
-    steps:
-      - name: Checkout
-        uses: actions/checkout@v2
-
-      - name: Create Docker image
-        run: |
-          docker build \
-              --tag pandocscholar/${{ matrix.distro }}:latest \
-              --file docker/${{ matrix.distro }}.Dockerfile \
-              .
-
-      - name: Run Docker on example
-        run: |
-          docker run --rm \
-                 --user "$(id -u):$(id -g)" \
-                 --volume "$(pwd)/example:/data" \
-                 pandocscholar/${{ matrix.distro }}:latest
-
-      - name: Login to Docker Hub
-        run: >-
-          echo "${{ secrets.DOCKER_HUB_TOKEN }}" |
-            docker login -u ${{ secrets.DOCKER_HUB_USERNAME }} --password-stdin
-
-      - name: Push image as latest
-        run: docker push pandocscholar/${{ matrix.distro }}:latest
-
-      - name: Push image as version
-        run: |
-          version=$(printf "${{ github.ref }}" | sed 's#.*v\(.*\)$#\1#')
-          if [ -n "${version}" ]; then
-              docker tag \
-                  pandocscholar/${{ matrix.distro }}:latest \
-                  pandocscholar/${{ matrix.distro }}:${version}
-              docker push pandocscholar/${{ matrix.distro }}:${version}
-          else
-              printf "Could not determine version" >&2
-              exit 1
-          fi

example/assets/pandoc-scholar/ChangeLog.md

@@ -1,170 +0,0 @@
-ChangeLog
-=========
-
-v2.3.0
-------
-
-Released 2020-12-01
-
-- Turned `example` dir into standalone example. The example is now
-  clearer about how pandoc-scholar can be used when it was installed
-  in a central location.
-
-- Provide Docker images. Each new release is now accompanied by
-  Docker images bundling all basic requirements into a single
-  container. See the README for more info.
-
-- Updated the LaTeX template. The template incorporates improvements
-  from the latest pandoc version and will now also work with pandoc
-  2.11.
-  
-- Renamed class given to the `<div>` wrapper around author
-  affiliations. The class was named `author_affiliations`, but the
-  CSS styles assumed `author-affiliations`. The HTML markup has been
-  updated to match the CSS.
-
-- Removed unneeded files from lua-filters. Files for testing have
-  been dropped; only the filter files and docs are kept. The next
-  major version will also change the directory structure below
-  `lua-filters` and get rid of the separate subdirectories for each
-  filter.
-
-v2.2.2
-------
-
-Released 2020-06-17
-
-- Update Lua filters to their most recent versions. This includes
-  a fix to the abstract-to-meta filter, which would sometimes
-  produce wrong results when used with pandoc 2.8 or newer.
-
-v2.2.1
-------
-
-Released 2020-04-25
-
-- Fixed incorrect path in JATS target: a file in the dependency
-  list of the JATS target was missing was missing a path prefix,
-  causing make to fail the Makefile was included in a different
-  directory.
-
-- Fixed bibliography and citation handling in JATS: citations
-  were formatted incorrectly if no CSL file was given. We also
-  make sure that `PANDOC_READER_OPTIONS` are respected for JATS.
-
-- Simplify bibliography handling for JSON-LD: it is now
-  sufficient to define a bibliography field in the article
-  metadata. Previously, JSON-LD generation failed unless the
-  `BIBLIOGRAPHY_FILE` variable was set; the requirement for this
-  variable has been removed.
-
-v2.2.0
-------
-
-Released 2020-04-21
-
-- Running `make clean` is now ensured to only remove generated
-  files (Sam Hiatt).
-
-- JATS support has been improved and produces valid JATS 1.2
-  documents using the Journal Archiving and Interchange tag set.
-  Bibliography entries in the documents are formatted with the
-  given CSL style.
-
-- The default LaTeX template has been updated to work with pandoc
-  2.9.
-
-  + The options for the natbib package can be passed via the
-    `natbiboptions` variable.
-
-  + A new environment `cslreferences` is defined. It is used to
-    contain pandoc-citeproc generated bibliographies.
-
-- New make target `default` has been introduced. It is run
-  instead of target `all` when make is called a specific target.
-
-- The example is now generated with links between examples and
-  references. Furthermore, the CSL file is explicitly defined to
-  make it clearer how an alternative style can be used.
-
-- The pandoc and pandoc-citeproc executables can now be set via
-  the `PANDOC` and `PANDOC_CITEPROC` variables, respectively.
-  The default is to use the binaries in the user's PATH.
-
-v2.1.1
-------
-
-Released 2019-04-16
-
-### Lua filters
-
-- Fix a bug which caused separators to be inserted even for
-  single authors. (#33)
-
-v2.1.0
-------
-
-Released 2019-01-16.
-
-### Templates
-
-- Removed a newline in the HTML template which caused an extra
-  space be inserted before institute addresses (Benjamin Lee).
-
-- Include subtitle in PDF output (solution taken from pandoc,
-  courtesy of Andrew Dunning).
-
-v2.0.1
-------
-
-Released 2018-12-26.
-
-### Makefile
-
-- Fix option for docx reference documents. (Mitchell Paulus)
-
-- Fix option for odt reference documents.
-
-### Lua filters
-
-- Fix filters for pandoc 2.3 and later; older versions should
-  continue to work.
-
-- author-info-blocks:
-
-  + Fix LaTeX output, surround `\dagger` with dollars.
-
-  + Keep authors as a list instead of joining them into a single
-    entry when the output is LaTeX. This fixes LaTeX layout
-    issues when many authors are given.
-
-- pagebreak: New filter to convert `\newpage` commands into
-  target-format appropriate page breaks. Not enabled by default.
-
-- multiple-bibliographies: a filter which allows the creation of
-  multiple bibliographies using `pandoc-citeproc`.
-  Not enabled by default.
-
-
-v2.0.0
-------
-
-- Update to pandoc 2. Pandoc scholar now requires pandoc 2.1 or later.
-
-- The internal document transformation system has been mostly
-  rewritten. Instead of custom writers based on panlunatic, the
-  new version now uses pandoc Lua filters. This builds on a
-  well-tested system and removes some bugs due caused by
-  panlunatic. Lua filters are also easier to use separately.
-  E.g., using Lua filters allows to integrate desired
-  functionality into a RMarkdown workflow.
-
-- Added support for CiTO property
-  *cites\_as\_recommended\_reading*.
-
-- Add missing author affiliations in HTML output (Thomas Sibley).
-
-- JATS support no longer relies on a custom writer; output is
-  generated directly via pandoc.
-
-- Fixed sub/sup styling in HTML output

example/assets/pandoc-scholar/LICENSE

@@ -1,339 +0,0 @@
-                    GNU GENERAL PUBLIC LICENSE
-                       Version 2, June 1991
-
- Copyright (C) 1989, 1991 Free Software Foundation, Inc.,
- 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
- Everyone is permitted to copy and distribute verbatim copies
- of this license document, but changing it is not allowed.
-
-                            Preamble
-
-  The licenses for most software are designed to take away your
-freedom to share and change it.  By contrast, the GNU General Public
-License is intended to guarantee your freedom to share and change free
-software--to make sure the software is free for all its users.  This
-General Public License applies to most of the Free Software
-Foundation's software and to any other program whose authors commit to
-using it.  (Some other Free Software Foundation software is covered by
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-a notice placed by the copyright holder saying it may be distributed
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-exercise the right to control the distribution of derivative or
-collective works based on the Program.
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-with the Program (or with a work based on the Program) on a volume of
-a storage or distribution medium does not bring the other work under
-the scope of this License.
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-under Section 2) in object code or executable form under the terms of
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-may add an explicit geographical distribution limitation excluding
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-later version", you have the option of following the terms and conditions
-either of that version or of any later version published by the Free
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-                            NO WARRANTY
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-FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW.  EXCEPT WHEN
-OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES
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-POSSIBILITY OF SUCH DAMAGES.
-
-                     END OF TERMS AND CONDITIONS
-
-            How to Apply These Terms to Your New Programs
-
-  If you develop a new program, and you want it to be of the greatest
-possible use to the public, the best way to achieve this is to make it
-free software which everyone can redistribute and change under these terms.
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-  To do so, attach the following notices to the program.  It is safest
-to attach them to the start of each source file to most effectively
-convey the exclusion of warranty; and each file should have at least
-the "copyright" line and a pointer to where the full notice is found.
-
-    <one line to give the program's name and a brief idea of what it does.>
-    Copyright (C) <year>  <name of author>
-
-    This program is free software; you can redistribute it and/or modify
-    it under the terms of the GNU General Public License as published by
-    the Free Software Foundation; either version 2 of the License, or
-    (at your option) any later version.
-
-    This program is distributed in the hope that it will be useful,
-    but WITHOUT ANY WARRANTY; without even the implied warranty of
-    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-    GNU General Public License for more details.
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-    You should have received a copy of the GNU General Public License along
-    with this program; if not, write to the Free Software Foundation, Inc.,
-    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
-
-Also add information on how to contact you by electronic and paper mail.
-
-If the program is interactive, make it output a short notice like this
-when it starts in an interactive mode:
-
-    Gnomovision version 69, Copyright (C) year name of author
-    Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
-    This is free software, and you are welcome to redistribute it
-    under certain conditions; type `show c' for details.
-
-The hypothetical commands `show w' and `show c' should show the appropriate
-parts of the General Public License.  Of course, the commands you use may
-be called something other than `show w' and `show c'; they could even be
-mouse-clicks or menu items--whatever suits your program.
-
-You should also get your employer (if you work as a programmer) or your
-school, if any, to sign a "copyright disclaimer" for the program, if
-necessary.  Here is a sample; alter the names:
-
-  Yoyodyne, Inc., hereby disclaims all copyright interest in the program
-  `Gnomovision' (which makes passes at compilers) written by James Hacker.
-
-  <signature of Ty Coon>, 1 April 1989
-  Ty Coon, President of Vice
-
-This General Public License does not permit incorporating your program into
-proprietary programs.  If your program is a subroutine library, you may
-consider it more useful to permit linking proprietary applications with the
-library.  If this is what you want to do, use the GNU Lesser General
-Public License instead of this License.

example/assets/pandoc-scholar/Makefile

@@ -1,126 +0,0 @@
-## The path to the directory in which this file resides. This allows users to
-## include this Makefile into theirs and to reuse all rules, given that they set
-## this variable to the correct value.
-PANDOC_SCHOLAR_PATH   ?= $(shell dirname $(realpath $(lastword $(MAKEFILE_LIST))))
-
-# include local makefile to allow easy overwriting of variables
--include local.mk
-include $(PANDOC_SCHOLAR_PATH)/pandoc-options.inc.mk
-
-LUA_FILTERS_PATH      ?= $(PANDOC_SCHOLAR_PATH)/lua-filters
-
-PANDOC ?= pandoc
-
-# Configuration (overwrite using Makefile.local.in if necessary)
-ARTICLE_FILE          ?= example/article.md
-OUTFILE_PREFIX        ?= outfile
-DEFAULT_EXTENSIONS    ?= latex pdf docx odt epub html
-ADDITIONAL_EXTENSIONS ?= xml jats jsonld txt
-JSON_FILE             ?= $(OUTFILE_PREFIX).enriched.json
-FLATTENED_JSON_FILE   ?= $(OUTFILE_PREFIX).flattened.json
-LUA_FILTERS           ?= $(LUA_FILTERS_PATH)/cito/cito.lua \
-                         $(LUA_FILTERS_PATH)/abstract-to-meta/abstract-to-meta.lua \
-                         $(LUA_FILTERS_PATH)/scholarly-metadata/scholarly-metadata.lua
-
-default: $(addprefix $(OUTFILE_PREFIX).,$(DEFAULT_EXTENSIONS))
-
-all: $(addprefix $(OUTFILE_PREFIX).,$(DEFAULT_EXTENSIONS)) \
-     $(addprefix $(OUTFILE_PREFIX).,$(ADDITIONAL_EXTENSIONS))
-
-$(JSON_FILE): $(ARTICLE_FILE) $(LUA_FILTERS)
-	$(PANDOC) $(PANDOC_READER_OPTIONS) \
-		     $(foreach filter, $(LUA_FILTERS), --lua-filter=$(filter)) \
-	       --to=json \
-	       --output=$@ $<
-
-$(OUTFILE_PREFIX).pdf $(OUTFILE_PREFIX).latex: \
-		$(JSON_FILE) \
-		$(TEMPLATE_FILE_LATEX) \
-		$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_LATEX_OPTIONS) \
-	       --lua-filter=$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua \
-	       --output $@ $<
-
-$(OUTFILE_PREFIX).docx: $(JSON_FILE) \
-		$(DOCX_REFERENCE_FILE) \
-		$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_DOCX_OPTIONS) \
-	       --lua-filter=$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua \
-	       --output $@ $<
-
-$(OUTFILE_PREFIX).odt: $(JSON_FILE) \
-		$(ODT_REFERENCE_FILE) \
-		$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_ODT_OPTIONS) \
-	       --lua-filter=$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua \
-	       --output $@ $<
-
-$(OUTFILE_PREFIX).epub: $(JSON_FILE) \
-		$(TEMPLATE_FILE_EPUB) \
-		$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_EPUB_OPTIONS) \
-	       --lua-filter=$(LUA_FILTERS_PATH)/author-info-blocks/author-info-blocks.lua \
-	       --output $@ $<
-
-$(OUTFILE_PREFIX).html: $(JSON_FILE) \
-		$(TEMPLATE_FILE_HTML) \
-		$(TEMPLATE_STYLE_HTML) \
-		$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_HTML_OPTIONS) \
-	       --lua-filter=$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua \
-	       --css=$(TEMPLATE_STYLE_HTML) \
-	       --mathjax \
-	       --output $@ $<
-
-$(OUTFILE_PREFIX).jsonld: $(JSON_FILE) \
-		$(BIBLIOGRAPHY_FILE) \
-		$(PANDOC_SCHOLAR_PATH)/scholar-filters/json-ld.lua \
-		$(PANDOC_SCHOLAR_PATH)/writers/jsonld.lua
-	$(PANDOC) --to $(PANDOC_SCHOLAR_PATH)/writers/jsonld.lua \
-	       --lua-filter=$(PANDOC_SCHOLAR_PATH)/scholar-filters/json-ld.lua \
-	       --output=$@ $<
-
-$(OUTFILE_PREFIX).txt: $(ARTICLE_FILE)
-	$(PANDOC) $(PANDOC_WRITER_OPTIONS) \
-	       --output $@ $<
-
-## The JSON file is required only for metadata (csl) extraction
-## by the jats-fixes.lua script, as pandoc overrides the CSL
-## field when converting to JATS.
-$(OUTFILE_PREFIX).jats $(OUTFILE_PREFIX).xml: $(ARTICLE_FILE) \
-		$(JSON_FILE) \
-		$(PANDOC_SCHOLAR_PATH)/templates/pandoc-scholar.jats \
-		$(PANDOC_SCHOLAR_PATH)/scholar-filters/jats-fixes.lua \
-		$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua \
-		$(PANDOC_SCHOLAR_PATH)/csl/chicago-author-date.csl \
-		$(PANDOC_SCHOLAR_PATH)/csl/jats.csl
-	$(PANDOC) \
-	       $(PANDOC_WRITER_OPTIONS) \
-	       $(PANDOC_JATS_OPTIONS) \
-		     $(foreach filter, $(LUA_FILTERS), --lua-filter=$(filter)) \
-	       --lua-filter=$(PANDOC_SCHOLAR_PATH)/scholar-filters/template-helper.lua \
-	       --to=jats_articleauthoring+element_citations \
-	       --output $@ $<
-
-clean:
-ifeq ($(OS),Windows_NT)
-	del $(OUTFILE_PREFIX).docx $(OUTFILE_PREFIX).epub $(OUTFILE_PREFIX).html
-	del $(OUTFILE_PREFIX).odt $(OUTFILE_PREFIX).latex $(OUTFILE_PREFIX).pdf
-	del $(JSON_FILE) $(FLATTENED_JSON_FILE)
-else
-	for ext in $(DEFAULT_EXTENSIONS) $(ADDITIONAL_EXTENSIONS); do\
-		rm -f $(OUTFILE_PREFIX).$$ext;\
-	done
-	rm -f $(JSON_FILE) $(FLATTENED_JSON_FILE)
-endif
-
-.PHONY: all clean
-
-# Include archive-generating targets. This makefile is not included in the
-# distributed archives
--include archives.inc.mk

example/assets/pandoc-scholar/README.md

@@ -1,326 +0,0 @@
-pandoc-scholar
-==============
-
-[![release shield]](https://github.com/pandoc-scholar/pandoc-scholar/releases)
-[![DOI]](https://zenodo.org/badge/latestdoi/82204858)
-[![license shield]](./LICENSE)
-[![Build status][GitHub Actions badge]][GitHub Actions]
-
-Create beautiful, semantically enriched articles with pandoc. This
-package provides utilities to make publishing of scientific articles as
-simple and pleasant as possible. It simplifies setting authors' metadata
-in YAML blocks, allows to add semantic annotation to citations, and only
-requires the programs pandoc and make.
-
-[release shield]: https://img.shields.io/github/release/pandoc-scholar/pandoc-scholar.svg
-[license shield]: https://img.shields.io/github/license/pandoc-scholar/pandoc-scholar.svg
-[GitHub Actions badge]: https://img.shields.io/github/workflow/status/pandoc-scholar/pandoc-scholar/CI?logo=github
-[GitHub Actions]: https://github.com/pandoc-scholar/pandoc-scholar/actions
-[DOI]: https://zenodo.org/badge/82204858.svg
-
-Overview
---------
-
-Plain pandoc is already excellent at document conversion, but it lacks
-in metadata handling. Pandoc-scholar offers simple ways to include
-metadata on authors, affiliations, contact details, and citations. The
-data is included into the final output as document headers. Additionally
-all entries can be exported as [JSON-LD], a standardized format for the
-semantic web.
-
-The background leading to the development of pandoc-scholar is described
-in the [paper published in PeerJ Computer Science][paper].
-
-Note that since version 2.0, most of the functionality of pandoc-scholar
-is now provided via [pandoc Lua filters]. If you prefer to mix-and-match
-selected functionalities provided by pandoc-scholar, you can now use the
-respective Lua filters directly. Integration with tools like RMarkdown
-is possible this way.
-
-[paper]: https://peerj.com/articles/cs-112/
-[JSON-LD]: https://en.wikipedia.org/wiki/JSON-LD
-[pandoc Lua filters]: https://github.com/pandoc/lua-filters
-
-### Demo
-
-An example document plus bibliography is provided in the *example*
-folder. Running `make` in the *example* folder will process the
-example article, generating output like below:
-
-![example article screenshot](https://pandoc-scholar.github.io/example/header.png)
-
-Get the full output as [pdf], [docx], or [epub], or take a look at the
-metadata in [JSON-LD] format.
-
-[pdf]: https://pandoc-scholar.github.io/example/example.pdf
-[docx]: https://pandoc-scholar.github.io/example/example.docx
-[epub]: https://pandoc-scholar.github.io/example/example.epub
-[JSON-LD]: https://pandoc-scholar.github.io/example/example.jsonld
-
-Usage via Docker
-----------------
-
-A very easy way to use pandoc-scholar is via Docker. The ready-made
-images contain all necessary software to generate a paper in
-multiple formats. This avoids any compatibility concerns; only
-Docker is required.
-
-The official images are in the [pandocscholar/ubuntu] and
-[pandocscholar/alpine] images. The Alpine image is a bit smaller,
-while the Ubuntu image may be more familiar for people looking to
-extend the image. Both images come with pandoc, pandoc-citeproc,
-pandoc-crossref, and LaTeX.
-
-### Example call
-
-Docker commands are often unwieldly due to the additional arguments.
-We recommend to define an alias or short script to simplify its use.
-
-Given an article in file `my-research-article.md` and a simple
-Makefile like
-
-```makefile
-ARTICLE_FILE = my-research-article.md
-OUTFILE_PREFIX = out
-include $(PANDOC_SCHOLAR_PATH)/Makefile
-```
-
-the conversion can be performed by running
-
-    docker run --rm -v "$(pwd):/data" -u "$(id -u)" pandocscholar/alpine
-
-This will generate a set of files whose names all start with `out.`.
-Please be aware that existing files of the same name will be
-overwritten. The pandoc-scholar container calls `make` internally;
-additional commands and options can be passed by appending them the
-above command.
-
-The images are based upon the official pandoc images; for more info
-and usage examples, see the [pandoc/dockerfiles] GitHub repo. The
-Docker images can easily be used in automatic document conversion
-pipelines; [pandoc-actions-example] gives a good overview.
-
-A major difference between pandoc and pandoc-scholar images is that
-pandoc-scholar doesn't use `pandoc` but `make` as entrypoint. A
-basic Makefile must be present in the article directory when running
-pandoc-scholar.
-
-[pandoc/dockerfiles]: https://github.com/pandoc/dockerfiles
-[pandoc-actions-example]: https://github.com/pandoc/pandoc-action-example
-
-Prerequisites
--------------
-
-This package builds on [pandoc](http://pandoc.org/), the universal
-document converter. See the pandoc website for [installation
-instructions](http://pandoc.org/installing.html) and suggestions for
-LaTeX packages, which we use for PDF generation.
-
-Starting with pandoc-scholar 3.0.0, the minimum required pandoc version
-is 2.11. If you have to use an older pandoc, please combine it with the
-last 2.* release of pandoc-scholar.
-
-Also note that pandoc's JATS support, especially citation handling, was
-buggy prior to pandoc v2.11.4. Please use that or a newer version when
-producing JATS XML.
-
-Installation
-------------
-
-Archives containing all required files are provided for each release.
-Use the *release* button above (or directly go to the [latest release])
-and download a `pandoc-scholar` archive; both archive files, `.zip` and
-`.tar.gz`, contain the same files. Choose the filetype that is the
-easiest to unpack on you system.
-
-A `pandoc-scholar` folder will be created on unpacking. The folder
-contains all required scripts and templates.
-
-[latest release]: https://github.com/pandoc-scholar/pandoc-scholar/releases/latest
-
-
-Usage
------
-
-### Quickstart
-
-Run `make` to convert the example article into all supported output formats. The
-markdown file used to create the output files can be configured via the
-`ARTICLE_FILE` variable, either directly in the Makefile or by specifying the
-value on the command line.
-
-    make ARTICLE_FILE=your-file.md
-
-### Includable Makefile
-
-The *Makefile*, which does most of the work, is written in a style that makes it
-simple to include it from within other Makefiles. This method allows to keep
-`pandoc-scholar` installed in a central location and to use the same instance
-for multiple projects. The `ARTICLE_FILE` and `PANDOC_SCHOLAR_PATH` variables
-must be defined in the including Makefile:
-
-``` Makefile
-ARTICLE_FILE        = your-file.md
-PANDOC_SCHOLAR_PATH = ../path-to-pandoc-scholar-folder
-include $(PANDOC_SCHOLAR_PATH)/Makefile
-```
-
-Calling `make` as usual will create all configured output formats. Per default,
-this creates *pdf*, *latex*, *docx*, *odt*, *epub*, *html*, and *jats* output.
-The set of output files can be reduced by setting the `DEFAULT_EXTENSIONS`
-variable to a subset of the aforementioned formats. For example `DEFAULT_EXTENSIONS = pdf odt docx`
-
-Alternative template files can be set using `TEMPLATE_FILE_<FORMAT>` variables,
-where `<FORMAT>` is one of *HTML*, *EPUB*, *JATS*, or *LATEX*. The reference
-files for ODT and DOCX output can be changed using `ODT_REFERENCE_FILE` and
-`DOCX_REFERENCE_FILE`, respectively.
-
-Additional pandoc options can be given on a per-format basis using
-`PANDOC_<FORMAT>_OPTIONS` variables. The following uses an actual Makefile as an
-example to demonstrate usage of those options.
-
-``` Makefile
-ARTICLE_FILE        = open-science-formatting.md
-
-PANDOC_LATEX_OPTIONS  = --latex-engine=xelatex
-PANDOC_LATEX_OPTIONS += --csl=peerj.csl
-PANDOC_LATEX_OPTIONS += --filter=pandoc-citeproc
-PANDOC_LATEX_OPTIONS += -M fontsize=10pt
-PANDOC_LATEX_OPTIONS += -M classoption=fleqn
-
-PANDOC_HTML_OPTIONS   = --toc
-PANDOC_EPUB_OPTIONS   = --toc
-
-DOCX_REFERENCE_FILE   = pandoc-manuscript.docx
-ODT_REFERENCE_FILE    = pandoc-manuscript.odt
-TEMPLATE_FILE_LATEX   = pandoc-peerj.latex
-
-PANDOC_SCHOLAR_PATH = pandoc-scholar
-include $(PANDOC_SCHOLAR_PATH)/Makefile
-```
-
-
-Metadata Features
------------------
-
-Pandoc-scholar supports additional functionality via metadata fields. Most
-notably, the augmentation of articles with author and affiliation data, which is
-essential for academic publishing, is greatly simplified when using
-pandoc-scholar.
-
-### Authors and affiliations
-
-Most metadata should be specified in the YAML block at the top of the article.
-Author data and affiliations are taken from the *author* and *institute* field,
-respectively. Institutes can be given via user-defined abbreviations, saving
-unnecessary repetitions while preserving readability.
-
-Example:
-
-``` yaml
-author:
-  - James Dewey Watson:
-      institute: cavendish
-  - Francis Harry Compton Crick:
-      institute: cavendish
-institute:
-  - cavendish: Cavendish Laboratory, Cambridge
-```
-
-Authors are given in the order in which they are listed, while institute order
-follows from author order.
-
-The separate institute field may add unwanted complexity in some cases. It is
-hence possible to omit it and to give the affiliations name directly in the
-author entry:
-
-``` yaml
-author:
-  - John MacFarlane:
-      institute: University of California, Berkeley
-```
-
-### Institute address
-
-Often it is not enough to give just a name for institutes. It is hence possible
-to add arbitrary fields. The name must then explicitly be set via the *name*
-field of the institute entry:
-
-``` yaml
-author:
-  - Robert Winkler:
-      institute: cinvestav
-institute:
-  - cinvestav:
-      name: 'CINVESTAV Unidad Irapuato, Department of Biochemistry and Biotechnology'
-      address: 'Km. 9.6 Libramiento Norte Carr. Irapuato-León, 36821 Irapuato Gto. México'
-      phone: +52 (462) 623 9635
-```
-
-Currently only the institute's address is used in the default template, but
-future extensions will be based on this convention.
-
-### Semantic citations
-
-Understanding the reason a citations is included in scholarly articles usually
-requires natural language processing of the article. However, navigating the
-current literature landscape can be improved and by having that information
-accesible and in a machine-readable form. Pandoc-scholar supports the CiTO
-ontology, allowing authors to specify important meta-information on the citation
-directly while writing the text. The property is simply prepended to the
-citation key, separated by a colon: `@<property>:citationKey`.
-
-The following table contains all supported keywords and the respective
-CiTO properties. Authors are free to use the short-form, the full-length
-property, or any of the alternatives listed below (i.e., all word in a
-row denote the property and have the same effect).
-
-CiTO property                  | Keyword             | alternatives
------------------------------- | ------------------- | ---------------------
-agrees\_with                   | agrees\_with        | agree\_with
-citation                       |                     |
-cites                          |                     |
-cites\_as\_authority           | authority           | as\_authority
-cites\_as\_data\_source        | data\_source        | as\_data_source
-cites\_as\_evidence            | evidence            | as\_evidence
-cites\_as\_metadata\_document  | metadata            | as\_metadata_document
-cites\_as\_recommended_reading | recommended_reading | as\_recommended\_reading
-disputes                       |                     |
-documents                      |                     |
-extends                        |                     |
-includes\_excerpt\_from        | excerpt             | excerpt\_from
-includes\_quotation\_from      | quotation           | quotation\_from
-obtaines\_background\_from     | background          | background\_from
-refutes                        |                     |
-replies\_to                    |                     |
-updates                        |                     |
-uses\_data\_from               | data\_from          | data
-uses\_method\_in               | method              | method\_in
-
-Example:
-
-    DNA strands form a double-helix [@evidence:watson_crick_1953].
-
-
-License
--------
-
-Copyright © 2016–2021 Albert Krewinkel and Robert Winkler except for the
-following components:
-
-- HTML template: © 2016 Andrew G. York and Diana Mounter
-- dkjson: © 2010-2013 David Heiko Kolf
-- lua-filters: © 2017-2021 Albert Krewinkel, John MacFarlane, and contributors.
-
-This program is free software; you can redistribute it and/or modify it under
-the terms of the GNU General Public License as published by the Free Software
-Foundation; either version 2 of the License, or (at your option) any later
-version.
-
-This program is distributed in the hope that it will be useful, but WITHOUT ANY
-WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
-PARTICULAR PURPOSE. See the GNU General Public License for more details.
-
-You should have received a copy of the GNU General Public License along with
-this program; if not, write to the Free Software Foundation, Inc., 51 Franklin
-Street, Fifth Floor, Boston, MA 02110-1301 USA.

example/assets/pandoc-scholar/archives.inc.mk

@@ -1,30 +0,0 @@
-# Generate Archives for distribution
-# ==================================
-
-archives: dist/pandoc-scholar.zip dist/pandoc-scholar.tar.gz
-
-dist/pandoc-scholar: \
-		csl \
-		$(LUA_FILTERS_PATH) \
-		scholar-filters \
-		LICENSE README.md \
-		Makefile pandoc-options.inc.mk \
-		example templates writers
-	rm -rf $@
-	mkdir -p $@
-	cp -av $^ $@
-
-dist/pandoc-scholar.tar.gz: dist/pandoc-scholar
-	rm -f $@
-	tar zvcf $@ -C $(dir $<) $(notdir $<)
-
-dist/pandoc-scholar.zip: dist/pandoc-scholar
-	rm -f $@
-	(cd $(dir $<) && zip -r $(notdir $@) $(notdir $<))
-
-clean-archives:
-	rm -rf dist
-
-dist-clean: clean-archives
-
-.PHONY: archives clean-archives dist-clean

example/assets/pandoc-scholar/csl/chicago-author-date.csl

@@ -1,648 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="display-and-sort" page-range-format="chicago">
-  <info>
-    <title>Chicago Manual of Style 17th edition (author-date)</title>
-    <id>http://www.zotero.org/styles/chicago-author-date</id>
-    <link href="http://www.zotero.org/styles/chicago-author-date" rel="self"/>
-    <link href="http://www.chicagomanualofstyle.org/tools_citationguide.html" rel="documentation"/>
-    <author>
-      <name>Julian Onions</name>
-      <email>julian.onions@gmail.com</email>
-    </author>
-    <contributor>
-      <name>Sebastian Karcher</name>
-    </contributor>
-    <contributor>
-      <name>Richard Karnesky</name>
-      <email>karnesky+zotero@gmail.com</email>
-      <uri>http://arc.nucapt.northwestern.edu/Richard_Karnesky</uri>
-    </contributor>
-    <contributor>
-      <name>Andrew Dunning</name>
-      <email>andrew.dunning@utoronto.ca</email>
-      <uri>https://orcid.org/0000-0003-0464-5036</uri>
-    </contributor>
-    <contributor>
-      <name>Matthew Roth</name>
-      <email>matthew.g.roth@yale.edu</email>
-      <uri> https://orcid.org/0000-0001-7902-6331</uri>
-    </contributor>
-    <category citation-format="author-date"/>
-    <category field="generic-base"/>
-    <summary>The author-date variant of the Chicago style</summary>
-    <updated>2018-01-24T12:00:00+00:00</updated>
-    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
-  </info>
-  <locale xml:lang="en">
-    <terms>
-      <term name="editor" form="verb-short">ed.</term>
-      <term name="container-author" form="verb">by</term>
-      <term name="translator" form="verb-short">trans.</term>
-      <term name="editortranslator" form="verb">edited and translated by</term>
-      <term name="translator" form="short">trans.</term>
-    </terms>
-  </locale>
-  <macro name="secondary-contributors">
-    <choose>
-      <if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="none">
-        <group delimiter=". ">
-          <names variable="editor translator" delimiter=". ">
-            <label form="verb" text-case="capitalize-first" suffix=" "/>
-            <name and="text" delimiter=", "/>
-          </names>
-          <names variable="director" delimiter=". ">
-            <label form="verb" text-case="capitalize-first" suffix=" "/>
-            <name and="text" delimiter=", "/>
-          </names>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="container-contributors">
-    <choose>
-      <if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="any">
-        <group prefix=", " delimiter=", ">
-          <names variable="container-author" delimiter=", ">
-            <label form="verb" suffix=" "/>
-            <name and="text" delimiter=", "/>
-          </names>
-          <names variable="editor translator" delimiter=", ">
-            <label form="verb" suffix=" "/>
-            <name and="text" delimiter=", "/>
-          </names>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="editor">
-    <names variable="editor">
-      <name name-as-sort-order="first" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" prefix=", "/>
-    </names>
-  </macro>
-  <macro name="translator">
-    <names variable="translator">
-      <name name-as-sort-order="first" and="text" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
-      <label form="short" prefix=", "/>
-    </names>
-  </macro>
-  <macro name="recipient">
-    <choose>
-      <if type="personal_communication">
-        <choose>
-          <if variable="genre">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-          <else>
-            <text term="letter" text-case="capitalize-first"/>
-          </else>
-        </choose>
-      </if>
-    </choose>
-    <names variable="recipient" delimiter=", ">
-      <label form="verb" prefix=" " text-case="lowercase" suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="substitute-title">
-    <choose>
-      <if type="article-magazine article-newspaper review review-book" match="any">
-        <text macro="container-title"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="contributors">
-    <group delimiter=". ">
-      <names variable="author">
-        <name and="text" name-as-sort-order="first" sort-separator=", " delimiter=", " delimiter-precedes-last="always"/>
-        <label form="short" prefix=", "/>
-        <substitute>
-          <names variable="editor"/>
-          <names variable="translator"/>
-          <names variable="director"/>
-          <text macro="substitute-title"/>
-          <text macro="title"/>
-        </substitute>
-      </names>
-      <text macro="recipient"/>
-    </group>
-  </macro>
-  <macro name="contributors-short">
-    <names variable="author">
-      <name form="short" and="text" delimiter=", " initialize-with=". "/>
-      <substitute>
-        <names variable="editor"/>
-        <names variable="translator"/>
-        <names variable="director"/>
-        <text macro="substitute-title"/>
-        <text macro="title"/>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="interviewer">
-    <names variable="interviewer" delimiter=", ">
-      <label form="verb" prefix=" " text-case="capitalize-first" suffix=" "/>
-      <name and="text" delimiter=", "/>
-    </names>
-  </macro>
-  <macro name="archive">
-    <group delimiter=". ">
-      <text variable="archive_location" text-case="capitalize-first"/>
-      <text variable="archive"/>
-      <text variable="archive-place"/>
-    </group>
-  </macro>
-  <macro name="access">
-    <group delimiter=". ">
-      <choose>
-        <if type="graphic report" match="any">
-          <text macro="archive"/>
-        </if>
-        <else-if type="article-journal bill book chapter legal_case legislation motion_picture paper-conference" match="none">
-          <text macro="archive"/>
-        </else-if>
-      </choose>
-      <choose>
-        <if type="webpage post-weblog" match="any">
-          <date variable="issued" form="text"/>
-        </if>
-      </choose>
-      <choose>
-        <if variable="issued" match="none">
-          <group delimiter=" ">
-            <text term="accessed" text-case="capitalize-first"/>
-            <date variable="accessed" form="text"/>
-          </group>
-        </if>
-      </choose>
-      <choose>
-        <if type="legal_case" match="none">
-          <choose>
-            <if variable="DOI">
-              <text variable="DOI" prefix="https://doi.org/"/>
-            </if>
-            <else>
-              <text variable="URL"/>
-            </else>
-          </choose>
-        </if>
-      </choose>
-    </group>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if variable="title" match="none">
-        <choose>
-          <if type="personal_communication" match="none">
-            <text variable="genre" text-case="capitalize-first"/>
-          </if>
-        </choose>
-      </if>
-      <else-if type="bill book graphic legislation motion_picture song" match="any">
-        <text variable="title" text-case="title" font-style="italic"/>
-        <group prefix=" (" suffix=")" delimiter=" ">
-          <text term="version"/>
-          <text variable="version"/>
-        </group>
-      </else-if>
-      <else-if variable="reviewed-author">
-        <choose>
-          <if variable="reviewed-title">
-            <group delimiter=". ">
-              <text variable="title" text-case="title" quotes="true"/>
-              <group delimiter=", ">
-                <text variable="reviewed-title" text-case="title" font-style="italic" prefix="Review of "/>
-                <names variable="reviewed-author">
-                  <label form="verb-short" text-case="lowercase" suffix=" "/>
-                  <name and="text" delimiter=", "/>
-                </names>
-              </group>
-            </group>
-          </if>
-          <else>
-            <group delimiter=", ">
-              <text variable="title" text-case="title" font-style="italic" prefix="Review of "/>
-              <names variable="reviewed-author">
-                <label form="verb-short" text-case="lowercase" suffix=" "/>
-                <name and="text" delimiter=", "/>
-              </names>
-            </group>
-          </else>
-        </choose>
-      </else-if>
-      <else-if type="legal_case interview patent" match="any">
-        <text variable="title"/>
-      </else-if>
-      <else>
-        <text variable="title" text-case="title" quotes="true"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="edition">
-    <choose>
-      <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=". ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short" strip-periods="true"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" text-case="capitalize-first" prefix=". "/>
-          </else>
-        </choose>
-      </if>
-      <else-if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="any">
-        <choose>
-          <if is-numeric="edition">
-            <group delimiter=" " prefix=", ">
-              <number variable="edition" form="ordinal"/>
-              <text term="edition" form="short"/>
-            </group>
-          </if>
-          <else>
-            <text variable="edition" prefix=", "/>
-          </else>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators">
-    <choose>
-      <if type="article-journal">
-        <choose>
-          <if variable="volume">
-            <text variable="volume" prefix=" "/>
-            <group prefix=" (" suffix=")">
-              <choose>
-                <if variable="issue">
-                  <text variable="issue"/>
-                </if>
-                <else>
-                  <date variable="issued">
-                    <date-part name="month"/>
-                  </date>
-                </else>
-              </choose>
-            </group>
-          </if>
-          <else-if variable="issue">
-            <group delimiter=" " prefix=", ">
-              <text term="issue" form="short"/>
-              <text variable="issue"/>
-              <date variable="issued" prefix="(" suffix=")">
-                <date-part name="month"/>
-              </date>
-            </group>
-          </else-if>
-          <else>
-            <date variable="issued" prefix=", ">
-              <date-part name="month"/>
-            </date>
-          </else>
-        </choose>
-      </if>
-      <else-if type="legal_case">
-        <text variable="volume" prefix=", "/>
-        <text variable="container-title" prefix=" "/>
-        <text variable="page" prefix=" "/>
-      </else-if>
-      <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-        <group prefix=". " delimiter=". ">
-          <group>
-            <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-            <number variable="volume" form="numeric"/>
-          </group>
-          <group>
-            <number variable="number-of-volumes" form="numeric"/>
-            <text term="volume" form="short" prefix=" " plural="true"/>
-          </group>
-        </group>
-      </else-if>
-      <else-if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="any">
-        <choose>
-          <if variable="page" match="none">
-            <group prefix=". ">
-              <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-              <number variable="volume" form="numeric"/>
-            </group>
-          </if>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="locators-chapter">
-    <choose>
-      <if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="any">
-        <choose>
-          <if variable="page">
-            <group prefix=", ">
-              <text variable="volume" suffix=":"/>
-              <text variable="page"/>
-            </group>
-          </if>
-        </choose>
-      </if>
-    </choose>
-  </macro>
-  <macro name="locators-article">
-    <choose>
-      <if type="article-newspaper">
-        <group prefix=", " delimiter=", ">
-          <group delimiter=" ">
-            <text variable="edition"/>
-            <text term="edition"/>
-          </group>
-          <group>
-            <text term="section" form="short" suffix=" "/>
-            <text variable="section"/>
-          </group>
-        </group>
-      </if>
-      <else-if type="article-journal">
-        <choose>
-          <if variable="volume issue" match="any">
-            <text variable="page" prefix=": "/>
-          </if>
-          <else>
-            <text variable="page" prefix=", "/>
-          </else>
-        </choose>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="point-locators">
-    <choose>
-      <if variable="locator">
-        <choose>
-          <if locator="page" match="none">
-            <choose>
-              <if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-                <choose>
-                  <if variable="volume">
-                    <group>
-                      <text term="volume" form="short" suffix=" "/>
-                      <number variable="volume" form="numeric"/>
-                      <label variable="locator" form="short" prefix=", " suffix=" "/>
-                    </group>
-                  </if>
-                  <else>
-                    <label variable="locator" form="short" suffix=" "/>
-                  </else>
-                </choose>
-              </if>
-              <else>
-                <label variable="locator" form="short" suffix=" "/>
-              </else>
-            </choose>
-          </if>
-          <else-if type="bill book graphic legal_case legislation motion_picture report song" match="any">
-            <number variable="volume" form="numeric" suffix=":"/>
-          </else-if>
-        </choose>
-        <text variable="locator"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="container-prefix">
-    <text term="in" text-case="capitalize-first"/>
-  </macro>
-  <macro name="container-title">
-    <choose>
-      <if type="chapter entry-dictionary entry-encyclopedia paper-conference" match="any">
-        <text macro="container-prefix" suffix=" "/>
-      </if>
-    </choose>
-    <choose>
-      <if type="webpage">
-        <text variable="container-title" text-case="title"/>
-      </if>
-      <else-if type="legal_case" match="none">
-        <group delimiter=" ">
-          <text variable="container-title" text-case="title" font-style="italic"/>
-          <choose>
-            <if type="post-weblog">
-              <text value="(blog)"/>
-            </if>
-          </choose>
-        </group>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <group delimiter=": ">
-      <text variable="publisher-place"/>
-      <text variable="publisher"/>
-    </group>
-  </macro>
-  <macro name="date">
-    <choose>
-      <if variable="issued">
-        <group delimiter=" ">
-          <date variable="original-date" form="text" date-parts="year" prefix="(" suffix=")"/>
-          <date variable="issued">
-            <date-part name="year"/>
-          </date>
-        </group>
-      </if>
-      <else-if variable="status">
-        <text variable="status" text-case="capitalize-first"/>
-      </else-if>
-      <else>
-        <text term="no date" form="short"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="date-in-text">
-    <choose>
-      <if variable="issued">
-        <group delimiter=" ">
-          <date variable="original-date" form="text" date-parts="year" prefix="[" suffix="]"/>
-          <date variable="issued">
-            <date-part name="year"/>
-          </date>
-        </group>
-      </if>
-      <else-if variable="status">
-        <text variable="status"/>
-      </else-if>
-      <else>
-        <text term="no date" form="short"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="day-month">
-    <date variable="issued">
-      <date-part name="month"/>
-      <date-part name="day" prefix=" "/>
-    </date>
-  </macro>
-  <macro name="collection-title">
-    <choose>
-      <if match="none" type="article-journal">
-        <choose>
-          <if match="none" is-numeric="collection-number">
-            <group delimiter=", ">
-              <text variable="collection-title" text-case="title"/>
-              <text variable="collection-number"/>
-            </group>
-          </if>
-          <else>
-            <group delimiter=" ">
-              <text variable="collection-title" text-case="title"/>
-              <text variable="collection-number"/>
-            </group>
-          </else>
-        </choose>
-      </if>
-    </choose>
-  </macro>
-  <macro name="collection-title-journal">
-    <choose>
-      <if type="article-journal">
-        <group delimiter=" ">
-          <text variable="collection-title"/>
-          <text variable="collection-number"/>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="event">
-    <group>
-      <text term="presented at" suffix=" "/>
-      <text variable="event"/>
-    </group>
-  </macro>
-  <macro name="description">
-    <choose>
-      <if type="interview">
-        <group delimiter=". ">
-          <text macro="interviewer"/>
-          <text variable="medium" text-case="capitalize-first"/>
-        </group>
-      </if>
-      <else-if type="patent">
-        <group delimiter=" " prefix=". ">
-          <text variable="authority"/>
-          <text variable="number"/>
-        </group>
-      </else-if>
-      <else>
-        <text variable="medium" text-case="capitalize-first" prefix=". "/>
-      </else>
-    </choose>
-    <choose>
-      <if variable="title" match="none"/>
-      <else-if type="thesis personal_communication speech" match="any"/>
-      <else>
-        <group delimiter=" " prefix=". ">
-          <text variable="genre" text-case="capitalize-first"/>
-          <choose>
-            <if type="report">
-              <text variable="number"/>
-            </if>
-          </choose>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <macro name="issue">
-    <choose>
-      <if type="legal_case">
-        <text variable="authority" prefix=". "/>
-      </if>
-      <else-if type="speech">
-        <group prefix=". " delimiter=", ">
-          <group delimiter=" ">
-            <text variable="genre" text-case="capitalize-first"/>
-            <text macro="event"/>
-          </group>
-          <text variable="event-place"/>
-          <text macro="day-month"/>
-        </group>
-      </else-if>
-      <else-if type="article-newspaper article-magazine personal_communication" match="any">
-        <date variable="issued" form="text" prefix=", "/>
-      </else-if>
-      <else-if type="patent">
-        <group delimiter=", " prefix=", ">
-          <group delimiter=" ">
-            <!--Needs Localization-->
-            <text value="filed"/>
-            <date variable="submitted" form="text"/>
-          </group>
-          <group delimiter=" ">
-            <choose>
-              <if variable="issued submitted" match="all">
-                <text term="and"/>
-              </if>
-            </choose>
-            <!--Needs Localization-->
-            <text value="issued"/>
-            <date variable="issued" form="text"/>
-          </group>
-        </group>
-      </else-if>
-      <else-if type="article-journal" match="any"/>
-      <else>
-        <group prefix=". " delimiter=", ">
-          <choose>
-            <if type="thesis">
-              <text variable="genre" text-case="capitalize-first"/>
-            </if>
-          </choose>
-          <text macro="publisher"/>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <citation et-al-min="4" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" givenname-disambiguation-rule="primary-name" collapse="year" after-collapse-delimiter="; ">
-    <layout prefix="(" suffix=")" delimiter="; ">
-      <group delimiter=", ">
-        <choose>
-          <if variable="issued accessed" match="any">
-            <group delimiter=" ">
-              <text macro="contributors-short"/>
-              <text macro="date-in-text"/>
-            </group>
-          </if>
-          <!---comma before forthcoming and n.d.-->
-          <else>
-            <group delimiter=", ">
-              <text macro="contributors-short"/>
-              <text macro="date-in-text"/>
-            </group>
-          </else>
-        </choose>
-        <text macro="point-locators"/>
-      </group>
-    </layout>
-  </citation>
-  <bibliography hanging-indent="true" et-al-min="11" et-al-use-first="7" subsequent-author-substitute="&#8212;&#8212;&#8212;" entry-spacing="0">
-    <sort>
-      <key macro="contributors"/>
-      <key variable="issued"/>
-      <key variable="title"/>
-    </sort>
-    <layout suffix=".">
-      <group delimiter=". ">
-        <text macro="contributors"/>
-        <text macro="date"/>
-        <text macro="title"/>
-      </group>
-      <text macro="description"/>
-      <text macro="secondary-contributors" prefix=". "/>
-      <text macro="container-title" prefix=". "/>
-      <text macro="container-contributors"/>
-      <text macro="edition"/>
-      <text macro="locators-chapter"/>
-      <text macro="collection-title-journal" prefix=", " suffix=", "/>
-      <text macro="locators"/>
-      <text macro="collection-title" prefix=". "/>
-      <text macro="issue"/>
-      <text macro="locators-article"/>
-      <text macro="access" prefix=". "/>
-    </layout>
-  </bibliography>
-</style>

example/assets/pandoc-scholar/csl/jats.csl

@@ -1,203 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" default-locale="en-US">
-  <info>
-    <title>Journal Article Tag Suite</title>
-    <title-short>JATS</title-short>
-    <id>http://www.zotero.org/styles/journal-article-tag-suite</id>
-    <link href="https://github.com/MartinPaulEve/JATS-CSL/blob/master/jats.csl" rel="self"/>
-    <link rel="documentation" href="http://jats.nlm.nih.gov/archiving/tag-library/1.0/index.html"/>
-    <author>
-      <name>Martin Paul Eve</name>
-      <email>martin@martineve.com</email>
-    </author>
-    <category citation-format="numeric"/>
-    <category field="medicine"/>
-    <category field="biology"/>
-    <summary>Use this style to generate bibliographic data in Journal Article Tagging Suite (JATS) 1.0 XML format</summary>
-    <updated>2014-06-21T17:41:26+00:00</updated>
-    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License. Originally by Martin Fenner.</rights>
-  </info>
-  <locale xml:lang="en">
-    <terms>
-        <term name="et-al">{{jats}}&lt;etal/&gt;{{/jats}}</term>
-    </terms>
-  </locale>
-  <macro name="citation-number">
-    <text variable="citation-number" prefix="{{jats}}id=&quot;ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
-  </macro>
-  <macro name="author">
-    <names variable="author" delimiter=" ">
-        <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator=" ">
-            <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
-            <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
-      </name>
-      <substitute>
-        <names variable="editor"/>
-      </substitute>
-    </names>
-  </macro>
-
-  <macro name="editor" delimiter=" ">
-    <names variable="editor" prefix="{{jats}}&lt;person-group person-group-type=&quot;editor&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}">
-      <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator=" ">
-        <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
-        <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;/given-names&gt;{{/jats}}"/>
-      </name>
-      <substitute>
-        <names variable="editor"/>
-      </substitute>
-    </names>
-  </macro>
-
-  <macro name="editor">
-    <group delimiter=": ">
-      <names variable="editor">
-        <name prefix="{{jats}}&lt;name&gt;{{/jats}}" suffix="{{jats}}&lt;/name&gt;{{/jats}}" name-as-sort-order="all" sort-separator="">
-          <name-part name="family" text-case="capitalize-first" prefix="{{jats}}&lt;surname&gt;{{/jats}}" suffix="{{jats}}&lt;/surname&gt;{{/jats}}"/>
-          <name-part name="given" text-case="capitalize-first" prefix="{{jats}}&lt;given-names&gt;{{/jats}}" suffix="{{jats}}&lt;given-names&gt;{{/jats}}"/>
-        </name>
-      </names>
-    </group>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if type="book" match="any">
-        <group prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}">
-	        <text variable="title"/>
-				</group>
-			</if>
-      <else>
-        <group prefix="{{jats}}&lt;article-title&gt;{{/jats}}" suffix="{{jats}}&lt;/article-title&gt;{{/jats}}">
-	        <text variable="title"/>
-				</group>
-      </else>
-    </choose>
-  </macro>
-  <macro name="container-title">
-    <text variable="container-title" form="short" prefix="{{jats}}&lt;source&gt;{{/jats}}" suffix="{{jats}}&lt;/source&gt;{{/jats}}"/>
-  </macro>
-  <macro name="publisher">
-    <text variable="publisher" prefix="{{jats}}&lt;publisher-name&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-name&gt;{{/jats}}"/>
-    <text variable="publisher-place" prefix="{{jats}}&lt;publisher-loc&gt;{{/jats}}" suffix="{{jats}}&lt;/publisher-loc&gt;{{/jats}}"/>
-  </macro>
-  <macro name="link">
-    <choose>
-      <if match="any" variable="DOI">
-        <group prefix="{{jats}}&lt;pub-id pub-id-type=&quot;doi&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/pub-id&gt;{{/jats}}">
-          <text variable="DOI"/>
-        </group>
-      </if>
-    </choose>
-    <choose>
-      <if match="any" variable="PMID">
-        <group prefix="{{jats}}&lt;pub-id pub-id-type=&quot;pmid&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/pub-id&gt;{{/jats}}">
-          <text variable="PMID"/>
-        </group>
-      </if>
-    </choose>
-    <choose>
-      <if variable="URL" match="any">
-        <text variable="URL" />
-      </if>
-    </choose>
-  </macro>
-  <macro name="date">
-    <choose>
-      <if type="article-journal article-magazine article-newspaper report patent book" match="any">
-        <group prefix="{{jats}}&lt;date&gt;{{/jats}}" suffix="{{jats}}&lt;/date&gt;{{/jats}}">
-          <date variable="issued">
-            <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
-            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
-            <date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
-          </date>
-        </group>
-      </if>
-      <else>
-        <group prefix="{{jats}}&lt;date-in-citation content-type=&quot;access-date&quot;{{/jats}}" suffix="{{jats}}&lt;/date-in-citation&gt;{{/jats}}">
-          <date variable="accessed" prefix="{{jats}} iso-8601-date=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
-            <date-part name="year"/>
-            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
-            <date-part name="day" form="numeric-leading-zeros" prefix="{{jats}}-{{/jats}}"/>
-          </date>
-          <date variable="accessed">
-            <date-part name="day" prefix="{{jats}}&lt;day&gt;{{/jats}}" suffix="{{jats}}&lt;/day&gt;{{/jats}}"/>
-            <date-part name="month" form="numeric-leading-zeros" prefix="{{jats}}&lt;month&gt;{{/jats}}" suffix="{{jats}}&lt;/month&gt;{{/jats}}"/>
-            <date-part name="year" prefix="{{jats}}&lt;year&gt;{{/jats}}" suffix="{{jats}}&lt;/year&gt;{{/jats}}"/>
-          </date>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <macro name="location">
-    <choose>
-      <if type="article-journal article-magazine" match="any">
-        <text variable="volume" prefix="{{jats}}&lt;volume&gt;{{/jats}}" suffix="{{jats}}&lt;/volume&gt;{{/jats}}"/>
-        <text variable="issue" prefix="{{jats}}&lt;issue&gt;{{/jats}}" suffix="{{jats}}&lt;/issue&gt;{{/jats}}"/>
-      </if>
-    </choose>
-    <choose>
-      <if type="article-journal article-magazine article-newspaper chapter" match="any">
-        <text variable="page-first" prefix="{{jats}}&lt;fpage&gt;{{/jats}}" suffix="{{jats}}&lt;/fpage&gt;{{/jats}}"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="publication-type">
-    <group prefix="{{jats}} publication-type=&quot;{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}">
-      <choose>
-        <if type="article-journal article-magazine article-newspaper" match="any">
-          <text value="journal"/>
-        </if>
-        <else-if type="book" match="any">
-          <text value="book"/>
-        </else-if>
-        <else-if type="chapter" match="any">
-          <text value="bookchapter"/>
-        </else-if>
-        <else-if type="dataset" match="any">
-          <text value="dataset"/>
-        </else-if>
-        <else-if type="patent" match="any">
-          <text value="patent"/>
-        </else-if>
-        <else-if type="report" match="any">
-          <text value="report"/>
-        </else-if>
-        <else-if type="review" match="any">
-          <text value="review"/>
-        </else-if>
-        <else>
-          <text value="standard"/>
-        </else>
-      </choose>
-    </group>
-  </macro>
-  <citation collapse="citation-number">
-    <sort>
-      <key variable="citation-number"/>
-    </sort>
-    <layout delimiter=",">
-      <group prefix="{{jats}}&lt;xref ref-type=&quot;bibr&quot; rid=&quot;{{/jats}}" suffix="{{jats}}&lt;/xref&gt;{{/jats}}">
-        <text variable="citation-number" prefix="{{jats}}ref-{{/jats}}" suffix="{{jats}}&quot;&gt;{{/jats}}"/>
-        <text variable="citation-number"/>
-      </group>
-    </layout>
-  </citation>
-  <bibliography sort-separator="">
-    <layout>
-      <group prefix="{{jats}}&lt;ref {{/jats}}" suffix="{{jats}}&lt;/ref&gt;{{/jats}}">
-        <text macro="citation-number"/>
-        <group prefix="{{jats}}&lt;element-citation{{/jats}}" suffix="{{jats}}&lt;/element-citation&gt;{{/jats}}">
-          <text macro="publication-type"/>
-          <text macro="author" prefix="{{jats}}&lt;person-group person-group-type=&quot;author&quot;&gt;{{/jats}}" suffix="{{jats}}&lt;/person-group&gt;{{/jats}}"/>
-          <text macro="title" />
-          <text macro="container-title"/>
-          <text macro="editor"/>
-          <text macro="publisher"/>
-          <text macro="date"/>
-          <text macro="location"/>
-          <text macro="link"/>
-        </group>
-      </group>
-    </layout>
-  </bibliography>
-</style>

example/assets/pandoc-scholar/docker/alpine.Dockerfile

@@ -1,19 +0,0 @@
-FROM alpine:3.12 AS builder
-RUN apk --no-cache add ca-certificates curl make zip
-
-WORKDIR /app
-COPY . /app
-env NO_GNU_TAR=true
-RUN make archives
-
-
-FROM pandoc/latex:2.10.1
-
-RUN apk --no-cache add make \
-  && tlmgr install preprint
-
-COPY --from=builder /app/dist/pandoc-scholar /opt/pandoc-scholar
-
-ENV PANDOC_SCHOLAR_PATH=/opt/pandoc-scholar
-
-ENTRYPOINT ["/usr/bin/make"]

example/assets/pandoc-scholar/docker/ubuntu.Dockerfile

@@ -1,24 +0,0 @@
-FROM ubuntu:focal AS builder
-RUN apt-get -q --no-allow-insecure-repositories update \
-  && DEBIAN_FRONTEND=noninteractive \
-     apt-get install --assume-yes --no-install-recommends \
-       ca-certificates curl make zip
-
-WORKDIR /app
-COPY . /app
-RUN make archives
-
-
-FROM pandoc/ubuntu-latex:2.10.1
-
-RUN apt-get -q --no-allow-insecure-repositories update \
-  && DEBIAN_FRONTEND=noninteractive \
-     apt-get install --assume-yes --no-install-recommends make \
-  && rm -rf /var/lib/apt/lists/* \
-  && tlmgr install preprint
-
-COPY --from=builder /app/dist/pandoc-scholar /opt/pandoc-scholar
-
-ENV PANDOC_SCHOLAR_PATH=/opt/pandoc-scholar
-
-ENTRYPOINT ["/usr/bin/make"]

example/assets/pandoc-scholar/example/.gitignore

@@ -1 +0,0 @@
-/outfile.*

example/assets/pandoc-scholar/example/Makefile

@@ -1,5 +0,0 @@
-# Assume pandoc-scholar is in the parent directory.
-# Should usually be overwritten or configured via an environment variable.
-PANDOC_SCHOLAR_PATH   ?= $(shell dirname $(PWD))
-ARTICLE_FILE=article.md
-include $(PANDOC_SCHOLAR_PATH)/Makefile

example/assets/pandoc-scholar/example/apa.csl

@@ -1,1916 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="never" page-range-format="expanded">
-  <info>
-    <title>American Psychological Association 7th edition</title>
-    <title-short>APA</title-short>
-    <id>http://www.zotero.org/styles/apa</id>
-    <link href="http://www.zotero.org/styles/apa" rel="self"/>
-    <link href="http://www.zotero.org/styles/apa-6th-edition" rel="template"/>
-    <link href="https://apastyle.apa.org/style-grammar-guidelines/references/examples" rel="documentation"/>
-    <author>
-      <name>Brenton M. Wiernik</name>
-      <email>zotero@wiernik.org</email>
-    </author>
-    <category citation-format="author-date"/>
-    <category field="psychology"/>
-    <category field="generic-base"/>
-    <updated>2019-12-04T13:09:49+00:00</updated>
-    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
-  </info>
-  <locale xml:lang="en">
-    <terms>
-      <term name="editortranslator" form="short">
-        <single>ed. &amp; trans.</single>
-        <multiple>eds. &amp; trans.</multiple>
-      </term>
-      <term name="translator" form="short">trans.</term>
-      <term name="interviewer" form="short">
-        <single>interviewer</single>
-        <multiple>interviewers</multiple>
-      </term>
-      <term name="collection-editor" form="short">
-        <single>ed.</single>
-        <multiple>eds.</multiple>
-      </term>
-      <term name="circa" form="short">ca.</term>
-      <term name="bc"> B.C.E.</term>
-      <term name="ad"> C.E.</term>
-      <term name="letter">personal communication</term>
-      <term name="letter" form="short">letter</term>
-      <term name="issue" form="long">
-        <single>issue</single>
-        <multiple>issues</multiple>
-      </term>
-    </terms>
-  </locale>
-  <locale xml:lang="af">
-    <terms>
-      <term name="letter">persoonlike kommunikasie</term>
-      <term name="letter" form="short">brief</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ar">
-    <terms>
-      <term name="letter">اتصال شخصي</term>
-      <term name="letter" form="short">خطاب</term>
-    </terms>
-  </locale>
-  <locale xml:lang="bg">
-    <terms>
-      <term name="letter">лична комуникация</term>
-      <term name="letter" form="short">писмо</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ca">
-    <terms>
-      <term name="letter">comunicació personal</term>
-      <term name="letter" form="short">carta</term>
-    </terms>
-  </locale>
-  <locale xml:lang="cs">
-    <terms>
-      <term name="letter">osobní komunikace</term>
-      <term name="letter" form="short">dopis</term>
-    </terms>
-  </locale>
-  <locale xml:lang="cy">
-    <terms>
-      <term name="letter">cyfathrebu personol</term>
-      <term name="letter" form="short">llythyr</term>
-    </terms>
-  </locale>
-  <locale xml:lang="da">
-    <terms>
-      <term name="et-al">et al.</term>
-      <term name="letter">personlig kommunikation</term>
-      <term name="letter" form="short">brev</term>
-    </terms>
-  </locale>
-  <locale xml:lang="de">
-    <terms>
-      <term name="et-al">et al.</term>
-      <term name="letter">persönliche Kommunikation</term>
-      <term name="letter" form="short">Brief</term>
-    </terms>
-  </locale>
-  <locale xml:lang="el">
-    <terms>
-      <term name="letter">προσωπική επικοινωνία</term>
-      <term name="letter" form="short">επιστολή</term>
-    </terms>
-  </locale>
-  <locale xml:lang="es">
-    <terms>
-      <term name="from">de</term>
-      <term name="letter">comunicación personal</term>
-      <term name="letter" form="short">carta</term>
-    </terms>
-  </locale>
-  <locale xml:lang="et">
-    <terms>
-      <term name="letter">isiklik suhtlus</term>
-      <term name="letter" form="short">kiri</term>
-    </terms>
-  </locale>
-  <locale xml:lang="eu">
-    <terms>
-      <term name="letter">komunikazio pertsonala</term>
-      <term name="letter" form="short">gutuna</term>
-    </terms>
-  </locale>
-  <locale xml:lang="fa">
-    <terms>
-      <term name="letter">ارتباط شخصی</term>
-      <term name="letter" form="short">نامه</term>
-    </terms>
-  </locale>
-  <locale xml:lang="fi">
-    <terms>
-      <term name="letter">henkilökohtainen viestintä</term>
-      <term name="letter" form="short">kirje</term>
-    </terms>
-  </locale>
-  <locale xml:lang="fr">
-    <terms>
-      <term name="letter">communication personnelle</term>
-      <term name="letter" form="short">lettre</term>
-      <term name="editor" form="short">
-        <single>éd.</single>
-        <multiple>éds.</multiple>
-      </term>
-    </terms>
-  </locale>
-  <locale xml:lang="he">
-    <terms>
-      <term name="letter">תקשורת אישית</term>
-      <term name="letter" form="short">מכתב</term>
-    </terms>
-  </locale>
-  <locale xml:lang="hr">
-    <terms>
-      <term name="letter">osobna komunikacija</term>
-      <term name="letter" form="short">pismo</term>
-    </terms>
-  </locale>
-  <locale xml:lang="hu">
-    <terms>
-      <term name="letter">személyes kommunikáció</term>
-      <term name="letter" form="short">levél</term>
-    </terms>
-  </locale>
-  <locale xml:lang="id">
-    <terms>
-      <term name="letter">komunikasi pribadi</term>
-      <term name="letter" form="short">surat</term>
-    </terms>
-  </locale>
-  <locale xml:lang="is">
-    <terms>
-      <term name="letter">persónuleg samskipti</term>
-      <term name="letter" form="short">bréf</term>
-    </terms>
-  </locale>
-  <locale xml:lang="it">
-    <terms>
-      <term name="letter">comunicazione personale</term>
-      <term name="letter" form="short">lettera</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ja">
-    <terms>
-      <term name="letter">個人的なやり取り</term>
-      <term name="letter" form="short">手紙</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ko">
-    <terms>
-      <term name="letter">개인 서신</term>
-      <term name="letter" form="short">편지</term>
-    </terms>
-  </locale>
-  <locale xml:lang="la">
-    <terms>
-      <term name="letter"/>
-      <term name="letter" form="short">epistula</term>
-    </terms>
-  </locale>
-  <locale xml:lang="lt">
-    <terms>
-      <term name="letter">communicationis personalis</term>
-      <term name="letter" form="short"/>
-    </terms>
-  </locale>
-  <locale xml:lang="lv">
-    <terms>
-      <term name="letter">personīga komunikācija</term>
-      <term name="letter" form="short">vēstule</term>
-    </terms>
-  </locale>
-  <locale xml:lang="mn">
-    <terms>
-      <term name="letter">хувийн харилцаа холбоо</term>
-      <term name="letter" form="short">захиа</term>
-    </terms>
-  </locale>
-  <locale xml:lang="nb">
-    <terms>
-      <term name="et-al">et al.</term>
-      <term name="letter">personlig kommunikasjon</term>
-      <term name="letter" form="short">brev</term>
-    </terms>
-  </locale>
-  <locale xml:lang="nl">
-    <terms>
-      <term name="et-al">et al.</term>
-      <term name="letter">persoonlijke communicatie</term>
-      <term name="letter" form="short">brief</term>
-    </terms>
-  </locale>
-  <locale xml:lang="nn">
-    <terms>
-      <term name="et-al">et al.</term>
-      <term name="letter">personlig kommunikasjon</term>
-      <term name="letter" form="short">brev</term>
-    </terms>
-  </locale>
-  <locale xml:lang="pl">
-    <terms>
-      <term name="letter">osobista komunikacja</term>
-      <term name="letter" form="short">list</term>
-    </terms>
-  </locale>
-  <locale xml:lang="pt">
-    <terms>
-      <term name="letter">comunicação pessoal</term>
-      <term name="letter" form="short">carta</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ro">
-    <terms>
-      <term name="letter">comunicare personală</term>
-      <term name="letter" form="short">scrisoare</term>
-    </terms>
-  </locale>
-  <locale xml:lang="ru">
-    <terms>
-      <term name="letter">личная переписка</term>
-      <term name="letter" form="short">письмо</term>
-    </terms>
-  </locale>
-  <locale xml:lang="sk">
-    <terms>
-      <term name="letter">osobná komunikácia</term>
-      <term name="letter" form="short">list</term>
-    </terms>
-  </locale>
-  <locale xml:lang="sl">
-    <terms>
-      <term name="letter">osebna komunikacija</term>
-      <term name="letter" form="short">pismo</term>
-    </terms>
-  </locale>
-  <locale xml:lang="sr">
-    <terms>
-      <term name="letter">лична комуникација</term>
-      <term name="letter" form="short">писмо</term>
-    </terms>
-  </locale>
-  <locale xml:lang="sv">
-    <terms>
-      <term name="letter">personlig kommunikation</term>
-      <term name="letter" form="short">brev</term>
-    </terms>
-  </locale>
-  <locale xml:lang="th">
-    <terms>
-      <term name="letter">การสื่อสารส่วนบุคคล</term>
-      <term name="letter" form="short">จดหมาย</term>
-    </terms>
-  </locale>
-  <locale xml:lang="tr">
-    <terms>
-      <term name="letter">kişisel iletişim</term>
-      <term name="letter" form="short">mektup</term>
-    </terms>
-  </locale>
-  <locale xml:lang="uk">
-    <terms>
-      <term name="letter">особисте спілкування</term>
-      <term name="letter" form="short">лист</term>
-    </terms>
-  </locale>
-  <locale xml:lang="vi">
-    <terms>
-      <term name="letter">giao tiếp cá nhân</term>
-      <term name="letter" form="short">thư</term>
-    </terms>
-  </locale>
-  <locale xml:lang="zh-CN">
-    <terms>
-      <term name="letter">的私人交流</term>
-      <term name="letter" form="short">信函</term>
-    </terms>
-  </locale>
-  <locale xml:lang="zh-TW">
-    <terms>
-      <term name="letter">私人通訊</term>
-      <term name="letter" form="short">信函</term>
-    </terms>
-  </locale>
-  <!-- General categories of item types:
-       Periodical: article-journal article-magazine article-newspaper post-weblog review review-book
-       Periodical or Booklike: paper-conference
-       Booklike: article book broadcast chapter dataset entry entry-dictionary entry-encyclopedia figure 
-                 graphic interview manuscript map motion_picture musical_score pamphlet patent 
-                 personal_communication report song speech thesis post webpage
-       Legal: bill legal_case legislation treaty
-  -->
-  <!-- APA references contain four parts: author, date, title, source -->
-  <macro name="author-bib">
-    <names variable="composer" delimiter=", ">
-      <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-      <substitute>
-        <names variable="author"/>
-        <names variable="illustrator"/>
-        <names variable="director">
-          <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-          <label form="long" prefix=" (" suffix=")" text-case="title"/>
-        </names>
-        <choose>
-          <if variable="container-title">
-            <choose>
-              <if type="book entry entry-dictionary entry-encyclopedia" match="any">
-                <choose>
-                  <if variable="title">
-                    <group delimiter=" ">
-                      <text macro="title"/>
-                      <text macro="parenthetical"/>
-                    </group>
-                  </if>
-                  <else>
-                    <text macro="title-and-descriptions"/>
-                  </else>
-                </choose>
-              </if>
-            </choose>
-          </if>
-        </choose>
-        <!-- Test for editortranslator and put that first as that becomes available -->
-        <names variable="editor" delimiter=", ">
-          <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-          <label form="short" prefix=" (" suffix=")" text-case="title"/>
-        </names>
-        <names variable="editorial-director">
-          <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-          <label form="short" prefix=" (" suffix=")" text-case="title"/>
-        </names>
-        <names variable="collection-editor">
-          <name name-as-sort-order="all" and="symbol" sort-separator=", " initialize-with=". " delimiter=", " delimiter-precedes-last="always"/>
-          <label form="short" prefix=" (" suffix=")" text-case="title"/>
-        </names>
-        <choose>
-          <if variable="title">
-            <group delimiter=" ">
-              <text macro="title"/>
-              <text macro="parenthetical"/>
-            </group>
-          </if>
-          <else>
-            <text macro="title-and-descriptions"/>
-          </else>
-        </choose>
-      </substitute>
-    </names>
-  </macro>
-  <macro name="author-intext">
-    <choose>
-      <if type="bill legal_case legislation treaty" match="any">
-        <text macro="title-intext"/>
-      </if>
-      <else-if type="interview personal_communication" match="any">
-        <choose>
-          <!-- These variables indicate that the letter is retrievable by the reader. 
-                If not, then use the APA in-text-only personal communication format -->
-          <if variable="archive container-title DOI publisher URL" match="none">
-            <group delimiter=", ">
-              <names variable="author">
-                <name and="symbol" delimiter=", " initialize-with=". "/>
-                <substitute>
-                  <text macro="title-intext"/>
-                </substitute>
-              </names>
-              <!-- Replace with term="personal-communication" if that becomes available -->
-              <text term="letter"/>
-            </group>
-          </if>
-          <else>
-            <names variable="author" delimiter=", ">
-              <name form="short" and="symbol" delimiter=", " initialize-with=". "/>
-              <substitute>
-                <text macro="title-intext"/>
-              </substitute>
-            </names>
-          </else>
-        </choose>
-      </else-if>
-      <else>
-        <names variable="composer" delimiter=", ">
-          <name form="short" and="symbol" delimiter=", " initialize-with=". "/>
-          <substitute>
-            <names variable="author"/>
-            <names variable="illustrator"/>
-            <names variable="director"/>
-            <choose>
-              <if variable="container-title">
-                <choose>
-                  <if type="book entry entry-dictionary entry-encyclopedia" match="any">
-                    <text macro="title-intext"/>
-                  </if>
-                </choose>
-              </if>
-            </choose>
-            <names variable="editor"/>
-            <names variable="editorial-director"/>
-            <text macro="title-intext"/>
-          </substitute>
-        </names>
-      </else>
-    </choose>
-  </macro>
-  <macro name="date-bib">
-    <group delimiter=" " prefix="(" suffix=")">
-      <choose>
-        <if is-uncertain-date="issued">
-          <text term="circa" form="short"/>
-        </if>
-      </choose>
-      <group>
-        <choose>
-          <if variable="issued">
-            <date variable="issued">
-              <date-part name="year"/>
-            </date>
-            <text variable="year-suffix"/>
-            <choose>
-              <if type="article-magazine article-newspaper broadcast interview motion_picture pamphlet personal_communication post post-weblog song speech webpage" match="any">
-                <!-- Many video and audio examples in manual give full dates. Err on the side of too much information. -->
-                <date variable="issued">
-                  <date-part prefix=", " name="month"/>
-                  <date-part prefix=" " name="day"/>
-                </date>
-              </if>
-              <else-if type="paper-conference">
-                <!-- Capture 'speech' stored as 'paper-conference' -->
-                <choose>
-                  <if variable="collection-editor editor editorial-director issue page volume" match="none">
-                    <date variable="issued">
-                      <date-part prefix=", " name="month"/>
-                      <date-part prefix=" " name="day"/>
-                    </date>
-                  </if>
-                </choose>
-              </else-if>
-              <!-- Only year: article article-journal book chapter entry entry-dictionary entry-encyclopedia dataset figure graphic 
-                   manuscript map musical_score paper-conference[published] patent report review review-book thesis -->
-            </choose>
-          </if>
-          <else-if variable="status">
-            <group>
-              <text variable="status" text-case="lowercase"/>
-              <text variable="year-suffix" prefix="-"/>
-            </group>
-          </else-if>
-          <else>
-            <group>
-              <text term="no date" form="short"/>
-              <text variable="year-suffix" prefix="-"/>
-            </group>
-          </else>
-        </choose>
-      </group>
-    </group>
-  </macro>
-  <macro name="date-sort-group">
-    <choose>
-      <if variable="issued">
-        <text value="1"/>
-      </if>
-      <else-if variable="status">
-        <text value="2"/>
-      </else-if>
-      <else>
-        <text value="0"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="date-sort-date">
-    <choose>
-      <if type="article-magazine article-newspaper broadcast interview pamphlet personal_communication post post-weblog speech treaty webpage" match="any">
-        <date variable="issued" form="numeric"/>
-      </if>
-      <else-if type="paper-conference">
-        <!-- Capture 'speech' stored as 'paper-conference' -->
-        <choose>
-          <if variable="collection-editor editor editorial-director issue page volume" match="none">
-            <date variable="issued" form="numeric"/>
-          </if>
-        </choose>
-      </else-if>
-      <else>
-        <date variable="issued" form="numeric"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="date-intext">
-    <choose>
-      <if variable="issued">
-        <group delimiter="/">
-          <group delimiter=" ">
-            <choose>
-              <if is-uncertain-date="original-date">
-                <text term="circa" form="short"/>
-              </if>
-            </choose>
-            <date variable="original-date">
-              <date-part name="year"/>
-            </date>
-          </group>
-          <group delimiter=" ">
-            <choose>
-              <if is-uncertain-date="issued">
-                <text term="circa" form="short"/>
-              </if>
-            </choose>
-            <group>
-              <choose>
-                <if type="interview personal_communication" match="any">
-                  <choose>
-                    <if variable="archive container-title DOI publisher URL" match="none">
-                      <!-- These variables indicate that the communication is retrievable by the reader. 
-                           If not, then use the in-text-only personal communication format -->
-                      <date variable="issued" form="text"/>
-                    </if>
-                    <else>
-                      <date variable="issued">
-                        <date-part name="year"/>
-                      </date>
-                    </else>
-                  </choose>
-                </if>
-                <else>
-                  <date variable="issued">
-                    <date-part name="year"/>
-                  </date>
-                </else>
-              </choose>
-              <text variable="year-suffix"/>
-            </group>
-          </group>
-        </group>
-      </if>
-      <else-if variable="status">
-        <text variable="status" text-case="lowercase"/>
-        <text variable="year-suffix" prefix="-"/>
-      </else-if>
-      <else>
-        <text term="no date" form="short"/>
-        <text variable="year-suffix" prefix="-"/>
-      </else>
-    </choose>
-  </macro>
-  <!-- APA has two description elements following the title:
-       title (parenthetical) [bracketed]  -->
-  <macro name="title-and-descriptions">
-    <choose>
-      <if variable="title">
-        <group delimiter=" ">
-          <text macro="title"/>
-          <text macro="parenthetical"/>
-          <text macro="bracketed"/>
-        </group>
-      </if>
-      <else>
-        <group delimiter=" ">
-          <text macro="bracketed"/>
-          <text macro="parenthetical"/>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <macro name="title">
-    <choose>
-      <if type="post webpage" match="any">
-        <!-- Webpages are always italicized -->
-        <text variable="title" font-style="italic"/>
-      </if>
-      <else-if variable="container-title" match="any">
-        <!-- Other types are italicized based on presence of container-title.
-             Assume that review and review-book are published in periodicals/blogs,
-             not just on a web page (ex. 69) -->
-        <text variable="title"/>
-      </else-if>
-      <else>
-        <choose>
-          <if type="article-journal article-magazine article-newspaper post-weblog review review-book" match="any">
-            <text variable="title" font-style="italic"/>
-          </if>
-          <else-if type="paper-conference">
-            <choose>
-              <if variable="collection-editor editor editorial-director" match="any">
-                <group delimiter=": " font-style="italic">
-                  <text variable="title"/>
-                  <!-- Replace with volume-title as that becomes available -->
-                  <choose>
-                    <if is-numeric="volume" match="none">
-                      <group delimiter=" ">
-                        <label variable="volume" form="short" text-case="capitalize-first"/>
-                        <text variable="volume"/>
-                      </group>
-                    </if>
-                  </choose>
-                </group>
-              </if>
-              <else>
-                <text variable="title" font-style="italic"/>
-              </else>
-            </choose>
-          </else-if>
-          <else>
-            <group delimiter=": " font-style="italic">
-              <text variable="title"/>
-              <!-- Replace with volume-title as that becomes available -->
-              <choose>
-                <if is-numeric="volume" match="none">
-                  <group delimiter=" ">
-                    <label variable="volume" form="short" text-case="capitalize-first"/>
-                    <text variable="volume"/>
-                  </group>
-                </if>
-              </choose>
-            </group>
-          </else>
-        </choose>
-      </else>
-    </choose>
-  </macro>
-  <macro name="title-intext">
-    <choose>
-      <if variable="title" match="none">
-        <text macro="bracketed-intext" prefix="[" suffix="]"/>
-      </if>
-      <else-if type="bill">
-        <!-- If a bill has no number or container-title, assume it is a hearing; italic -->
-        <choose>
-          <if variable="number container-title" match="none">
-            <text variable="title" form="short" font-style="italic" text-case="title"/>
-          </if>
-          <else-if variable="title">
-            <text variable="title" form="short" text-case="title"/>
-          </else-if>
-          <else>
-            <group delimiter=" ">
-              <text variable="genre"/>
-              <group delimiter=" ">
-                <choose>
-                  <if variable="chapter-number container-title" match="none">
-                    <!-- Replace with label variable="number" as that becomes available -->
-                    <text term="issue" form="short"/>
-                  </if>
-                </choose>
-                <text variable="number"/>
-              </group>
-            </group>
-          </else>
-        </choose>
-      </else-if>
-      <else-if type="legal_case" match="any">
-        <!-- Cases are italicized -->
-        <text variable="title" font-style="italic"/>
-      </else-if>
-      <else-if type="legislation treaty" match="any">
-        <!-- Legislation and treaties not italicized or quoted -->
-        <text variable="title" form="short" text-case="title"/>
-      </else-if>
-      <else-if type="post webpage" match="any">
-        <!-- Webpages are always italicized -->
-        <text variable="title" form="short" font-style="italic" text-case="title"/>
-      </else-if>
-      <else-if variable="container-title" match="any">
-        <!-- Other types are italicized or quoted based on presence of container-title. As in title macro. -->
-        <text variable="title" form="short" quotes="true" text-case="title"/>
-      </else-if>
-      <else>
-        <text variable="title" form="short" font-style="italic" text-case="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="parenthetical">
-    <!-- (Secondary contributors; Database location; Genre no. 123; Report Series 123, Version, Edition, Volume, Page) -->
-    <group prefix="(" suffix=")">
-      <choose>
-        <if type="patent">
-          <!-- authority: U.S. ; genre: patent ; number: 123,445 -->
-          <group delimiter=" ">
-            <text variable="authority" form="short"/>
-            <choose>
-              <if variable="genre">
-                <text variable="genre" text-case="capitalize-first"/>
-              </if>
-              <else>
-                <!-- This should be localized -->
-                <text value="patent" text-case="capitalize-first"/>
-              </else>
-            </choose>
-            <group delimiter=" ">
-              <!-- Replace with label variable="number" if that becomes available -->
-              <text term="issue" form="short" text-case="capitalize-first"/>
-              <text variable="number"/>
-            </group>
-          </group>
-        </if>
-        <else-if type="post webpage" match="any">
-          <!-- For post webpage, container-title is treated as publisher -->
-          <group delimiter="; ">
-            <text macro="secondary-contributors"/>
-            <text macro="database-location"/>
-            <text macro="number"/>
-            <text macro="locators-booklike"/>
-          </group>
-        </else-if>
-        <else-if variable="container-title">
-          <group delimiter="; ">
-            <text macro="secondary-contributors"/>
-            <choose>
-              <if type="broadcast graphic map motion_picture song" match="any">
-                <!-- For audiovisual media, number information comes after title, not container-title -->
-                <text macro="number"/>
-              </if>
-            </choose>
-          </group>
-        </else-if>
-        <else>
-          <group delimiter="; ">
-            <text macro="secondary-contributors"/>
-            <text macro="database-location"/>
-            <text macro="number"/>
-            <text macro="locators-booklike"/>
-          </group>
-        </else>
-      </choose>
-    </group>
-  </macro>
-  <macro name="parenthetical-container">
-    <choose>
-      <if variable="container-title" match="any">
-        <group prefix="(" suffix=")">
-          <group delimiter="; ">
-            <text macro="database-location"/>
-            <choose>
-              <if type="broadcast graphic map motion_picture song" match="none">
-                <!-- For audiovisual media, number information comes after title, not container-title -->
-                <text macro="number"/>
-              </if>
-            </choose>
-            <text macro="locators-booklike"/>
-          </group>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="bracketed">
-    <!-- [Descriptive information] -->
-    <!-- If there is a number, genre is already printed in macro="number" -->
-    <group prefix="[" suffix="]">
-      <choose>
-        <if variable="reviewed-author reviewed-title" type="review review-book" match="any">
-          <!-- Reviewed item -->
-          <group delimiter="; ">
-            <group delimiter=", ">
-              <group delimiter=" ">
-                <!-- Assume that genre is entered as 'Review of the book' or similar -->
-                <choose>
-                  <if variable="number" match="none">
-                    <choose>
-                      <if variable="genre">
-                        <text variable="genre" text-case="capitalize-first"/>
-                      </if>
-                      <else-if variable="medium">
-                        <text variable="medium" text-case="capitalize-first"/>
-                      </else-if>
-                      <else>
-                        <!-- Replace with term="review" as that becomes available -->
-                        <text value="Review of"/>
-                      </else>
-                    </choose>
-                  </if>
-                  <else>
-                    <choose>
-                      <if variable="medium">
-                        <text variable="medium" text-case="capitalize-first"/>
-                      </if>
-                      <else>
-                        <!-- Replace with term="review" as that becomes available -->
-                        <text value="Review of"/>
-                      </else>
-                    </choose>
-                  </else>
-                </choose>
-                <text macro="reviewed-title"/>
-              </group>
-              <names variable="reviewed-author">
-                <label form="verb-short" suffix=" "/>
-                <name and="symbol" initialize-with=". " delimiter=", "/>
-              </names>
-            </group>
-            <choose>
-              <if variable="genre" match="any">
-                <choose>
-                  <if variable="number" match="none">
-                    <text variable="medium" text-case="capitalize-first"/>
-                  </if>
-                </choose>
-              </if>
-            </choose>
-          </group>
-        </if>
-        <else-if type="thesis">
-          <!-- Thesis type and institution -->
-          <group delimiter="; ">
-            <choose>
-              <if variable="number" match="none">
-                <group delimiter=", ">
-                  <text variable="genre" text-case="capitalize-first"/>
-                  <choose>
-                    <if variable="archive DOI URL" match="any">
-                      <!-- Include the university in brackets if thesis is published -->
-                      <text variable="publisher"/>
-                    </if>
-                  </choose>
-                </group>
-              </if>
-            </choose>
-            <text variable="medium" text-case="capitalize-first"/>
-          </group>
-        </else-if>
-        <else-if variable="interviewer" type="interview" match="any">
-          <!-- Interview information -->
-          <choose>
-            <if variable="title">
-              <text macro="format"/>
-            </if>
-            <else-if variable="genre">
-              <group delimiter="; ">
-                <group delimiter=" ">
-                  <text variable="genre" text-case="capitalize-first"/>
-                  <group delimiter=" ">
-                    <text term="author" form="verb"/>
-                    <names variable="interviewer">
-                      <name and="symbol" initialize-with=". " delimiter=", "/>
-                    </names>
-                  </group>
-                </group>
-              </group>
-            </else-if>
-            <else-if variable="interviewer">
-              <group delimiter="; ">
-                <names variable="interviewer">
-                  <label form="verb" suffix=" " text-case="capitalize-first"/>
-                  <name and="symbol" initialize-with=". " delimiter=", "/>
-                </names>
-                <text variable="medium" text-case="capitalize-first"/>
-              </group>
-            </else-if>
-            <else>
-              <text macro="format"/>
-            </else>
-          </choose>
-        </else-if>
-        <else-if type="personal_communication">
-          <!-- Letter information -->
-          <choose>
-            <if variable="recipient">
-              <group delimiter="; ">
-                <group delimiter=" ">
-                  <choose>
-                    <if variable="number" match="none">
-                      <choose>
-                        <if variable="genre">
-                          <text variable="genre" text-case="capitalize-first"/>
-                        </if>
-                        <else-if variable="medium">
-                          <text variable="medium" text-case="capitalize-first"/>
-                        </else-if>
-                        <else>
-                          <text term="letter" form="short" text-case="capitalize-first"/>
-                        </else>
-                      </choose>
-                    </if>
-                    <else>
-                      <choose>
-                        <if variable="medium">
-                          <text variable="medium" text-case="capitalize-first"/>
-                        </if>
-                        <else>
-                          <text term="letter" form="short" text-case="capitalize-first"/>
-                        </else>
-                      </choose>
-                    </else>
-                  </choose>
-                  <names variable="recipient" delimiter=", ">
-                    <label form="verb" suffix=" "/>
-                    <name and="symbol" delimiter=", "/>
-                  </names>
-                </group>
-                <choose>
-                  <if variable="genre" match="any">
-                    <choose>
-                      <if variable="number" match="none">
-                        <text variable="medium" text-case="capitalize-first"/>
-                      </if>
-                    </choose>
-                  </if>
-                </choose>
-              </group>
-            </if>
-            <else>
-              <text macro="format"/>
-            </else>
-          </choose>
-        </else-if>
-        <else-if variable="composer" type="song" match="all">
-          <!-- Performer of classical music works -->
-          <group delimiter="; ">
-            <choose>
-              <if variable="number" match="none">
-                <group delimiter=" ">
-                  <choose>
-                    <if variable="genre">
-                      <text variable="genre" text-case="capitalize-first"/>
-                      <!-- Replace prefix with performer label as that becomes available -->
-                      <names variable="author" prefix="recorded by ">
-                        <name and="symbol" initialize-with=". " delimiter=", "/>
-                      </names>
-                    </if>
-                    <else-if variable="medium">
-                      <text variable="medium" text-case="capitalize-first"/>
-                      <!-- Replace prefix with performer label as that becomes available -->
-                      <names variable="author" prefix="recorded by ">
-                        <name and="symbol" initialize-with=". " delimiter=", "/>
-                      </names>
-                    </else-if>
-                    <else>
-                      <!-- Replace prefix with performer label as that becomes available -->
-                      <names variable="author" prefix="Recorded by ">
-                        <name and="symbol" initialize-with=". " delimiter=", "/>
-                      </names>
-                    </else>
-                  </choose>
-                </group>
-              </if>
-              <else>
-                <group delimiter=" ">
-                  <choose>
-                    <if variable="medium">
-                      <text variable="medium" text-case="capitalize-first"/>
-                      <!-- Replace prefix with performer label as that becomes available -->
-                      <names variable="author" prefix="recorded by ">
-                        <name and="symbol" initialize-with=". " delimiter=", "/>
-                      </names>
-                    </if>
-                    <else>
-                      <!-- Replace prefix with performer label as that becomes available -->
-                      <names variable="author" prefix="Recorded by ">
-                        <name and="symbol" initialize-with=". " delimiter=", "/>
-                      </names>
-                    </else>
-                  </choose>
-                </group>
-              </else>
-            </choose>
-            <choose>
-              <if variable="genre" match="any">
-                <choose>
-                  <if variable="number" match="none">
-                    <text variable="medium" text-case="capitalize-first"/>
-                  </if>
-                </choose>
-              </if>
-            </choose>
-          </group>
-        </else-if>
-        <else-if variable="container-title" match="none">
-          <!-- Other description -->
-          <text macro="format"/>
-        </else-if>
-        <else>
-          <!-- For conference presentations, chapters in reports, software, place bracketed after the container title -->
-          <choose>
-            <if type="paper-conference speech" match="any">
-              <choose>
-                <if variable="collection-editor editor editorial-director issue page volume" match="any">
-                  <text macro="format"/>
-                </if>
-              </choose>
-            </if>
-            <else-if type="book">
-              <choose>
-                <if variable="version" match="none">
-                  <text macro="format"/>
-                </if>
-              </choose>
-            </else-if>
-            <else-if type="report" match="none">
-              <text macro="format"/>
-            </else-if>
-          </choose>
-        </else>
-      </choose>
-    </group>
-  </macro>
-  <macro name="bracketed-intext">
-    <group prefix="[" suffix="]">
-      <choose>
-        <if variable="reviewed-author reviewed-title" type="review review-book" match="any">
-          <!-- This should be localized -->
-          <text macro="reviewed-title-intext" prefix="Review of "/>
-        </if>
-        <else-if variable="interviewer" type="interview" match="any">
-          <names variable="interviewer">
-            <label form="verb" suffix=" " text-case="capitalize-first"/>
-            <name and="symbol" initialize-with=". " delimiter=", "/>
-            <substitute>
-              <text macro="format-intext"/>
-            </substitute>
-          </names>
-        </else-if>
-        <else-if type="personal_communication">
-          <!-- Letter information -->
-          <choose>
-            <if variable="recipient">
-              <group delimiter=" ">
-                <choose>
-                  <if variable="number" match="none">
-                    <text variable="genre" text-case="capitalize-first"/>
-                  </if>
-                  <else>
-                    <text term="letter" form="short" text-case="capitalize-first"/>
-                  </else>
-                </choose>
-                <names variable="recipient" delimiter=", ">
-                  <label form="verb" suffix=" "/>
-                  <name and="symbol" delimiter=", "/>
-                </names>
-              </group>
-            </if>
-            <else>
-              <text macro="format-intext"/>
-            </else>
-          </choose>
-        </else-if>
-        <else>
-          <text macro="format-intext"/>
-        </else>
-      </choose>
-    </group>
-  </macro>
-  <macro name="bracketed-container">
-    <group prefix="[" suffix="]">
-      <choose>
-        <if type="paper-conference speech" match="any">
-          <!-- Conference presentations should describe the session [container] in bracketed unless published in a proceedings -->
-          <choose>
-            <if variable="collection-editor editor editorial-director issue page volume" match="none">
-              <text macro="format"/>
-            </if>
-          </choose>
-        </if>
-        <else-if type="book" variable="version" match="all">
-          <!-- For entries in mobile app reference works, place bracketed after the container-title -->
-          <text macro="format"/>
-        </else-if>
-        <else-if type="report">
-          <!-- For chapters in reports, place bracketed after the container title -->
-          <text macro="format"/>
-        </else-if>
-      </choose>
-    </group>
-  </macro>
-  <macro name="secondary-contributors">
-    <choose>
-      <if type="article-journal article-magazine article-newspaper post-weblog review review-book" match="any">
-        <text macro="secondary-contributors-periodical"/>
-      </if>
-      <else-if type="paper-conference">
-        <choose>
-          <if variable="collection-editor editor editorial-director" match="any">
-            <text macro="secondary-contributors-booklike"/>
-          </if>
-          <else>
-            <text macro="secondary-contributors-periodical"/>
-          </else>
-        </choose>
-      </else-if>
-      <else>
-        <text macro="secondary-contributors-booklike"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="secondary-contributors-periodical">
-    <group delimiter="; ">
-      <choose>
-        <if variable="title">
-          <names variable="interviewer" delimiter="; ">
-            <name and="symbol" initialize-with=". " delimiter=", "/>
-            <label form="short" prefix=", " text-case="title"/>
-          </names>
-        </if>
-      </choose>
-      <names variable="translator" delimiter="; ">
-        <name and="symbol" initialize-with=". " delimiter=", "/>
-        <label form="short" prefix=", " text-case="title"/>
-      </names>
-    </group>
-  </macro>
-  <macro name="secondary-contributors-booklike">
-    <group delimiter="; ">
-      <choose>
-        <if variable="title">
-          <names variable="interviewer">
-            <name and="symbol" initialize-with=". " delimiter=", "/>
-            <label form="short" prefix=", " text-case="title"/>
-          </names>
-        </if>
-      </choose>
-      <!-- When editortranslator becomes available, add a test: variable="editortranslator" match="none"; then print translator -->
-      <choose>
-        <if type="post webpage" match="none">
-          <!-- Webpages treat container-title like publisher -->
-          <choose>
-            <if variable="container-title" match="none">
-              <group delimiter="; ">
-                <names variable="container-author">
-                  <label form="verb-short" suffix=" " text-case="title"/>
-                  <name and="symbol" initialize-with=". " delimiter=", "/>
-                </names>
-                <names variable="editor translator" delimiter="; ">
-                  <name and="symbol" initialize-with=". " delimiter=", "/>
-                  <label form="short" prefix=", " text-case="title"/>
-                </names>
-              </group>
-            </if>
-          </choose>
-        </if>
-        <else>
-          <group delimiter="; ">
-            <names variable="container-author">
-              <label form="verb-short" suffix=" " text-case="title"/>
-              <name and="symbol" initialize-with=". " delimiter=", "/>
-            </names>
-            <names variable="editor translator" delimiter="; ">
-              <name and="symbol" initialize-with=". " delimiter=", "/>
-              <label form="short" prefix=", " text-case="title"/>
-            </names>
-          </group>
-        </else>
-      </choose>
-    </group>
-  </macro>
-  <macro name="database-location">
-    <choose>
-      <if variable="archive-place" match="none">
-        <!-- With `archive-place`: physical archives. Without: online archives. -->
-        <!-- Add archive_collection as that becomes available -->
-        <text variable="archive_location"/>
-      </if>
-    </choose>
-  </macro>
-  <macro name="number">
-    <choose>
-      <if variable="number">
-        <group delimiter=", ">
-          <group delimiter=" ">
-            <text variable="genre" text-case="title"/>
-            <choose>
-              <if is-numeric="number">
-                <!-- Replace with label variable="number" if that becomes available -->
-                <text term="issue" form="short" text-case="capitalize-first"/>
-                <text variable="number"/>
-              </if>
-              <else>
-                <text variable="number"/>
-              </else>
-            </choose>
-          </group>
-          <choose>
-            <if type="thesis">
-              <choose>
-                <!-- Include the university in brackets if thesis is published -->
-                <if variable="archive DOI URL" match="any">
-                  <text variable="publisher"/>
-                </if>
-              </choose>
-            </if>
-          </choose>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="locators-booklike">
-    <choose>
-      <if type="article-journal article-magazine article-newspaper broadcast interview patent post post-weblog review review-book speech webpage" match="any"/>
-      <else-if type="paper-conference">
-        <choose>
-          <if variable="collection-editor editor editorial-director" match="any">
-            <group delimiter=", ">
-              <text macro="version"/>
-              <text macro="edition"/>
-              <text macro="volume-booklike"/>
-            </group>
-          </if>
-        </choose>
-      </else-if>
-      <else>
-        <group delimiter=", ">
-          <text macro="version"/>
-          <text macro="edition"/>
-          <text macro="volume-booklike"/>
-        </group>
-      </else>
-    </choose>
-  </macro>
-  <macro name="version">
-    <choose>
-      <if is-numeric="version">
-        <group delimiter=" ">
-          <!-- replace with label variable="version" if that becomes available -->
-          <text term="version" text-case="capitalize-first"/>
-          <text variable="version"/>
-        </group>
-      </if>
-      <else>
-        <text variable="version"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="edition">
-    <choose>
-      <if is-numeric="edition">
-        <group delimiter=" ">
-          <number variable="edition" form="ordinal"/>
-          <label variable="edition" form="short"/>
-        </group>
-      </if>
-      <else>
-        <text variable="edition"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="volume-booklike">
-    <group delimiter=", ">
-      <!-- Report series [ex. 52] -->
-      <choose>
-        <if type="report">
-          <group delimiter=" ">
-            <text variable="collection-title" text-case="title"/>
-            <text variable="collection-number"/>
-          </group>
-        </if>
-      </choose>
-      <choose>
-        <if variable="volume" match="any">
-          <choose>
-            <!-- Non-numeric volumes are already printed as part of the book title -->
-            <if is-numeric="volume" match="none"/>
-            <else>
-              <group delimiter=" ">
-                <label variable="volume" form="short" text-case="capitalize-first"/>
-                <number variable="volume" form="numeric"/>
-              </group>
-            </else>
-          </choose>
-        </if>
-        <else>
-          <group>
-            <!-- Replace with label variable="number-of-volumes" if that becomes available -->
-            <text term="volume" form="short" text-case="capitalize-first" suffix=" "/>
-            <text term="page-range-delimiter" prefix="1"/>
-            <number variable="number-of-volumes" form="numeric"/>
-          </group>
-        </else>
-      </choose>
-      <group delimiter=" ">
-        <label variable="issue" text-case="capitalize-first"/>
-        <text variable="issue"/>
-      </group>
-      <group delimiter=" ">
-        <label variable="page" form="short" suffix=" "/>
-        <text variable="page"/>
-      </group>
-    </group>
-  </macro>
-  <macro name="reviewed-title">
-    <choose>
-      <if variable="reviewed-title">
-        <!-- Not possible to distinguish TV series episode from other reviewed 
-              works [Ex. 69] -->
-        <text variable="reviewed-title" font-style="italic"/>
-      </if>
-      <else>
-        <!-- Assume title is title of reviewed work -->
-        <text variable="title" font-style="italic"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="reviewed-title-intext">
-    <choose>
-      <if variable="reviewed-title">
-        <!-- Not possible to distinguish TV series episode from other reviewed works [Ex. 69] -->
-        <text variable="reviewed-title" form="short" font-style="italic" text-case="title"/>
-      </if>
-      <else>
-        <!-- Assume title is title of reviewed work -->
-        <text variable="title" form="short" font-style="italic" text-case="title"/>
-      </else>
-    </choose>
-  </macro>
-  <macro name="format">
-    <choose>
-      <if variable="genre medium" match="any">
-        <group delimiter="; ">
-          <choose>
-            <if variable="number" match="none">
-              <text variable="genre" text-case="capitalize-first"/>
-            </if>
-          </choose>
-          <text variable="medium" text-case="capitalize-first"/>
-        </group>
-      </if>
-      <!-- Generic labels for specific types -->
-      <!-- These should be localized when possible -->
-      <else-if type="dataset">
-        <text value="Data set"/>
-      </else-if>
-      <else-if type="book" variable="version" match="all">
-        <!-- Replace with type="software" and term="software" as that becomes available -->
-        <text value="Computer software"/>
-      </else-if>
-      <else-if type="interview personal_communication" match="any">
-        <choose>
-          <if variable="archive container-title DOI publisher URL" match="none">
-            <text term="letter" text-case="capitalize-first"/>
-          </if>
-          <else-if type="interview">
-            <text term="interview" text-case="capitalize-first"/>
-          </else-if>
-        </choose>
-      </else-if>
-      <else-if type="map">
-        <text value="Map"/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="format-intext">
-    <choose>
-      <if variable="genre" match="any">
-        <text variable="genre" text-case="capitalize-first"/>
-      </if>
-      <else-if variable="medium">
-        <text variable="medium" text-case="capitalize-first"/>
-      </else-if>
-      <!-- Generic labels for specific types -->
-      <!-- These should be localized when possible -->
-      <else-if type="dataset">
-        <text value="Data set"/>
-      </else-if>
-      <else-if type="book" variable="version" match="all">
-        <!-- Replace with type="software" and term="software" as that becomes available -->
-        <text value="Computer software"/>
-      </else-if>
-      <else-if type="interview personal_communication" match="any">
-        <choose>
-          <if variable="archive container-title DOI publisher URL" match="none">
-            <text term="letter" text-case="capitalize-first"/>
-          </if>
-          <else-if type="interview">
-            <text term="interview" text-case="capitalize-first"/>
-          </else-if>
-        </choose>
-      </else-if>
-      <else-if type="map">
-        <text value="Map"/>
-      </else-if>
-    </choose>
-  </macro>
-  <!-- APA 'source' element contains four parts:
-       container, event, publisher, access -->
-  <macro name="container">
-    <choose>
-      <if type="article-journal article-magazine article-newspaper post-weblog review review-book" match="any">
-        <!-- Periodical items -->
-        <text macro="container-periodical"/>
-      </if>
-      <else-if type="paper-conference">
-        <!-- Determine if paper-conference is a periodical or booklike -->
-        <choose>
-          <if variable="editor editorial-director collection-editor container-author" match="any">
-            <text macro="container-booklike"/>
-          </if>
-          <else>
-            <text macro="container-periodical"/>
-          </else>
-        </choose>
-      </else-if>
-      <else-if type="post webpage" match="none">
-        <!-- post and webpage treat container-title like publisher -->
-        <text macro="container-booklike"/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="container-periodical">
-    <group delimiter=". ">
-      <group delimiter=", ">
-        <text variable="container-title" font-style="italic" text-case="title"/>
-        <choose>
-          <if variable="volume">
-            <group>
-              <text variable="volume" font-style="italic"/>
-              <text variable="issue" prefix="(" suffix=")"/>
-            </group>
-          </if>
-          <else>
-            <text variable="issue" font-style="italic"/>
-          </else>
-        </choose>
-        <choose>
-          <if variable="page">
-            <text variable="page"/>
-          </if>
-          <else>
-            <!-- Ex. 6: Journal article with article number or eLocator -->
-            <!-- This should be localized -->
-            <text variable="number" prefix="Article "/>
-          </else>
-        </choose>
-      </group>
-      <choose>
-        <if variable="issued">
-          <choose>
-            <if variable="issue page volume" match="none">
-              <text variable="status" text-case="capitalize-first"/>
-            </if>
-          </choose>
-        </if>
-      </choose>
-    </group>
-  </macro>
-  <macro name="container-booklike">
-    <choose>
-      <if variable="container-title" match="any">
-        <group delimiter=" ">
-          <text term="in" text-case="capitalize-first"/>
-          <group delimiter=", ">
-            <names variable="editor translator" delimiter=", &amp; ">
-              <!-- Change to editortranslator and move editor to substitute as that becomes available -->
-              <name and="symbol" initialize-with=". " delimiter=", "/>
-              <label form="short" text-case="title" prefix=" (" suffix=")"/>
-              <substitute>
-                <names variable="editorial-director"/>
-                <names variable="collection-editor"/>
-                <names variable="container-author"/>
-              </substitute>
-            </names>
-            <group delimiter=": " font-style="italic">
-              <text variable="container-title"/>
-              <!-- Replace with volume-title as that becomes available -->
-              <choose>
-                <if is-numeric="volume" match="none">
-                  <group delimiter=" ">
-                    <label variable="volume" form="short" text-case="capitalize-first"/>
-                    <text variable="volume"/>
-                  </group>
-                </if>
-              </choose>
-            </group>
-          </group>
-          <text macro="parenthetical-container"/>
-          <text macro="bracketed-container"/>
-        </group>
-      </if>
-    </choose>
-  </macro>
-  <macro name="publisher">
-    <group delimiter="; ">
-      <choose>
-        <if type="thesis">
-          <choose>
-            <if variable="archive DOI URL" match="none">
-              <text variable="publisher"/>
-            </if>
-          </choose>
-        </if>
-        <else-if type="post webpage" match="any">
-          <!-- For websites, treat container title like publisher -->
-          <group delimiter="; ">
-            <text variable="container-title" text-case="title"/>
-            <text variable="publisher"/>
-          </group>
-        </else-if>
-        <else-if type="paper-conference">
-          <!-- For paper-conference, don't print publisher if in a journal-like proceedings -->
-          <choose>
-            <if variable="collection-editor editor editorial-director" match="any">
-              <text variable="publisher"/>
-            </if>
-          </choose>
-        </else-if>
-        <else-if type="article-journal article-magazine article-newspaper post-weblog" match="none">
-          <text variable="publisher"/>
-        </else-if>
-      </choose>
-      <group delimiter=", ">
-        <choose>
-          <if variable="archive-place">
-            <!-- With `archive-place`: physical archives. Without: online archives. -->
-            <!-- For physical archives, print the location before the archive name.
-                For electronic archives, these are printed in macro="description". -->
-            <!-- Split "archive_location" into "archive_collection" and "archive_location" as that becomes available -->
-            <!-- Must test for archive_collection:
-                With collection: archive_collection (archive_location), archive, archive-place
-                No collection: archive (archive_location), archive-place
-            -->
-            <text variable="archive_location"/>
-          </if>
-        </choose>
-        <text variable="archive"/>
-        <text variable="archive-place"/>
-      </group>
-    </group>
-  </macro>
-  <macro name="access">
-    <choose>
-      <if variable="DOI" match="any">
-        <text variable="DOI" prefix="https://doi.org/"/>
-      </if>
-      <else-if variable="URL">
-        <group delimiter=" ">
-          <choose>
-            <if variable="issued status" match="none">
-              <group delimiter=" ">
-                <text term="retrieved" text-case="capitalize-first"/>
-                <date variable="accessed" form="text" suffix=","/>
-                <text term="from"/>
-              </group>
-            </if>
-          </choose>
-          <text variable="URL"/>
-        </group>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="event">
-    <choose>
-      <if variable="event">
-        <!-- To prevent Zotero from printing event-place due to its double-mapping of all 'place' to
-             both publisher-place and event-place. Remove this 'choose' when that is changed. -->
-        <choose>
-          <if variable="collection-editor editor editorial-director issue page volume" match="none">
-            <!-- Don't print event info if published in a proceedings -->
-            <group delimiter=", ">
-              <text variable="event"/>
-              <text variable="event-place"/>
-            </group>
-          </if>
-        </choose>
-      </if>
-    </choose>
-  </macro>
-  <!-- After 'source', APA also prints publication history (original publication, reprint info, retraction info) -->
-  <macro name="publication-history">
-    <choose>
-      <if type="patent" match="none">
-        <group prefix="(" suffix=")">
-          <choose>
-            <if variable="references">
-              <!-- This provides the option for more elaborate description 
-                   of publication history, such as full "reprinted" references
-                   (examples 11, 43, 44) or retracted references -->
-              <text variable="references"/>
-            </if>
-            <else>
-              <group delimiter=" ">
-                <text value="Original work published"/>
-                <choose>
-                  <if is-uncertain-date="original-date">
-                    <text term="circa" form="short"/>
-                  </if>
-                </choose>
-                <date variable="original-date">
-                  <date-part name="year"/>
-                </date>
-              </group>
-            </else>
-          </choose>
-        </group>
-      </if>
-      <else>
-        <text variable="references" prefix="(" suffix=")"/>
-      </else>
-    </choose>
-  </macro>
-  <!-- Legal citations have their own rules -->
-  <macro name="legal-cites">
-    <choose>
-      <if type="legal_case">
-        <group delimiter=". ">
-          <group delimiter=", ">
-            <text variable="title"/>
-            <group delimiter=" ">
-              <text macro="container-legal"/>
-              <text macro="date-legal"/>
-            </group>
-            <text variable="references"/>
-          </group>
-          <text macro="access"/>
-        </group>
-      </if>
-      <else-if type="bill">
-        <!-- Currently designed to handle bills, resolutions, hearings, rederal reports. -->
-        <group delimiter=". ">
-          <group delimiter=", ">
-            <choose>
-              <if variable="number container-title" match="none">
-                <!-- If no number or container-title, then assume it is a hearing -->
-                <text variable="title" font-style="italic"/>
-              </if>
-              <else>
-                <text variable="title"/>
-              </else>
-            </choose>
-            <group delimiter=" ">
-              <text macro="container-legal"/>
-              <text macro="date-legal"/>
-              <choose>
-                <if variable="number container-title" match="none">
-                  <!-- If no number or container-title, then assume it is a hearing -->
-                  <names variable="author" prefix="(testimony of " suffix=")">
-                    <name and="symbol" delimiter=", "/>
-                  </names>
-                </if>
-                <else>
-                  <text variable="status" prefix="(" suffix=")"/>
-                </else>
-              </choose>
-            </group>
-            <text variable="references"/>
-          </group>
-          <text macro="access"/>
-        </group>
-      </else-if>
-      <else-if type="legislation">
-        <!-- Currently designed to handle statutes, codified regulations, executive orders.
-             For uncodified regulations, assume future code section is in status. -->
-        <group delimiter=". ">
-          <group delimiter=", ">
-            <text variable="title"/>
-            <group delimiter=" ">
-              <text macro="container-legal"/>
-              <text macro="date-legal"/>
-              <text variable="status" prefix="(" suffix=")"/>
-            </group>
-            <text variable="references"/>
-          </group>
-          <text macro="access"/>
-        </group>
-      </else-if>
-      <else-if type="treaty">
-        <!-- APA generally defers to Bluebook for legal citations, but diverges without
-             explanation for treaty items. The Bluebook format that was used in APA 6th
-             ed. is used here. -->
-        <group delimiter=", ">
-          <text variable="title" text-case="title"/>
-          <names variable="author">
-            <name initialize-with="." form="short" delimiter="-"/>
-          </names>
-          <text macro="date-legal"/>
-          <text macro="container-legal"/>
-          <text macro="access"/>
-        </group>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="date-legal">
-    <choose>
-      <if type="legal_case">
-        <group prefix="(" suffix=")" delimiter=" ">
-          <text variable="authority"/>
-          <choose>
-            <if variable="container-title" match="any">
-              <!-- Print only year for cases published in reporters-->
-              <date variable="issued" form="numeric" date-parts="year"/>
-            </if>
-            <else>
-              <date variable="issued" form="text"/>
-            </else>
-          </choose>
-        </group>
-      </if>
-      <else-if type="bill legislation" match="any">
-        <group prefix="(" suffix=")" delimiter=" ">
-          <group delimiter=" ">
-            <date variable="original-date">
-              <date-part name="year"/>
-            </date>
-            <text term="and" form="symbol"/>
-          </group>
-          <date variable="issued">
-            <date-part name="year"/>
-          </date>
-        </group>
-      </else-if>
-      <else-if type="treaty">
-        <date variable="issued" form="text"/>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="container-legal">
-    <!-- Expect legal item container-titles to be stored in short form -->
-    <choose>
-      <if type="legal_case">
-        <group delimiter=" ">
-          <choose>
-            <if variable="container-title">
-              <group delimiter=" ">
-                <text variable="volume"/>
-                <text variable="container-title"/>
-                <group delimiter=" ">
-                  <!-- Change to label variable="section" as that becomes available -->
-                  <text term="section" form="symbol"/>
-                  <text variable="section"/>
-                </group>
-                <choose>
-                  <if variable="page page-first" match="any">
-                    <text variable="page-first"/>
-                  </if>
-                  <else>
-                    <text value="___"/>
-                  </else>
-                </choose>
-              </group>
-            </if>
-            <else>
-              <group delimiter=" ">
-                <choose>
-                  <if is-numeric="number">
-                    <!-- Replace with label variable="number" if that becomes available -->
-                    <text term="issue" form="short" text-case="capitalize-first"/>
-                  </if>
-                </choose>
-                <text variable="number"/>
-              </group>
-            </else>
-          </choose>
-        </group>
-      </if>
-      <else-if type="bill">
-        <group delimiter=", ">
-          <group delimiter=" ">
-            <text variable="genre"/>
-            <group delimiter=" ">
-              <choose>
-                <if variable="chapter-number container-title" match="none">
-                  <!-- Replace with label variable="number" as that becomes available -->
-                  <text term="issue" form="short"/>
-                </if>
-              </choose>
-              <text variable="number"/>
-            </group>
-          </group>
-          <text variable="authority"/>
-          <text variable="chapter-number"/>
-          <group delimiter=" ">
-            <text variable="volume"/>
-            <text variable="container-title"/>
-            <text variable="page-first"/>
-          </group>
-        </group>
-      </else-if>
-      <else-if type="legislation">
-        <choose>
-          <if variable="number">
-            <!--There's a public law number-->
-            <group delimiter=", ">
-              <text variable="number" prefix="Pub. L. No. "/>
-              <group delimiter=" ">
-                <text variable="volume"/>
-                <text variable="container-title"/>
-                <text variable="page-first"/>
-              </group>
-            </group>
-          </if>
-          <else>
-            <group delimiter=" ">
-              <text variable="volume"/>
-              <text variable="container-title"/>
-              <choose>
-                <if variable="section">
-                  <group delimiter=" ">
-                    <!-- Change to label variable="section" as that becomes available -->
-                    <text term="section" form="symbol"/>
-                    <text variable="section"/>
-                  </group>
-                </if>
-                <else>
-                  <text variable="page-first"/>
-                </else>
-              </choose>
-            </group>
-          </else>
-        </choose>
-      </else-if>
-      <else-if type="treaty">
-        <group delimiter=" ">
-          <number variable="volume"/>
-          <text variable="container-title"/>
-          <choose>
-            <if variable="page page-first" match="any">
-              <text variable="page-first"/>
-            </if>
-            <else>
-              <group delimiter=" ">
-                <!-- Replace with label variable="number" if that becomes available -->
-                <text term="issue" form="short" text-case="capitalize-first"/>
-                <text variable="number"/>
-              </group>
-            </else>
-          </choose>
-        </group>
-      </else-if>
-    </choose>
-  </macro>
-  <macro name="citation-locator">
-    <group delimiter=" ">
-      <choose>
-        <if locator="chapter">
-          <label variable="locator" text-case="capitalize-first"/>
-        </if>
-        <else>
-          <label variable="locator" form="short"/>
-        </else>
-      </choose>
-      <text variable="locator"/>
-    </group>
-  </macro>
-  <citation et-al-min="3" et-al-use-first="1" disambiguate-add-year-suffix="true" disambiguate-add-names="true" disambiguate-add-givenname="true" collapse="year" givenname-disambiguation-rule="primary-name">
-    <sort>
-      <key macro="author-bib" names-min="3" names-use-first="1"/>
-      <key macro="date-sort-group"/>
-      <key macro="date-sort-date" sort="ascending"/>
-      <key variable="status"/>
-    </sort>
-    <layout prefix="(" suffix=")" delimiter="; ">
-      <group delimiter=", ">
-        <text macro="author-intext"/>
-        <text macro="date-intext"/>
-        <text macro="citation-locator"/>
-      </group>
-    </layout>
-  </citation>
-  <bibliography hanging-indent="true" et-al-min="21" et-al-use-first="19" et-al-use-last="true" entry-spacing="0" line-spacing="2">
-    <sort>
-      <key macro="author-bib"/>
-      <key macro="date-sort-group"/>
-      <key macro="date-sort-date" sort="ascending"/>
-      <key variable="status"/>
-      <key macro="title"/>
-    </sort>
-    <layout>
-      <choose>
-        <if type="bill legal_case legislation treaty" match="any">
-          <!-- Legal items have different orders and delimiters -->
-          <choose>
-            <if variable="DOI URL" match="any">
-              <text macro="legal-cites"/>
-            </if>
-            <else>
-              <text macro="legal-cites" suffix="."/>
-            </else>
-          </choose>
-        </if>
-        <else>
-          <group delimiter=" ">
-            <group delimiter=". " suffix=".">
-              <text macro="author-bib"/>
-              <text macro="date-bib"/>
-              <text macro="title-and-descriptions"/>
-              <text macro="container"/>
-              <text macro="event"/>
-              <text macro="publisher"/>
-            </group>
-            <text macro="access"/>
-            <text macro="publication-history"/>
-          </group>
-        </else>
-      </choose>
-    </layout>
-  </bibliography>
-</style>

example/assets/pandoc-scholar/example/article.md

@@ -1,138 +0,0 @@
----
-title: Example article written in pandoc-flavored Markdown
-author:
-  - Jane Doe:
-      institute:
-        - fosg
-        - fop
-      email: jane.doe@example.com
-      orcid: 0000-0000-0000-0000
-      equal_contributor: "yes"
-      correspondence: "yes"
-  - John Q. Doe:
-      institute: fosg
-      equal_contributor: "yes"
-  - Peder Ås:
-      institute: fosg
-  - Juan Pérez:
-      institute: acme
-      email: juan.perez@example.edu
-      correspondence: "yes"
-institute:
-  - fosg:
-      name: Formatting Open Science Group
-      address: 23 Science Street, Eureka, Mississippi, USA
-      phone: +1 (555) 423 1338
-      email: '{firstname}.{lastname}\@fosg.example.com'
-  - fop: Federation of Planets
-  - acme:
-      name: Acme Corporation
-bibliography: bibliography.bib
-csl: apa.csl
-link-citations: true
-project:
-  title: Pandoc Scholar Example
-  zip-url: https://github.com/pandoc-scholar/pandoc-scholar/releases
-  github-url: https://github.com/pandoc-scholar/pandoc-scholar/
-...
-
-# Abstract
-
-This is an example article.  There is not much to see but filler text.
-
-
-# Further reading
-
-See the [pandoc manual](http://pandoc.org/MANUAL.html) for more information on
-pandoc.
-
-Authors struggling to fill this document with content are referred to
-@Upper_writers_1974.
-
-
-# Lorem Ipsum
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
-incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
-nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
-Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
-fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
-culpa qui officia deserunt mollit anim id est laborum.
-
-
-## Dolor sit amet
-
-Deserunt excepturi commodi sit qui velit quis. Delectus sit omnis culpa
-accusamus repellat iusto vel. Quod deserunt quasi nisi dolor. Quo eum id
-reiciendis dolor. Est qui illum et.
-
-Quo dolore molestiae et laboriosam occaecati explicabo corrupti. Earum expedita
-ducimus quaerat est quam ut molestiae. Illum deleniti vel labore facilis et cum
-est. Est nemo est vel ad. Assumenda consequatur rerum officiis atque officia.
-Est nihil iste cumque ad qui.
-
-Eaque sed sit totam enim. Et explicabo illum rerum aut. Aspernatur sit dolor
-animi tempora cum. Maxime in soluta aut. Explicabo id maiores voluptates aut
-voluptas id. Dolore sed labore voluptatem omnis doloribus mollitia aliquid
-cupiditate.
-
-In rerum saepe placeat. Deleniti suscipit sed quam fugit assumenda sit et
-tempora. Veniam illum expedita quia error qui quibusdam rerum. Qui ut sunt est
-eos.
-
-Recusandae et sit ut. Impedit deserunt consequatur et dignissimos vel et.
-Eveniet voluptatem magni quis est dolore excepturi officia nihil. Debitis quae
-commodi error.
-
-Modi debitis et ut saepe saepe dolorem. Quis sed autem expedita est voluptate
-esse neque. Quod aspernatur quam velit placeat nihil omnis debitis. Corporis sit
-rerum consectetur possimus rerum consequuntur. Rerum quas ut repellendus
-tenetur. Consequuntur adipisci dolores eveniet qui est ipsum.
-
-Atque deserunt necessitatibus unde facere amet molestiae. Ipsam at quia placeat
-aliquam autem. Enim corporis accusamus consequatur.
-
-Et vitae unde perferendis tenetur cupiditate non exercitationem. Aut molestiae
-sed est. Deserunt repudiandae non quia esse ad vitae vel in. Et reprehenderit
-dolore et aut distinctio.
-
-Vel quia molestiae quod sint fuga omnis est fuga. Minus quaerat repellat quod.
-Rerum rerum enim repellendus rerum consequatur non perspiciatis. Illo sapiente
-sed natus ipsa quia temporibus. Est nostrum fugit odio non voluptatem odit
-rerum. Et consequatur aut nostrum accusamus earum.
-
-Sit explicabo iure eligendi consequatur. Consequatur atque praesentium
-consequatur dolores quam. Neque eius provident harum placeat. Quo aut pariatur
-illum laborum porro minima. Dolorem nobis esse laudantium. Perspiciatis
-voluptate deleniti voluptatem et.
-
-Quos assumenda magnam non inventore. Adipisci repellendus eligendi possimus
-voluptate numquam voluptatem natus. Deleniti cupiditate facilis commodi aliquid
-voluptatem laudantium autem similique. Vel sunt cupiditate consequatur. Dolorum
-voluptatem nihil culpa fugiat non itaque animi iusto. Unde incidunt numquam
-vitae.
-
-Eius provident voluptatem animi quidem quia. Velit omnis voluptas atque.
-Voluptatem accusamus atque blanditiis commodi aspernatur ullam ad. Nulla quidem
-fugiat explicabo quo dolor hic.
-
-Rerum dolore quo ratione sed aspernatur doloremque. Ut neque laudantium quae
-enim dolores et. Laudantium dolores id assumenda autem aspernatur. Accusamus
-doloribus nihil rerum et atque est aut delectus.
-
-Nulla itaque mollitia vitae accusamus. Eveniet soluta praesentium dolore harum
-culpa. Totam voluptatem non aspernatur.
-
-Eveniet in illo consequatur. Fugiat et totam unde nihil quis. Non et velit
-recusandae blanditiis unde. Eaque fugiat id pariatur. Non numquam minima aut.
-Iste eos et autem et exercitationem velit officiis vero.
-
-Ullam minima quisquam est ducimus iste. Commodi occaecati inventore provident
-voluptatem repudiandae. Quia est qui dolore sit nisi officia doloremque dolor.
-Perspiciatis tempore laudantium quia repellendus quia deleniti. Sed consequuntur
-autem quisquam aliquam.
-
-Ut dolores natus et sunt delectus nulla. Ipsum eum quia ex est ut quia. Ratione
-et eius consequatur veritatis hic expedita ea.
-
-# References

example/assets/pandoc-scholar/example/bibliography.bib

@@ -1,13 +0,0 @@
-@article {Upper_writers_1974,
-  author = {Upper, Dennis},
-  title = {The unsuccessful self-treatment of a case of “writer's block”},
-  journal = {Journal of Applied Behavior Analysis},
-  volume = {7},
-  number = {3},
-  publisher = {Blackwell Publishing Ltd},
-  issn = {1938-3703},
-  url = {http://dx.doi.org/10.1901/jaba.1974.7-497a},
-  doi = {10.1901/jaba.1974.7-497a},
-  pages = {497--497},
-  year = {1974},
-}

example/assets/pandoc-scholar/example/rmarkdown-scholarpandoc.Rmd

@@ -1,173 +0,0 @@
----
-title: "Testing author list with scholarpandoc"
-author:
-- Jane Doe:
-    institute:
-    - fosg
-    - fop
-    email: jane.doe@example.com
-    orcid: 0000-0000-0000-0000
-    equal_contributor: 'yes'
-    correspondence: 'yes'
-- John Q. Doe:
-    institute: fosg
-    equal_contributor: 'yes'
-- Peder Ås:
-    institute: fosg
-- Juan Pérez:
-    institute: acme
-    email: juan.perez@example.edu
-    correspondence: 'yes'
-date: "1/20/2020"
-output:
-  bookdown::word_document2:
-    fig_caption: yes
-    reference_docx: ../templates/template.docx
-    pandoc_args:
-    - --lua-filter=../lua-filters/scholarly-metadata/scholarly-metadata.lua
-    - --lua-filter=../lua-filters/author-info-blocks/author-info-blocks.lua
-    - --lua-filter=../lua-filters/abstract-to-meta/abstract-to-meta.lua
-    - --lua-filter=../lua-filters/pagebreak/pagebreak.lua
-  bookdown::html_document2:    
-    fig_caption: yes
-    template: ../templates/pandoc-scholar.html
-    css: ../templates/styles/pandoc-scholar.css
-    self_contained: true
-    pandoc_args:
-      - --lua-filter=../lua-filters/cito/cito.lua
-      - --lua-filter=../lua-filters/abstract-to-meta/abstract-to-meta.lua
-      - --lua-filter=../lua-filters/scholarly-metadata/scholarly-metadata.lua
-      - --lua-filter=../scholar-filters/template-helper.lua
-  bookdown::pdf_document2:
-    keep_tex: true
-    toc: false
-    fig_caption: yes
-    template: ../templates/pandoc-scholar.latex
-    pandoc_args:
-      - --lua-filter=../lua-filters/cito/cito.lua
-      - --lua-filter=../lua-filters/abstract-to-meta/abstract-to-meta.lua
-      - --lua-filter=../lua-filters/scholarly-metadata/scholarly-metadata.lua
-      - --lua-filter=../scholar-filters/template-helper.lua  
-institute:
-- fosg:
-    name: Formatting Open Science Group
-    address: 23 Science Street, Eureka, Mississippi, USA
-    phone: +1 (555) 423 1338
-    email: '{firstname}.{lastname}\@fosg.example.com'
-- fop: Federation of Planets
-- acme:
-    name: Acme Corporation
-bibliography: ../example/bibliography.bib
-csl: ../csl/chicago-author-date.csl
-link-citations: yes
-project:
-  title: Pandoc Scholar Example
-  zip-url: https://github.com/pandoc-scholar/pandoc-scholar/releases
-  github-url: https://github.com/pandoc-scholar/pandoc-scholar/
-...
-
-# Abstract
-
-This is an example article.  There is not much to see but filler text.
-
-
-# Further reading
-
-See the [pandoc manual](http://pandoc.org/MANUAL.html) for more information on
-pandoc.
-
-Authors struggling to fill this document with content are referred to
-@Upper_writers_1974.
-
-
-# Lorem Ipsum
-
-Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do eiusmod tempor
-incididunt ut labore et dolore magna aliqua. Ut enim ad minim veniam, quis
-nostrud exercitation ullamco laboris nisi ut aliquip ex ea commodo consequat.
-Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu
-fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in
-culpa qui officia deserunt mollit anim id est laborum.
-
-
-## Dolor sit amet
-
-Deserunt excepturi commodi sit qui velit quis. Delectus sit omnis culpa
-accusamus repellat iusto vel. Quod deserunt quasi nisi dolor. Quo eum id
-reiciendis dolor. Est qui illum et.
-
-Quo dolore molestiae et laboriosam occaecati explicabo corrupti. Earum expedita
-ducimus quaerat est quam ut molestiae. Illum deleniti vel labore facilis et cum
-est. Est nemo est vel ad. Assumenda consequatur rerum officiis atque officia.
-Est nihil iste cumque ad qui.
-
-Eaque sed sit totam enim. Et explicabo illum rerum aut. Aspernatur sit dolor
-animi tempora cum. Maxime in soluta aut. Explicabo id maiores voluptates aut
-voluptas id. Dolore sed labore voluptatem omnis doloribus mollitia aliquid
-cupiditate.
-
-In rerum saepe placeat. Deleniti suscipit sed quam fugit assumenda sit et
-tempora. Veniam illum expedita quia error qui quibusdam rerum. Qui ut sunt est
-eos.
-
-Recusandae et sit ut. Impedit deserunt consequatur et dignissimos vel et.
-Eveniet voluptatem magni quis est dolore excepturi officia nihil. Debitis quae
-commodi error.
-
-Modi debitis et ut saepe saepe dolorem. Quis sed autem expedita est voluptate
-esse neque. Quod aspernatur quam velit placeat nihil omnis debitis. Corporis sit
-rerum consectetur possimus rerum consequuntur. Rerum quas ut repellendus
-tenetur. Consequuntur adipisci dolores eveniet qui est ipsum.
-
-Atque deserunt necessitatibus unde facere amet molestiae. Ipsam at quia placeat
-aliquam autem. Enim corporis accusamus consequatur.
-
-Et vitae unde perferendis tenetur cupiditate non exercitationem. Aut molestiae
-sed est. Deserunt repudiandae non quia esse ad vitae vel in. Et reprehenderit
-dolore et aut distinctio.
-
-Vel quia molestiae quod sint fuga omnis est fuga. Minus quaerat repellat quod.
-Rerum rerum enim repellendus rerum consequatur non perspiciatis. Illo sapiente
-sed natus ipsa quia temporibus. Est nostrum fugit odio non voluptatem odit
-rerum. Et consequatur aut nostrum accusamus earum.
-
-Sit explicabo iure eligendi consequatur. Consequatur atque praesentium
-consequatur dolores quam. Neque eius provident harum placeat. Quo aut pariatur
-illum laborum porro minima. Dolorem nobis esse laudantium. Perspiciatis
-voluptate deleniti voluptatem et.
-
-Quos assumenda magnam non inventore. Adipisci repellendus eligendi possimus
-voluptate numquam voluptatem natus. Deleniti cupiditate facilis commodi aliquid
-voluptatem laudantium autem similique. Vel sunt cupiditate consequatur. Dolorum
-voluptatem nihil culpa fugiat non itaque animi iusto. Unde incidunt numquam
-vitae.
-
-Eius provident voluptatem animi quidem quia. Velit omnis voluptas atque.
-Voluptatem accusamus atque blanditiis commodi aspernatur ullam ad. Nulla quidem
-fugiat explicabo quo dolor hic.
-
-Rerum dolore quo ratione sed aspernatur doloremque. Ut neque laudantium quae
-enim dolores et. Laudantium dolores id assumenda autem aspernatur. Accusamus
-doloribus nihil rerum et atque est aut delectus.
-
-Nulla itaque mollitia vitae accusamus. Eveniet soluta praesentium dolore harum
-culpa. Totam voluptatem non aspernatur.
-
-Eveniet in illo consequatur. Fugiat et totam unde nihil quis. Non et velit
-recusandae blanditiis unde. Eaque fugiat id pariatur. Non numquam minima aut.
-Iste eos et autem et exercitationem velit officiis vero.
-
-Ullam minima quisquam est ducimus iste. Commodi occaecati inventore provident
-voluptatem repudiandae. Quia est qui dolore sit nisi officia doloremque dolor.
-Perspiciatis tempore laudantium quia repellendus quia deleniti. Sed consequuntur
-autem quisquam aliquam.
-
-Ut dolores natus et sunt delectus nulla. Ipsum eum quia ex est ut quia. Ratione
-et eius consequatur veritatis hic expedita ea.
-
-# References
-
-pandoc_args:
-    - --lua-filter=../lua-filters/scholarly-metadata/scholarly-metadata.lua
-    - --lua-filter=../lua-filters/author-info-blocks/author-info-blocks.lua
-    - --lua-filter=../lua-filters/abstract-to-meta/abstract-to-meta.lua

example/assets/pandoc-scholar/lua-filters/LICENSE

@@ -1,21 +0,0 @@
-MIT License
-
-Copyright (c) 2017-2020 John MacFarlane and contributors
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.

example/assets/pandoc-scholar/lua-filters/README.md

@@ -1,40 +0,0 @@
-[![travis build
-status](https://img.shields.io/travis/pandoc/lua-filters/master.svg?label=travis+build)](https://travis-ci.org/pandoc/lua-filters)
-
-# Lua Filters
-
-This repository collects Lua filters for pandoc.
-
-To learn about Lua filters, see the
-[documentation](http://pandoc.org/lua-filters.html).
-
-Structure
----------
-
-Each filter goes in its own subdirectory.  Each subdirectory contains:
-
-- the filter itself (e.g. `wordcount.lua`)
-- a `README.md` describing the use of the filter
-- a `Makefile` with a `test` target to test the filter
-- some data files used for the tests, which may also serve
-  as examples
-
-Requirements
-------------
-
-Filters are tested against the latest pandoc version.  There is
-no guarantee that filters will work with older versions, but
-many do.
-
-Some filters depend on external programs, which must be installed
-separately.  Refer to the filters' README for detailed
-requirements.
-
-Contributing
-------------
-
-PRs for new filters are welcome, provided they conform to these
-guidelines. Lua code should ideally follow the Olivine Labs [Lua
-style guide].
-
-[Lua style guide]: https://github.com/Olivine-Labs/lua-style-guide

example/assets/pandoc-scholar/lua-filters/abstract-to-meta/README.md

@@ -1,37 +0,0 @@
-# abstract-to-meta
-
-This moves a document's abstract from the main text into the
-metadata. Metadata elements usually allow for finer placement
-control in the final output, but writing body text is easier and
-more natural.
-
-## Defining an Abstract
-
-A document abstract can either be put directly in the document
-metadata, for example by inserting an *abstract* attribute into a
-YAML block.
-
-    ---
-    abstract: |
-      Place abstract here.
-
-      Multiple paragraphs are possible.
-    ---
-
-The additional indentation and formatting requirements in YAML
-headers can be confusing or annoying for authors. It is hence
-preferable to allow abstracts be written as normal sections.
-
-    # Abstract
-
-    Place abstract here.
-
-    Multiple paragraphs are possible.
-
-This filter turns the latter into the former by looking for a
-top-level header whose ID is `abstract`. Pandoc auto-creates IDs
-based on header contents, so a header titled *Abstract* will
-satisfy this condition.^[1]
-
-[1]: This requires the `auto_identifier` extension. It is
-     enabled by default.

example/assets/pandoc-scholar/lua-filters/abstract-to-meta/abstract-to-meta.lua

@@ -1,55 +0,0 @@
---[[
-abstract-to-meta – move an "abstract" section into document metadata
-
-Copyright: © 2017–2020 Albert Krewinkel
-License:   MIT – see LICENSE file for details
-]]
-local abstract = {}
-
---- Extract abstract from a list of blocks.
-function abstract_from_blocklist (blocks)
-  local body_blocks = {}
-  local looking_at_abstract = false
-
-  for _, block in ipairs(blocks) do
-    if block.t == 'Header' and block.level == 1 then
-      if block.identifier == 'abstract' then
-        looking_at_abstract = true
-      else
-        looking_at_abstract = false
-        body_blocks[#body_blocks + 1] = block
-      end
-    elseif looking_at_abstract then
-      abstract[#abstract + 1] = block
-    else
-      body_blocks[#body_blocks + 1] = block
-    end
-  end
-
-  return body_blocks
-end
-
-if PANDOC_VERSION >= {2,9,2} then
-  -- Check all block lists with pandoc 2.9.2 or later
-  return {{
-      Blocks = abstract_from_blocklist,
-      Meta = function (meta)
-        if not meta.abstract and #abstract > 0 then
-          meta.abstract = pandoc.MetaBlocks(abstract)
-        end
-        return meta
-      end
-  }}
-else
-  -- otherwise, just check the top-level block-list
-  return {{
-      Pandoc = function (doc)
-        local meta = doc.meta
-        local other_blocks = abstract_from_blocklist(doc.blocks)
-        if not meta.abstract and #abstract > 0 then
-          meta.abstract = pandoc.MetaBlocks(abstract)
-        end
-        return pandoc.Pandoc(other_blocks, meta)
-      end,
-  }}
-end

example/assets/pandoc-scholar/lua-filters/author-info-blocks/README.md

@@ -1,59 +0,0 @@
-# author-info-blocks
-
-This filter adds author-related header blocks usually included in
-scholarly articles, such as a list of author affiliations,
-correspondence information, and on notes equal contributors.
-
-
-## Dependencies
-
-This filter assumes metadata in the canonical format generated by
-the [scholarly-metadata filter](../scholarly-metadata).
-
-## Usage
-
-The filter should be run after *scholarly-metadata.lua*:
-
-    pandoc --lua-filter=scholarly-metadata/scholarly-metadata.lua \
-           --lua-filter=author-info-blocks/author-inffo-blocks.lua \
-           --output=outfile.pdf --pdf-engine=xelatex \
-           article.md
-
-The ways in which affiliation data should be given is described
-in the docs for **scholarly-metadata.lua*. Additionally, authors
-who contributed equally to an article can be marked by adding
-`equal_contributor: yes` to the respective YAML objects.
-Similarly, corresponding authors should be marked with
-`correspondence: yes` and have an `email` listed.
-
-### Example
-
-Take the following example YAML block:
-
-``` yaml
----
-title: Affiliation Blocks Example 
-author:
-  - Jane Doe:
-      institute:
-        - federation
-      equal_contributor: "yes"
-      correspondence: "yes"
-      email: jane.doe@example.com
-  - John Q. Doe:
-      institute: [federation, acme]
-      equal_contributor: "yes"
-  - Juan Pérez:
-      institute: acme
-institute:
-  - federation: Federation of Planets
-  - acme:
-      name: Acme Corporation
----
-```
-
-This will mark Jane Doe and John Q. Doe as equal contributors and
-Jane Doe as the sole corresponding author. Below is a screenshot
-of a document header created from this metadata.
-
-![sample output](sample.png)

example/assets/pandoc-scholar/lua-filters/author-info-blocks/author-info-blocks.lua

@@ -1,176 +0,0 @@
---[[
-affiliation-blocks – generate title components
-
-Copyright © 2017–2020 Albert Krewinkel
-
-Permission to use, copy, modify, and/or distribute this software for any purpose
-with or without fee is hereby granted, provided that the above copyright notice
-and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-THIS SOFTWARE.
-]]
-local List = require 'pandoc.List'
-local utils = require 'pandoc.utils'
-local stringify = utils.stringify
-
-local default_marks
-local default_marks = {
-  corresponding_author = FORMAT == 'latex'
-    and {pandoc.RawInline('latex', '*')}
-    or {pandoc.Str '✉'},
-  equal_contributor = FORMAT == 'latex'
-    and {pandoc.RawInline('latex', '$\\dagger{}$')}
-    or {pandoc.Str '*'},
-}
-
-local function intercalate(lists, elem)
-  local result = List:new{}
-  for i = 1, (#lists - 1) do
-    result:extend(lists[i])
-    result:extend(elem)
-  end
-  if #lists > 0 then
-    result:extend(lists[#lists])
-  end
-  return result
-end
-
---- Check whether the given author is a corresponding author
-local function is_corresponding_author(author)
-  return author.correspondence and author.email
-end
-
---- Create inlines for a single author (includes all author notes)
-local function author_inline_generator (get_mark)
-  return function (author)
-    local author_marks = List:new{}
-    if author.equal_contributor then
-      author_marks[#author_marks + 1] = get_mark 'equal_contributor'
-    end
-    local idx_str
-    for _, idx in ipairs(author.institute) do
-      if type(idx) ~= 'table' then
-        idx_str = tostring(idx)
-      else
-        idx_str = stringify(idx)
-      end
-      author_marks[#author_marks + 1] = {pandoc.Str(idx_str)}
-    end
-    if is_corresponding_author(author) then
-      author_marks[#author_marks + 1] = get_mark 'corresponding_author'
-    end
-    local res = List.clone(author.name)
-    res[#res + 1] = pandoc.Superscript(intercalate(author_marks, {pandoc.Str ','}))
-    return res
-  end
-end
-
-local function is_equal_contributor (author)
-  return author.equal_contributor
-end
-
---- Create equal contributors note.
-local function create_equal_contributors_block(authors, mark)
-  local has_equal_contribs = List:new(authors):find_if(is_equal_contributor)
-  if not has_equal_contribs then
-    return nil
-  end
-  local contributors = {
-    pandoc.Superscript(mark'equal_contributor'),
-    pandoc.Space(),
-    pandoc.Str 'These authors contributed equally to this work.'
-  }
-  return List:new{pandoc.Para(contributors)}
-end
-
---- Generate a block list all affiliations, marked with arabic numbers.
-local function create_affiliations_blocks(affiliations)
-  local affil_lines = List:new(affiliations):map(
-    function (affil, i)
-      local num_inlines = List:new{
-        pandoc.Superscript{pandoc.Str(tostring(i))},
-        pandoc.Space()
-      }
-      return num_inlines .. affil.name
-    end
-                                                )
-  return {pandoc.Para(intercalate(affil_lines, {pandoc.LineBreak()}))}
-end
-
---- Generate a block element containing the correspondence information
-local function create_correspondence_blocks(authors, mark)
-  local corresponding_authors = List:new{}
-  for _, author in ipairs(authors) do
-    if is_corresponding_author(author) then
-      local mailto = 'mailto:' .. pandoc.utils.stringify(author.email)
-      local author_with_mail = List:new(
-        author.name .. List:new{pandoc.Space(),  pandoc.Str '<'} ..
-        author.email .. List:new{pandoc.Str '>'}
-      )
-      local link = pandoc.Link(author_with_mail, mailto)
-      table.insert(corresponding_authors, {link})
-    end
-  end
-  if #corresponding_authors == 0 then
-    return nil
-  end
-  local correspondence = List:new{
-    pandoc.Superscript(mark'corresponding_author'),
-    pandoc.Space(),
-    pandoc.Str'Correspondence:',
-    pandoc.Space()
-  }
-  local sep = List:new{pandoc.Str',',  pandoc.Space()}
-  return {
-    pandoc.Para(correspondence .. intercalate(corresponding_authors, sep))
-  }
-end
-
---- Generate a list of inlines containing all authors.
-local function create_authors_inlines(authors, mark)
-  local inlines_generator = author_inline_generator(mark)
-  local inlines = List:new(authors):map(inlines_generator)
-  local and_str = List:new{pandoc.Space(), pandoc.Str'and', pandoc.Space()}
-
-  local last_author = inlines[#inlines]
-  inlines[#inlines] = nil
-  local result = intercalate(inlines, {pandoc.Str ',', pandoc.Space()})
-  if #authors > 1 then
-    result:extend(List:new{pandoc.Str ","} .. and_str)
-  end
-  result:extend(last_author)
-  return result
-end
-
-return {
-  {
-    Pandoc = function (doc)
-      local meta = doc.meta
-      local body = List:new{}
-
-      local mark = function (mark_name) return default_marks[mark_name] end
-
-      body:extend(create_equal_contributors_block(doc.meta.author, mark) or {})
-      body:extend(create_affiliations_blocks(doc.meta.institute) or {})
-      body:extend(create_correspondence_blocks(doc.meta.author, mark) or {})
-      body:extend(doc.blocks)
-
-      -- Overwrite authors with formatted values. We use a single, formatted
-      -- string for most formats. LaTeX output, however, looks nicer if we
-      -- provide a authors as a list.
-      meta.author = FORMAT:match 'latex'
-        and pandoc.MetaList(doc.meta.author):map(author_inline_generator(mark))
-        or pandoc.MetaInlines(create_authors_inlines(doc.meta.author, mark))
-      -- Institute info is now baked into the affiliations block.
-      meta.institute = nil
-
-      return pandoc.Pandoc(body, meta)
-    end
-  }
-}

example/assets/pandoc-scholar/lua-filters/bibexport/README.md

@@ -1,39 +0,0 @@
-# bibexport
-
-Export all cited references into a single bibtex file. This is
-most useful when writing collaboratively while using a large,
-private bibtex collection. Using the bibexport filter allows to
-create a reduced bibtex file suitable for sharing with
-collaborators.
-
-## Prerequisites
-
-This filter expects the `bibexport` executable to be installed
-and in the user's PATH. Installation differs across systems.
-Users of the TeX Live distribution can install the [bibexport]
-package by running
-
-    tlmgr install bibexport
-
-Windows appears to be unsupported at the moment.
-
-[bibexport]: https://www.ctan.org/pkg/bibexport
-
-## Usage
-
-The filter runs `bibexport` on a temporary *aux* file, creating
-the file *bibexport.bib* on success. The name of the temporary
-*.aux* file can be set via the `auxfile` meta value; if no value
-is specified, *bibexport.aux* will be used as filename.
-
-Please note that `bibexport` prints messages to stdout. Pandoc
-should be called with the `-o` or `--output` option instead of
-redirecting stdout to a file. E.g.
-
-    pandoc --lua-filter=bibexport.lua article.md -o article.html
-
-or, when the filter is called in a one-off fashion
-
-    pandoc --lua-filter=bibexport.lua article.md -o /dev/null
-    
-

example/assets/pandoc-scholar/lua-filters/bibexport/bibexport.lua

@@ -1,89 +0,0 @@
-local utils = require 'pandoc.utils'
-local List = require 'pandoc.List'
-
-local citation_id_set = {}
-
--- Collect all citation IDs.
-function Cite (c)
-  local cs = c.citations
-  for i = 1, #cs do
-    citation_id_set[cs[i].id or cs[i].citationId] = true
-  end
-end
-
---- Return a list of citation IDs
-function citation_ids ()
-  local citations = {};
-  for cid, _ in pairs(citation_id_set) do
-    citations[#citations + 1] = cid
-  end
-  return citations
-end
-
---- stringify meta inline elements. Pandoc prior to version 2.8
--- didn't properly tag MetaInline values, so making it necessary to use an
--- auxiliary Span.
-local stringifyMetaInlines = function (el)
-  return el.t
-    and utils.stringify(el)
-    or utils.stringify(pandoc.Span(el))
-end
-
-function bibdata (bibliography)
-  function bibname (bibitem)
-    return type(bibitem) == 'string'
-      and bibitem:gsub('%.bib$', '')
-      -- bibitem is assumed to be a list of inlines or MetaInlines element
-      or stringifyMetaInlines(bibitem):gsub('%.bib$', '')
-  end
-
-  local bibs = bibliography.t == 'MetaList'
-    and List.map(bibliography, bibname)
-    or {bibname(bibliography)}
-  return table.concat(bibs, ',')
-end
-
-function aux_content(bibliography)
-  local cites = citation_ids()
-  table.sort(cites)
-  local citations = table.concat(cites, ',')
-  return table.concat(
-    {
-      '\\bibstyle{alpha}',
-      '\\bibdata{' .. bibdata(bibliography) .. '}',
-      '\\citation{' .. citations .. '}',
-      '',
-    },
-    '\n'
-  )
-end
-
-function write_dummy_aux (bibliography, auxfile)
-  local filename
-  if type(auxfile) == 'string' then
-    filename = auxfile
-  elseif type(auxfile) == 'table' then
-    -- assume list of inlines
-    filename = utils.stringify(pandoc.Span(auxfile))
-  else
-    filename = 'bibexport.aux'
-  end
-  local fh = io.open(filename, 'w')
-  fh:write(aux_content(bibliography))
-  fh:close()
-  io.stdout:write('Aux written to ' .. filename .. '\n')
-  return filename
-end
-
-function Pandoc (doc)
-  local meta = doc.meta
-  if not meta.bibliography then
-    return nil
-  else
-    -- create a dummy .aux file
-    local auxfile_name = write_dummy_aux(meta.bibliography, meta.auxfile)
-    os.execute('bibexport ' .. auxfile_name)
-    io.stdout:write('Output written to bibexport.bib\n')
-    return nil
-  end
-end

example/assets/pandoc-scholar/lua-filters/cito/README.md

@@ -1,85 +0,0 @@
-# cito
-
-This filter extracts optional CiTO (Citation Typing Ontology)
-information from citations and stores the information in the
-document's metadata. The extracted info is intended to be used in
-combination with other filters, templates, or custom writers. It
-is mandatory to run pandoc-citeproc *after* this filter if CiTO
-data is embedded in the document; otherwise pandoc-citeproc will
-interpret CiTO properties as part of the citation ID.
-
-## Using the Citation Typing Ontology
-
-The [citation typing ontology] (CiTO) allows authors to specify the
-reason a citation is given. This is helpful for the authors and
-their co-authors, and furthermore adds data that can be used by
-readers to search and navigate relevant publications.
-
-A CiTO annotation must come before the citation key and be
-followed by a colon. E.g., `@method_in:towbin_1979` signifies
-that the citation with ID *towbin_1979* is cited because the
-method described in that paper has been used in the paper at
-hand.
-
-[citation typing ontology]: http://purl.org/spar/cito
-
-## Recognized CiTO properties
-
-Below is the list of CiTO properties recognized by the filter,
-together with the aliases that can be used as shorthands.
-
-- agrees_with
-  - agree_with
-- citation
-- cites
-- cites_as_authority
-  - as_authority
-  - authority
-- cites_as_data_source
-- cites_as_evidence
-  - as_evidence
-  - evidence
-- cites_as_metadata_document
-  - as_metadata_document
-  - metadata_document
-  - metadata
-- cites_as_recommended_reading
-  - as_recommended_reading
-  - recommended_reading
-- disagrees_with
-  - disagree
-  - disagrees
-- disputes
-- documents
-- extends
-- includes_excerpt_from
-  - excerpt
-  - excerpt_from
-- includes_quotation_from
-  - quotation
-  - quotation_from
-- obtains_background_from
-  - background
-  - background_from
-- refutes
-- replies_to
-- updates
-- uses_data_from
-  - data
-  - data_from
-- uses_method_in
-  - method
-  - method_in
-
-## Filter interactions
-
-Note that the [pandoc-crossref] filter uses citations to link to
-other elements. The crossref extensions are not understood by
-cito.lua. pandoc-crossref, if used, should always be invoked
-first: `pandoc --lua-filter=cito.lua --filter=pandoc-crossref …`
-
-[pandoc-crossref]: https://lierdakil.github.io/pandoc-crossref/
-
-## References
-
-This approach was described in <https://doi.org/10.7717/peerj-cs.112>.

example/assets/pandoc-scholar/lua-filters/cito/cito.lua

@@ -1,138 +0,0 @@
--- Copyright © 2017–2020 Albert Krewinkel, Robert Winkler
---
--- This library is free software; you can redistribute it and/or modify it
--- under the terms of the MIT license. See LICENSE for details.
-
-local _version = '1.0.0'
-local properties_and_aliases = {
-  agrees_with = {
-    'agree_with'
-  },
-  citation = {
-  },
-  cites = {
-  },
-  cites_as_authority = {
-    'as_authority',
-    'authority'
-  },
-  cites_as_data_source = {
-    "as_data_source",
-    "data_source"
-  },
-  cites_as_evidence = {
-    'as_evidence',
-    'evidence'
-  },
-  cites_as_metadata_document = {
-    'as_metadata_document',
-    'metadata_document',
-    'metadata'
-  },
-  cites_as_recommended_reading = {
-    'as_recommended_reading',
-    'recommended_reading'
-  },
-  disagrees_with = {
-    'disagree',
-    'disagrees'
-  },
-  disputes = {
-  },
-  documents = {
-  },
-  extends = {
-  },
-  includes_excerpt_from = {
-    'excerpt',
-    'excerpt_from'
-  },
-  includes_quotation_from = {
-    'quotation',
-    'quotation_from'
-  },
-  obtains_background_from = {
-    'background',
-    'background_from'
-  },
-  refutes = {
-  },
-  replies_to = {
-  },
-  updates = {
-  },
-  uses_data_from = {
-    'data',
-    'data_from'
-  },
-  uses_method_in = {
-    'method',
-    'method_in'
-  },
-}
-
-local default_cito_property = 'citation'
-
---- Map from cito aliases to the actual cito property.
-local properties_by_alias = {}
-for property, aliases in pairs(properties_and_aliases) do
-  -- every property is an alias for itself
-  properties_by_alias[property] = property
-  for _, alias in pairs(aliases) do
-    properties_by_alias[alias] = property
-  end
-end
-
---- Split citation ID into cito property and the actual citation ID. If
---- the ID does not seem to contain a CiTO property, the
---- `default_cito_property` will be returned, together with the
---- unchanged input ID.
-local function split_cito_from_id (citation_id)
-  local pattern = '^(.+):(.+)$'
-  local prop_alias, split_citation_id = citation_id:match(pattern)
-
-  if properties_by_alias[prop_alias] then
-    return properties_by_alias[prop_alias], split_citation_id
-  end
-
-  return default_cito_property, citation_id
-end
-
---- Citations by CiTO properties.
-local function store_cito (cito_cites, prop, cite_id)
-  if not prop then
-    return
-  end
-  if not cito_cites[prop] then
-    cito_cites[prop] = {}
-  end
-  table.insert(cito_cites[prop], cite_id)
-end
-
---- Returns a Cite filter function which extracts CiTO information and
---- add it to the given collection table.
-local function extract_cito (cito_cites)
-  return function (cite)
-    for k, citation in pairs(cite.citations) do
-      local cito_prop, cite_id = split_cito_from_id(citation.id)
-      store_cito(cito_cites, cito_prop, cite_id)
-      citation.id = cite_id
-    end
-    return cite
-  end
-end
-
---- Lists of citation IDs, indexed by CiTO properties.
-local citations_by_property = {}
-
-return {
-  {
-    Cite = extract_cito(citations_by_property)
-  },
-  {
-    Meta = function (meta)
-      meta.cito_cites = citations_by_property
-      return meta
-    end
-  }
-}

example/assets/pandoc-scholar/lua-filters/diagram-generator/README.md

@@ -1,252 +0,0 @@
-# Diagram Generator Lua Filter
-
-## Introduction
-This Lua filter is used to create images with or without captions from code
-blocks. Currently PlantUML, Graphviz, Ti*k*Z and Python can be processed.
-This document also serves as a test document, which is why the subsequent
-test diagrams are integrated in every supported language.
-
-## Prerequisites
-To be able to use this Lua filter, the respective external tools must be
-installed. However, it is sufficient if the tools to be used are installed.
-If you only want to use PlantUML, you don't need LaTeX or Python, etc.
-
-### PlantUML
-To use PlantUML, you must install PlantUML itself. See the
-[PlantUML website](http://plantuml.com/) for more details. It should be
-noted that PlantUML is a Java program and therefore Java must also
-be installed.
-
-By default, this filter expects the plantuml.jar file to be in the
-working directory. Alternatively, the environment variable
-`PLANTUML` can be set with a path. If, for example, a specific
-PlantUML version is to be used per pandoc document, the
-`plantumlPath` meta variable can be set.
-
-Furthermore, this filter assumes that Java is located in the
-system or user path. This means that from any place of the system
-the `java` command is understood. Alternatively, the `JAVA_HOME`
-environment variable gets used. To use a specific Java version per
-pandoc document, use the `javaPath` meta variable. Please notice
-that `JAVA_HOME` must be set to the java's home directory e.g.
-`c:\Program Files\Java\jre1.8.0_201\` whereas `javaPath` must be
-set to the absolute path of `java.exe` e.g.
-`c:\Program Files\Java\jre1.8.0_201\bin\java.exe`.
-
-Example usage:
-
-~~~~~~~~~~~~~~~~
-```{.plantuml caption="This is an image, created by **PlantUML**."}
-@startuml
-Alice -> Bob: Authentication Request Bob --> Alice: Authentication Response
-Alice -> Bob: Another authentication Request Alice <-- Bob: another Response
-@enduml
-```
-~~~~~~~~~~~~~~~~
-
-### Graphviz
-To use Graphviz you only need to install Graphviz, as you can read
-on its [website](http://www.graphviz.org/). There are no other
-dependencies.
-
-This filter assumes that the `dot` command is located in the path
-and therefore can be used from any location. Alternatively, you can
-set the environment variable `DOT` or use the pandoc's meta variable
-`dotPath`.
-
-Example usage from [the Graphviz
-gallery](https://graphviz.gitlab.io/_pages/Gallery/directed/fsm.html):
-
-~~~~~~~~~~~~~~~~
-```{.graphviz caption="This is an image, created by **Graphviz**'s dot."}
-digraph finite_state_machine {
-	rankdir=LR;
-	size="8,5"
-	node [shape = doublecircle]; LR_0 LR_3 LR_4 LR_8;
-	node [shape = circle];
-	LR_0 -> LR_2 [ label = "SS(B)" ];
-	LR_0 -> LR_1 [ label = "SS(S)" ];
-	LR_1 -> LR_3 [ label = "S($end)" ];
-	LR_2 -> LR_6 [ label = "SS(b)" ];
-	LR_2 -> LR_5 [ label = "SS(a)" ];
-	LR_2 -> LR_4 [ label = "S(A)" ];
-	LR_5 -> LR_7 [ label = "S(b)" ];
-	LR_5 -> LR_5 [ label = "S(a)" ];
-	LR_6 -> LR_6 [ label = "S(b)" ];
-	LR_6 -> LR_5 [ label = "S(a)" ];
-	LR_7 -> LR_8 [ label = "S(b)" ];
-	LR_7 -> LR_5 [ label = "S(a)" ];
-	LR_8 -> LR_6 [ label = "S(b)" ];
-	LR_8 -> LR_5 [ label = "S(a)" ];
-}
-```
-~~~~~~~~~~~~~~~~
-
-### Ti*k*Z
-Ti*k*Z (cf. [Wikipedia](https://en.wikipedia.org/wiki/PGF/TikZ)) is a
-description language for graphics of any kind that can be used within
-LaTeX (cf. [Wikipedia](https://en.wikipedia.org/wiki/LaTeX)).
-
-Therefore a LaTeX system must be installed on the system. The Ti*k*Z code is
-embedded into a dynamic LaTeX document. This temporary document gets
-translated into a PDF document using LaTeX (`pdflatex`). Finally,
-Inkscape is used to convert the PDF file to the desired format.
-
-Note: We are using Inkscape here to use a stable solution for the
-convertion. Formerly ImageMagick was used instead. ImageMagick is
-not able to convert PDF files. Hence, it uses Ghostscript to do
-so, cf. [1](https://stackoverflow.com/a/6599718/2258393).
-Unfortunately, Ghostscript behaves unpredictable during Windows and
-Linux tests cases, cf. [2](https://stackoverflow.com/questions/21774561/some-pdfs-are-converted-improperly-using-imagemagick),
-[3](https://stackoverflow.com/questions/9064706/imagemagic-convert-command-pdf-convertion-with-bad-size-orientation), [4](https://stackoverflow.com/questions/18837093/imagemagic-renders-image-with-black-background),
-[5](https://stackoverflow.com/questions/37392798/pdf-to-svg-is-not-perfect),
-[6](https://stackoverflow.com/q/10288065/2258393), etc. By using Inkscape,
-we need one dependency less and get rid of unexpected Ghostscript issues.
-
-Due to this more complicated process, the use of Ti*k*Z is also more
-complicated overall. The process is error-prone: An insufficiently
-configured LaTeX installation or an insufficiently configured
-Inkscape installation can lead to errors. Overall, this results in
-the following dependencies:
-
-- Any LaTeX installation. This should be configured so that
-missing packages are installed automatically. This filter uses the
-`pdflatex` command which is available by the system's path. Alternatively,
-you can set the `PDFLATEX` environment variable. In case you have to use
-a specific LaTeX version on a pandoc document basis, you might set the
-`pdflatexPath` meta variable.
-
-- An installation of [Inkscape](https://inkscape.org/).
-It is assumed that the `inkscape` command is in the path and can be
-executed from any location. Alternatively, the environment
-variable `INKSCAPE` can be set with a path. If a specific
-version per pandoc document is to be used, the `inkscapePath`
-meta-variable can be set.
-
-In order to use additional LaTeX packages, use the optional
-`additionalPackages` attribute in your document, as in the
-example below.
-
-Example usage from [TikZ
-examples](http://www.texample.net/tikz/examples/parallelepiped/) by
-[Kjell Magne Fauske](http://www.texample.net/tikz/examples/nav1d/):
-
-~~~~~~~~~~~~~~~~
-```{.tikz caption="This is an image, created by **TikZ i.e. LaTeX**."
-     additionalPackages="\usepackage{adjustbox}"}
-\usetikzlibrary{arrows}
-\tikzstyle{int}=[draw, fill=blue!20, minimum size=2em]
-\tikzstyle{init} = [pin edge={to-,thin,black}]
-
-\resizebox{16cm}{!}{%
-  \trimbox{3.5cm 0cm 0cm 0cm}{
-    \begin{tikzpicture}[node distance=2.5cm,auto,>=latex']
-      \node [int, pin={[init]above:$v_0$}] (a) {$\frac{1}{s}$};
-      \node (b) [left of=a,node distance=2cm, coordinate] {a};
-      \node [int, pin={[init]above:$p_0$}] at (0,0) (c)
-        [right of=a] {$\frac{1}{s}$};
-      \node [coordinate] (end) [right of=c, node distance=2cm]{};
-      \path[->] (b) edge node {$a$} (a);
-      \path[->] (a) edge node {$v$} (c);
-      \draw[->] (c) edge node {$p$} (end) ;
-    \end{tikzpicture}
-  }
-}
-```
-~~~~~~~~~~~~~~~~
-
-### Python
-In order to use Python to generate a diagram, your Python code must store the
-final image data in a temporary file with the correct format. In case you use
-matplotlib for a diagram, add the following line to do so:
-
-```python
-plt.savefig("$DESTINATION$", dpi=300, fomat="$FORMAT$")
-```
-
-The placeholder `$FORMAT$` gets replace by the necessary format. Most of the
-time, this will be `png` or `svg`. The second placeholder, `$DESTINATION$`
-gets replaced by the path and file name of the destination. Both placeholders
-can be used as many times as you want. Example usage from the [Matplotlib 
-examples](https://matplotlib.org/gallery/lines_bars_and_markers/cohere.html#sphx-glr-gallery-lines-bars-and-markers-cohere-py):
-
-~~~~~~~~~~~~~~~~
-```{.py2image caption="This is an image, created by **Python**."}
-import matplotlib
-matplotlib.use('Agg')
-
-import sys
-import numpy as np
-import matplotlib.pyplot as plt
-
-# Fixing random state for reproducibility
-np.random.seed(19680801)
-
-dt = 0.01
-t = np.arange(0, 30, dt)
-nse1 = np.random.randn(len(t))                 # white noise 1
-nse2 = np.random.randn(len(t))                 # white noise 2
-
-# Two signals with a coherent part at 10Hz and a random part
-s1 = np.sin(2 * np.pi * 10 * t) + nse1
-s2 = np.sin(2 * np.pi * 10 * t) + nse2
-
-fig, axs = plt.subplots(2, 1)
-axs[0].plot(t, s1, t, s2)
-axs[0].set_xlim(0, 2)
-axs[0].set_xlabel('time')
-axs[0].set_ylabel('s1 and s2')
-axs[0].grid(True)
-
-cxy, f = axs[1].cohere(s1, s2, 256, 1. / dt)
-axs[1].set_ylabel('coherence')
-
-fig.tight_layout()
-plt.savefig("$DESTINATION$", dpi=300, fomat="$FORMAT$")
-```
-~~~~~~~~~~~~~~~~
-
-Precondition to use Python is a Python environment which contains all
-necessary libraries you want to use. To use, for example, the standard
-[Anaconda Python](https://www.anaconda.com/distribution/) environment
-on a Microsoft Windows system ...
-
-- set the environment variable `PYTHON` or the meta key `pythonPath`
-to `c:\ProgramData\Anaconda3\python.exe`
-
-- set the environment variable `PYTHON_ACTIVATE` or the meta
-key `activatePythonPath` to `c:\ProgramData\Anaconda3\Scripts\activate.bat`.
-
-Pandoc will activate this Python environment and starts Python with your code.
-
-## How to run pandoc
-This section will show, how to call Pandoc in order to use this filter with
-meta keys. The following command assume, that the filters are stored in the
-subdirectory `filters`. Further, this is a example for a Microsoft Windows
-system.
-
-Command to use PlantUML (a single line):
-
-```
-pandoc.exe README.md -f markdown -t docx --self-contained --standalone --lua-filter=filters\diagram-generator.lua --metadata=plantumlPath:"c:\ProgramData\chocolatey\lib\plantuml\tools\plantuml.jar" --metadata=javaPath:"c:\Program Files\Java\jre1.8.0_201\bin\java.exe" -o README.docx
-```
-
-All available environment variables:
-
-- `PLANTUML` e.g. `c:\ProgramData\chocolatey\lib\plantuml\tools\plantuml.jar`; Default: `plantuml.jar`
-- `INKSCAPE` e.g. `c:\Program Files\Inkscape\inkscape.exe`; Default: `inkscape`
-- `PYTHON` e.g. `c:\ProgramData\Anaconda3\python.exe`; Default: n/a
-- `PYTHON_ACTIVATE` e.g. `c:\ProgramData\Anaconda3\Scripts\activate.bat`; Default: n/a
-- `JAVA_HOME` e.g. `c:\Program Files\Java\jre1.8.0_201`; Default: n/a
-- `DOT` e.g. `c:\ProgramData\chocolatey\bin\dot.exe`; Default: `dot`
-- `PDFLATEX` e.g. `c:\Program Files\MiKTeX 2.9\miktex\bin\x64\pdflatex.exe`; Default: `pdflatex`
-
-All available meta keys:
-
-- `plantumlPath`
-- `inkscapePath`
-- `pythonPath`
-- `activatePythonPath`
-- `javaPath`
-- `dotPath`
-- `pdflatexPath`

example/assets/pandoc-scholar/lua-filters/diagram-generator/diagram-generator.lua

@@ -1,316 +0,0 @@
---[[
-diagram-generator – create images and figures from code blocks.
-
-This Lua filter is used to create images with or without captions
-from code blocks. Currently PlantUML, GraphViz, Tikz, and Python
-can be processed. For further details, see README.md.
-
-Copyright: © 2018-2020 John MacFarlane <jgm@berkeley.edu>,
-             2018 Florian Schätzig <florian@schaetzig.de>,
-             2019 Thorsten Sommer <contact@sommer-engineering.com>,
-             2019-2020 Albert Krewinkel <albert+pandoc@zeitkraut.de>
-License:   MIT – see LICENSE file for details
-]]
--- Module pandoc.system is required and was added in version 2.7.3
-PANDOC_VERSION:must_be_at_least '2.7.3'
-
-local system = require 'pandoc.system'
-local with_temporary_directory = system.with_temporary_directory
-local with_working_directory = system.with_working_directory
-
--- The PlantUML path. If set, uses the environment variable PLANTUML or the
--- value "plantuml.jar" (local PlantUML version). In order to define a
--- PlantUML version per pandoc document, use the meta data to define the key
--- "plantumlPath".
-local plantumlPath = os.getenv("PLANTUML") or "plantuml.jar"
-
--- The Inkscape path. In order to define an Inkscape version per pandoc
--- document, use the meta data to define the key "inkscapePath".
-local inkscapePath = os.getenv("INKSCAPE") or "inkscape"
-
--- The Python path. In order to define a Python version per pandoc document,
--- use the meta data to define the key "pythonPath".
-local pythonPath = os.getenv("PYTHON")
-
--- The Python environment's activate script. Can be set on a per document
--- basis by using the meta data key "activatePythonPath".
-local pythonActivatePath = os.getenv("PYTHON_ACTIVATE")
-
--- The Java path. In order to define a Java version per pandoc document,
--- use the meta data to define the key "javaPath".
-local javaPath = os.getenv("JAVA_HOME")
-if javaPath then
-    javaPath = javaPath .. package.config:sub(1,1) .. "bin"
-        .. package.config:sub(1,1) .. "java"
-else
-    javaPath = "java"
-end
-
--- The dot (Graphviz) path. In order to define a dot version per pandoc
--- document, use the meta data to define the key "dotPath".
-local dotPath = os.getenv("DOT") or "dot"
-
--- The pdflatex path. In order to define a pdflatex version per pandoc
--- document, use the meta data to define the key "pdflatexPath".
-local pdflatexPath = os.getenv("PDFLATEX") or "pdflatex"
-
--- The default format is SVG i.e. vector graphics:
-local filetype = "svg"
-local mimetype = "image/svg+xml"
-
--- Check for output formats that potentially cannot use SVG
--- vector graphics. In these cases, we use a different format
--- such as PNG:
-if FORMAT == "docx" then
-    filetype = "png"
-    mimetype = "image/png"
-elseif FORMAT == "pptx" then
-    filetype = "png"
-    mimetype = "image/png"
-elseif FORMAT == "rtf" then
-    filetype = "png"
-    mimetype = "image/png"
-end
-
--- Execute the meta data table to determine the paths. This function
--- must be called first to get the desired path. If one of these
--- meta options was set, it gets used instead of the corresponding
--- environment variable:
-function Meta(meta)
-    plantumlPath = meta.plantumlPath or plantumlPath
-    inkscapePath = meta.inkscapePath or inkscapePath
-    pythonPath = meta.pythonPath or pythonPath
-    pythonActivatePath = meta.activatePythonPath or pythonActivatePath
-    javaPath = meta.javaPath or javaPath
-    dotPath = meta.dotPath or dotPath
-    pdflatexPath = meta.pdflatexPath or pdflatexPath
-end
-
--- Call plantuml.jar with some parameters (cf. PlantUML help):
-local function plantuml(puml, filetype)
-    local final = pandoc.pipe(javaPath, {"-jar", plantumlPath, "-t" .. filetype, "-pipe", "-charset", "UTF8"}, puml)
-    return final
-end
-
--- Call dot (GraphViz) in order to generate the image
--- (thanks @muxueqz for this code):
-local function graphviz(code, filetype)
-    local final = pandoc.pipe(dotPath, {"-T" .. filetype}, code)
-    return final
-end
-
---
--- TikZ
---
-
---- LaTeX template used to compile TikZ images. Takes additional
---- packages as the first, and the actual TikZ code as the second
---- argument.
-local tikz_template = [[
-\documentclass{standalone}
-\usepackage{tikz}
-%% begin: additional packages
-%s
-%% end: additional packages
-\begin{document}
-%s
-\end{document}
-]]
-
---- Returns a function which takes the filename of a PDF and a
--- target filename, and writes the input as the given format.
--- Returns `nil` if conversion into the target format is not
--- possible.
-local function convert_from_pdf(filetype)
-  -- Build the basic Inkscape command for the conversion
-  local inkscape_output_args
-  if filetype == 'png' then
-    inkscape_output_args = '--export-png="%s" --export-dpi=300'
-  elseif filetype == 'svg' then
-    inkscape_output_args = '--export-plain-svg="%s"'
-  else
-    return nil
-  end
-  return function (pdf_file, outfile)
-    local inkscape_command = string.format(
-      '"%s" --without-gui --file="%s" ' .. inkscape_output_args,
-      inkscapePath,
-      pdf_file,
-      outfile
-    )
-    io.stderr:write(inkscape_command .. '\n')
-    local command_output = io.popen(inkscape_command)
-    -- TODO: print output when debugging.
-    command_output:close()
-  end
-end
-
---- Compile LaTeX with Tikz code to an image
-local function tikz2image(src, filetype, additional_packages)
-  local convert = convert_from_pdf(filetype)
-  -- Bail if there is now known way from PDF to the target format.
-  if not convert then
-    error(string.format("Don't know how to convert pdf to %s.", filetype))
-  end
-  return with_temporary_directory("tikz2image", function (tmpdir)
-    return with_working_directory(tmpdir, function ()
-      -- Define file names:
-      local file_template = "%s/tikz-image.%s"
-      local tikz_file = file_template:format(tmpdir, "tex")
-      local pdf_file = file_template:format(tmpdir, "pdf")
-      local outfile = file_template:format(tmpdir, filetype)
-
-      -- Build and write the LaTeX document:
-      local f = io.open(tikz_file, 'w')
-      f:write(tikz_template:format(additional_packages or '', src))
-      f:close()
-
-      -- Execute the LaTeX compiler:
-      pandoc.pipe(pdflatexPath, {'-output-directory', tmpdir, tikz_file}, '')
-
-      convert(pdf_file, outfile)
-
-      -- Try to open and read the image:
-      local img_data
-      local r = io.open(outfile, 'rb')
-      if r then
-        img_data = r:read("*all")
-        r:close()
-      else
-        -- TODO: print warning
-      end
-
-      return img_data
-    end)
-  end)
-end
-
--- Run Python to generate an image:
-local function py2image(code, filetype)
-
-    -- Define the temp files:
-    local outfile = string.format('%s.%s', os.tmpname(), filetype)
-    local pyfile = os.tmpname()
-
-    -- Replace the desired destination's file type in the Python code:
-    local extendedCode = string.gsub(code, "%$FORMAT%$", filetype)
-
-    -- Replace the desired destination's path in the Python code:
-    extendedCode = string.gsub(extendedCode, "%$DESTINATION%$", outfile)
-
-    -- Write the Python code:
-    local f = io.open(pyfile, 'w')
-    f:write(extendedCode)
-    f:close()
-
-    -- Execute Python in the desired environment:
-    local pycmd = pythonPath .. ' ' .. pyfile
-    local command = pythonActivatePath
-      and pythonActivatePath .. ' && ' .. pycmd
-      or pycmd
-    os.execute(command)
-
-    -- Try to open the written image:
-    local r = io.open(outfile, 'rb')
-    local imgData = nil
-
-    -- When the image exist, read it:
-    if r then
-        imgData = r:read("*all")
-        r:close()
-    else
-        io.stderr:write(string.format("File '%s' could not be opened", outfile))
-        error 'Could not create image from python code.'
-    end
-
-    -- Delete the tmp files:
-    os.remove(pyfile)
-    os.remove(outfile)
-
-    return imgData
-end
-
--- Executes each document's code block to find matching code blocks:
-function CodeBlock(block)
-
-    -- Predefine a potential image:
-    local fname = nil
-
-    -- Using a table with all known generators i.e. converters:
-    local converters = {
-        plantuml = plantuml,
-        graphviz = graphviz,
-        tikz = tikz2image,
-        py2image = py2image,
-    }
-
-    -- Check if a converter exists for this block. If not, return the block
-    -- unchanged.
-    local img_converter = converters[block.classes[1]]
-    if not img_converter then
-      return nil
-    end
-
-    -- Call the correct converter which belongs to the used class:
-    local success, img = pcall(img_converter, block.text,
-        filetype, block.attributes["additionalPackages"] or nil)
-
-    -- Was ok?
-    if success and img then
-        -- Hash the figure name and content:
-        fname = pandoc.sha1(img) .. "." .. filetype
-
-        -- Store the data in the media bag:
-        pandoc.mediabag.insert(fname, mimetype, img)
-
-    else
-
-        -- an error occured; img contains the error message
-        io.stderr:write(tostring(img))
-        io.stderr:write('\n')
-        error 'Image conversion failed. Aborting.'
-
-    end
-
-    -- Case: This code block was an image e.g. PlantUML or dot/Graphviz, etc.:
-    if fname then
-
-        -- Define the default caption:
-        local caption = {}
-        local enableCaption = nil
-
-        -- If the user defines a caption, use it:
-        if block.attributes["caption"] then
-            caption = pandoc.read(block.attributes.caption).blocks[1].content
-
-            -- This is pandoc's current hack to enforce a caption:
-            enableCaption = "fig:"
-        end
-
-        -- Create a new image for the document's structure. Attach the user's
-        -- caption. Also use a hack (fig:) to enforce pandoc to create a
-        -- figure i.e. attach a caption to the image.
-        local imgObj = pandoc.Image(caption, fname, enableCaption)
-
-        -- Now, transfer the attribute "name" from the code block to the new
-        -- image block. It might gets used by the figure numbering lua filter.
-        -- If the figure numbering gets not used, this additional attribute
-        -- gets ignored as well.
-        if block.attributes["name"] then
-            imgObj.attributes["name"] = block.attributes["name"]
-        end
-
-        -- Finally, put the image inside an empty paragraph. By returning the
-        -- resulting paragraph object, the source code block gets replaced by
-        -- the image:
-        return pandoc.Para{ imgObj }
-    end
-end
-
--- Normally, pandoc will run the function in the built-in order Inlines ->
--- Blocks -> Meta -> Pandoc. We instead want Meta -> Blocks. Thus, we must
--- define our custom order:
-return {
-    {Meta = Meta},
-    {CodeBlock = CodeBlock},
-}

example/assets/pandoc-scholar/lua-filters/include-files/README.md

@@ -1,70 +0,0 @@
-# include-files
-
-Filter to include other files in the document.
-
-## Usage
-
-Use a special code block with class `include` to include files of
-the same format as the input. Each code line is treated as the
-filename of a file, parsed, and the result is added to the
-document.
-
-Metadata from included files is discarded.
-
-### Shifting Headings
-
-The default is to include the subdocuments unchanged, but it can
-be convenient to modify the level of headers; a top-level header
-in an included file should be a second or third-level header in
-the final document. Use the `shift-heading-level-by` attribute to
-control header shifting.
-
-### Comments
-
-Comment lines can be added in the include block by beginning a
-line with two `//` characters.
-
-### Different formats
-
-Files are assumed to be written in Markdown, but sometimes one
-will want to include files written in a different format. An
-alternative format can be specified via the `format` attribute.
-Only plain-text formats are accepted.
-
-## Example
-
-Let's assume we are writing a longer document, like a thesis.
-Each chapter and appendix section resides in its own file, with
-some additional information in the main file `main.md`:
-
-    ---
-    author: me
-    title: Thesis
-    ---
-
-    # Frontmatter
-
-    Thanks everyone!
-
-    <!-- actual chapters start here -->
-
-    ``` {.include}
-    chapters/introduction.md
-    chapters/methods.md
-    chapters/results.md
-    chapters/discussion.md
-    ```
-
-    # Appendix
-
-    More info goes here.
-
-    ``` {.include shift-heading-level-by=1}
-    // headings in included documents are shifted down a level,
-    // a level 1 heading becomes level 2.
-    appendix/questionaire.md
-    ```
-
-An HTML can be produced with this command:
-
-    pandoc --lua-filter=include-files.lua main.md --output result.html

example/assets/pandoc-scholar/lua-filters/include-files/include-files.lua

@@ -1,48 +0,0 @@
---- include-files.lua – filter to include Markdown files
----
---- Copyright: © 2019–2020 Albert Krewinkel
---- License:   MIT – see LICENSE file for details
-
--- pandoc's List type
-local List = require 'pandoc.List'
-
---- Shift headings in block list by given number
-function shift_headings(blocks, shift_by)
-  if not shift_by then
-    return blocks
-  end
-
-  local shift_headings_filter = {
-    Header = function (header)
-      header.level = header.level + shift_by
-      return header
-    end
-  }
-
-  return pandoc.walk_block(pandoc.Div(blocks), shift_headings_filter).content
-end
-
---- Filter function for code blocks
-function CodeBlock(cb)
-  -- ignore code blocks which are not of class "include".
-  if not cb.classes:includes 'include' then
-    return
-  end
-
-  -- Markdown is used if this is nil.
-  local format = cb.attributes['format']
-  local shift_heading_level_by =
-    tonumber(cb.attributes['shift-heading-level-by'])
-
-
-  local blocks = List:new()
-  for line in cb.text:gmatch('[^\n]+') do
-    if line:sub(1,2) ~= '//' then
-      local fh = io.open(line)
-      local contents = pandoc.read(fh:read '*a', format).blocks
-      blocks:extend(shift_headings(contents, shift_heading_level_by))
-      fh:close()
-    end
-  end
-  return blocks
-end

example/assets/pandoc-scholar/lua-filters/latex-hyphen/README.md

@@ -1,49 +0,0 @@
-# latex-hyphen.lua
-
-`latex-hyphen.lua` is a [pandoc](https://pandoc.org/) filter that replaces
-intra-word hyphens with the raw LaTeX expression `"=` for improved
-hyphenation.
-
-## Purpose
-
-The regular hyphen `-` prevents LaTeX from breaking a word at any other
-position than the explicit hyphen. With long, hyphenated words as they occur
-in languages like German, this can lead to undesirable visual results. The
-expression `"=` outputs a normal hyphen while still allowing LaTeX to break
-the word at any other position according to its regular hyphenation rules.
-
-Before:
-
-![](without-filter.png)
-
-After:
-
-![](with-filter.png)
-
-## Usage
-
-For this to work, babel shorthands have to be activated. With XeLaTeX or
-LuaTeX as PDF engine, this can be done using the YAML frontmatter:
-
-```yaml
-polyglossia-lang:
-    name: german
-    options:
-        - spelling=new,babelshorthands=true
-
-```
-
-For pdflatex, a custom template has to be used, as the built-in template
-explicitly deactivates babel’s shorthands.
-
-The filter can then be called like this:
-
-```sh
-pandoc -o mydoc.pdf --pdf-engine xelatex \
-    --lua-filter latex-hyphen.lua mydoc.md
-```
-
-## Caveat
-
-pandoc strips LaTeX expressions from PDF strings like bookmarks. Thus, the
-document outline in the resulting PDF file will lack any hyphens.

example/assets/pandoc-scholar/lua-filters/latex-hyphen/latex-hyphen.lua

@@ -1,81 +0,0 @@
---- Replace intra-word hyphens with LaTeX shorthand "= for better hyphenation.
---
--- PURPOSE
---
--- The regular hyphen - prevents LaTeX from breaking a word at any other
--- position than the explicit hyphen. With long, hyphenated words as they occur
--- in languages like German, this can lead to undesirable visual results. The
--- expression "= outputs a normal hyphen while still allowing LaTeX to break
--- the word at any other position according to its regular hyphenation rules.
---
--- USAGE
---
--- For this to work, babel shorthands have to be activated. With XeLaTeX or
--- LuaTeX as PDF engine, this can be done using the YAML frontmatter:
-
--- polyglossia-lang:
---     name: german
---     options:
---         - spelling=new,babelshorthands=true
---
--- For pdflatex, a custom template has to be used, as the built-in template
--- explicitly deactivates babel’s shorthands.
---
--- The filter can then be called like this:
---
--- pandoc -o doc.pdf --pdf-engine xelatex --lua-filter latex-hyphen.lua doc.md
---
--- AUTHOR
---
--- Copyright 2020 Frederik Elwert <frederik.elwert@rub.de>
---
--- LICENSE
---
--- Permission is hereby granted, free of charge, to any person obtaining a copy
--- of this software and associated documentation files (the "Software"), to
--- deal in the Software without restriction, including without limitation the
--- rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
--- sell copies of the Software, and to permit persons to whom the Software is
--- furnished to do so, subject to the following conditions:
---
--- The above copyright notice and this permission notice shall be included in
--- all copies or substantial portions of the Software.
---
--- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
--- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
--- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
--- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
--- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
--- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
--- IN THE SOFTWARE.
-
-
-if FORMAT ~= 'latex' then
-  return {}
-end
-
-function split_hyphen(inputstr)
-  local sep = '-'
-  local t = {}
-  for str in string.gmatch(inputstr, '([^'..sep..']+)') do
-    table.insert(t, str)
-  end
-  return t
-end
-
-function Str(elem)
-  local parts = split_hyphen(elem.c)
-  -- if not more than one part, string contains no hyphen, return unchanged.
-  if #parts <= 1 then
-    return nil
-  end
-  -- otherwise, splice raw latex "= between parts
-  local o = {}
-  for index, part in ipairs(parts) do
-    table.insert(o, pandoc.Str(part))
-    if index < #parts then
-      table.insert(o, pandoc.RawInline('latex', '"='))
-    end
-  end
-  return o
-end

example/assets/pandoc-scholar/lua-filters/lilypond/README.md

@@ -1,81 +0,0 @@
-# lilypond
-This filter renders [LilyPond](http://lilypond.org) inline code and
-code blocks into embedded images of musical notation. It's designed with
-(pandoc-flavored) Markdown input in mind.
-
-See the accompanying test files for some examples of how the filter works.
-
-## Rationale
-LilyPond is the tool of choice for generating musical notation from
-text input.  Integrating it with pandoc lets us write documents that include the
-code for musical examples alongside their main content and compile them with a
-single command. Because filters operate directly on pandoc's AST, support for
-any sufficiently rich output format is free.
-
-The LilyPond distribution includes a program called
-[`lilypond-book`](http://lilypond.org/doc/v2.19/Documentation/usage/lilypond_002dbook.en.html)
-that's intended to serve a similar purpose. Unfortunately, it has some
-significant limitations: only HTML and Texinfo are supported for input,
-compilation is messy, and the [source
-code](https://git.savannah.gnu.org/cgit/lilypond.git/tree/scripts/lilypond-book.py)
-is complex, running to over 700 lines of Python 2. This filter aims to be a
-superior alternative.
-
-## Usage
-The filter operates on inline code (type `Code`) and code block (type
-`CodeBlock`) elements that are marked with the `lilypond` class. Each such
-element is replaced by an image element, with the underlying PNG image generated
-by feeding the contents of the original element to LilyPond. (Eventually the
-filter will support SVG output as well.)
-
-You can configure the filter's behavior in two ways: by adding classes and
-attributes to individual code elements, and by adding metadata to the input
-document. Classes and attributes naturally only affect the element they're
-attached to, while metadata options affect all code elements in the document.
-
-The available classes are:
-
-* `ly-fragment`: the code in this element will be wrapped in some additional
-  boilerplate before compilation, meaning you can start writing notes
-  immediately without a bunch of setup. Inline code elements are always treated
-  as fragments.
-* `ly-norender`: this element will be ignored by the filter.
-
-The available (key-value) attributes are:
-
-* `ly-caption`: caption for the image generated from this element.  Default:
-  `"Musical notation"`.
-* `ly-name`: base filename (without path) for the image generated from this
-  element; an file extension will be appended. Default: the SHA1 digest of the
-  element's contents.
-* `ly-resolution`: resolution (in DPI) for the image generated from this
-  element. Default: set by LilyPond.
-* `ly-title`: title for the image generated from this element. Default: the
-  element's contents.
-
-The available metadata options are:
-
-* `lilypond.image_directory` (string): directory where generated images should
-  be saved. Will be resolved relative to the output file for this run of pandoc.
-  Default: `"."`.
-* `lilypond.relativize` (boolean): if enabled, use relative paths for the `src`
-  attributes of generated images.
-
-The classes and attributes listed above will *not* be copied to the generated
-image, but all other classes and attributes will be, and so will the identifier
-if one is present. The `lilypond` block (if present) will be stripped from the
-document metadata. Images generated from inline code will be tagged with the
-`lilypond-image-inline` class, and those generated from code blocks with the
-`lilypond-image-standalone` class.
-
-## Requirements
-The `lilypond` executable must be installed to a location on
-your `PATH`. You can obtain it [here](http://lilypond.org/download.html) or
-through your package manager.
-
-The filter uses some path-manipulation commands from the GNU coreutils,
-specifically `realpath` and `dirname`, so you'll also need those installed.
-
-Finally, because `lilypond.lua` uses functions from the `pandoc.system`
-submodule, it requires pandoc version 2.7.3 or later.
-

example/assets/pandoc-scholar/lua-filters/lilypond/lilypond.lua

@@ -1,189 +0,0 @@
-if PANDOC_VERSION and PANDOC_VERSION.must_be_at_least then
-  -- Actually, this check is redundant since `Version' objects were
-  -- introduced in pandoc v2.7.3, but I've left it in for clarity.
-  PANDOC_VERSION:must_be_at_least("2.7.3")
-else
-  error("pandoc version >=2.7.3 is required")
-end
-
-local OPTIONS = {
-        image_directory = ".",
-        relativize = false
-      }
-
-local SPECIAL_CLASSES = {
-        ["lilypond"] = true,
-        ["ly-fragment"] = true,
-        ["ly-norender"] = true
-      }
-
-local SPECIAL_ATTRIBUTES = {
-        ["ly-caption"] = true,
-        ["ly-name"] = true,
-        ["ly-resolution"] = true,
-        ["ly-title"] = true
-      }
-
--- pandoc.system.with_temporary_directory had a different (undocumented)
--- name in the 2.7.3 release.
-local with_temporary_directory = tostring(PANDOC_VERSION) == "2.7.3"
-                                   and pandoc.system.with_temp_directory
-                                    or pandoc.system.with_temporary_directory
-
--- This is the extra boilerplate that's added to code snippets when the
--- `ly-fragment' class is present. It's adapted from what `lilypond-book'
--- does. (The file `lilypond-book-preamble.ly' is placed on the include
--- path as part of the default LilyPond installation.)
-local function wrap_fragment(src)
-  return table.concat(
-           {
-             [[\include "lilypond-book-preamble.ly"]],
-             [[\paper { indent = 0\mm }]],
-             src,
-           },
-           "\n"
-         )
-end
-
-local function get_output_directory()
-  return PANDOC_STATE.output_file
-           and pandoc.pipe(
-                 "dirname",
-                 {PANDOC_STATE.output_file},
-                 ""
-               ):gsub("\n", "")
-end
-
-local function resolve_relative_path(what, where)
-  return pandoc.system.with_working_directory(
-           where,
-           function ()
-             return pandoc.pipe("realpath", {what}, ""):gsub("\n", "")
-           end
-         )
-end
-
-local function generate_image(name, input, dpi, whither)
-  local fullname = name .. ".png"
-  with_temporary_directory(
-    "lilypond-lua-XXXXX",
-    function (tmp_dir)
-      pandoc.system.with_working_directory(
-        tmp_dir,
-        function ()
-          pandoc.pipe(
-            "lilypond",
-            {
-              "--silent",
-              "--png", dpi and "-dresolution=" .. dpi or "",
-              "--output=" .. name, "-"
-            },
-            input
-          )
-          pandoc.pipe("cp", {fullname, whither}, "")
-        end
-      )
-    end
-  )
-  return whither .. "/" .. fullname
-end
-
-local function make_relative_path(to, from)
-  return pandoc.pipe(
-           "realpath",
-           {"--relative-to=" .. from, to},
-           ""
-         ):gsub("\n", "")
-end
-
-local function process_lilypond(elem, inline)
-  local code = elem.text
-  local fragment = elem.classes:includes("ly-fragment") or inline
-  local input = fragment
-                  and wrap_fragment(code)
-                   or code
-  local dpi = elem.attributes["ly-resolution"]
-  local name = elem.attributes["ly-name"] or pandoc.sha1(code)
-
-  local out_dir = get_output_directory() or "."
-  local dest = resolve_relative_path(OPTIONS.image_directory, out_dir)
-
-  local path = generate_image(name, input, dpi, dest)
-  local img = io.open(path, "rb")
-  pandoc.mediabag.insert(path, "image/png", img:read("*a"))
-  img:close()
-
-  local caption = elem.attributes["ly-caption"] or "Musical notation"
-  local src = OPTIONS.relativize
-                and make_relative_path(path, out_dir)
-                 or path
-  -- The "fig:" prefix causes this image to be rendered as a proper figure
-  -- in HTML ouput (this is a rather ugly pandoc feature and may be replaced
-  -- by something more elegant in the future).
-  local fudge = inline and "" or "fig:"
-  -- Strip newlines, indendation, etc. from the code for a more readable title.
-  local title = fudge .. (elem.attributes["ly-title"]
-                            or code:gsub("%s+", " "))
-
-  -- Strip most of the LilyPond-related attributes from this code element, for
-  -- tidiness.
-  local classes = elem.classes:filter(
-    function (cls)
-      return not SPECIAL_CLASSES[cls]
-    end
-  )
-  table.insert(
-    classes,
-    -- Add one special class for styling/manipulation purposes.
-    inline and "lilypond-image-inline"
-            or "lilypond-image-standalone"
-  )
-  local attributes = elem.attributes
-  for a, t in pairs(SPECIAL_ATTRIBUTES) do
-    attributes[a] = nil
-  end
-  local attrs = pandoc.Attr(elem.identifier, classes, attributes)
-
-  return pandoc.Image(caption, src, title, attrs)
-end
-
--- Update `OPTIONS' based on the document metadata.
-local function meta_transformer(md)
-  local ly_block = md.lilypond or {}
-  local dir_conf = ly_block.image_directory
-  OPTIONS.image_directory = dir_conf
-                              and pandoc.utils.stringify(dir_conf)
-                               or OPTIONS.image_directory
-  OPTIONS.relativize = ly_block.relativize
-                         or OPTIONS.relativize
-
-  md.lilypond = nil
-  return md
-end
-
-local function code_transformer(elem)
-  if elem.classes:includes("lilypond")
-       and not elem.classes:includes("ly-norender") then
-    return process_lilypond(elem, true)
-  else
-    return elem
-  end
-end
-
-local function code_block_transformer(elem)
-  if elem.classes:includes("lilypond")
-       and not elem.classes:includes("ly-norender") then
-    -- When replacing a block element we must wrap the generated image
-    -- in a `Para' since `Image' is an inline element.
-    return pandoc.Para({process_lilypond(elem, false)})
-  else
-    return elem
-  end
-end
-
--- Make sure the metadata transformation runs first so that the code
--- transformations operate with the correct options.
-return {
-         {Meta = meta_transformer},
-         {Code = code_transformer, CodeBlock = code_block_transformer},
-       }

example/assets/pandoc-scholar/lua-filters/minted/README.md

@@ -1,316 +0,0 @@
-# minted
-
-This filter enables users to use the [`minted`][minted] package with the
-`beamer` and `latex` writers.  Users may attach any desired `minted` specific
-styling / attributes to their code-blocks (or via document metadata).  These
-`minted` specific attributes will be _removed_ for any writers that are not
-`beamer` or `latex`, since many of the `minted` options require using `latex`
-specific syntax that can cause problems in other output formats.  For example,
-if the `fontsize=\footnotesize` attribute were applied to a code block, an
-`html` export would include `data-fontsize="\footnotesize"`, which may produce
-errors or more commonly be entirely meaningless for non-latex writers.
-
-The `minted` package will be used as a _replacement_ for the existing `pandoc`
-inline code and code block elements.  Behind the scenes, `minted` builds on top
-of the `fancyvrb` latex package, using [pygments][pygments] to perform the
-highlighting.  The `minted` package contains _many_ options for customizing
-output, users are encouraged to read / review section 5.3 of the
-[minted documentation][minted_docs].  **This filter does not make any attempts
-to validate arguments supplied to the `minted` package**.  Invalid / conflicting
-arguments are a usage error.
-
-**Contents**
-
-- [Setup](#setup)
-    - [LaTeX Preamble Configuration](#latex-preamble-configuration)
-    - [PDF Compilation](#pdf-compilation)
-- [Minted Filter Settings](#minted-filter-settings)
-    - [Default Settings](#default-settings)
-    - [All Metadata Settings](#all-metadata-settings)
-        - [`no_default_autogobble`](#no_default_autogobble-boolean)
-        - [`no_mintinline`](#no_mintinline-boolean)
-        - [`default_block_language`](#default_block_language-string)
-        - [`default_inline_language`](#default_inline_language-string)
-        - [`block_attributes`](#block_attributes-list-of-strings)
-        - [`inline_attributes`](#inline_attributes-list-of-strings)
-- [Important Usage Notes](#important-usage-notes)
-- [Bonus](#bonus)
-
-# Setup
-
-## LaTeX Preamble Configuration
-
-Since this filter will emit `\mintline` commands for inline code, and
-`\begin{minted} ... \end{minted}` environments for code blocks, you must ensure
-that your document includes the `minted` package in the preamble of your
-`beamer` or `latex` document.  The filter cannot accomplish this for you.
-
-**Option 1**
-
-Use the `header-includes` feature of `pandoc` (`-H` / `--include-in-header`).
-This will be injected into the preamble section of your `beamer` or `latex`
-document.  The bare minimum you need in this file is
-
-```latex
-\usepackage{minted}
-```
-
-However, there are many other things you can set here (related or unrelated to
-this filter), and this is a good opportunity to perform some global setup on the
-`minted` package.  Some examples:
-
-```latex
-\usepackage{minted}
-
-% Set the `style=tango` attribute for all minted blocks.  Can still be overriden
-% per block (e.g., you want to change just one).  Run `pygmentize -L` to see
-% all available options.
-\usemintedstyle{tango}
-
-% Depending on which pygments style you choose, comments and preprocessor
-% directives may be italic.  The `tango` style is one of these.  This disables
-% all italics in the `minted` environment.
-\AtBeginEnvironment{minted}{\let\itshape\relax}
-
-% This disables italics for the `\mintinline` commands.
-% Credit: https://tex.stackexchange.com/a/469702/113687
-\usepackage{xpatch}
-\xpatchcmd{\mintinline}{\begingroup}{\begingroup\let\itshape\relax}{}{}
-```
-
-The `minted` package has many options, see the
-[minted documentation][minted_docs] for more information.  For example, see the
-`bgcolor` option for the `minted` package.  In this "header-include" file would
-be an excellent location to `\definecolor`s that you want to use with `bgcolor`.
-
-**Option 1.5**
-
-You can also set `header-includes` in the metadata of your document.  The above
-example could be set as (noting the escaped backslashes):
-
-```yaml
-colorlinks: true
-header-includes:
-  # Include the minted package, set global style, define colors, etc.
-  - "\\usepackage{minted}"
-  - "\\usemintedstyle{tango}"
-  # Prevent italics in the `minted` environment.
-  - "\\AtBeginEnvironment{minted}{\\let\\itshape\\relax}"
-  # Prevent italics in the `\mintinline` command.
-  - "\\usepackage{xpatch}"
-  - "`\\xpatchcmd{\\mintinline}{\\begingroup}{\\begingroup\\let\\itshape\\relax}{}{}`{=latex}"
-```
-
-Note on the last line calling `\xpatchcmd`, we escape the backslashes and
-additionally force `pandoc` to treat this as `latex` code by making it an inline
-`latex` code element.  See [pandoc issue 2139 (comment)][pandoc_issue_2139] for
-more information.
-
-Formally, you may want to apply the ``-"`\\raw_tex`{=latex}"`` trick to all
-metadata to indicate it is `latex` specific code.  However, since `pandoc`
-strips out any raw `latex` when converting to other writers, it isn't necessary.
-
-**Option 2**
-
-You can also create your own custom `beamer` or `latex` template to have much
-finer control over what is / is not included in your document.  You may obtain
-a copy of the template that `pandoc` uses by default by running
-`pandoc -D beamer` or `pandoc -D latex` depending on your document type.
-
-After you have modified the template to suit your needs (including at the very
-least a `\usepackage{minted}`), specify your template file to `pandoc` using
-the `--template <path/to/template/file>` command line argument.
-
-## PDF Compilation
-
-To compile a PDF, there are two things that the `minted` package requires be
-available: an escaped shell to be able to run external commands (the
-`-shell-escape` command line flag), and the ability to create and later read
-auxiliary files (`minted` runs `pygmentize` for the highlighting).
-
-At the time of writing this, only one of these is accessible using `pandoc`
-directly.  One may pass `--pdf-engine-opt=-shell-escape` to forward the
-`-shell-escape` flag to the latex engine being used.  Unfortunately, though,
-the second component (related to temporary files being created) is not supported
-by `pandoc`.  See [pandoc issue 4271][pandoc_issue_4271].
-
-**However**, in reality this is an minor issue that can easily be worked around.
-Instead of generating `md => pdf`, you just use `pandoc` to generate `md => tex`
-and then compile `tex => pdf` yourself.  See the [sample Makefile](Makefile) for
-examples of how to execute both stages.  **Furthermore**, you will notice a
-significant advantage of managing the `pdf` compilation yourself: the generated
-`minted` files are cached and unless you `make clean` (or remove them manually),
-unchanged code listings will be reused.  That is, you will have faster
-compilation times :slightly_smiling_face:
-
-# Minted Filter Settings
-
-Direct control over the settings of this filter are performed by setting
-sub-keys of a `minted` metadata key for your document.
-
-## Default Settings
-
-By default, this filter
-
-1. Transforms all inline `Code` elements to `\mintinline`.  This can be disabled
-   globally by setting `no_mintinline: true`.
-
-2. Transforms all `CodeBlock` elements to `\begin{minted} ... \end{minted}` raw
-   latex code.  This cannot be disabled.
-
-3. Both (1) and (2) default to the `"text"` pygments lexer, meaning that inline
-   code or code blocks without a specific code class applied will receive no
-   syntax highlighting.  This can be changed globally by setting
-   `default_block_language: "lexer"` or `default_inline_language: "lexer"`.
-
-4. All `CodeBlock` elements have the `autogobble` attribute applied to them,
-   which informs `minted` to trim all common preceding whitespace.  This can be
-   disabled globally by setting `no_default_autogobble: true`.  However, doing
-   this is **strongly discouraged**.  Consider a code block nested underneath
-   a list item.  Pandoc will (correctly) generate indented code, meaning you
-   will need to manually inform `minted` to `gobble=indent` where `indent` is
-   the number of spaces to trim.  Note that `pandoc` may not reproduce the same
-   indentation level of the original document.
-
-## All Metadata Settings
-
-Each of the following are nested under the `minted` metadata key.
-
-### `no_default_autogobble` (boolean)
-
-By default this filter will always use `autogobble` with minted, which will
-automatically trim common preceding whitespace.  This is important because
-code blocks nested under a list or other block elements _will_ have common
-preceding whitespace that you _will_ want trimmed.
-
-### `no_mintinline` (boolean)
-
-Globally prevent this filter from emitting `\mintinline` calls for inline
-Code elements, emitting `\texttt` instead.  Possibly useful in saving
-compile time for large documents that do not seek to have syntax
-highlighting on inline code elements.
-
-### `default_block_language` (string)
-
-The default pygments lexer class to use for code blocks.  By default this
-is `"text"`, meaning no syntax highlighting.  This is a fallback value, code
-blocks that explicitly specify a lexer will not use it.
-
-### `default_inline_language` (string)
-
-Same as `default_block_language`, only for inline code (typed in single
-backticks).  The default is also `"text"`, and changing is discouraged.
-
-### `block_attributes` (list of strings)
-
-Any default attributes to apply to _all_ code blocks.  These may be
-overriden on a per-code-block basis.  See section 5.3 of the
-[minted documentation][minted_docs] for available options.
-
-### `inline_attributes` (list of strings)
-
-Any default attributes to apply to _all_ inline code.  These may be
-overriden on a per-code basis.  See section 5.3 of the
-[minted documentation][minted_docs] for available options.
-
-[minted_docs]: http://mirrors.ctan.org/macros/latex/contrib/minted/minted.pdf
-[minted]: https://ctan.org/pkg/minted?lang=en
-[pygments]: http://pygments.org/
-[pandoc_issue_2139]: https://github.com/jgm/pandoc/issues/2139#issuecomment-310522113
-[pandoc_issue_4271]: https://github.com/jgm/pandoc/issues/4721
-
-# Important Usage Notes
-
-Refer to the [`sample.md`](sample.md) file for some live examples of how to use
-this filter.  If you execute `make` in this directory, `sample_beamer.pdf`,
-`sample_latex.pdf`, and `sample.html` will all be generated to demonstrate the
-filter in action.
-
-`pandoc` allows you to specify additional attributes on either the closing
-backtick of an inline code element, or after the third backtick of a fenced
-code block.  This is done using `{curly braces}`, an example:
-
-```md
-`#include <type_traits>`{.cpp .showspaces style=bw}
-```
-
-or
-
-    ```{.cpp .showspaces style=bw}
-    #include <type_traits>
-    ```
-
-In order, these are
-
-- `.cpp`: specify the language lexer class.
-- `.showspaces`: a `minted` boolean attribute.
-- `style=bw`: a `minted` attribute that takes an argument (`bw` is a pygments
-  style, black-white, just an example).
-
-There are two rules that must not be violated:
-
-1. Any time you want to supply extra arguments to `minted` to a specific inline
-   code or code block element, **the lexer class must always be first, and
-   always be present**.
-
-   This is a limitation of the implementation of this filter.
-
-2. Observe the difference between specifying boolean attributes vs attributes
-   that take an argument.  Boolean `minted` attributes **must** have a leading
-   `.`, and `minted` attributes that take an argument **may not** have a leading
-   `.`.
-
-    - **Yes**: `{.cpp .showspaces}`, **No**: `{.cpp showspaces}`
-    - **Yes**: `{.cpp style=bw}`, **No**: `{.cpp .style=bw}`
-
-   If you violate this, then `pandoc` will likely not produce an actual inline
-   `Code` or `CodeBlock` element, but instead something else (undefined).
-
-Last, but not least, you will see that the `--no-highlight` flag is used in the
-`Makefile` for the latex targets.  This is added in the spirit of the filter
-being a "full replacement" for `pandoc` highlighting with `minted`.  This only
-affects inline code elements that meet the following criteria:
-
-1. The inline code element has a lexer, e.g., `{.cpp}`.
-2. The inline code element can actually be parsed for that language by `pandoc`.
-
-If these two conditions are met, and you do **not** specify `--no-highlight`,
-the `pandoc` highlighting engine will take over.  Users are encouraged to build
-the samples (`make` in this directory) and look at the end of the
-`Special Characters are Supported` section.  If you remove `--no-highlight`,
-`make realclean`, and then `make` again, you will see that the pandoc
-highlighting engine will colorize the `auto foo = [](){};`.
-
-Simply put: if you do not want any pandoc highlighting in your LaTeX, **make
-sure you add `--no-highlight`** and it will not happen.
-
-It is advantageous for this filter to rely on this behavior, because it means
-that the filter does not need to worry about escaping special characters for
-LaTeX -- `pandoc` will do that for us.  Inspect the generated `sample_*.tex`
-files (near the end) to see the difference.  `--no-highlight` will produce
-`\texttt` commands, but omitting this flag will result in some `\VERB` commands
-from `pandoc`.
-
-# Bonus
-
-Included here is a simple python script to help you get the right color
-definitions for `bgcolor` with minted.  Just run
-[`background_color.py`](background_color.py) with a single argument that is the
-name of the pygments style you want the `latex` background color definition for:
-
-```console
-$ ./background_color.py monokai
-Options for monokai (choose *one*):
-
-  (*) \definecolor{monokai_bg}{HTML}{272822}
-  (*) \definecolor{monokai_bg}{RGB}{39,40,34}
-  (*) \definecolor{monokai_bg}{rgb}{0.1529,0.1569,0.1333}
-                   |--------/
-                   |
-                   +--> You can rename this too :)
-```
-
-See the contents of [`sample.md`](sample.md) (click on "View Raw" to see the
-comments in the metadata section).  Notably, in order to use `\definecolor` you
-should make sure that the `xcolor` package is actually included.  Comments in
-the file explain the options.

example/assets/pandoc-scholar/lua-filters/minted/minted.lua

@@ -1,456 +0,0 @@
---[[
-minted -- enable the minted environment for code listings in beamer and latex.
-
-MIT License
-
-Copyright (c) 2019 Stephen McDowell
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-]]
-
---------------------------------------------------------------------------------
--- Quick documentation.  See full documentation here:                         --
--- https://github.com/pandoc/lua-filters/blob/master/minted                   --
---------------------------------------------------------------------------------
---[[
-Brief overview of metadata keys that you can use in your document:
-
-minted:
-  no_default_autogobble:   <boolean>, *DISCOURAGED*
-  no_mintinline:           <boolean>
-  default_block_language:  <string>
-  default_inline_language: <string>
-  block_attributes:        <list of strings>
-    - attr_1
-    - attr_2
-    - ...
-  inline_attributes:       <list of strings>
-    - attr_1
-    - attr_2
-    - ...
-
-In words, underneath the `minted` metadata key, you have the following options:
-
-### `no_default_autogobble` (boolean)
-
-By default this filter will always use `autogobble` with minted, which will
-automatically trim common preceding whitespace.  This is important because
-code blocks nested under a list or other block elements _will_ have common
-preceding whitespace that you _will_ want trimmed.
-
-### `no_mintinline` (boolean)
-
-Globally prevent this filter from emitting `\mintinline` calls for inline
-Code elements, emitting `\texttt` instead.  Possibly useful in saving
-compile time for large documents that do not seek to have syntax
-highlighting on inline code elements.
-
-### `default_block_language` (string)
-
-The default pygments lexer class to use for code blocks.  By default this
-is `"text"`, meaning no syntax highlighting.  This is a fallback value, code
-blocks that explicitly specify a lexer will not use it.
-
-### `default_inline_language` (string)
-
-Same as `default_block_language`, only for inline code (typed in single
-backticks).  The default is also `"text"`, and changing is discouraged.
-
-### `block_attributes` (list of strings)
-
-Any default attributes to apply to _all_ code blocks.  These may be
-overriden on a per-code-block basis.  See section 5.3 of the
-[minted documentation][minted_docs] for available options.
-
-### `inline_attributes` (list of strings)
-
-Any default attributes to apply to _all_ inline code.  These may be
-overriden on a per-code basis.  See section 5.3 of the
-[minted documentation][minted_docs] for available options.
-
-[minted_docs]: http://mirrors.ctan.org/macros/latex/contrib/minted/minted.pdf
-]]
-
-local List = require('pandoc.List')
-
---------------------------------------------------------------------------------
--- Potential metadata elements to override.                                   --
---------------------------------------------------------------------------------
-local minted_no_mintinline           = false
-local minted_default_block_language  = "text"
-local minted_default_inline_language = "text"
-local minted_block_attributes        = {}
-local minted_inline_attributes       = {}
-
---------------------------------------------------------------------------------
--- Constants used to differentiate Code and CodeBlock elements.               --
---------------------------------------------------------------------------------
-local MintedInline = 0
-local MintedBlock  = 1
-
---------------------------------------------------------------------------------
--- Utility functions.                                                         --
---------------------------------------------------------------------------------
--- Return the string lexer class to be used with minted.  `elem` should be
--- either a Code or CodeBlock element (whose `classes` list will be inspected
--- first).  `kind` is assumed to be either `MintedInline` or `MintedBlock` in
--- order to choose the appropriate fallback lexer when unspecified.
-local function minted_language(elem, kind)
-  -- If the code [block] attached classes, we assume the first one is the
-  -- lexer class to use.
-  if #elem.classes > 0 then
-    return elem.classes[1]
-  end
-  -- Allow user-level metadata to override the inline language.
-  if kind == MintedInline then
-    return minted_default_inline_language
-  end
-  -- Allow user-level metadata to override the block language.
-  if kind == MintedBlock then
-    return minted_default_block_language
-  end
-
-  -- Failsafe, should not hit here unless function called incorrectly.
-  return "text"
-end
-
--- Returns a boolean specifying whether or not the specified string `cls` is an
--- option that is supported by the minted package.
-local function is_minted_class(cls)
-  -- Section 5.3 Available Options of Minted documentation.  Note that many of
-  -- these do not apply to \mintinline (inline Code).  Users are responsible
-  -- for supplying valid arguments to minted.  For example, specifying
-  -- `autogobble` and `gobble` at the same time is a usage error.
-  --
-  -- http://mirrors.ctan.org/macros/latex/contrib/minted/minted.pdf
-  local all_minted_options = List:new{
-    "autogobble", "baselinestretch", "beameroverlays", "breakafter",
-    "breakaftergroup", "breakaftersymbolpre", "breakaftersymbolpost",
-    "breakanywhere", "breakanywheresymbolpre", "breakanywheresymbolpost",
-    "breakautoindent", "breakbefore", "breakbeforegroup",
-    "breakbeforesymbolpre", "breakbeforesymbolpost", "breakbytoken",
-    "breakbytokenanywhere", "breakindent", "breakindentnchars", "breaklines",
-    "breaksymbol", "breaksymbolleft", "breaksymbolright", "breaksymbolindent",
-    "breaksymbolindentnchars", "breaksymbolindentleft",
-    "breaksymbolindentleftnchars", "breaksymbolindentright",
-    "breaksymbolindentrightnchars", "breaksymbolsep", "breaksymbolsepnchars",
-    "breaksymbolsepleft", "breaksymbolsepleftnchars", "breaksymbolsepright",
-    "breaksymbolseprightnchars", "bgcolor", "codetagify", "curlyquotes",
-    "encoding", "escapeinside", "firstline", "firstnumber", "fontfamily",
-    "fontseries", "fontsize", "fontshape", "formatcom", "frame", "framerule",
-    "framesep", "funcnamehighlighting", "gobble", "highlightcolor",
-    "highlightlines", "keywordcase", "label", "labelposition", "lastline",
-    "linenos", "numberfirstline", "numbers", "mathescape", "numberblanklines",
-    "numbersep", "obeytabs", "outencoding", "python3", "resetmargins",
-    "rulecolor", "samepage", "showspaces", "showtabs", "space", "spacecolor",
-    "startinline", "style", "stepnumber", "stepnumberfromfirst",
-    "stepnumberoffsetvalues", "stripall", "stripnl", "tab", "tabcolor",
-    "tabsize", "texcl", "texcomments", "xleftmargin", "xrightmargin"
-  }
-  return all_minted_options:includes(cls, 0)
-end
-
--- Return a string for the minted attributes `\begin{minted}[attributes]` or
--- `\mintinline[attributes]`.  Attributes are acquired by inspecting the
--- specified element's `classes` and `attr` fields.  Any global attributes
--- provided in the document metadata will be included _only_ if they do not
--- override the element-level attributes.
---
--- `elem` should either be a Code or CodeBlock element, and `kind` is assumed to
--- be either `MintedInline` or `MintedBlock`.  The `kind` determines which
--- global default attribute list to use.
-local function minted_attributes(elem, kind)
-  -- The full listing of attributes that will be joined and returned.
-  local minted_attributes = {}
-
-  -- Book-keeping, track xxx=yyy keys `xxx` that have been added to
-  -- `minted_attributes` to make checking optional global defaults via the
-  -- `block_attributes` or `inline_attributes` easier.
-  local minted_keys = {}
-
-  -- Boolean style options for minted (e.g., ```{.bash .autogobble}) will appear
-  -- in the list of classes.
-  for _, cls in ipairs(elem.classes) do
-    if is_minted_class(cls) then
-      table.insert(minted_attributes, cls)
-      table.insert(minted_keys, cls)
-    end
-  end
-
-  -- Value options using key=value (e.g., ```{.bash fontsize=\scriptsize}) show
-  -- up in the list of attributes.
-  for _, attr in ipairs(elem.attributes) do
-    cls, value = attr[1], attr[2]
-    if is_minted_class(cls) then
-      table.insert(minted_attributes, cls .. "=" .. value)
-      table.insert(minted_keys, cls)
-    end
-  end
-
-  -- Add any global defaults _only_ if they do not conflict.  Note that conflict
-  -- is only in the literal sense.  If a user has `autogobble` and `gobble=2`
-  -- specified, these do conflict in the minted sense, but this filter makes no
-  -- checks on validity ;)
-  local global_defaults = nil
-  if kind == MintedInline then
-    global_defaults = minted_inline_attributes
-  elseif kind == MintedBlock then
-    global_defaults = minted_block_attributes
-  end
-  for _, global_attr in ipairs(global_defaults) do
-    -- Either use the index of `=` minus one, or -1 if no `=` present.  Fallback
-    -- on -1 means that the substring is the original string.
-    local end_idx = (string.find(global_attr, "=") or 0) - 1
-    local global_key = string.sub(global_attr, 1, end_idx)
-    local can_insert_global = true
-    for _, existing_key in ipairs(minted_keys) do
-      if existing_key == global_key then
-        can_insert_global = false
-        break
-      end
-    end
-
-    if can_insert_global then
-      table.insert(minted_attributes, global_attr)
-    end
-  end
-
-  -- Return a comma delimited string for specifying the attributes to minted.
-  return table.concat(minted_attributes, ",")
-end
-
--- Return the specified `elem` with any minted data removed from the `classes`
--- and `attr`.  Otherwise writers such as the HTML writer might produce invalid
--- code since latex makes heavy use of the \backslash.
-local function remove_minted_attibutes(elem)
-  -- Remove any minted items from the classes.
-  classes = {}
-  for _, cls in ipairs(elem.classes) do
-    if not is_minted_class(cls) and cls ~= "no_minted" then
-      table.insert(classes, cls)
-    end
-  end
-  elem.classes = classes
-
-  -- Remove any minted items from the attributes.
-  extra_attrs = {}
-  for _, attr in ipairs(elem.attributes) do
-    cls, value = attr[1], attr[2]
-    if not is_minted_class(cls) then
-      table.insert(extra_attrs, {cls, value})
-    end
-  end
-  elem.attributes = extra_attrs
-
-  -- Return the (potentially modified) element for pandoc to take over.
-  return elem
-end
-
--- Return a `start_delim` and `end_delim` that can safely wrap around the
--- specified `text` when used inline. If no special characters occur in `text`,
--- then a pair of braces are returned. Otherwise, if any character of
--- `possible_delims` are not in `text`, then it is returned. If no delimiter
--- could be found, an error is raised.
-local function minted_inline_delims(text)
-  local start_delim, end_delim
-  if text:find('[{}]') then
-    -- Try some other delimiter (the alphanumeric digits are in Python's
-    -- string.digits + string.ascii_letters order)
-    possible_delims = ('|!@#^&*-=+' .. '0123456789' ..
-                       'abcdefghijklmnopqrstuvwxyz' ..
-                       'ABCDEFGHIJKLMNOPQRSTUVWXYZ')
-    for char in possible_delims:gmatch('.') do
-      if not text:find(char, 1, true) then
-        start_delim = char
-        end_delim = char
-        break
-      end
-    end
-    if not start_delim then
-      local msg = 'Unable to determine delimiter to use around inline code %q'
-      error(msg:format(text))
-    end
-  else
-    start_delim = '{'
-    end_delim = '}'
-  end
-
-  return start_delim, end_delim
-end
-
---------------------------------------------------------------------------------
--- Pandoc overrides.                                                          --
---------------------------------------------------------------------------------
--- Override the pandoc Meta function so that we can parse the metadata for the
--- document and store the necessary variables locally to use in other functions
--- such as Code and CodeBlock (helper methods).
-function Meta(m)
-  -- Grab the `minted` metadata, quit early if not present.
-  local minted = m["minted"]
-  local found_autogobble = false
-  local always_autogobble = true
-  if minted ~= nil then
-    -- Parse and set the global bypass to turn off all \mintinline calls.
-    local no_mintinline = minted["no_mintinline"]
-    if no_mintinline ~= nil then
-      minted_no_mintinline = no_mintinline
-    end
-
-    -- Parse and set the default block language.
-    local default_block_language = minted.default_block_language
-      and pandoc.utils.stringify(minted.default_block_language)
-    if default_block_language ~= nil then
-      minted_default_block_language = default_block_language
-    end
-
-    -- Parse and set the default inline language.
-    local default_inline_language = minted.default_inline_language
-      and pandoc.utils.stringify(minted.default_inline_language)
-    if default_inline_language ~= nil then
-      minted_default_inline_language = default_inline_language
-    end
-
-    -- Parse the global default minted attributes to use on every block.
-    local block_attributes = minted["block_attributes"]
-    if block_attributes ~= nil then
-      for _, attr in ipairs(block_attributes) do
-        if attr == "autogobble" then
-          found_autogobble = true
-        end
-        table.insert(minted_block_attributes, attr[1].text)
-      end
-    end
-
-    -- Allow users to turn off autogobble for blocks, but really they should not
-    -- ever seek to do this (indented code blocks under list for example).
-    local no_default_autogobble = minted["no_default_autogobble"]
-    if no_default_autogobble ~= nil then
-      always_autogobble = not no_default_autogobble
-    end
-
-    -- Parse the global default minted attributes to use on ever inline.
-    local inline_attributes = minted["inline_attributes"]
-    if inline_attributes ~= nil then
-      for _, attr in ipairs(inline_attributes) do
-        table.insert(minted_inline_attributes, attr[1].text)
-      end
-    end
-  end
-
-  -- Make sure autogobble is turned on by default if no `minted` meta key is
-  -- provided for the document.
-  if always_autogobble and not found_autogobble then
-    table.insert(minted_block_attributes, "autogobble")
-  end
-
-  -- Return the metadata to pandoc (unchanged).
-  return m
-end
-
--- Override inline code elements to use \mintinline for beamer / latex writers.
--- Other writers have all minted attributes removed.
-function Code(elem)
-  if FORMAT == "beamer" or FORMAT == "latex" then
-    -- Allow a bypass to turn off \mintinline via adding .no_minted class.
-    local found_no_minted_class = false
-    for _, cls in ipairs(elem.classes) do
-      if cls == "no_minted" then
-        found_no_minted_class = true
-        break
-      end
-    end
-
-    -- Check for local or global bypass to turn off \mintinline
-    if minted_no_mintinline or found_no_minted_class then
-      return nil -- Return `nil` signals to `pandoc` that elem is not changed.
-    end
-
-    local start_delim, end_delim = minted_inline_delims(elem.text)
-    local language   = minted_language(elem, MintedInline)
-    local attributes = minted_attributes(elem, MintedInline)
-    local raw_minted = string.format(
-      "\\mintinline[%s]{%s}%s%s%s",
-      attributes,
-      language,
-      start_delim,
-      elem.text,
-      end_delim
-    )
-    -- NOTE: prior to pandoc commit 24a0d61, `beamer` cannot be used as the
-    -- RawBlock format.  Using `latex` should not cause any problems.
-    return pandoc.RawInline("latex", raw_minted)
-  else
-    return remove_minted_attibutes(elem)
-  end
-end
-
--- Override code blocks to use \begin{minted}...\end{minted} for beamer / latex
--- writers.  Other writers have all minted attributes removed.
-function CodeBlock(block)
-  if FORMAT == "beamer" or FORMAT == "latex" then
-    local language   = minted_language(block, MintedBlock)
-    local attributes = minted_attributes(block, MintedBlock)
-    local raw_minted = string.format(
-      "\\begin{minted}[%s]{%s}\n%s\n\\end{minted}",
-      attributes,
-      language,
-      block.text
-    )
-    -- NOTE: prior to pandoc commit 24a0d61, `beamer` cannot be used as the
-    -- RawBlock format.  Using `latex` should not cause any problems.
-    return pandoc.RawBlock("latex", raw_minted)
-  else
-    return remove_minted_attibutes(block)
-  end
-end
-
--- Override headers to make all beamer frames fragile, since any minted
--- environments or \mintinline invocations will halt compilation if the frame
--- is not marked as fragile.
-function Header(elem)
-  if FORMAT == 'beamer' then
-    -- Check first that 'fragile' is not already present.
-    local has_fragile = false
-    for _, val in ipairs(elem.classes) do
-      if val == 'fragile' then
-        has_fragile = true
-        break
-      end
-    end
-
-    -- If not found, add fragile to the list of classes.
-    if not has_fragile then
-      table.insert(elem.classes, 'fragile')
-    end
-
-    -- NOTE: pass the remaining work to pandoc, noting that 2.5 and below
-    -- may duplicate the 'fragile' specifier.  Duplicated fragile does *not*
-    -- cause compile errors.
-    return elem
-  end
-end
-
--- NOTE: order of return matters, Meta needs to be first otherwise the metadata
--- from the document will not be loaded _first_.
-return {
-  {Meta = Meta},
-  {Code = Code},
-  {CodeBlock = CodeBlock},
-  {Header = Header}
-}

example/assets/pandoc-scholar/lua-filters/multiple-bibliographies/README.md

@@ -1,33 +0,0 @@
-# multiple-bibliographies
-
-This filter allows to create multiple bibliographies using
-`pandoc-citeproc`. The content of each bibliography is controlled
-via YAML values and the file in which a bibliographic entry is
-specified.
-
-## Usage
-
-Instead of using the usual *bibliography* metadata field, all
-bibliographies must be defined via a separate field of the scheme
-*bibliographyX*, e.g.
-
-    ---
-    bibliography_main: main-bibliography.bib
-    bibliography_software: software.bib
-    ---
-
-The placement of bibliographies is controlled via special divs.
-
-    # References
-    
-    ::: {#refs_main}
-    :::
-    
-    # Software
-    
-    ::: {#refs_software}
-    :::
-
-Each refsX div should have a matching bibliographyX entry in the
-header. These divs are filled with citations from the respective
-bib-file.

example/assets/pandoc-scholar/lua-filters/multiple-bibliographies/multiple-bibliographies.lua

@@ -1,110 +0,0 @@
---[[
-multiple-bibliographies – create multiple bibliographies
-
-Copyright © 2018-2020 Albert Krewinkel
-
-Permission to use, copy, modify, and/or distribute this software for any
-purpose with or without fee is hereby granted, provided that the above
-copyright notice and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-]]
-local List = require 'pandoc.List'
-local utils = require 'pandoc.utils'
-local stringify = utils.stringify
-local run_json_filter = utils.run_json_filter
-
---- Collection of all cites in the document
-local all_cites = {}
---- Document meta value
-local doc_meta = pandoc.Meta{}
-
---- Div used by pandoc-citeproc to insert the bibliography.
-local refs_div = pandoc.Div({}, pandoc.Attr('refs'))
-
-local supports_quiet_flag = (function ()
-  local version = pandoc.pipe('pandoc-citeproc', {'--version'}, '')
-  local major, minor, patch = version:match 'pandoc%-citeproc (%d+)%.(%d+)%.?(%d*)'
-  major, minor, patch = tonumber(major), tonumber(minor), tonumber(patch)
-  return major > 0
-    or minor > 14
-    or (minor == 14 and patch >= 5)
-end)()
-
---- Resolve citations in the document by combining all bibliographies
--- before running pandoc-citeproc on the full document.
-local function resolve_doc_citations (doc)
-  -- combine all bibliographies
-  local meta = doc.meta
-  local orig_bib = meta.bibliography
-  meta.bibliography = pandoc.MetaList{orig_bib}
-  for name, value in pairs(meta) do
-    if name:match('^bibliography_') then
-      table.insert(meta.bibliography, value)
-    end
-  end
-  -- add dummy div to catch the created bibliography
-  table.insert(doc.blocks, refs_div)
-  -- resolve all citations
-  doc = run_json_filter(doc, 'pandoc-citeproc')
-  -- remove catch-all bibliography
-  table.remove(doc.blocks)
-  -- restore bibliography to original value
-  doc.meta.bibliography = orig_bib
-  return doc
-end
-
---- Explicitly create a new meta object with all fields relevant for
---- pandoc-citeproc.
-local function meta_for_pandoc_citeproc (bibliography)
-  -- We could just indiscriminately copy all meta fields, but let's be
-  -- explicit about what's important.
-  local fields = {
-    'bibliography', 'references', 'csl', 'citation-style',
-    'link-citations', 'citation-abbreviations', 'lang',
-    'suppress-bibliography', 'reference-section-title',
-    'notes-after-punctuation', 'nocite'
-  }
-  local new_meta = pandoc.Meta{}
-  for _, field in ipairs(fields) do
-    new_meta[field] = doc_meta[field]
-  end
-  new_meta.bibliography = bibliography
-  return new_meta
-end
-
---- Create a bibliography for a given topic. This acts on all divs whose
--- ID starts with "refs", followed by nothing but underscores and
--- alphanumeric characters.
-local function create_topic_bibliography (div)
-  local name = div.identifier:match('^refs([_%w]*)$')
-  local bibfile = name and doc_meta['bibliography' .. name]
-  if not bibfile then
-    return nil
-  end
-  local tmp_blocks = {pandoc.Para(all_cites), refs_div}
-  local tmp_meta = meta_for_pandoc_citeproc(bibfile)
-  local tmp_doc = pandoc.Pandoc(tmp_blocks, tmp_meta)
-  local filter_args = {FORMAT, supports_quiet_flag and '-q' or nil}
-  local res = run_json_filter(tmp_doc, 'pandoc-citeproc', filter_args)
-  -- First block of the result contains the dummy paragraph, second is
-  -- the refs Div filled by pandoc-citeproc.
-  div.content = res.blocks[2].content
-  return div
-end
-
-return {
-  {
-    -- Collect all citations and the doc's Meta value for other filters.
-    Cite = function (c) all_cites[#all_cites + 1] = c end,
-    Meta = function (m) doc_meta = m end,
-  },
-  { Pandoc = resolve_doc_citations },
-  { Div = create_topic_bibliography },
-}

example/assets/pandoc-scholar/lua-filters/pagebreak/README.md

@@ -1,68 +0,0 @@
-pagebreak
-=========
-
-This filter converts paragraps containing only the LaTeX
-`\newpage` or `\pagebreak` command into appropriate pagebreak
-markup for other formats. The command must be the only contents
-of a raw TeX block in order to be recognized. I.e., for Markdown
-the following is sufficient:
-
-    Paragraph before page break
-
-    \newpage
-
-    Paragraph after page break
-
-
-Usage
------
-
-Fully supported output formats are:
-
-- Docx,
-- LaTeX,
-- HTML, and
-- EPUB.
-
-ODT is supported, but requires additional settings in the
-reference document (see below).
-
-In all other formats, the page break is represented using the
-form feed character.
-
-
-### Usage with HTML
-If you want to use an HTML class rather than an inline style set
-the value of the metadata key `newpage_html_class` or the
-environment variable `PANDOC_NEWPAGE_HTML_CLASS` (the metadata
-'wins' if both are defined) to the name of the class and use CSS
-like this:
-
-    @media all {
-        .page-break	{ display: none; }
-    }
-    @media print {
-        .page-break	{ display: block; page-break-after: always; }
-    }
-
-
-### Usage with ODT
-
-To use with ODT you must create a reference ODT with a named
-paragraph style called `Pagebreak` (or whatever you set the
-metadata field `newpage_odt_style` or the environment variable
-`PANDOC_NEWPAGE_ODT_STYLE` to) and define it as having no extra
-space before or after but set it to have a pagebreak after it
-<https://help.libreoffice.org/Writer/Text_Flow>.
-
-(There will be an empty dummy paragraph, which means some extra
-vertical space, and you probably want that space to go at the
-bottom of the page before the break rather than at the top of
-the page after the break!)
-
-
-Alternative syntax
-------------------
-
-The form feed character as the only element in a paragraph is
-supported as an alternative to the LaTeX syntax described above.

example/assets/pandoc-scholar/lua-filters/pagebreak/pagebreak.lua

@@ -1,100 +0,0 @@
---[[
-pagebreak – convert raw LaTeX page breaks to other formats
-
-Copyright © 2017-2020 Benct Philip Jonsson, Albert Krewinkel
-
-Permission to use, copy, modify, and/or distribute this software for any
-purpose with or without fee is hereby granted, provided that the above
-copyright notice and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES
-WITH REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF
-MERCHANTABILITY AND FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR
-ANY SPECIAL, DIRECT, INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES
-WHATSOEVER RESULTING FROM LOSS OF USE, DATA OR PROFITS, WHETHER IN AN
-ACTION OF CONTRACT, NEGLIGENCE OR OTHER TORTIOUS ACTION, ARISING OUT OF
-OR IN CONNECTION WITH THE USE OR PERFORMANCE OF THIS SOFTWARE.
-]]
-local stringify_orig = (require 'pandoc.utils').stringify
-
-local function stringify(x)
-  return type(x) == 'string' and x or stringify_orig(x)
-end
-
---- configs – these are populated in the Meta filter.
-local pagebreak = {
-  epub = '<p style="page-break-after: always;"> </p>',
-  html = '<div style="page-break-after: always;"></div>',
-  latex = '\\newpage{}',
-  ooxml = '<w:p><w:r><w:br w:type="page"/></w:r></w:p>',
-  odt = '<text:p text:style-name="Pagebreak"/>'
-}
-
-local function pagebreaks_from_config (meta)
-  local html_class =
-    (meta.newpage_html_class and stringify(meta.newpage_html_class))
-    or os.getenv 'PANDOC_NEWPAGE_HTML_CLASS'
-  if html_class and html_class ~= '' then
-    pagebreak.html = string.format('<div class="%s"></div>', html_class)
-  end
-
-  local odt_style =
-    (meta.newpage_odt_style and stringify(meta.newpage_odt_style))
-    or os.getenv 'PANDOC_NEWPAGE_ODT_STYLE'
-  if odt_style and odt_style ~= '' then
-    pagebreak.odt = string.format('<text:p text:style-name="%s"/>', odt_style)
-  end
-end
-
---- Return a block element causing a page break in the given format.
-local function newpage(format)
-  if format == 'docx' then
-    return pandoc.RawBlock('openxml', pagebreak.ooxml)
-  elseif format:match 'latex' then
-    return pandoc.RawBlock('tex', pagebreak.latex)
-  elseif format:match 'odt' then
-    return pandoc.RawBlock('opendocument', pagebreak.odt)
-  elseif format:match 'html.*' then
-    return pandoc.RawBlock('html', pagebreak.html)
-  elseif format:match 'epub' then
-    return pandoc.RawBlock('html', pagebreak.epub)
-  else
-    -- fall back to insert a form feed character
-    return pandoc.Para{pandoc.Str '\f'}
-  end
-end
-
-local function is_newpage_command(command)
-  return command:match '^\\newpage%{?%}?$'
-    or command:match '^\\pagebreak%{?%}?$'
-end
-
--- Filter function called on each RawBlock element.
-function RawBlock (el)
-  -- Don't do anything if the output is TeX
-  if FORMAT:match 'tex$' then
-    return nil
-  end
-  -- check that the block is TeX or LaTeX and contains only
-  -- \newpage or \pagebreak.
-  if el.format:match 'tex' and is_newpage_command(el.text) then
-    -- use format-specific pagebreak marker. FORMAT is set by pandoc to
-    -- the targeted output format.
-    return newpage(FORMAT)
-  end
-  -- otherwise, leave the block unchanged
-  return nil
-end
-
--- Turning paragraphs which contain nothing but a form feed
--- characters into line breaks.
-function Para (el)
-  if #el.content == 1 and el.content[1].text == '\f' then
-    return newpage(FORMAT)
-  end
-end
-
-return {
-  {Meta = pagebreaks_from_config},
-  {RawBlock = RawBlock, Para = Para}
-}

example/assets/pandoc-scholar/lua-filters/pandoc-quotes.lua/LICENSE.txt

@@ -1,19 +0,0 @@
-Copyright (c) 2018 Odin Kroeger
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.
-IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,
-DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR
-OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE
-OR OTHER DEALINGS IN THE SOFTWARE.

example/assets/pandoc-scholar/lua-filters/pandoc-quotes.lua/README.md

@@ -1,110 +0,0 @@
-# pandoc-quotes.lua
-
-`pandoc-quotes.lua` is a filter for [Pandoc](https://www.pandoc.org/) that
-replaces non-typographic quotation marks with typographic ones for languages
-other than American English.
-
-You can define which typographic quotation marks to replace plain ones with by
-setting either a document's `quot-marks`, `quot-lang`, or `lang` metadata
-field. Typically, it should 'just work'.
-
-See the [manual page](man/pandoc-quotes.lua.md) for details.
-
-
-## Installing `pandoc-quotes.lua`
-
-You use `pandoc-quotes.lua` **at your own risk**. You have been warned.
-
-### Requirements
-
-You need [Pandoc](https://www.pandoc.org/) 2.0 or later.
-
-
-### Installation
-
-1. Download the
-   [latest release](https://github.com/odkr/pandoc-quotes.lua/releases/latest).
-2. Unpack it.
-3. Move `pandoc-quotes.lua` from the repository directory to the
-   `filters` sub-directory of your Pandoc data directory
-   (`pandoc --version` will tell you where that is).
-
-### POSIX-compliant systems
-
-If you have [curl](https://curl.haxx.se/) or
-[wget](https://www.gnu.org/software/wget/), you can (probably)
-install `pandoc-quotes.lua` by copy-pasting the
-following commands into a bourne shell:
-
-```sh
-(
-    set -Cefu
-    NAME=pandoc-quotes.lua VERS=0.1.10
-    URL="https://github.com/odkr/${NAME:?}/archive/v${VERS:?}.tar.gz"
-    FILTERS="${HOME:?}/.pandoc/filters"
-    mkdir -p "${FILTERS:?}"
-    {
-        curl -L "$URL" || ERR=$?
-        [ "${ERR-0}" -eq 127 ] && wget -q -O - "$URL"
-    } | tar xz
-    mv "$NAME-$VERS/pandoc-quotes.lua" "$FILTERS"
-)
-```
-
-You may also want to copy the manual page from the `man` directory in the
-repository to wherever your operating system searches for manual pages.
-
-
-## Test suite
-
-For the test suite to work, you need a POSIX-compliant operating system,
-[make](https://en.wikipedia.org/wiki/Make_(software)), and
-[Pandoc](https://www.pandoc.org/) 2.7.2. The test suite may or may not
-work with other versions of Pandoc.
-
-To run the test suite, just say:
-
-```sh
-    make test
-```
-
-## Documentation
-
-See the [manual page](man/pandoc-quotes.lua.md)
-and the source for details.
-
-
-## Contact
-
-If there's something wrong with `pandoc-quotes.lua`,
-[open an issue](https://github.com/odkr/pandoc-quotes.lua/issues).
-
-
-## License
-
-Copyright 2018, 2019 Odin Kroeger
-
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
-
-The above copyright notice and this permission notice shall be included in
-all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
-
-## Further Information
-
-
-GitHub:
-    <https://github.com/odkr/pandoc-quotes.lua>

example/assets/pandoc-scholar/lua-filters/pandoc-quotes.lua/pandoc-quotes.lua

@@ -1,474 +0,0 @@
---- Replaces plain quotation marks with typographic ones.
--- 
--- # SYNOPSIS
--- 
---      pandoc --lua-filter pandoc-quotes.lua
--- 
--- 
--- # DESCRIPTION
--- 
--- pandoc-quotes.lua is a filter for pandoc that replaces non-typographic
--- quotation marks with typographic ones for languages other than American
--- English.
--- 
--- You can define which typographic quotation marks to replace plain ones with
--- by setting either a document's quot-marks, quot-lang, or lang
--- metadata field. If none of these is set, pandoc-quotes.lua does nothing.
--- 
--- You can add your own mapping of a language to quotation marks or override
--- the default ones by setting quot-marks-by-lang.
--- 
--- ## quot-marks
--- 
--- A list of four strings, where the first item lists the primary left
--- quotation mark, the second the primary right quotation mark, the third
--- the secondary left quotation mark, and the fourth the secondary right
--- quotation mark.
--- 
--- For example:
--- 
--- ```yaml
--- ---
--- quot-marks:
---     - ''
---     - ''
---     - '
---     - '
--- ...
--- ```
--- 
--- You always have to set all four.
--- 
--- If each quotation mark consists of one character only,
--- you can write the whole list as a simple string.
--- 
--- For example:
--- 
--- ```yaml
--- ---
--- quot-marks: ""''
--- ...
--- ```
--- 
--- If quot-marks is set, the other fields are ignored.
--- 
--- 
--- # quotation-lang
--- 
--- An RFC 5646-like code for the language the quotation marks of
--- which shall be used (e.g., "pt-BR", "es").
--- 
--- For example:
--- 
--- ```yaml
--- ---
--- quot-lang: de-AT
--- ...
--- ```
--- 
--- Note: Only the language and the country tags of RFC 5646 are supported.
--- For example, "it-CH" (i.e., Italian as spoken in Switzerland) is fine, 
--- but "it-756" (also Italian as spoken in Switzerland) will return the 
--- quotation marks for "it" (i.e., Italian as spoken in general).
--- 
--- If quot-marks is set, quot-lang is ignored.
--- 
--- 
--- # lang
--- 
--- The format of lang is the same as for quot-lang. If quot-marks
--- or quot-lang is set, lang is ignored. 
--- 
--- For example:
--- 
--- ```yaml
--- ---
--- lang: de-AT
--- ...
--- ```
--- 
--- 
--- # ADDING LANGUAGES
--- 
--- You can add quotation marks for unsupported languages, or override the
--- defaults, by setting the metadata field quot-marks-by-lang to a maping
--- of RFC 5646-like language codes (e.g., "pt-BR", "es") to lists of quotation
--- marks, which are given in the same format as for the quot-marks
--- metadata field.
--- 
--- For example:
--- 
--- ```yaml
--- ---
--- quot-marks-by-lang:
---     abc-XYZ: ""''
--- lang: abc-XYZ
--- ...
--- ```
--- 
--- 
--- # CAVEATS
--- 
--- pandoc represents documents as abstract syntax trees internally, and
--- quotations are nodes in that tree. However, pandoc-quotes.lua replaces
--- those nodes with their content, adding proper quotation marks. That is,
--- pandoc-quotes.lua pushes quotations from the syntax of a document's
--- representation into its semantics. That being so, you should not 
--- use pandoc-quotes.lua with output formats that represent quotes
--- syntactically (e.g., HTML, LaTeX, ConTexT). Moroever, filters running after
--- pandoc-quotes won't recognise quotes. So, it should be the last or
--- one of the last filters you apply.
--- 
--- Support for quotation marks of different languages is certainly incomplete
--- and likely erroneous. See <https://github.com/odkr/pandoc-quotes.lua> if
--- you'd like to help with this.
--- 
--- pandoc-quotes.lua is Unicode-agnostic.
--- 
--- 
--- # SEE ALSO
--- 
--- pandoc(1)
---
---
--- # AUTHOR
---
--- Copyright 2019 Odin Kroeger
---
---
--- # LICENSE
---
--- Permission is hereby granted, free of charge, to any person obtaining a copy
--- of this software and associated documentation files (the "Software"), to
--- deal in the Software without restriction, including without limitation the
--- rights to use, copy, modify, merge, publish, distribute, sublicense, and/or
--- sell copies of the Software, and to permit persons to whom the Software is
--- furnished to do so, subject to the following conditions:
---
--- The above copyright notice and this permission notice shall be included in
--- all copies or substantial portions of the Software.
---
--- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
--- IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
--- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
--- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
--- LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
--- FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS
--- IN THE SOFTWARE.
---
---
--- @script pandoc-quotes.lua
--- @release 0.1.10
--- @author Odin Kroeger
--- @copyright 2018, 2020 Odin Kroeger
--- @license MIT
-
-
--- # INITIALISATION
-
-local M = {}
-
-local pairs = pairs
-local require = require
-
-local io = io
-local table = table
-local package = package
-
-local pandoc = pandoc
-if not pandoc.utils then pandoc.utils = require 'pandoc.utils' end
-
-local _ENV = M
-
-local text = require 'text'
-
-
--- # CONSTANTS
-
---- The name of this script.
-SCRIPT_NAME = 'pandoc-quotes.lua'
-
---- The path seperator of the operating system.
-PATH_SEP = package.config:sub(1, 1)
-
---- The character sequence to end a line.
-if PATH_SEP == '\\' then EOL = '\r\n'
-                    else EOL = '\n'   end
-
-
---- A list of mappings from RFC 5646-ish language codes to quotation marks.
--- 
--- I have adopted the list below from:
--- <https://en.wikipedia.org/w/index.php?title=Quotation_mark&oldid=836731669>
--- 
--- I tried to come up with reasonable defaults for secondary quotes for
--- language that, according to the Wikipedia, don't have any.
---
--- Adding languages:
---
--- Add an ordered pair, where the first item is an RFC 5646 language
--- code (though only the language and country tags are supported) and the
--- second item is a list of quotation marks, in the following order:
--- primary left, primary right, secondary left, secondary right.
---
--- You have to list four quotation marks, even if the langauge you add does
--- not use secondary quotation marks. Just come up with something that makes
--- sense. This is because a user may, rightly, find that just because their
--- language does not 'officially' have secondary quotation marks, they
--- are going to use them anyway. And they should get a reasonable result,
--- not a runtime error.
---
--- The order in which languages are listed is meaningless. If you define 
--- variants for a language that is spoken in different countries, also
--- define a 'default' for the language alone, without the country tag.
-QUOT_MARKS_BY_LANG = {
-    bo          = {'「', '」',    '『', '』'     },
-    bs          = {'”',  '”',     '’',  '’'    },
-    cn          = {'「', '」',    '『', '』'     },
-    cs          = {'„',  '“',     '‚',  '‘'    },
-    cy          = {'‘',  '’',     '“',  '”'    },
-    da          = {'»',  '«',     '›',  '‹'    },
-    de          = {'„',  '“',     '‚',  '‘'    },
-    ['de-CH']   = {'«',  '»',     '‹',  '›'    },
-    el          = {'«',  '»',     '“',  '”'    },
-    en          = {'“',  '”',     '‘',  '’'    },
-    ['en-US']   = {'“',  '”',     '‘',  '’'    },
-    ['en-GB']   = {'‘',  '’',     '“',  '”'    },
-    ['en-UK']   = {'‘',  '’',     '“',  '”'    },
-    ['en-CA']   = {'“',  '”',     '‘',  '’'    },
-    eo          = {'“',  '”',     '‘',  '’'    },
-    es          = {'«',  '»',     '“',  '”'    },
-    et          = {'„',  '“',     '‚',  '‘'    },
-    fi          = {'”',  '”',     '’',  '’'    },
-    fil         = {'“',  '”',     '‘',  '’'    },
-    fa          = {'«',  '»',     '‹',  '›'    },
-    fr          = {'«',  '»',     '‹',  '›'    },
-    ga          = {'“',  '”',     '‘',  '’'    },
-    gd          = {'‘',  '’',     '“',  '”'    },
-    gl          = {'«',  '»',     '‹',  '›'    },
-    he          = {'“',  '”',     '‘',  '’'    },
-    hi          = {'“',  '”',     '‘',  '’'    },
-    hu          = {'„',  '”',     '»',  '«'    },
-    hr          = {'„',  '“',     '‚',  '‘'    },
-    ia          = {'“',  '”',     '‘',  '’'    },
-    id          = {'“',  '”',     '‘',  '’'    },
-    is          = {'„',  '“',     '‚',  '‘'    },
-    it          = {'«',  '»',     '“',  '”'    },
-    ['it-CH']   = {'«',  '»',     '‹',  '›'    },
-    ja          = {'「', '」',    '『',  '』'    },
-    jbo         = {'lu', 'li\'u', 'lu', 'li\'u'},
-    ka          = {'„',  '“',     '‚',  '‘'    },
-    khb         = {'《', '》',    '〈',  '〉'    },
-    kk          = {'«',  '»',     '‹',  '›'    },
-    km          = {'«',  '»',     '‹',  '›'    },
-    ko          = {'《', '》',    '〈',  '〉'    },
-    ['ko-KR']   = {'“',  '”',     '‘',  '’'    },
-    lt          = {'„',  '“',     '‚',  '‘'    },
-    lv          = {'„',  '“',     '‚',  '‘'    },
-    lo          = {'«',  '»',     '‹',  '›'    },
-    nl          = {'„',  '”',     '‚',  '’'    },
-    mk          = {'„',  '“',     '’',  '‘'    },
-    mn          = {'«',  '»',     '‹',  '›'    },
-    mt          = {'“',  '”',     '‘',  '’'    },
-    no          = {'«',  '»',     '«',  '»'    },
-    pl          = {'„',  '”',     '»',  '«'    },
-    ps          = {'«',  '»',     '‹',  '›'    },
-    pt          = {'«',  '»',     '“',  '”'    },
-    ['pt-BR']   = {'“',  '”',     '‘',  '’'    },
-    rm          = {'«',  '»',     '‹',  '›'    },
-    ro          = {'„',  '”',     '«',  '»'    },
-    ru          = {'«',  '»',     '“',  '”'    },
-    sk          = {'„',  '“',     '‚',  '‘'    },
-    sl          = {'„',  '“',     '‚',  '‘'    },
-    sq          = {'„',  '“',     '‚',  '‘'    },
-    sr          = {'„',  '“',     '’',  '’'    },
-    sv          = {'”',  '”',     '’',  '’'    },
-    tdd         = {'「', '」',    '『',  '』'    },
-    ti          = {'«',  '»',     '‹',  '›'    },
-    th          = {'“',  '”',     '‘',  '’'    },
-    thi         = {'「', '」',    '『',  '』'    },
-    tr          = {'«',  '»',     '‹',  '›'    },
-    ug          = {'«',  '»',     '‹',  '›'    },
-    uk          = {'«',  '»',     '„',  '“'    },
-    uz          = {'«',  '»',     '„',  '“'    },
-    vi          = {'“',  '”',     '‘',  '’'    },
-    wen         = {'„',  '“',     '‚',  '‘'    },
-    ka          = {'„',  '“',     '‚',  '‘'    },
-    khb         = {'《', '》',     '〈', '〉'    },
-    kk          = {'«',  '»',     '‹',  '›'    },
-    km          = {'«',  '»',     '‹',  '›'    },
-    ko          = {'《', '》',     '〈', '〉'    },
-    ['ko-KR']   = {'“',  '”',     '‘',  '’'    },
-    lt          = {'„',  '“',     '‚',  '‘'    },
-    lv          = {'„',  '“',     '‚',  '‘'    },
-    lo          = {'«',  '»',     '‹',  '›'    },
-    nl          = {'„',  '”',     '‚',  '’'    },
-    mk          = {'„',  '“',     '’',  '‘'    },
-    mn          = {'«',  '»',     '‹',  '›'    },
-    mt          = {'“',  '”',     '‘',  '’'    },
-    no          = {'«',  '»',     '«',  '»'    },
-    pl          = {'„',  '”',     '»',  '«'    },
-    ps          = {'«',  '»',     '‹',  '›'    },
-    pt          = {'«',  '»',     '“',  '”'    },
-    ['pt-BR']   = {'“',  '”',     '‘',  '’'    },
-    rm          = {'«',  '»',     '‹',  '›'    },
-    ro          = {'„',  '”',     '«',  '»'    },
-    ru          = {'«',  '»',     '“',  '”'    },
-    sk          = {'„',  '“',     '‚',  '‘'    },
-    sl          = {'„',  '“',     '‚',  '‘'    },
-    sq          = {'„',  '“',     '‚',  '‘'    },
-    sr          = {'„',  '“',     '’',  '’'    },
-    sv          = {'”',  '”',     '’',  '’'    },
-    tdd         = {'「', '」',     '『', '』'    },
-    ti          = {'«',  '»',     '‹',  '›'    },
-    th          = {'“',  '”',     '‘',  '’'    },
-    thi         = {'「', '」',     '『', '』'    },
-    tr          = {'«',  '»',     '‹',  '›'    },
-    ug          = {'«',  '»',     '‹',  '›'    },
-    uk          = {'«',  '»',     '„',  '“'    },
-    uz          = {'«',  '»',     '„',  '“'    },
-    vi          = {'“',  '”',     '‘',  '’'    },
-    wen         = {'„',  '“',     '‚',  '‘'    }
-}
-
-
--- # FUNCTIONS
-
---- Prints warnings to STDERR.
---
--- Prefixes messages with `SCRIPT_NAME` and ": ".
--- Also appends an end of line sequence.
---
--- @tparam string str A string format to be written to STDERR.
--- @tparam string ... Arguments to that format.
-function warn (str, ...)
-    io.stderr:write(SCRIPT_NAME, ': ', string.format(str, ...), EOL)
-end
-
-
---- Applies a function to every element of a list.
---
--- @tparam func f The function.
--- @tparam tab list The list.
--- @treturn tab The return values of `f`.
-function map (f, list)
-    local ret = {}
-    for k, v in pairs(list) do ret[k] = f(v) end
-    return ret
-end
-
-do
-    local stringify = pandoc.utils.stringify
-
-    --- Reads quotation marks from a `quot-marks` metadata field.
-    --
-    -- @tparam pandoc.MetaValue The content of a metadata field.
-    --  Must be either of type pandoc.MetaInlines or pandoc.MetaList.
-    -- @treturn[1] {pandoc.Str,pandoc.Str,pandoc.Str,pandoc.Str} 
-    --  A table of quotation marks 
-    -- @treturn[2] `nil` if an error occurred.
-    -- @treturn[2] string An error message.
-    function get_quotation_marks (meta)
-        if meta.t == 'MetaInlines' then
-            local marks = stringify(meta)
-            if text.len(marks) ~= 4 then
-                return nil, 'not four quotation marks'
-            end
-            local ret = {}
-            for i = 1, 4 do ret[i] = text.sub(marks, i, i) end
-            return ret
-        elseif meta.t == 'MetaList' then
-            local marks = map(stringify, meta)
-            if #marks ~= 4 then
-                return nil, 'not four quotation marks'
-            end
-            return marks
-        end
-        return nil, 'neither a string nor a list'
-    end
-end
-
-
-do
-    local stringify = pandoc.utils.stringify
-    
-    -- Holds the quotation marks for the language of the document.
-    -- Common to `configure` and `insert_quot_marks`.
-    local QUOT_MARKS = nil
-
-    --- Determines the quotation marks for the document.
-    --
-    -- Stores them in `QUOT_MARKS`, which it shares with `insert_quot_marks`.
-    -- Prints errors to STDERR.
-    --
-    -- @tparam pandoc.Meta The document's metadata.
-    function configure (meta)
-        local quot_marks, lang
-        if meta['quot-marks-by-lang'] then
-            for k, v in pairs(meta['quot-marks-by-lang']) do
-                local quot_marks, err = get_quotation_marks(v)
-                if not quot_marks then 
-                    warn('metadata field "quot-marks-by-lang": lang "%s": %s.',
-                         k, err) 
-                    return
-                end
-                QUOT_MARKS_BY_LANG[k] = quot_marks
-            end
-        end
-        if meta['quot-marks'] then
-            local err
-            quot_marks, err = get_quotation_marks(meta['quot-marks'])
-            if not quot_marks then 
-                warn('metadata field "quot-marks": %s.', err)
-                return
-            end
-        elseif meta['quot-lang'] then
-            lang = stringify(meta['quot-lang'])
-        elseif meta['lang'] then
-            lang = stringify(meta['lang'])
-        end
-        if lang then
-            for i = 1, 3 do
-                if     i == 2 then lang = lang:match '^(%a+)'
-                elseif i == 3 then
-                    local expr = '^' .. lang .. '-'
-                    for k, v in pairs(QUOT_MARKS_BY_LANG) do
-                        if k:match(expr) then quot_marks = v break end
-                    end
-                end
-                if     i  < 3 then quot_marks = QUOT_MARKS_BY_LANG[lang] end
-                if quot_marks then break end
-            end
-        end
-        if quot_marks then QUOT_MARKS = map(pandoc.Str, quot_marks) 
-        elseif lang then warn('%s: unknown language.', lang) end
-    end
-
-
-    do
-        local insert = table.insert
-        --- Replaces quoted elements with quoted text.
-        --
-        -- Uses the quotation marks stored in `QUOT_MARKS`, 
-        -- which it shares with `configure`.
-        --
-        -- @tparam pandoc.Quoted quoted A quoted element.
-        -- @treturn {pandoc.Str,pandoc.Inline,...,pandoc.Str}
-        --  A list with the opening quote (as `pandoc.Str`),
-        --  the content of `quoted`, and the closing quote (as `pandoc.Str`).
-        function insert_quot_marks (quoted)
-            if not QUOT_MARKS then return end
-            local quote_type = quoted.c[1]
-            local inlines    = quoted.c[2]
-            local left, right
-            if     quote_type == 'DoubleQuote' then left, right = 1, 2
-            elseif quote_type == 'SingleQuote' then left, right = 3, 4
-            else   error('unknown quote type') end
-            insert(inlines, 1, QUOT_MARKS[left])
-            insert(inlines,    QUOT_MARKS[right])
-            return inlines
-        end
-    end
-end
-
-return {{Meta = configure}, {Quoted = insert_quot_marks}}

example/assets/pandoc-scholar/lua-filters/plantuml/plantuml.lua

@@ -1,56 +0,0 @@
---[[
-# PlantUML Pandoc filter
-PlantUML Pandoc filter to process code blocks with class "plantuml" containing PlantUML notation into images.
-
-* For textual output formats, use --extract-media=DIR
-* For HTML formats, you may alternatively use --self-contained
-
-## Example in markdown-file
-```plantuml
-@startuml
-Alice -> Bob: Authentication Request Bob --> Alice: Authentication Response
-Alice -> Bob: Another authentication Request Alice <-- Bob: another authentication Response @enduml
-```
-## Run pandoc
-```
-pandoc --self-contained --lua-filter=plantuml.lua readme.md -o output.htm
-```
-
-## Prerequisites
-* download PlantUML from http://plantuml.com (needs JAVA)
-* 3 ways to set the environment
-    1. plantuml.lua and plantuml.jar in the same folder and start pandoc always from this folder
-    2. set a Environment Variable PLANTUML with the path to plantuml.jar
-        * Windows - with powershell: Set-Item env:PLANTUML "c:\bin\plantuml.jar"
-    3. change path to plantuml.jar in plantuml.lua
-
-This script based on the example "Converting ABC code to music notation" from https://pandoc.org/lua-filters.html
-**This script was only tested with markdown to html on a windows environment!**
-]]
-
--- Path to PlantUML.jar
--- if you use opinion 3 change the path to plantuml.jar like this:
--- local plantumlPath = os.getenv("PLANTUML") or "c:\\bin\\plantuml.jar"
-local plantumlPath = os.getenv("PLANTUML") or "plantuml.jar"
-
--- SVG has a much better quality
--- local filetype = "png"
--- local mimetype = "image/png"
-local filetype = "svg"
-local mimetype = "image/svg+xml"
-
--- call plantuml.jar wit some parameters (see plantuml help)
-local function plantuml(puml, filetype, plantumlPath)
-    local final = pandoc.pipe("java", {"-jar", plantumlPath, "-t" .. filetype, "-pipe", "-charset", "UTF8"}, puml)
-    return final
-end
-
--- search for class "plantuml" and replace with image
-function CodeBlock(block)
-    if block.classes[1] == "plantuml" then
-        local img = plantuml(block.text, filetype, plantumlPath)
-        local fname = pandoc.sha1(img) .. "." .. filetype
-        pandoc.mediabag.insert(fname, mimetype, img)
-        return pandoc.Para{ pandoc.Image({pandoc.Str("PlantUML Diagramm")}, fname) }
-    end
-end

example/assets/pandoc-scholar/lua-filters/plantuml/readme.md

@@ -1,30 +0,0 @@
-# PlantUML Pandoc filter
-PlantUML Pandoc filter to process code blocks with class "plantuml" containing PlantUML notation into images.
-
-* For textual output formats, use --extract-media=DIR
-* For HTML formats, you may alternatively use --self-contained
-
-## Example in markdown-file
-```plantuml
-@startuml
-Alice -> Bob: Authentication Request Bob --> Alice: Authentication Response
-Alice -> Bob: Another authentication Request Alice <-- Bob: another authentication Response
-@enduml
-```
-## Run pandoc
-```
-pandoc --self-contained --lua-filter=plantuml.lua readme.md -o output.htm
-```
-
-## Prerequisites
-* download PlantUML from http://plantuml.com (needs JAVA)
-* 3 ways to set the environment
-    1. plantuml.lua and plantuml.jar in the same folder and start pandoc always from this folder
-    2. set a Environment Variable PLANTUML with the path to plantuml.jar
-        * Windows - with powershell: Set-Item env:PLANTUML "c:\bin\plantuml.jar"
-    3. change path to plantuml.jar in plantuml.lua
-
-
-This script based on the example "Converting ABC code to music notation" from https://pandoc.org/lua-filters.html
-
-This script was only tested with markdown to html on a windows environment!

example/assets/pandoc-scholar/lua-filters/scholarly-metadata/README.md

@@ -1,91 +0,0 @@
-# scholarly-metadata
-
-The filter turns metadata entries for authors and their
-affiliations into a canonical form. This allows users to
-conveniently declare document authors and their affiliations,
-while making it possible to rely on default object metadata
-structures when using the data in other filters or when accessing
-the data from custom templates.
-
-
-## Canonical format for authors and affiliations
-
-Authors and affiliations entries are treated as *named objects*.
-All named objects will have an ID and a name, i.e. they are
-metadata objects with *at least* those two keys:
-
-    - id: namedObjectExample
-      name: Example for a named object.
-
-The filter converts the *author* and *institute* metadata fields
-into lists of named objects.
-
-E.g., the following YAML data
-
-    author:
-      - Jane Doe:
-          email: 'jane.doe@example.edu'
-      - John Q. Doe
-
-
-will be transformed into
-
-    author:
-    - email: 'jane.doe\@example.edu'
-      id: Jane Doe
-      name: Jane Doe
-    - id: 'John Q. Doe'
-      name: 'John Q. Doe'
-      
-Internally, `id` will be a simple string, while `name` is of type
-`MetaInlines`.
-      
-
-## Referencing affiliations
-
-Author affiliations are a common feature of scholarly
-publications. It is possible to add institutes to each author
-object. Three methods of doing this are supported.
-
-1.  **Referencing institutes by list index**: affiliations can be
-    listed in the *institute* metadata field and then referenced
-    by using the numerical index:
-    
-        institute:
-          - Acme Corporation
-          - Federation of Planets
-        author:
-          - Jane Doe:
-              institute: [1, 2]
-          - John Q. Doe:
-              institute: [2]
-        
-    This is also the canonical representation used to keep track
-    of author affiliations.
-
-2.  **Referencing institutes by ID**: using numerical indices is
-    error prone and difficult to maintain when adding or removing
-    authors or affilications. It is hence possible to use IDs
-    instead:
-
-        institute:
-          - acme: Acme Corporation
-          - federation: Federation of Planets
-        author:
-          - Jane Doe:
-              institute: [acme, federation]
-          - John Q. Doe:
-              institute: [federation]
-
-3.  **Adding institute as an attribute**: sometimes it might be
-    more convenient to give an affiliation directly in the
-    author's YAML object. Those objects can still be referenced
-    by ID from authors listed below such entry.
-    
-        author:
-          - Jane Doe:
-              institute:
-               - Acme Cooproration
-               - federation: Federation of Planets
-          - John Q. Doe:
-              institute: [federation]

example/assets/pandoc-scholar/lua-filters/scholarly-metadata/scholarly-metadata.lua

@@ -1,185 +0,0 @@
---[[
-ScholarlyMeta – normalize author/affiliation meta variables
-
-Copyright (c) 2017-2020 Albert Krewinkel, Robert Winkler
-
-Permission to use, copy, modify, and/or distribute this software for any purpose
-with or without fee is hereby granted, provided that the above copyright notice
-and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-THIS SOFTWARE.
-]]
-local List = require 'pandoc.List'
-
--- Split a string at commas.
-local function comma_separated_values(str)
-  local acc = List:new{}
-  for substr in str:gmatch('([^,]*)') do
-    acc[#acc + 1] = substr:gsub('^%s*', ''):gsub('%s*$', '') -- trim
-  end
-  return acc
-end
-
---- Ensure the return value is a list.
-local function ensure_list (val)
-  if type(val) ~= 'table' then
-    -- create singleton list (or empty list if val == nil).
-    return List:new{val}
-  elseif val.t == 'MetaInlines' then
-    -- check if this is really a comma-separated list
-    local csv = comma_separated_values(pandoc.utils.stringify(val))
-    if #csv >= 2 then
-      return csv
-    end
-    return List:new{val}
-  elseif val.t == 'MetaList' then
-    return List:new(val)
-  else
-    -- MetaBlocks or MetaMap, use as a singleton
-    return List:new{val}
-  end
-end
-
---- Returns a function which checks whether an object has the given ID.
-local function has_id (id)
-  return function(x) return x.id == id end
-end
-
---- Copy all key-value pairs of the first table into the second iff there is no
--- such key yet in the second table.
--- @returns the second argument
-function add_missing_entries(a, b)
-  for k, v in pairs(a) do
-    b[k] = b[k] or v
-  end
-  return b
-end
-
---- Create an object with a name. The name is either taken directly from the
--- `name` field, or from the *only* field name (i.e., key) if the object is a
--- dictionary with just one entry. If neither exists, the name is left unset
--- (`nil`).
-function to_named_object (obj)
-  local named = {}
-  if type(obj) ~= 'table' then
-    -- if the object isn't a table, just use its value as a name.
-    named.name = pandoc.MetaInlines{pandoc.Str(tostring(obj))}
-    named.id = tostring(obj)
-  elseif obj.t == 'MetaInlines' then
-      -- Treat inlines as the name
-      named.name = obj
-      named.id = pandoc.utils.stringify(obj)
-  elseif obj.name ~= nil then
-    -- object has name attribute → just create a copy of the object
-    add_missing_entries(obj, named)
-    named.id = pandoc.utils.stringify(named.id or named.name)
-  elseif next(obj) and next(obj, next(obj)) == nil then
-    -- the entry's key is taken as the name, the value contains the
-    -- attributes.
-    key, attribs = next(obj)
-    if type(attribs) == "string" or attribs.t == 'MetaInlines' then
-      named.name = attribs
-    else
-      add_missing_entries(attribs, named)
-      named.name = named.name or pandoc.MetaInlines{pandoc.Str(tostring(key))}
-    end
-    named.id = named.id and pandoc.utils.stringify(named.id) or key
-  else
-    -- this is not a named object adhering to the usual conventions.
-    error('not a named object: ' .. tostring(obj))
-  end
-  return named
-end
-
---- Resolve institute placeholders to full named objects
-local function resolve_institutes (institute, known_institutes)
-  local unresolved_institutes
-  if institute == nil then
-    unresolved_institutes = {}
-  elseif type(institute) == "string" or type(institute) == "number" then
-    unresolved_institutes = {institute}
-  else
-    unresolved_institutes = institute
-  end
-
-  local result = List:new{}
-  for i, inst in ipairs(unresolved_institutes) do
-    result[i] =
-      known_institutes[tonumber(inst)] or
-      known_institutes:find_if(has_id(pandoc.utils.stringify(inst))) or
-      to_named_object(inst)
-  end
-  return result
-end
-
---- Insert a named object into a list; if an object of the same name exists
--- already, add all properties only present in the new object to the existing
--- item.
-function merge_on_id (list, namedObj)
-  local elem, idx = list:find_if(has_id(namedObj.id))
-  local res = elem and add_missing_entries(namedObj, elem) or namedObj
-  local obj_idx = idx or (#list + 1)
-  -- return res, obj_idx
-  list[obj_idx] = res
-  return res, #list
-end
-
---- Flatten a list of lists.
-local function flatten (lists)
-  local result = List:new{}
-  for _, lst in ipairs(lists) do
-    result:extend(lst)
-  end
-  return result
-end
-
---- Canonicalize authors and institutes
-local function canonicalize(raw_author, raw_institute)
-  local institutes = ensure_list(raw_institute):map(to_named_object)
-  local authors = ensure_list(raw_author):map(to_named_object)
-
-  for _, author in ipairs(authors) do
-    author.institute = resolve_institutes(
-      ensure_list(author.institute),
-      institutes
-    )
-  end
-
-  -- Merge institutes defined in author objects with those defined in the
-  -- top-level list.
-  local author_insts = flatten(authors:map(function(x) return x.institute end))
-  for _, inst in ipairs(author_insts) do
-    merge_on_id(institutes, inst)
-  end
-
-  -- Add list indices to institutes for numbering and reference purposes
-  for idx, inst in ipairs(institutes) do
-    inst.index = pandoc.MetaInlines{pandoc.Str(tostring(idx))}
-  end
-
-  -- replace institutes with their indices
-  local to_index = function (inst)
-    return tostring(select(2, institutes:find_if(has_id(inst.id))))
-  end
-  for _, author in ipairs(authors) do
-    author.institute = pandoc.MetaList(author.institute:map(to_index))
-  end
-
-  return authors, institutes
-end
-
-
-return {
-  {
-    Meta = function(meta)
-      meta.author, meta.institute = canonicalize(meta.author, meta.institute)
-      return meta
-    end
-  }
-}

example/assets/pandoc-scholar/lua-filters/scrlttr2/README.md

@@ -1,60 +0,0 @@
-# scrlttr2
-
-This filter allows to write DIN 5008 letter using the [scrlttr2]
-LaTeX document class from KOMA script. It converts metadata to
-the appropriate KOMA variables and allows using the default LaTeX
-template shipped with pandoc.
-
-[scrlttr2]: https://www.ctan.org/pkg/scrlttr2
-
-## Base variables
-
-  - `opening`: phrase used as an opening;
-    defaults to "Dear Sir/Madam,"
-  - `closing`: closing phrase; defaults to "Sincerely,"
-  - `address`: recipient's street address;
-    defaults to "no address given"
-  - `date`: the date of the letter; defaults to the current day.
-
-## KOMA Variables
-
-Currently, the following metadata fields are translated to KOMA
-variables:
-
-- `fromaddress` (alias: `return-address`): address of the sender
-- `fromfax` (alias: `fax`): sender's fax number
-- `fromemail` (alias: `email`): sender's email
-- `fromlogo` (alias: `logo`): value to be used as the sender's logo
-- `fromname` (alias: `author`): sender name
-- `fromphone` (alias: `phone`): sender's phone number
-- `fromurl` (alias: `url`): sender's URL
-- `customer`: customer number
-- `invoice`: invoice number
-- `myref`: sender's reference
-- `place`: sender's place used near date
-- `signature`: sender's signature
-- `subject`: letter's subject
-- `title`: letter title
-- `yourref`: addressee's reference
-
-The values of these variables are converted to MetaInlines. If a
-list is given, then each list item is used as a line, e.g.,
-
-    fromaddress:
-      - 35 Industry Way
-      - Springfield
-      
-The `KOMAoptions` value is inferred from the given variables, but
-can be overwritten by specifying it explicitly.
-
-See the scrlttr2 documentation for details.
-
-## Intended Usage
-
-Many sender variables don't change, so it is sensible to provide
-default values for these. Authors using Markdown to draft letters
-can use a separate YAML file for this. E.g., if there is a file
-`default.yml` which contains the sender's details, then only the
-addressee's data must be specified.
-
-    pandoc --lua-filter=scrlttr2 letter.md default.yml -o out.pdf

example/assets/pandoc-scholar/lua-filters/scrlttr2/scrlttr2.lua

@@ -1,161 +0,0 @@
--- Ensure unpack also works if pandoc was compiled against Lua 5.1
-local unpack = unpack or table.unpack
-local List = require 'pandoc.List'
-local stringify = (require 'pandoc.utils')['stringify']
-
---- Set some default options
-local default = {
-  opening = 'Dear Sir/Madam,',
-  closing = 'Sincerely,',
-  address = 'no address given'
-}
-
---- Return a list of inlines representing a call to a latex command.
-local function latex_command (command, ...)
-  local entry = {
-    pandoc.RawInline('latex', '\\' .. command),
-  }
-  for _, arg in ipairs{...} do
-    entry[#entry + 1] = pandoc.RawInline('latex', '{')
-    if type(arg) ~= 'table' then
-      entry[#entry + 1] = pandoc.RawInline('latex', tostring(arg))
-    else
-      List.extend(entry, arg)
-    end
-    entry[#entry + 1] = pandoc.RawInline('latex', '}')
-  end
-  return entry
-end
-
---- Convert the given meta-value to a list of inlines
-local function ensure_inlines (val)
-  if not val or type(val) == 'string' or type(val) == 'boolean' then
-    return pandoc.MetaInlines{pandoc.Str(tostring(val))}
-  elseif type(val) == 'table' and val.t == 'MetaInlines' then
-      return val
-  elseif type(val) == 'table' then
-    local res = List:new{}
-    for i = 1, #val do
-      res:extend(val[i])
-      res[#res + 1] = pandoc.RawInline('latex', '\\\\ ')
-    end
-    res[#res] = nil -- drop last linebreak
-    return pandoc.MetaInlines(res)
-  else
-    return pandoc.MetaInlines{pandoc.Str(pandoc.utils.stringify(val))}
-  end
-end
-
---- Convert the given value to a MetaList
-local function ensure_meta_list (val)
-  if not val or val.t ~= 'MetaList'  then
-    return pandoc.MetaList{}
-  else
-    return val
-  end
-end
-
---- Set supported variables as KOMA variables.
-function setkomavar_commands (meta)
-  local set_vars = {}
-  local res = {}
-  local function set_koma_var (name, value, enable)
-    if value ~= nil then
-      res[#res + 1] = latex_command('setkomavar', name, ensure_inlines(value))
-      if enable then
-        set_vars[#set_vars + 1] = name
-      end
-    end
-  end
-
-  set_koma_var('fromname', meta.fromname or meta.author)
-  set_koma_var('fromaddress', meta.fromaddress or meta['return-address'])
-  set_koma_var('subject', meta.subject)
-  set_koma_var('title', meta.title)
-  set_koma_var('signature', meta.signature)
-  set_koma_var('customer', meta.customer)
-  set_koma_var('yourref', meta.yourref)
-  set_koma_var('myref', meta.myref)
-  set_koma_var('invoice', meta.invoice)
-  set_koma_var('place', meta.place)
-
-  set_koma_var('fromfax', meta.fromfax or meta.fax, true)
-  set_koma_var('fromurl', meta.fromurl or meta.url, true)
-  set_koma_var('fromlogo', meta.fromlogo or meta.logo, true)
-  set_koma_var('fromemail', meta.fromemail or meta.email, true)
-  set_koma_var('fromphone', meta.fromphone or meta.phone, true)
-
-  -- don't set date if date is set to `false`
-  if meta.date == nil or meta.date == true then
-    if meta['date-format'] then
-      set_koma_var('date', os.date(stringify(date_format)))
-    else
-      set_koma_var('date', pandoc.MetaInlines{pandoc.RawInline('latex', '\\today')})
-    end
-  elseif meta.date then
-    set_koma_var('date', meta.date)
-  end
-
-  if meta['KOMAoptions'] or #set_vars >= 1 then
-    res[#res + 1] = latex_command(
-      'KOMAoptions',
-      meta['KOMAoptions']
-        or table.concat(set_vars, '=true,') .. '=true'
-    )
-  end
-
-  return res
-end
-
---- Bring Metadata in a form suitable for the scrlttr KOMA class
-local function make_koma_metadata(meta)
-  local header_includes = ensure_meta_list(meta['header-includes'])
-  List.extend(header_includes, setkomavar_commands(meta))
-
-  local include_before = ensure_meta_list(meta['include-before'])
-  List.extend(
-    include_before,
-    {
-      pandoc.MetaInlines(
-        latex_command(
-          'begin',
-          'letter',
-          ensure_inlines(meta.address or default.address)
-        )
-      ),
-
-      pandoc.MetaInlines(
-        latex_command('opening', meta.opening or default.opening)
-      ),
-    }
-  )
-
-  local include_after = ensure_meta_list(meta['include-after'])
-  List.extend(
-    include_after,
-    {
-      pandoc.MetaInlines(
-        latex_command('closing', meta.closing or default.closing)
-      ),
-      pandoc.MetaInlines(latex_command('end', 'letter')),
-    }
-  )
-
-  -- unset or reset some unwanted vars
-  meta.data   = nil  -- set via komavar 'date'
-  meta.title  = nil  -- set via komavar 'subject'
-  meta.indent = true -- disable parskib
-  -- set documentclass to scrlttr2 if it's unset
-  meta.documentclass = meta.documentclass or pandoc.MetaString'scrlttr2'
-
-
-  meta['header-includes'] = header_includes
-  meta['include-before'] = include_before
-  meta['include-after'] = include_after
-
-  return meta
-end
-
-return {
-  {Meta = make_koma_metadata}
-}

example/assets/pandoc-scholar/lua-filters/section-refs/README.md

@@ -1,47 +0,0 @@
-# section-refs
-
-This filter allows the user to put bibliographies at the end of
-each section, containing only those references in the section. It
-works by splitting the document up into sections, and then
-treating each section as a separate document for pandoc-citeproc
-to process.
-
-## Usage
-
-This filter interferes with the default operation of
-pandoc-citeproc. The `pandoc-citeproc` filter must either be run
-*before* this filter, or not at all. The `section-refs.lua`
-filter calls `pandoc-citeproc` as necessary. For example:
-
-    pandoc input.md -F pandoc-citeproc --lua-filter section-refs.lua
-
-or
-
-    pandoc input.md --lua-filter section-refs.lua
-
-### Configuration
-
-The filter allows customization through these metadata fields:
-
-`section-refs-level`
-:   This variable controls what level the biblography will occur
-    at the end of. The header of the generated references section
-    will be one level lower than the section that it appears on
-    (so if it occurs at the end of a level-1 section, it will
-    receive a level-2 header, and so on).
-
-`section-refs-bibliography`
-:   Behaves like `bibliography` in the context of this filter.
-    This variable exists because pandoc automatically invokes
-    `pandoc-citeproc` as the final filter if it is called with
-    either `--bibliography`, or if the `bibliography` metadata is
-    given via a command line option. Using
-    `section-refs-bibliography` on the command line avoids this
-    unwanted invocation.
-
-## Dependencies
-
-This filter requires
-
-  * pandoc version 2.8 or later, and
-  * pandoc-citeproc version 0.14.5 or later.

example/assets/pandoc-scholar/lua-filters/section-refs/section-refs.lua

@@ -1,137 +0,0 @@
--- pandoc.utils.make_sections exists since pandoc 2.8
-if PANDOC_VERSION == nil then -- if pandoc_version < 2.1
-  error("ERROR: pandoc >= 2.1 required for section-refs filter")
-else
-  PANDOC_VERSION:must_be_at_least {2,8}
-end
-
-local utils = require 'pandoc.utils'
-local run_json_filter = utils.run_json_filter
-
---- The document's metadata
-local meta
--- Lowest level at which bibliographies should be generated.
-local section_refs_level
--- original bibliography value
-local orig_bibliography
-
--- Returns true iff a div is a section div.
-local function is_section_div (div)
-  return div.t == 'Div'
-    and div.classes[1] == 'section'
-    and div.attributes.number
-end
-
-local function section_header (div)
-  local header = div.content and div.content[1]
-  local is_header = is_section_div(div)
-    and header
-    and header.t == 'Header'
-  return is_header and header or nil
-end
-
-local function adjust_refs_components (div)
-  local header = section_header(div)
-  if not header then
-    return div
-  end
-  local blocks = div.content
-  local bib_header = blocks:find_if(function (b)
-      return b.identifier == 'bibliography'
-  end)
-  local refs = blocks:find_if(function (b)
-      return b.identifier == 'refs'
-  end)
-  if bib_header then
-    bib_header.identifier = 'bibliography-' .. header.attributes.number
-    bib_header.level = header.level + 1
-  end
-  if refs and refs.identifier == 'refs' then
-    refs.identifier = 'refs-' .. header.attributes.number
-  end
-  return div
-end
-
---- Create a bibliography for a given topic. This acts on all
--- section divs at or above `section_refs_level`
-local function create_section_bibliography (div)
-  -- don't do anything if there is no bibliography
-  if not meta.bibliography and not meta.references then
-    return nil
-  end
-  local header = section_header(div)
-  -- Blocks for which a bibliography will be generated
-  local subsections
-  local blocks
-  if not header or section_refs_level < header.level then
-    -- Don't do anything for lower level sections.
-    return nil
-  elseif section_refs_level == header.level then
-    blocks = div.content
-    subsections = pandoc.List:new{}
-  else
-    blocks = div.content:filter(function (b)
-        return not is_section_div(b)
-    end)
-    subsections = div.content:filter(is_section_div)
-  end
-  local tmp_doc = pandoc.Pandoc(blocks, meta)
-  local filter_args = {FORMAT, '-q'} -- keep pandoc-citeproc quiet
-  local new_doc = run_json_filter(tmp_doc, 'pandoc-citeproc', filter_args)
-  div.content = new_doc.blocks .. subsections
-  return adjust_refs_components(div)
-end
-
---- Remove remaining section divs
-local function flatten_sections (div)
-  local header = section_header(div)
-  if not header then
-    return nil
-  else
-    header.identifier = div.identifier
-    header.attributes.number = nil
-    div.content[1] = header
-    return div.content
-  end
-end
-
---- Filter to the references div and bibliography header added by
---- pandoc-citeproc.
-local remove_pandoc_citeproc_results = {
-  Header = function (header)
-    return header.identifier == 'bibliography'
-      and {}
-      or nil
-  end,
-  Div = function (div)
-    return div.identifier == 'refs'
-      and {}
-      or nil
-  end
-}
-
-local function restore_bibliography (meta)
-  meta.bibliography = orig_bibliography
-  return meta
-end
-
---- Setup the document for further processing by wrapping all
---- sections in Div elements.
-function setup_document (doc)
-  -- save meta for other filter functions
-  meta = doc.meta
-  section_refs_level = tonumber(meta["section-refs-level"]) or 1
-  orig_bibliography = meta.bibliography
-  meta.bibliography = meta['section-refs-bibliography'] or meta.bibliography
-  local sections = utils.make_sections(true, nil, doc.blocks)
-  return pandoc.Pandoc(sections, doc.meta)
-end
-
-return {
-  -- remove result of previous pandoc-citeproc run (for backwards
-  -- compatibility)
-  remove_pandoc_citeproc_results,
-  {Pandoc = setup_document},
-  {Div = create_section_bibliography},
-  {Div = flatten_sections, Meta = restore_bibliography}
-}

example/assets/pandoc-scholar/lua-filters/short-captions/README.md

@@ -1,52 +0,0 @@
----
-title: "short-captions.lua"
-lof: true
----
-
-# Short captions in \LaTeX\ output
-
-For latex output, this filter uses the attribute `short-caption` for
-figures so that the attribute value appears in the List of Figures, if
-one is desired.
-
-# Usage
-
-Where you would have a figure in, say, markdown as 
-
-    ![The caption](foo.png ) 
-
-You can now specify the figure as 
-
-    ![The long caption](foo.png){short-caption="a short caption"} 
-
-If the document metadata includes `lof:true`, then the List of Figures
-will use the short caption. This is particularly useful for students
-writing dissertations, who often have to include a List of Figures in
-the front matter, but where figure captions themselves can be quite
-lengthy.
-
-    pandoc --lua-filter=short-captions.lua article.md -o article.tex
-
-    pandoc --lua-filter=short-captions.lua article.md -o article.pdf
-    
-
-
-# Example
-
-@Fig:shortcap is an interesting figure with a long caption, but a short
-caption in the List of Figures.
-
-![This is an *extremely* interesting figure that has a lot of detail I
-will need to describe in a few sentences. This figure has a short
-caption that will appear in the list of figures. Other attributes are
-preserved](fig.pdf){#fig:shortcap short-caption="A short caption with
-math $x^n + y^n = z^n$" width="50%"}
-
-
-# Limitations
-
-- The filter will process the `short-caption` attribute value as pandoc
-  markdown, regardless of the input format.
-- It does not work for tables and listings yet.
-- But it works with pandoc-crossref, regardless of the order of
-  application.

example/assets/pandoc-scholar/lua-filters/short-captions/short-captions.lua

@@ -1,37 +0,0 @@
-if FORMAT ~= "latex" then
-  return
-end
-
-local function latex(str)
-  return pandoc.RawInline('latex', str)
-end
-
-function figure_image (elem)
-  local image = elem.content and elem.content[1]
-  return (image.t == 'Image' and image.title == 'fig:')
-    and image
-    or nil
-end
-
-function Para (para)
-  local img = figure_image(para)
-  if not img or not img.caption or not img.attributes['short-caption'] then
-    return nil
-  end
-
-  local short_caption = pandoc.Span(
-    pandoc.read(img.attributes['short-caption']).blocks[1].c
-  )
-  local hypertarget = "{%%\n"
-  local label = "\n"
-  if img.identifier ~= img.title then
-    hypertarget = string.format("\\hypertarget{%s}{%%\n",img.identifier)
-    label = string.format("\n\\label{%s}",img.identifier)
-  end
-  return pandoc.Para {
-    latex(hypertarget .. "\\begin{figure}\n\\centering\n"),
-    img,
-    latex("\n\\caption["), short_caption, latex("]"), pandoc.Span(img.caption),
-    latex(label .."\n\\end{figure}\n}\n")
-  }
-end

example/assets/pandoc-scholar/lua-filters/spellcheck/README.md

@@ -1,42 +0,0 @@
-# spellcheck
-
-This filter checks the spelling of words in the body of the
-document (omitting metadata).  The external program `aspell` is
-used for the checking, and must be present in the path.
-
-Why use this instead of just running `aspell` on the
-document's source?  Because this filter is sensitive to
-the semantics of the document in ways that `aspell` is
-not:
-
-- Material in code spans, raw HTML, URLs in links,
-  and math is not spell-checked, eliminating a big
-  class of false positives.
-
-- The filter is sensitive to the `lang` specified in
-  the document's metadata; this will be treated as the
-  default language for the document.
-
-- It is also sensitive to `lang` attributes on native
-  divs and spans. Thus, for example, in an English
-  document, `[chevaux]{lang=fr}` will not be registered
-  as a spelling error.
-
-To run it,
-
-    pandoc --lua-filter spellcheck.lua sample.md
-
-A list of misspelled words (or at any rate, words not
-in the appropriate dictionary) will be printed to stdout.
-If the word is in a div or span with a non-default `lang`
-attribute, the relevant language will be indicated in
-brackets after the word, separated by a tab.
-
-To add words to the list for a language, you can add files
-with names `.aspell.LANG.pws` in your home directory.  Example:
-
-```
-% cat ~/.aspell.en.pws
-personal_ws-1.1 en 0
-goopy
-```

example/assets/pandoc-scholar/lua-filters/spellcheck/spellcheck.lua

@@ -1,70 +0,0 @@
--- lua filter for spell checking: requires 'aspell'.
--- Copyright (C) 2017-2020 John MacFarlane, released under MIT license
-
-local text = require('text')
-local words = {}
-local deflang
-
-local function add_to_dict(lang, t)
-  if not words[lang] then
-    words[lang] = {}
-  end
-  if not words[lang][t] then
-    words[lang][t] = (words[lang][t] or 0) + 1
-  end
-end
-
-local function get_deflang(meta)
-  deflang = (meta.lang and meta.lang[1] and meta.lang[1].c) or 'en'
-  -- the following is better but won't work in pandoc 2.0.6.
-  -- it requires pandoc commit ecc46e229fde934f163d1f646383d24bfe2039e1:
-  -- deflang = (meta.lang and pandoc.utils.stringify(meta.lang)) or 'en'
-  return {} -- eliminate meta so it doesn't get spellchecked
-end
-
-local function run_spellcheck(lang)
-  local keys = {}
-  local wordlist = words[lang]
-  for k,_ in pairs(wordlist) do
-    keys[#keys + 1] = k
-  end
-  local inp = table.concat(keys, '\n')
-  local outp = pandoc.pipe('aspell', {'list','-l',lang}, inp)
-  for w in string.gmatch(outp, "([%S]+)\n") do
-    io.write(w)
-    if lang ~= deflang then
-      io.write("\t[" .. lang .. "]")
-    end
-    io.write("\n")
-  end
-end
-
-local function results(el)
-    pandoc.walk_block(pandoc.Div(el.blocks), {Str = function(e) add_to_dict(deflang, e.text) end})
-    for lang,v in pairs(words) do
-        run_spellcheck(lang)
-    end
-    os.exit(0)
-end
-
-local function checkstr(el)
-  add_to_dict(deflang, el.text)
-end
-
-local function checkspan(el)
-  local lang = el.attributes.lang
-  if not lang then return nil end
-  pandoc.walk_inline(el, {Str = function(e) add_to_dict(lang, e.text) end})
-  return {} -- remove span, so it doesn't get checked again
-end
-
-local function checkdiv(el)
-  local lang = el.attributes.lang
-  if not lang then return nil end
-  pandoc.walk_block(el, {Str = function(e) add_to_dict(lang, e.text) end})
-  return {} -- remove div, so it doesn't get checked again
-end
-
-return {{Meta = get_deflang},
-        {Div = checkdiv, Span = checkspan},
-        {Str = function(e) add_to_dict(deflang, e.text) end, Pandoc = results}}

example/assets/pandoc-scholar/lua-filters/table-short-captions/README.md

@@ -1,66 +0,0 @@
----
-title: "table-short-captions.lua"
----
-
-# Short captions in \LaTeX\ tables output
-
-For LaTeX output, this filter enables use of the attribute
-`short-caption` for tables. The attribute value will appear in the List
-of Tables.
-
-This filter also enables the class `.unlisted` for tables. This will
-prevent the table caption from appearing in the List of Tables.
-
-# Usage
-
-In Pandoc Markdown, you can add a caption to a table with
-
-    Table: This is the *italicised long caption* of my table, which has
-    a very long caption.
-
-If the document metadata includes `lot:true`, then the List of Tables
-will be inserted at the beginning of the document.
-
-The [pandoc-crossref](http://lierdakil.github.io/pandoc-crossref/)
-filter extends this, and enables you to specify a custom label for the
-table.
-
-    Table: This is the *italicised long caption* of my table, which has
-    a very long caption.  {#tbl:full-of-juicy-data}
-
-This filter, when run _before_ pandoc-crossref, allows you to add short
-captions to the table as a `short-caption` attribute. What is between
-the quotes will be parsed as Markdown.
-
-**Important!:** You _must_ use empty square brackets before the
-attributes tag.
-
-    Table: This is the *italicised long caption* of my table, which has
-    a very long caption.
-    []{#tbl:full-of-juicy-data short-caption="Short caption for *juicy* data table."}
-
-Alternatively, if you wish to create a table which is unlisted in the
-List of Tables, you can use the `.unlisted` class in the attributes tag.
-
-    Table: This is the *italicised long caption* of my table, which will
-    not appear in the List of Tables. []{#tbl:full-of-juicy-data .unlisted}
-
-This filter should prove useful for students writing dissertations, who
-often have to include a List of Tables in the front matter, but where
-table captions themselves can be quite lengthy.
-
-    pandoc --lua-filter=table-short-captions.lua \
-           --filter pandoc-crossref \
-           article.md -o article.tex
-
-    pandoc --lua-filter=table-short-captions.lua \
-           --filter pandoc-crossref \
-           article.md -o article.pdf
-
-
-# Limitations
-
-- The filter will process the `short-caption` attribute value as pandoc
-  markdown, regardless of the input format.
-- pandoc-crossref should be run after it.
-- I have only tested this from a Markdown source.

example/assets/pandoc-scholar/lua-filters/table-short-captions/table-short-captions.lua

@@ -1,160 +0,0 @@
----LaTeXTableShortCapts – enable `.unlisted` and `short-caption=""` properties
---                        for Pandoc conversion to LaTeX
-
---[[
-Copyright (c) 2019 Blake Riley
-
-Permission to use, copy, modify, and/or distribute this software for any purpose
-with or without fee is hereby granted, provided that the above copyright notice
-and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-THIS SOFTWARE.
-]]
-local List = require 'pandoc.List'
-
--- don't do anything unless we target latex
-if FORMAT ~= "latex" then
-  return {}
-end
-
---- Code for injection into the LaTeX header,
---  to overwrite a macro in longtable captions.
-longtable_caption_mod = [[
-% -- begin:latex-table-short-captions --
-\makeatletter\AtBeginDocument{%
-\def\LT@c@ption#1[#2]#3{%                 % Overwrite the workhorse macro used in formatting a longtable caption.
-  \LT@makecaption#1\fnum@table{#3}%
-  \@ifundefined{pandoctableshortcapt}
-     {\def\@tempa{#2}}                    % Use default behaviour: argument in square brackets
-     {\let\@tempa\pandoctableshortcapt}   % If defined (even if blank), use to override
-  \ifx\@tempa\@empty\else                 % If @tempa is blank, no lot entry! Otherwise, @tempa becomes the lot title.
-     {\let\\\space
-     \addcontentsline{lot}{table}{\protect\numberline{\thetable}{\@tempa}}}%
-  \fi}
-}\makeatother
-% -- end:latex-table-short-captions --
-]]
-
---- Creates a def shortcaption block to be placed before the table
--- @tparam ?string sc : The short-caption property value
--- @treturn Plain : The def shortcaption block
-local function defshortcapt(sc)
-  local scblock = List:new{}
-  scblock:extend {pandoc.RawInline('tex', "\\def\\pandoctableshortcapt{")}
-  if sc then
-    scblock:extend (pandoc.read(sc).blocks[1].c)
-  end
-  scblock:extend {pandoc.RawInline('tex', "}")}
-  if not sc then
-    scblock:extend {pandoc.RawInline('tex', "  % .unlisted")}
-  end
-  return pandoc.Plain(scblock)
-end
-
---- The undef shortcaption block to be placed after the table
-local undefshortcapt = pandoc.RawBlock('tex', "\\let\\pandoctableshortcapt\\relax")
-
---- Parses a mock "Table Attr".
--- We use the Attr of an empty Span as if it were Table Attr.
--- This function extracts what is needed to build a short-caption.
--- @tparam Attr attr : The Attr of the property Span in the table caption
--- @treturn ?string : The identifier
--- @treturn ?string : The "short-caption" property, if present.
--- @treturn bool : Whether ".unlisted" appeared in the classes
-local function parse_table_attrs(attr)
-  -- Find label
-  local label = nil
-  if attr.identifier and (#attr.identifier > 0) then
-    label = attr.identifier
-  end
-
-  -- Look for ".unlisted" in classes
-  local unlisted = false
-  if attr.classes:includes("unlisted") then
-    unlisted = true
-  end
-
-  -- If not unlisted, then find the property short-caption.
-  local short_caption = nil
-  if not unlisted then
-    if (attr.attributes["short-caption"]) and
-       (#attr.attributes["short-caption"] > 0) then
-      short_caption = attr.attributes['short-caption']
-    end
-  end
-
-  return label, short_caption, unlisted
-end
-
---- Wraps a table with shortcaption code
--- @tparam Table tbl : The table with {}-wrapped properties in the caption
--- @treturn List[Blocks] : The table with {label} in the caption,
---                         optionally wrapped in shortcaption code
-function rewrite_longtable_caption(tbl)
-  -- Escape if there is no caption present.
-  if not tbl.caption then
-    return nil
-  end
-
-  -- Try find the properties block
-  local is_properties_span = function (inl)
-    return (inl.t) and (inl.t == "Span")                      -- is span
-                   and (inl.content) and (#inl.content == 0)  -- is empty span
-  end
-  local propspan, idx = tbl.caption:find_if(is_properties_span)
-
-  -- If we couldn't find properties, escape.
-  if not propspan then
-    return nil
-  end
-
-  -- Otherwise, parse it all
-  local label, short_caption, unlisted = parse_table_attrs(propspan.attr)
-
-  -- Excise the span from the caption
-  tbl.caption[idx] = nil
-
-  -- Put label back into caption for pandoc-crossref
-  if label then
-    tbl.caption:extend {pandoc.Str("{#"..label.."}")}
-  end
-
-  -- Place new table
-  local result = List:new{}
-  if short_caption or unlisted then
-    result:extend {defshortcapt(short_caption)}
-  end
-  result:extend {tbl}
-  if short_caption or unlisted then
-    result:extend {undefshortcapt}
-  end
-  return result
-end
-
---- Inserts longtable_caption_mod into the header_includes
--- @tparam Meta meta : The document metadata
--- @treturn Meta : The document metadata, with replacement LaTeX macro
---                 in header_includes
-function add_longtable_caption_mod(meta)
-  local header_includes = -- test ? a : b
-    (meta['header-includes'] and meta['header-includes'].t == 'MetaList')
-    and meta['header-includes']
-    or pandoc.MetaList{meta['header-includes']}
-  header_includes[#header_includes + 1] =
-    pandoc.MetaBlocks{pandoc.RawBlock('tex', longtable_caption_mod)}
-  meta['header-includes'] = header_includes
-  return meta
-end
-
-return {
-  {
-    Meta = add_longtable_caption_mod,
-    Table = rewrite_longtable_caption,
-  }
-}

example/assets/pandoc-scholar/lua-filters/track-changes/README.md

@@ -1,18 +0,0 @@
-# Tracks changes in LaTeX and HTML or removes them in other output formats
-
-The Pandoc Docx reader and writer supports track changes of MS Word
-(command line parameter `--track-changes=accept|reject|all`).
-
-If `--track-changes=all` was used to read a docx file, track changes
-and/or comments are included in the AST as spans and are written to any
-other output formats than docx and clutters the output.
-
-This Lua filter addresses this problem by interpreting the parameter
-`--track-changes` (pandoc version >= 2.1.1) or the metadata variable
-`trackChanges: accept|reject|all` (set either in a YAML block or with
-`-M`) and accepts/rejects changes and removes comments for all output
-formats including docx. In case of `--track-changes=all` and for html
-and latex, it converts track changings and comments to appropriate
-commands (for LaTex provided by the [changes
-package](https://ctan.org/pkg/changes)) and tries to mimic the
-visualization as in MS Word.

example/assets/pandoc-scholar/lua-filters/track-changes/track-changes.lua

@@ -1,247 +0,0 @@
-local authors = {}
-
-local function is_tex(format)
-    return format == 'latex' or format == 'tex' or format == 'context'
-end
-
-local function is_html (format)
-    return format == 'html' or format == 'html4' or format == 'html5'
-end
-
-local function is_wordprocessing (format)
-    return format == 'docx' or format == 'odt'
-end
-
-header_track_changes = [[
-
-\makeatletter
-\PassOptionsToPackage{textsize=scriptsize}{todonotes}
-\PassOptionsToPackage{markup=underlined,authormarkup=none,commentmarkup=todo}{changes}
-\usepackage{changes}
-\@ifpackagelater{changes}{2018/11/03}{%
-}{%
-  \usepackage{todonotes}
-  \setremarkmarkup{\todo[color=Changes@Color#1!20]{\sffamily\textbf{#1:}~#2}}
-}%
-\makeatother
-\definecolor{auth1}{HTML}{4477AA}
-\definecolor{auth2}{HTML}{117733}
-\definecolor{auth3}{HTML}{999933}
-\definecolor{auth4}{HTML}{CC6677}
-\definecolor{auth5}{HTML}{AA4499}
-\definecolor{auth6}{HTML}{332288}
-\setlength{\marginparwidth}{3cm}
-\newcommand{\note}[2][]{\added[#1,remark={#2}]{}}
-\newcommand\hlnotesingle{%
-  \bgroup
-  \expandafter\def\csname sout\space\endcsname{\bgroup \ULdepth =-.8ex \ULset}%
-  \markoverwith{\textcolor{yellow}{\rule[-.5ex]{.1pt}{2.5ex}}}%
-  \ULon}
-\newcommand\hlnote[1]{\let\helpcmd\hlnotesingle\parhelp#1\par\relax\relax}
-\long\def\parhelp#1\par#2\relax{%
-  \helpcmd{#1}\ifx\relax#2\else\par\parhelp#2\relax\fi%
-}
-
-\makeatletter
-\newcommand\ifmoving{%
-  \ifx\protect\@unexpandable@protect
-      \expandafter\@firstoftwo
-  \else
-      \expandafter\@secondoftwo
-  \fi
-}
-
-\newcommand{\gobbletwo}[2][]{\@bsphack\@esphack}
-\newcommand{\gobbleone}[1][]{\@bsphack\@esphack}
-
-\let\oldadded\added
-\let\olddeleted\deleted
-\let\oldhlnote\hlnote
-\let\oldnote\note
-\renewcommand{\added}{\ifmoving{\gobbleone}{\oldadded}}
-\renewcommand{\deleted}{\ifmoving{\gobbletwo}{\olddeleted}}
-\renewcommand{\hlnote}{\ifmoving{}{\oldhlnote}}
-\renewcommand{\note}{\ifmoving{\gobbletwo}{\oldnote}}
-\makeatother
-]]
-
-local function initials(s)
-    local ignore = { -- list of words to ignore
-        ['dr'] = true, ['mr'] = true, ['ms'] = true, ['mrs'] = true, ['prof'] = true,
-        ['mx'] = true, ['sir'] = true,
-    }
-
-    local ans = {}
-    for w in s:gmatch '[%w\']+' do
-        if not ignore[w:lower()] then ans[#ans+1] = w:sub(1,1):upper() end
-    end
-    return table.concat(ans)
-end
-
-relinerHtml = {
-    Str = function (s)
-        if s.text == "¶" then
-            return pandoc.Str('
')
-        end
-    end
-}
-
-relinerTex = {
-    Str = function (s)
-        if s.text == "¶" then
-            return pandoc.Str('\\newline')
-        end
-    end
-}
-
-reliner = {
-    Str = function (s)
-        if s.text == "¶" then
-           return pandoc.LineBreak()
-        end
-    end
-}
-
-function SpanReliner(elem)
-    local classes = elem.classes or elem.attr.classes
-    if classes:includes("comment-start") then
-        return pandoc.walk_inline(elem, reliner)
-    end
-end
-
-local toTex = {["comment-start"] = "\\note", insertion = "\\added", deletion = "\\deleted"}
-
-local function TrackingSpanToTex(elem)
-    if toTex[elem.classes[1]] ~= nil then
-        local author = elem.attributes.author
-        local inits = author:find' ' and initials(author) or author
-        authors[inits] = author
-        local s = toTex[elem.classes[1]] .. '[id=' .. inits .. ']{'
-        if elem.classes:includes("comment-start") then
-            s = s .. pandoc.utils.stringify(pandoc.walk_inline(elem, relinerTex)) .. '}\\hlnote{'
-        else
-            s = s .. pandoc.utils.stringify(elem.content) .. '}'
-        end
-        return pandoc.RawInline('latex', s)
-    elseif elem.classes:includes("comment-end") then
-        return pandoc.RawInline('latex', '}')
-    end
-end
-
-local function pairsByKeys(t, f)
-    local a = {}
-    for n in pairs(t) do table.insert(a, n) end
-    table.sort(a, f)
-    local i = 0
-    local iter = function ()
-      i = i + 1
-      return a[i], t[a[i]]
-    end
-    return iter
-end
-
---- Add packages to the header includes.
-local function add_track_changes(meta)
-    local header_includes
-    if meta['header-includes'] and meta['header-includes'].t == 'MetaList' then
-        header_includes = meta['header-includes']
-    else
-        header_includes = pandoc.MetaList{meta['header-includes']}
-    end
-    header_includes[#header_includes + 1] =
-        pandoc.MetaBlocks{pandoc.RawBlock('latex', header_track_changes)}
-    local a = 1
-    for key,value in pairsByKeys(authors) do -- sorted author list; otherwise make test may fail
-        header_includes[#header_includes + 1] =
-            pandoc.MetaBlocks{pandoc.RawBlock('latex', '\\definechangesauthor[name={' .. value .. '}, color=auth' .. a .. ']{' .. key .. '}')}
-        a = a + 1
-    end
-    meta['header-includes'] = header_includes
-    return meta
-end
-
-local toHtml = {["comment-start"] = "mark", insertion = "ins", deletion = "del"}
-
-local function TrackingSpanToHtml(elem)
-    if toHtml[elem.classes[1]] ~= nil then
-        local author = elem.attributes.author
-        local inits = author:find' ' and initials(author) or author
-        authors[inits] = author
-        local s = '<' .. toHtml[elem.classes[1]]
-        for k,v in pairs(elem.attributes) do
-            local hattr = k
-            if hattr ~= 'date' then hattr = 'data-' .. hattr end
-            s = s .. ' ' .. hattr .. '="' .. v .. '"'
-        end
-        if elem.classes:includes("comment-start") then
-            if elem.identifier then
-                s = s .. ' data-id="' .. elem.identifier .. '"'
-            end
-            s = s .. ' title="' .. pandoc.utils.stringify(pandoc.walk_inline(elem, relinerHtml)) .. '">'
-        else
-            s = s .. '>' .. pandoc.utils.stringify(elem.content) .. '</' .. toHtml[elem.classes[1]] .. '>'
-        end
-        return pandoc.RawInline('html', s)
-    elseif elem.classes:includes("comment-end") then
-        return pandoc.RawInline('html', '</mark>')
-    end
-end
-
-local function SpanAcceptChanges(elem)
-    if elem.classes:includes("comment-start") or elem.classes:includes("comment-end") then
-        return {}
-    elseif elem.classes:includes("insertion") then
-        return elem.content
-    elseif elem.classes:includes("deletion") then
-        return {}
-    end
-end
-
-local function SpanRejectChanges(elem)
-    if elem.classes:includes("comment-start") or elem.classes:includes("comment-end") then
-        return {}
-    elseif elem.classes:includes("insertion") then
-        return {}
-    elseif elem.classes:includes("deletion") then
-        return elem.content
-    end
-end
-
-function Pandoc(doc)
-    local meta = doc.meta
-    local trackChangesOptions = {all = 'AllChanges', accept = 'AcceptChanges', reject = 'RejectChanges' }
-    local tc = meta and meta['trackChanges']
-    tc = type(meta['trackChanges']) == 'table' and pandoc.utils.stringify(meta['trackChanges']) or meta['trackChanges'] or 'accept'
-    local trackChanges = PANDOC_READER_OPTIONS and PANDOC_READER_OPTIONS.trackChanges or trackChangesOptions[tc]
-    meta.trackChanges = nil -- remove it from the matadata
-    
-    local M = {}
-    if trackChanges == 'AllChanges' then
-        if is_html(FORMAT) then
-            M[#M + 1] = {
-                Span = TrackingSpanToHtml
-            }
-        elseif is_tex(FORMAT) then
-            M[#M + 1] = {
-                Span = TrackingSpanToTex,
-            }
-        elseif is_wordprocessing(FORMAT) then
-            M[#M + 1] = { Span = SpanReliner }
-        end
-    elseif trackChanges == 'RejectChanges' then
-        M[#M + 1] = { Span = SpanRejectChanges }
-    else -- otherwise assumes AcceptChanges
-        M[#M + 1] = { Span = SpanAcceptChanges }
-    end
-
-    if #M then
-        local blocks = doc.blocks
-        for i = 1, #M do
-            blocks = pandoc.walk_block(pandoc.Div(blocks), M[i]).content
-        end
-        if trackChanges == 'AllChanges' and is_tex(FORMAT) then
-            meta = add_track_changes(meta)
-        end
-        return pandoc.Pandoc(blocks, meta)
-    end
-end

example/assets/pandoc-scholar/lua-filters/wordcount/README.md

@@ -1,11 +0,0 @@
-# wordcount
-
-This filter counts the words in the body of a document (omitting
-metadata like titles and abstracts), including words in code.
-It should be more accurate than `wc -w` run directly on a
-Markdown document, since the latter will count markup
-characters, like the `#` in front of an ATX header, or
-tags in HTML documents, as words.
-
-To run it, `pandoc --lua-filter wordcount.lua myfile.md`.
-The word count will be printed to stdout.

example/assets/pandoc-scholar/lua-filters/wordcount/wordcount.lua

@@ -1,29 +0,0 @@
--- counts words in a document 
-
-words = 0 
-
-wordcount = { 
-  Str = function(el) 
-    -- we don't count a word if it's entirely punctuation: 
-    if el.text:match("%P") then 
-        words = words + 1 
-    end 
-  end, 
-
-  Code = function(el) 
-    _,n = el.text:gsub("%S+","") 
-    words = words + n 
-  end, 
-
-  CodeBlock = function(el) 
-    _,n = el.text:gsub("%S+","") 
-    words = words + n 
-  end 
-} 
-
-function Pandoc(el) 
-    -- skip metadata, just count body: 
-    pandoc.walk_block(pandoc.Div(el.blocks), wordcount) 
-    print(words .. " words in body") 
-    os.exit(0) 
-end

example/assets/pandoc-scholar/pandoc-options.inc.mk

@@ -1,50 +0,0 @@
-# Settings for Pandoc
-# ===================
-
-TEMPLATE_FILE_LATEX   ?= $(PANDOC_SCHOLAR_PATH)/templates/pandoc-scholar.latex
-TEMPLATE_FILE_HTML    ?= $(PANDOC_SCHOLAR_PATH)/templates/pandoc-scholar.html
-TEMPLATE_FILE_JATS    ?= $(PANDOC_SCHOLAR_PATH)/templates/pandoc-scholar.jats
-
-TEMPLATE_STYLE_HTML   ?= $(PANDOC_SCHOLAR_PATH)/templates/styles/pandoc-scholar.css
-
-## Pandoc options
-PANDOC_READER_OPTIONS ?=
-ifdef BIBLIOGRAPHY_FILE
-PANDOC_READER_OPTIONS += --metadata "bibliography:$(BIBLIOGRAPHY_FILE)"
-endif
-
-ifndef PANDOC_WRITER_OPTIONS
-PANDOC_WRITER_OPTIONS  = --standalone
-PANDOC_WRITER_OPTIONS += --citeproc
-ifdef BIBLIOGRAPHY_FILE
-PANDOC_WRITER_OPTIONS += --metadata "bibliography:$(BIBLIOGRAPHY_FILE)"
-PANDOC_WRITER_OPTIONS += --bibliography=$(BIBLIOGRAPHY_FILE)
-endif
-endif
-
-PANDOC_ODT_OPTIONS    ?=
-PANDOC_DOCX_OPTIONS   ?=
-PANDOC_HTML_OPTIONS   ?=
-PANDOC_EPUB_OPTIONS   ?=
-ifndef PANDOC_LATEX_OPTIONS
-PANDOC_LATEX_OPTIONS   = --pdf-engine=xelatex
-endif
-
-ifdef ODT_REFERENCE_FILE
-PANDOC_ODT_OPTIONS    += --reference-doc=$(ODT_REFERENCE_FILE)
-endif
-ifdef DOCX_REFERENCE_FILE
-PANDOC_DOCX_OPTIONS   += --reference-doc=$(DOCX_REFERENCE_FILE)
-endif
-ifdef TEMPLATE_FILE_LATEX
-PANDOC_LATEX_OPTIONS  += --template=$(TEMPLATE_FILE_LATEX)
-endif
-ifdef TEMPLATE_FILE_HTML
-PANDOC_HTML_OPTIONS   += --template=$(TEMPLATE_FILE_HTML)
-endif
-ifdef TEMPLATE_FILE_EPUB
-PANDOC_EPUB_OPTIONS   += --template=$(TEMPLATE_FILE_EPUB)
-endif
-ifdef TEMPLATE_FILE_JATS
-PANDOC_JATS_OPTIONS   += --template=$(TEMPLATE_FILE_JATS)
-endif

example/assets/pandoc-scholar/scholar-filters/dkjson.lua

@@ -1,714 +0,0 @@
--- Module options:
-local always_try_using_lpeg = true
-local register_global_module_table = false
-local global_module_name = 'json'
-
---[==[
-
-David Kolf's JSON module for Lua 5.1/5.2
-
-Version 2.5
-
-
-For the documentation see the corresponding readme.txt or visit
-<http://dkolf.de/src/dkjson-lua.fsl/>.
-
-You can contact the author by sending an e-mail to 'david' at the
-domain 'dkolf.de'.
-
-
-Copyright (C) 2010-2013 David Heiko Kolf
-
-Permission is hereby granted, free of charge, to any person obtaining
-a copy of this software and associated documentation files (the
-"Software"), to deal in the Software without restriction, including
-without limitation the rights to use, copy, modify, merge, publish,
-distribute, sublicense, and/or sell copies of the Software, and to
-permit persons to whom the Software is furnished to do so, subject to
-the following conditions:
-
-The above copyright notice and this permission notice shall be
-included in all copies or substantial portions of the Software.
-
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
-EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
-MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
-NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
-BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
-ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
-CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
-
---]==]
-
--- global dependencies:
-local pairs, type, tostring, tonumber, getmetatable, setmetatable, rawset =
-      pairs, type, tostring, tonumber, getmetatable, setmetatable, rawset
-local error, require, pcall, select = error, require, pcall, select
-local floor, huge = math.floor, math.huge
-local strrep, gsub, strsub, strbyte, strchar, strfind, strlen, strformat =
-      string.rep, string.gsub, string.sub, string.byte, string.char,
-      string.find, string.len, string.format
-local strmatch = string.match
-local concat = table.concat
-
-local json = { version = "dkjson 2.5" }
-
-if register_global_module_table then
-  _G[global_module_name] = json
-end
-
-local _ENV = nil -- blocking globals in Lua 5.2
-
-pcall (function()
-  -- Enable access to blocked metatables.
-  -- Don't worry, this module doesn't change anything in them.
-  local debmeta = require "debug".getmetatable
-  if debmeta then getmetatable = debmeta end
-end)
-
-json.null = setmetatable ({}, {
-  __tojson = function () return "null" end
-})
-
-local function isarray (tbl)
-  local max, n, arraylen = 0, 0, 0
-  for k,v in pairs (tbl) do
-    if k == 'n' and type(v) == 'number' then
-      arraylen = v
-      if v > max then
-        max = v
-      end
-    else
-      if type(k) ~= 'number' or k < 1 or floor(k) ~= k then
-        return false
-      end
-      if k > max then
-        max = k
-      end
-      n = n + 1
-    end
-  end
-  if max > 10 and max > arraylen and max > n * 2 then
-    return false -- don't create an array with too many holes
-  end
-  return true, max
-end
-
-local escapecodes = {
-  ["\""] = "\\\"", ["\\"] = "\\\\", ["\b"] = "\\b", ["\f"] = "\\f",
-  ["\n"] = "\\n",  ["\r"] = "\\r",  ["\t"] = "\\t"
-}
-
-local function escapeutf8 (uchar)
-  local value = escapecodes[uchar]
-  if value then
-    return value
-  end
-  local a, b, c, d = strbyte (uchar, 1, 4)
-  a, b, c, d = a or 0, b or 0, c or 0, d or 0
-  if a <= 0x7f then
-    value = a
-  elseif 0xc0 <= a and a <= 0xdf and b >= 0x80 then
-    value = (a - 0xc0) * 0x40 + b - 0x80
-  elseif 0xe0 <= a and a <= 0xef and b >= 0x80 and c >= 0x80 then
-    value = ((a - 0xe0) * 0x40 + b - 0x80) * 0x40 + c - 0x80
-  elseif 0xf0 <= a and a <= 0xf7 and b >= 0x80 and c >= 0x80 and d >= 0x80 then
-    value = (((a - 0xf0) * 0x40 + b - 0x80) * 0x40 + c - 0x80) * 0x40 + d - 0x80
-  else
-    return ""
-  end
-  if value <= 0xffff then
-    return strformat ("\\u%.4x", value)
-  elseif value <= 0x10ffff then
-    -- encode as UTF-16 surrogate pair
-    value = value - 0x10000
-    local highsur, lowsur = 0xD800 + floor (value/0x400), 0xDC00 + (value % 0x400)
-    return strformat ("\\u%.4x\\u%.4x", highsur, lowsur)
-  else
-    return ""
-  end
-end
-
-local function fsub (str, pattern, repl)
-  -- gsub always builds a new string in a buffer, even when no match
-  -- exists. First using find should be more efficient when most strings
-  -- don't contain the pattern.
-  if strfind (str, pattern) then
-    return gsub (str, pattern, repl)
-  else
-    return str
-  end
-end
-
-local function quotestring (value)
-  -- based on the regexp "escapable" in https://github.com/douglascrockford/JSON-js
-  value = fsub (value, "[%z\1-\31\"\\\127]", escapeutf8)
-  if strfind (value, "[\194\216\220\225\226\239]") then
-    value = fsub (value, "\194[\128-\159\173]", escapeutf8)
-    value = fsub (value, "\216[\128-\132]", escapeutf8)
-    value = fsub (value, "\220\143", escapeutf8)
-    value = fsub (value, "\225\158[\180\181]", escapeutf8)
-    value = fsub (value, "\226\128[\140-\143\168-\175]", escapeutf8)
-    value = fsub (value, "\226\129[\160-\175]", escapeutf8)
-    value = fsub (value, "\239\187\191", escapeutf8)
-    value = fsub (value, "\239\191[\176-\191]", escapeutf8)
-  end
-  return "\"" .. value .. "\""
-end
-json.quotestring = quotestring
-
-local function replace(str, o, n)
-  local i, j = strfind (str, o, 1, true)
-  if i then
-    return strsub(str, 1, i-1) .. n .. strsub(str, j+1, -1)
-  else
-    return str
-  end
-end
-
--- locale independent num2str and str2num functions
-local decpoint, numfilter
-
-local function updatedecpoint ()
-  decpoint = strmatch(tostring(0.5), "([^05+])")
-  -- build a filter that can be used to remove group separators
-  numfilter = "[^0-9%-%+eE" .. gsub(decpoint, "[%^%$%(%)%%%.%[%]%*%+%-%?]", "%%%0") .. "]+"
-end
-
-updatedecpoint()
-
-local function num2str (num)
-  return replace(fsub(tostring(num), numfilter, ""), decpoint, ".")
-end
-
-local function str2num (str)
-  local num = tonumber(replace(str, ".", decpoint))
-  if not num then
-    updatedecpoint()
-    num = tonumber(replace(str, ".", decpoint))
-  end
-  return num
-end
-
-local function addnewline2 (level, buffer, buflen)
-  buffer[buflen+1] = "\n"
-  buffer[buflen+2] = strrep ("  ", level)
-  buflen = buflen + 2
-  return buflen
-end
-
-function json.addnewline (state)
-  if state.indent then
-    state.bufferlen = addnewline2 (state.level or 0,
-                           state.buffer, state.bufferlen or #(state.buffer))
-  end
-end
-
-local encode2 -- forward declaration
-
-local function addpair (key, value, prev, indent, level, buffer, buflen, tables, globalorder, state)
-  local kt = type (key)
-  if kt ~= 'string' and kt ~= 'number' then
-    return nil, "type '" .. kt .. "' is not supported as a key by JSON."
-  end
-  if prev then
-    buflen = buflen + 1
-    buffer[buflen] = ","
-  end
-  if indent then
-    buflen = addnewline2 (level, buffer, buflen)
-  end
-  buffer[buflen+1] = quotestring (key)
-  buffer[buflen+2] = ":"
-  return encode2 (value, indent, level, buffer, buflen + 2, tables, globalorder, state)
-end
-
-local function appendcustom(res, buffer, state)
-  local buflen = state.bufferlen
-  if type (res) == 'string' then
-    buflen = buflen + 1
-    buffer[buflen] = res
-  end
-  return buflen
-end
-
-local function exception(reason, value, state, buffer, buflen, defaultmessage)
-  defaultmessage = defaultmessage or reason
-  local handler = state.exception
-  if not handler then
-    return nil, defaultmessage
-  else
-    state.bufferlen = buflen
-    local ret, msg = handler (reason, value, state, defaultmessage)
-    if not ret then return nil, msg or defaultmessage end
-    return appendcustom(ret, buffer, state)
-  end
-end
-
-function json.encodeexception(reason, value, state, defaultmessage)
-  return quotestring("<" .. defaultmessage .. ">")
-end
-
-encode2 = function (value, indent, level, buffer, buflen, tables, globalorder, state)
-  local valtype = type (value)
-  local valmeta = getmetatable (value)
-  valmeta = type (valmeta) == 'table' and valmeta -- only tables
-  local valtojson = valmeta and valmeta.__tojson
-  if valtojson then
-    if tables[value] then
-      return exception('reference cycle', value, state, buffer, buflen)
-    end
-    tables[value] = true
-    state.bufferlen = buflen
-    local ret, msg = valtojson (value, state)
-    if not ret then return exception('custom encoder failed', value, state, buffer, buflen, msg) end
-    tables[value] = nil
-    buflen = appendcustom(ret, buffer, state)
-  elseif value == nil then
-    buflen = buflen + 1
-    buffer[buflen] = "null"
-  elseif valtype == 'number' then
-    local s
-    if value ~= value or value >= huge or -value >= huge then
-      -- This is the behaviour of the original JSON implementation.
-      s = "null"
-    else
-      s = num2str (value)
-    end
-    buflen = buflen + 1
-    buffer[buflen] = s
-  elseif valtype == 'boolean' then
-    buflen = buflen + 1
-    buffer[buflen] = value and "true" or "false"
-  elseif valtype == 'string' then
-    buflen = buflen + 1
-    buffer[buflen] = quotestring (value)
-  elseif valtype == 'table' then
-    if tables[value] then
-      return exception('reference cycle', value, state, buffer, buflen)
-    end
-    tables[value] = true
-    level = level + 1
-    local isa, n = isarray (value)
-    if n == 0 and valmeta and valmeta.__jsontype == 'object' then
-      isa = false
-    end
-    local msg
-    if isa then -- JSON array
-      buflen = buflen + 1
-      buffer[buflen] = "["
-      for i = 1, n do
-        buflen, msg = encode2 (value[i], indent, level, buffer, buflen, tables, globalorder, state)
-        if not buflen then return nil, msg end
-        if i < n then
-          buflen = buflen + 1
-          buffer[buflen] = ","
-        end
-      end
-      buflen = buflen + 1
-      buffer[buflen] = "]"
-    else -- JSON object
-      local prev = false
-      buflen = buflen + 1
-      buffer[buflen] = "{"
-      local order = valmeta and valmeta.__jsonorder or globalorder
-      if order then
-        local used = {}
-        n = #order
-        for i = 1, n do
-          local k = order[i]
-          local v = value[k]
-          if v then
-            used[k] = true
-            buflen, msg = addpair (k, v, prev, indent, level, buffer, buflen, tables, globalorder, state)
-            prev = true -- add a seperator before the next element
-          end
-        end
-        for k,v in pairs (value) do
-          if not used[k] then
-            buflen, msg = addpair (k, v, prev, indent, level, buffer, buflen, tables, globalorder, state)
-            if not buflen then return nil, msg end
-            prev = true -- add a seperator before the next element
-          end
-        end
-      else -- unordered
-        for k,v in pairs (value) do
-          buflen, msg = addpair (k, v, prev, indent, level, buffer, buflen, tables, globalorder, state)
-          if not buflen then return nil, msg end
-          prev = true -- add a seperator before the next element
-        end
-      end
-      if indent then
-        buflen = addnewline2 (level - 1, buffer, buflen)
-      end
-      buflen = buflen + 1
-      buffer[buflen] = "}"
-    end
-    tables[value] = nil
-  else
-    return exception ('unsupported type', value, state, buffer, buflen,
-      "type '" .. valtype .. "' is not supported by JSON.")
-  end
-  return buflen
-end
-
-function json.encode (value, state)
-  state = state or {}
-  local oldbuffer = state.buffer
-  local buffer = oldbuffer or {}
-  state.buffer = buffer
-  updatedecpoint()
-  local ret, msg = encode2 (value, state.indent, state.level or 0,
-                   buffer, state.bufferlen or 0, state.tables or {}, state.keyorder, state)
-  if not ret then
-    error (msg, 2)
-  elseif oldbuffer == buffer then
-    state.bufferlen = ret
-    return true
-  else
-    state.bufferlen = nil
-    state.buffer = nil
-    return concat (buffer)
-  end
-end
-
-local function loc (str, where)
-  local line, pos, linepos = 1, 1, 0
-  while true do
-    pos = strfind (str, "\n", pos, true)
-    if pos and pos < where then
-      line = line + 1
-      linepos = pos
-      pos = pos + 1
-    else
-      break
-    end
-  end
-  return "line " .. line .. ", column " .. (where - linepos)
-end
-
-local function unterminated (str, what, where)
-  return nil, strlen (str) + 1, "unterminated " .. what .. " at " .. loc (str, where)
-end
-
-local function scanwhite (str, pos)
-  while true do
-    pos = strfind (str, "%S", pos)
-    if not pos then return nil end
-    local sub2 = strsub (str, pos, pos + 1)
-    if sub2 == "\239\187" and strsub (str, pos + 2, pos + 2) == "\191" then
-      -- UTF-8 Byte Order Mark
-      pos = pos + 3
-    elseif sub2 == "//" then
-      pos = strfind (str, "[\n\r]", pos + 2)
-      if not pos then return nil end
-    elseif sub2 == "/*" then
-      pos = strfind (str, "*/", pos + 2)
-      if not pos then return nil end
-      pos = pos + 2
-    else
-      return pos
-    end
-  end
-end
-
-local escapechars = {
-  ["\""] = "\"", ["\\"] = "\\", ["/"] = "/", ["b"] = "\b", ["f"] = "\f",
-  ["n"] = "\n", ["r"] = "\r", ["t"] = "\t"
-}
-
-local function unichar (value)
-  if value < 0 then
-    return nil
-  elseif value <= 0x007f then
-    return strchar (value)
-  elseif value <= 0x07ff then
-    return strchar (0xc0 + floor(value/0x40),
-                    0x80 + (floor(value) % 0x40))
-  elseif value <= 0xffff then
-    return strchar (0xe0 + floor(value/0x1000),
-                    0x80 + (floor(value/0x40) % 0x40),
-                    0x80 + (floor(value) % 0x40))
-  elseif value <= 0x10ffff then
-    return strchar (0xf0 + floor(value/0x40000),
-                    0x80 + (floor(value/0x1000) % 0x40),
-                    0x80 + (floor(value/0x40) % 0x40),
-                    0x80 + (floor(value) % 0x40))
-  else
-    return nil
-  end
-end
-
-local function scanstring (str, pos)
-  local lastpos = pos + 1
-  local buffer, n = {}, 0
-  while true do
-    local nextpos = strfind (str, "[\"\\]", lastpos)
-    if not nextpos then
-      return unterminated (str, "string", pos)
-    end
-    if nextpos > lastpos then
-      n = n + 1
-      buffer[n] = strsub (str, lastpos, nextpos - 1)
-    end
-    if strsub (str, nextpos, nextpos) == "\"" then
-      lastpos = nextpos + 1
-      break
-    else
-      local escchar = strsub (str, nextpos + 1, nextpos + 1)
-      local value
-      if escchar == "u" then
-        value = tonumber (strsub (str, nextpos + 2, nextpos + 5), 16)
-        if value then
-          local value2
-          if 0xD800 <= value and value <= 0xDBff then
-            -- we have the high surrogate of UTF-16. Check if there is a
-            -- low surrogate escaped nearby to combine them.
-            if strsub (str, nextpos + 6, nextpos + 7) == "\\u" then
-              value2 = tonumber (strsub (str, nextpos + 8, nextpos + 11), 16)
-              if value2 and 0xDC00 <= value2 and value2 <= 0xDFFF then
-                value = (value - 0xD800)  * 0x400 + (value2 - 0xDC00) + 0x10000
-              else
-                value2 = nil -- in case it was out of range for a low surrogate
-              end
-            end
-          end
-          value = value and unichar (value)
-          if value then
-            if value2 then
-              lastpos = nextpos + 12
-            else
-              lastpos = nextpos + 6
-            end
-          end
-        end
-      end
-      if not value then
-        value = escapechars[escchar] or escchar
-        lastpos = nextpos + 2
-      end
-      n = n + 1
-      buffer[n] = value
-    end
-  end
-  if n == 1 then
-    return buffer[1], lastpos
-  elseif n > 1 then
-    return concat (buffer), lastpos
-  else
-    return "", lastpos
-  end
-end
-
-local scanvalue -- forward declaration
-
-local function scantable (what, closechar, str, startpos, nullval, objectmeta, arraymeta)
-  local len = strlen (str)
-  local tbl, n = {}, 0
-  local pos = startpos + 1
-  if what == 'object' then
-    setmetatable (tbl, objectmeta)
-  else
-    setmetatable (tbl, arraymeta)
-  end
-  while true do
-    pos = scanwhite (str, pos)
-    if not pos then return unterminated (str, what, startpos) end
-    local char = strsub (str, pos, pos)
-    if char == closechar then
-      return tbl, pos + 1
-    end
-    local val1, err
-    val1, pos, err = scanvalue (str, pos, nullval, objectmeta, arraymeta)
-    if err then return nil, pos, err end
-    pos = scanwhite (str, pos)
-    if not pos then return unterminated (str, what, startpos) end
-    char = strsub (str, pos, pos)
-    if char == ":" then
-      if val1 == nil then
-        return nil, pos, "cannot use nil as table index (at " .. loc (str, pos) .. ")"
-      end
-      pos = scanwhite (str, pos + 1)
-      if not pos then return unterminated (str, what, startpos) end
-      local val2
-      val2, pos, err = scanvalue (str, pos, nullval, objectmeta, arraymeta)
-      if err then return nil, pos, err end
-      tbl[val1] = val2
-      pos = scanwhite (str, pos)
-      if not pos then return unterminated (str, what, startpos) end
-      char = strsub (str, pos, pos)
-    else
-      n = n + 1
-      tbl[n] = val1
-    end
-    if char == "," then
-      pos = pos + 1
-    end
-  end
-end
-
-scanvalue = function (str, pos, nullval, objectmeta, arraymeta)
-  pos = pos or 1
-  pos = scanwhite (str, pos)
-  if not pos then
-    return nil, strlen (str) + 1, "no valid JSON value (reached the end)"
-  end
-  local char = strsub (str, pos, pos)
-  if char == "{" then
-    return scantable ('object', "}", str, pos, nullval, objectmeta, arraymeta)
-  elseif char == "[" then
-    return scantable ('array', "]", str, pos, nullval, objectmeta, arraymeta)
-  elseif char == "\"" then
-    return scanstring (str, pos)
-  else
-    local pstart, pend = strfind (str, "^%-?[%d%.]+[eE]?[%+%-]?%d*", pos)
-    if pstart then
-      local number = str2num (strsub (str, pstart, pend))
-      if number then
-        return number, pend + 1
-      end
-    end
-    pstart, pend = strfind (str, "^%a%w*", pos)
-    if pstart then
-      local name = strsub (str, pstart, pend)
-      if name == "true" then
-        return true, pend + 1
-      elseif name == "false" then
-        return false, pend + 1
-      elseif name == "null" then
-        return nullval, pend + 1
-      end
-    end
-    return nil, pos, "no valid JSON value at " .. loc (str, pos)
-  end
-end
-
-local function optionalmetatables(...)
-  if select("#", ...) > 0 then
-    return ...
-  else
-    return {__jsontype = 'object'}, {__jsontype = 'array'}
-  end
-end
-
-function json.decode (str, pos, nullval, ...)
-  local objectmeta, arraymeta = optionalmetatables(...)
-  return scanvalue (str, pos, nullval, objectmeta, arraymeta)
-end
-
-function json.use_lpeg ()
-  local g = require ("lpeg")
-
-  if g.version() == "0.11" then
-    error "due to a bug in LPeg 0.11, it cannot be used for JSON matching"
-  end
-
-  local pegmatch = g.match
-  local P, S, R = g.P, g.S, g.R
-
-  local function ErrorCall (str, pos, msg, state)
-    if not state.msg then
-      state.msg = msg .. " at " .. loc (str, pos)
-      state.pos = pos
-    end
-    return false
-  end
-
-  local function Err (msg)
-    return g.Cmt (g.Cc (msg) * g.Carg (2), ErrorCall)
-  end
-
-  local SingleLineComment = P"//" * (1 - S"\n\r")^0
-  local MultiLineComment = P"/*" * (1 - P"*/")^0 * P"*/"
-  local Space = (S" \n\r\t" + P"\239\187\191" + SingleLineComment + MultiLineComment)^0
-
-  local PlainChar = 1 - S"\"\\\n\r"
-  local EscapeSequence = (P"\\" * g.C (S"\"\\/bfnrt" + Err "unsupported escape sequence")) / escapechars
-  local HexDigit = R("09", "af", "AF")
-  local function UTF16Surrogate (match, pos, high, low)
-    high, low = tonumber (high, 16), tonumber (low, 16)
-    if 0xD800 <= high and high <= 0xDBff and 0xDC00 <= low and low <= 0xDFFF then
-      return true, unichar ((high - 0xD800)  * 0x400 + (low - 0xDC00) + 0x10000)
-    else
-      return false
-    end
-  end
-  local function UTF16BMP (hex)
-    return unichar (tonumber (hex, 16))
-  end
-  local U16Sequence = (P"\\u" * g.C (HexDigit * HexDigit * HexDigit * HexDigit))
-  local UnicodeEscape = g.Cmt (U16Sequence * U16Sequence, UTF16Surrogate) + U16Sequence/UTF16BMP
-  local Char = UnicodeEscape + EscapeSequence + PlainChar
-  local String = P"\"" * g.Cs (Char ^ 0) * (P"\"" + Err "unterminated string")
-  local Integer = P"-"^(-1) * (P"0" + (R"19" * R"09"^0))
-  local Fractal = P"." * R"09"^0
-  local Exponent = (S"eE") * (S"+-")^(-1) * R"09"^1
-  local Number = (Integer * Fractal^(-1) * Exponent^(-1))/str2num
-  local Constant = P"true" * g.Cc (true) + P"false" * g.Cc (false) + P"null" * g.Carg (1)
-  local SimpleValue = Number + String + Constant
-  local ArrayContent, ObjectContent
-
-  -- The functions parsearray and parseobject parse only a single value/pair
-  -- at a time and store them directly to avoid hitting the LPeg limits.
-  local function parsearray (str, pos, nullval, state)
-    local obj, cont
-    local npos
-    local t, nt = {}, 0
-    repeat
-      obj, cont, npos = pegmatch (ArrayContent, str, pos, nullval, state)
-      if not npos then break end
-      pos = npos
-      nt = nt + 1
-      t[nt] = obj
-    until cont == 'last'
-    return pos, setmetatable (t, state.arraymeta)
-  end
-
-  local function parseobject (str, pos, nullval, state)
-    local obj, key, cont
-    local npos
-    local t = {}
-    repeat
-      key, obj, cont, npos = pegmatch (ObjectContent, str, pos, nullval, state)
-      if not npos then break end
-      pos = npos
-      t[key] = obj
-    until cont == 'last'
-    return pos, setmetatable (t, state.objectmeta)
-  end
-
-  local Array = P"[" * g.Cmt (g.Carg(1) * g.Carg(2), parsearray) * Space * (P"]" + Err "']' expected")
-  local Object = P"{" * g.Cmt (g.Carg(1) * g.Carg(2), parseobject) * Space * (P"}" + Err "'}' expected")
-  local Value = Space * (Array + Object + SimpleValue)
-  local ExpectedValue = Value + Space * Err "value expected"
-  ArrayContent = Value * Space * (P"," * g.Cc'cont' + g.Cc'last') * g.Cp()
-  local Pair = g.Cg (Space * String * Space * (P":" + Err "colon expected") * ExpectedValue)
-  ObjectContent = Pair * Space * (P"," * g.Cc'cont' + g.Cc'last') * g.Cp()
-  local DecodeValue = ExpectedValue * g.Cp ()
-
-  function json.decode (str, pos, nullval, ...)
-    local state = {}
-    state.objectmeta, state.arraymeta = optionalmetatables(...)
-    local obj, retpos = pegmatch (DecodeValue, str, pos, nullval, state)
-    if state.msg then
-      return nil, state.pos, state.msg
-    else
-      return obj, retpos
-    end
-  end
-
-  -- use this function only once:
-  json.use_lpeg = function () return json end
-
-  json.using_lpeg = true
-
-  return json -- so you can get the module using json = require "dkjson".use_lpeg()
-end
-
-if always_try_using_lpeg then
-  pcall (json.use_lpeg)
-end
-
-return json
-

example/assets/pandoc-scholar/scholar-filters/json-ld.lua

@@ -1,234 +0,0 @@
--- json-ld.lua: add a JSON-LD metadata field describing the document.
---
--- Copyright (c) 2017-2021 Albert Krewinkel
---
--- This program is free software; you can redistribute it and/or modify it
--- under the terms of the GNU public license version 2 or later.
--- See the LICENSE file for details.
-local SCRIPT_DIR = PANDOC_SCRIPT_FILE:gsub('/[^/]*$', '')
-
-package.path =  SCRIPT_DIR .. '/?.lua;' .. package.path
-
-local json = require "dkjson"
-local List = require 'pandoc.List'
-
-local function stringify(x)
-  if x == nil then
-    return nil
-  elseif type(x) == 'string' then
-    return x
-  end
-  return pandoc.utils.stringify(x)
-end
-
-local function Organizations(orgs)
-  local orgs_json = {}
-  for i, org in ipairs(orgs) do
-    orgs_json[i] = {
-      ["@type"] = "Organization",
-      ["name"]  = org.name and stringify(org.name),
-      ['url']   = org.url and stringify(org.url),
-    }
-  end
-  return orgs_json
-end
-
-local function Authors(authors)
-  local authors_json = pandoc.MetaList{}
-  for i, author in ipairs(authors) do
-    authors_json[i] = {
-      ['@type']       = "Person",
-      ['@id']         = authors[i].orcid and
-                          ("https://orcid.org/" .. stringify(authors[i].orcid)),
-      ["name"]        = author.name and stringify(author.name),
-      ["affiliation"] = author.institute and Organizations(author.institute),
-      ['email']       = author.email and stringify(author.email),
-      ['url']         = author.url and stringify(author.url),
-    }
-  end
-  return authors_json
-end
-
-local function Cito (bibjson, cites_by_cito_property)
-  function find_citation(id)
-    -- sloooow
-    for i = 1, #bibjson do
-      if bibjson[i].id == id then
-        return bibjson[i]
-      end
-    end
-  end
-
-  local result = {}
-  local bibentry, citation_ld
-  for citation_type, typed_citation_ids in pairs(cites_by_cito_property) do
-    for i = 1, #typed_citation_ids do
-      bibentry = find_citation(typed_citation_ids[i])
-      if bibentry and bibentry.DOI then
-        citation_ld = {
-          ["@id"] = "http://dx.doi.org/" .. bibentry.DOI
-        }
-        cito_type_str = "cito:" .. citation_type
-        if not result[cito_type_str] then
-          result[cito_type_str] = {}
-        end
-        table.insert(result[cito_type_str], citation_ld)
-      end
-    end
-  end
-  return result
-end
-
-local function Citations (bibjson, citation_ids)
-  function find_citation(id)
-    -- sloooow
-    for i = 1, #bibjson do
-      if bibjson[i].id == id then
-        return bibjson[i]
-      end
-    end
-  end
-
-  function CitationSchema(record)
-    local type
-    if record.type == "report" then
-      type = "Report"
-    elseif record.type == "article-journal" then
-      type = "ScholarlyArticle"
-    else
-      type = "Article"
-    end
-
-    local authors = {}
-    if record.author then
-      for i = 1, #record.author do
-        local name = {
-          record.author[i].family,
-          record.author[i].given
-        }
-        authors[i] = {
-          name = table.concat(name, ", ")
-        }
-      end
-    end
-
-    return {
-      ["@context"] = {
-        ["@vocab"]    = "http://schema.org/",
-        ["title"]     = "headline",
-        ["page"]      = "pagination",
-        ["date"]      = "datePublished",
-        ["publisher"] = "publisher",
-        ["author"]    = "author",
-      },
-      ["@type"]     = type,
-      ["@id"]       = record.DOI and ("http://dx.doi.org/" .. record.DOI),
-      ["title"]     = record.title,
-      ["author"]    = Authors(authors),
-      ["date"]      = record.issued and
-        record.issued["date-parts"] and
-        table.concat(record.issued["date-parts"][1], "-"),
-      ["publisher"] = record.publisher and
-        { ["@type"] = "Organization", ["name"] = record.publisher },
-      ["page"]      = record.page,
-    }
-  end
-
-  local res = {}
-  for cit_id, _ in pairs(citation_ids) do
-    local citation_record = find_citation(cit_id)
-    if citation_record then
-      res[#res + 1] = CitationSchema(citation_record)
-    end
-  end
-  return res
-end
-
-function json_ld (meta)
-  local default_image = "https://upload.wikimedia.org/wikipedia/commons/f/fa/Globe.svg"
-  local accessible_for_free
-  if meta.accessible_for_free ~= nil then
-    accessible_for_free = meta.accessible_for_free
-  else
-    accessible_for_free = true
-  end
-  local context = {
-    ["@vocab"]    = "http://schema.org/",
-    ["cito"]      = "http://purl.org/spar/cito/",
-    ["author"]    = "author",
-    ["name"]      = "name",
-    ["title"]     = "headline",
-    ["subtitle"]  = "alternativeTitle",
-    ["publisher"] = "publisher",
-    ["date"]      = "datePublished",
-    ["isFree"]    = accessible_for_free and "isAccessibleForFree" or nil,
-    ["image"]     = "image",
-    ["citation"]  = "citation",
-  }
-
-  local citation_ids = {}
-  for _, ids in pairs(meta.cito_cites) do
-    for _, id in ipairs(ids) do citation_ids[id] = true end
-  end
-  local result = {
-    ["@context"]  = context,
-    ["@type"]     = "ScholarlyArticle",
-    ["author"]    = Authors(meta.author),
-    ["name"]      = stringify(meta.title),
-    ["title"]     = stringify(meta.title),
-    ["subtitle"]  = meta.subtitle and stringify(meta.subtitle),
-    ["date"]      = meta.date and stringify(meta.date) or os.date("%Y-%m-%d"),
-    -- -- ["image"]     = meta.image or default_image,
-    ["isFree"]    = accessible_for_free,
-    ["citation"]  = Citations(meta.bibliography_records, citation_ids),
-  }
-  for k, v in pairs(Cito(meta.bibliography_records, meta.cito_cites)) do
-    result[k] = v
-  end
-  return result
-end
-
-local function bibliography(bibfilename)
-  if not bibfilename or bibfilename == '' then
-    return {}
-  end
-  local bibfile = io.popen("pandoc-citeproc --bib2json " .. bibfilename, "r")
-  local jsonstr = bibfile:read("*a")
-  bibfile:close()
-  return json.decode(jsonstr)
-end
-
-local function institute_resolver (institutes)
-  return function (inst_idx)
-    return institutes[tonumber(stringify(inst_idx))]
-  end
-end
-
-function Meta (meta)
-  local function clone (obj)
-    local result = {}
-    for k, v in pairs(obj) do result[k] = v end
-    return result
-  end
-  local metadata = clone(meta)
-
-  local resolve_institute = function (idx)
-    return meta.institute[tonumber(idx)]
-  end
-  local tmp_authors = {}
-  for i, author_orig in ipairs(meta.author) do
-    local author = clone(author_orig)
-    if author.institute then
-      author.institute = List.map(author.institute, resolve_institute)
-    end
-    tmp_authors[i] = author
-  end
-  metadata.author = tmp_authors
-
-  local bib = pandoc.utils.stringify(meta.bibliography)
-  metadata.bibliography_records = bibliography(bib)
-  local jsonld_object = json_ld(metadata)
-  meta.jsonld = json.encode(jsonld_object)
-
-  return meta
-end

example/assets/pandoc-scholar/scholar-filters/template-helper.lua

@@ -1,48 +0,0 @@
---[[
-template-helper: generate meta fields to be used in templates.
-
-Copyright © 2017–2021 Albert Krewinkel
-
-Permission to use, copy, modify, and/or distribute this software for any purpose
-with or without fee is hereby granted, provided that the above copyright notice
-and this permission notice appear in all copies.
-
-THE SOFTWARE IS PROVIDED "AS IS" AND THE AUTHOR DISCLAIMS ALL WARRANTIES WITH
-REGARD TO THIS SOFTWARE INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND
-FITNESS. IN NO EVENT SHALL THE AUTHOR BE LIABLE FOR ANY SPECIAL, DIRECT,
-INDIRECT, OR CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS
-OF USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR OTHER
-TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR PERFORMANCE OF
-THIS SOFTWARE.
-]]
-
-local List = require 'pandoc.List'
-
-function Meta (meta)
-  local function resolve_institute (idx)
-    return meta.institute[tonumber(idx)]
-  end
-
-  for i, author in ipairs(meta.author) do
-    local institute_indices = List:new(author.institute)
-    local institutes = institute_indices:map(resolve_institute)
-    author.institute_indices = institute_indices
-    author.institute = institutes
-    meta.has_equal_contributors = meta.has_equal_contributors
-      or author.equal_contributor
-    meta.has_correspondence = meta.has_correspondence
-      or author.correspondence and author.email
-  end
-  -- helper attributes
-  if #meta.author > 0 then
-    meta.author[1].first = true
-    meta.author[#meta.author].last = true
-  end
-
-  for i, institute in ipairs(meta.institute) do
-    institute.index = tostring(i)
-  end
-
-  return meta
-end
-

example/assets/pandoc-scholar/templates/pandoc-scholar.html

@@ -1,119 +0,0 @@
-<!doctype html>
-<!--
-Template created by Andrew G. York, based on this theme by Diana Mounter:
-https://github.com/broccolini/dinky, which mentioned that
-attribution is appreciated. Thanks, broccolini! -->
-<html lang="en">
-<head>
-  <base target="_blank"/>
-  <meta charset="utf-8"/>
-  <meta http-equiv="X-UA-Compatible" content="IE=edge"/>
-  <meta name="viewport" content="width=device-width, initial-scale=1, user-scalable=no"/>
-$for(author-meta)$
-  <meta name="author" content="$author-meta$"/>
-$endfor$
-$if(date-meta)$
-  <meta name="dcterms.date" content="$date-meta$"/>
-$endif$
-$if(keywords)$
-  <meta name="keywords" content="$for(keywords)$$keywords$$sep$, $endfor$"/>
-$endif$
-  <title>$if(title-prefix)$$title-prefix$ – $endif$$pagetitle$</title>
-  <style type="text/css">code{white-space: pre;}</style>
-$if(quotes)$
-  <style type="text/css">q { quotes: "“" "”" "‘" "’"; }</style>
-$endif$
-$if(highlighting-css)$
-  <style type="text/css">
-$highlighting-css$
-  </style>
-$endif$
-$for(css)$
-  <link rel="stylesheet" href="$css$">
-$endfor$
-$if(math)$
-$if(mathjax)$
-$-- MathJax is handled specially.  We need to add the data-external attribute
-$-- so it doesn't get inlined (and thus broken) by the --self-contained option.
-$-- (2.7.2 is the default MathJax version as of Pandoc 2.2.1.)
-  <script data-external="1" src="https://cdnjs.cloudflare.com/ajax/libs/mathjax/2.7.2/MathJax.js?config=TeX-AMS_CHTML-full"></script>
-$else$
-  $math$
-$endif$
-$endif$
-  <!--[if lt IE 9]>
-    <script src="//cdnjs.cloudflare.com/ajax/libs/html5shiv/3.7.3/html5shiv-printshiv.min.js"></script>
-  <![endif]-->
-$for(header-includes)$
-  $header-includes$
-$endfor$
-</head>
-<body>
-<div class="wrapper">
-$if(project)$
-<header class="page-header">
-  <h1 class="header">$project.title$</h1>
-  <ul>
-$if(project.zip-url)$
-    <li class="download"><a class="buttons" href="$project.zip-url$">Download ZIP</a></li>
-$endif$
-$if(project.github-url)$
-    <li><a class="buttons github" href="$project.github-url$">View On GitHub</a></li>
-$endif$
-$if(project.pdf-url)$
-    <li><a class="buttons pdf" href="$project.pdf-url$">Download PDF</a></li>
-$endif$
-  </ul>
-  <p class="header">This project is maintained by $project.maintainer$</p>
-</header>
-$endif$
-<article typeof="ScholarlyArticle" vocab="http://schema.org/">
-    <!-- <header class="article-header"> -->
-<h1 property="headline">$title$</h1>
-$if(subtitle)$
-<p property="alternativeHeadline" class="subtitle">$subtitle$</p>
-$endif$
-<!-- </header> -->
-<p class="author-list">
-$for(author)$
-  $if(author.last)$and $endif$<span property="author" typeof="Person">
-    $author.name$</span><sup>$if(author.correspondence)$$if(author.email)$<a href="mailto:$author.email$">✉</a> $endif$$endif$$for(author.institute_indices)$$author.institute_indices$$sep$,$endfor$$if(author.equal_contributor)$,$if(equal_contributor_symbol)$$equal_contributor_symbol$$else$*$endif$$endif$</sup>$sep$,
-$endfor$
-</p>
-<div class="author-affiliations">
-$for(institute)$
-  <div class="affiliation"><sup>$institute.index$</sup>$institute.name$$if(institute.address)$, $institute.address$$endif$
-  </div>
-$endfor$
-</div>
-<div class="author-info">
-    $if(has_equal_contributors)$
-    <div class="author-contrib">
-        <sup>$if(equal_contributor_symbol)$$equal_contributor_symbol$$else$*$endif$</sup>These authors contributed equally to this work
-    </div>
-    $endif$
-    $if(has_correspondence)$
-    <div class="author-correspondence">
-        Correspondence: $for(author)$$if(author.correspondence)$$if(author.email)$$author.name$ <a href="mailto:$author.email$">&lt;$author.email$&gt;</a> $endif$$endif$$endfor$
-    </div>
-    $endif$
-</div>
-$if(abstract)$<p class="abstract" property="description">$abstract$</p>$endif$
-$if(doi)$<p><a href="https://doi.org/$doi$">doi: $doi$</a></p>$endif$
-
-$for(include-before)$
-$include-before$
-
-$endfor$
-
-<div property="articleBody" class="article-body">
-$body$
-</div>
-</article>
-<footer>
-  <p><small>Generated using <a href="https://github.com/pandoc-scholar/pandoc-scholar">pandoc scholar</a></small></p>
-</footer>
-</div>
- <!--[if !IE]><script>fixScale(document);</script><![endif]-->
-</body>
-</html>

example/assets/pandoc-scholar/templates/pandoc-scholar.jats

@@ -1,118 +0,0 @@
-<?xml version="1.0" encoding="utf-8" ?>
-$if(xml-stylesheet)$
-<?xml-stylesheet type="text/xsl" href="$xml-stylesheet$"?>
-$endif$
-<!DOCTYPE article PUBLIC "-//NLM//DTD JATS (Z39.96) Article Authoring DTD v1.2 20190208//EN"
-          "JATS-articleauthoring1.dtd">
-<article xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink" dtd-version="1.2" article-type="research-article">
-<front>
-<article-meta>
-$if(title)$
-<title-group>
-<article-title>$title$</article-title>
-</title-group>
-$endif$
-$if(author)$
-<contrib-group>
-$for(author)$
-<contrib contrib-type="author" corresp="$if(author.correspondence)$yes$else$no$endif$">
-$if(author.orcid)$
-<contrib-id contrib-id-type="orcid">$author.orcid$</contrib-id>
-$endif$
-<name-alternatives>
-<string-name>$author.name$</string-name>
-</name-alternatives>
-$for(author.institute)$
-<aff>
-$author.institute.name$
-$if(author.institute.phone)$
-<phone>$author.institute.phone$</phone>
-$endif$
-</aff>
-$endfor$
-$if(author.email)$
-<email>$author.email$</email>
-$endif$
-</contrib>
-$endfor$
-</contrib-group>
-$endif$
-$if(date)$
-<pub-date pub-type="epub"$if(date.iso-8601)$ iso-8601-date="$date.iso-8601$"$endif$>
-$if(date.day)$
-<day>$date.day$</day>
-$endif$
-$if(date.month)$
-<month>$date.month$</month>
-$endif$
-<year>$date.year$</year>
-</pub-date>
-$endif$
-$if(article.volume)$
-<volume>$article.volume$</volume>
-$endif$
-$if(article.issue)$
-<issue>$article.issue$</issue>
-$endif$
-$if(article.fpage)$
-<fpage>$article.fpage$</fpage>
-$endif$
-$if(article.lpage)$
-<lpage>$article.lpage$</lpage>
-$endif$
-$if(article.elocation-id)$
-<elocation-id>$article.elocation-id$</elocation-id>
-$endif$
-$if(history)$
-<history>
-</history>
-$endif$
-$if(copyright)$
-<permissions>
-$if(copyright.statement)$
-<copyright-statement>$copyright.statement$</copyright-statement>
-$endif$
-$if(copyright.year)$
-<copyright-year>$copyright.year$</copyright-year>
-$endif$
-$if(copyright.holder)$
-<copyright-holder>$copyright.holder$</copyright-holder>
-$endif$
-$if(copyright.text)$
-<license license-type="$copyright.type$" xlink:href="$copyright.link$">
-<license-p>$copyright.text$</license-p>
-</license>
-</permissions>
-$endif$
-$endif$
-$if(abstract)$
-<abstract>
-$abstract$
-</abstract>
-$endif$
-$if(tags)$
-<kwd-group kwd-group-type="author">
-$for(tags)$
-<kwd>$tags$</kwd>
-$endfor$
-</kwd-group>
-$endif$
-$if(article.funding-statement)$
-<funding-group>
-<funding-statement>$article.funding-statement$</funding-statement>
-</funding-group>
-$endif$
-</article-meta>
-$if(notes)$
-<notes>$notes$</notes>
-$endif$
-</front>
-<body>
-$body$
-</body>
-<back>
-$if(back)$
-$back$
-$endif$
-</back>
-</article>

example/assets/pandoc-scholar/templates/pandoc-scholar.latex

@@ -1,399 +0,0 @@
-% Options for packages loaded elsewhere
-\PassOptionsToPackage{unicode$for(hyperrefoptions)$,$hyperrefoptions$$endfor$}{hyperref}
-\PassOptionsToPackage{hyphens}{url}
-$if(colorlinks)$
-\PassOptionsToPackage{dvipsnames,svgnames*,x11names*}{xcolor}
-$endif$
-$if(dir)$
-$if(latex-dir-rtl)$
-\PassOptionsToPackage{RTLdocument}{bidi}
-$endif$
-$endif$
-$if(CJKmainfont)$
-\PassOptionsToPackage{space}{xeCJK}
-$endif$
-%
-\documentclass[
-$if(fontsize)$
-  $fontsize$,
-$endif$
-$if(lang)$
-  $babel-lang$,
-$endif$
-$if(papersize)$
-  $papersize$paper,
-$endif$
-$for(classoption)$
-  $classoption$$sep$,
-$endfor$
-]{$documentclass$}
-\usepackage{amsmath,amssymb}
-$if(fontfamily)$
-\usepackage[$for(fontfamilyoptions)$$fontfamilyoptions$$sep$,$endfor$]{$fontfamily$}
-$else$
-\usepackage{lmodern}
-$endif$
-$if(linestretch)$
-\usepackage{setspace}
-$endif$
-\usepackage{ifxetex,ifluatex}
-\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
-  \usepackage[$if(fontenc)$$fontenc$$else$T1$endif$]{fontenc}
-  \usepackage[utf8]{inputenc}
-  \usepackage{textcomp} % provide euro and other symbols
-\else % if luatex or xetex
-$if(mathspec)$
-  \ifxetex
-    \usepackage{mathspec}
-  \else
-    \usepackage{unicode-math}
-  \fi
-$else$
-  \usepackage{unicode-math}
-$endif$
-  \defaultfontfeatures{Scale=MatchLowercase}
-  \defaultfontfeatures[\rmfamily]{Ligatures=TeX,Scale=1}
-$if(mainfont)$
-  \setmainfont[$for(mainfontoptions)$$mainfontoptions$$sep$,$endfor$]{$mainfont$}
-$endif$
-$if(sansfont)$
-  \setsansfont[$for(sansfontoptions)$$sansfontoptions$$sep$,$endfor$]{$sansfont$}
-$endif$
-$if(monofont)$
-  \setmonofont[$for(monofontoptions)$$monofontoptions$$sep$,$endfor$]{$monofont$}
-$endif$
-$for(fontfamilies)$
-  \newfontfamily{$fontfamilies.name$}[$for(fontfamilies.options)$$fontfamilies.options$$sep$,$endfor$]{$fontfamilies.font$}
-$endfor$
-$if(mathfont)$
-$if(mathspec)$
-  \ifxetex
-    \setmathfont(Digits,Latin,Greek)[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
-  \else
-    \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
-  \fi
-$else$
-  \setmathfont[$for(mathfontoptions)$$mathfontoptions$$sep$,$endfor$]{$mathfont$}
-$endif$
-$endif$
-$if(CJKmainfont)$
-  \ifxetex
-    \usepackage{xeCJK}
-    \setCJKmainfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
-  \fi
-$endif$
-$if(luatexjapresetoptions)$
-  \ifluatex
-    \usepackage[$for(luatexjapresetoptions)$$luatexjapresetoptions$$sep$,$endfor$]{luatexja-preset}
-  \fi
-$endif$
-$if(CJKmainfont)$
-  \ifluatex
-    \usepackage[$for(luatexjafontspecoptions)$$luatexjafontspecoptions$$sep$,$endfor$]{luatexja-fontspec}
-    \setmainjfont[$for(CJKoptions)$$CJKoptions$$sep$,$endfor$]{$CJKmainfont$}
-  \fi
-$endif$
-\fi
-% Use upquote if available, for straight quotes in verbatim environments
-\IfFileExists{upquote.sty}{\usepackage{upquote}}{}
-\IfFileExists{microtype.sty}{% use microtype if available
-  \usepackage[$for(microtypeoptions)$$microtypeoptions$$sep$,$endfor$]{microtype}
-  \UseMicrotypeSet[protrusion]{basicmath} % disable protrusion for tt fonts
-}{}
-$if(indent)$
-$else$
-\makeatletter
-\@ifundefined{KOMAClassName}{% if non-KOMA class
-  \IfFileExists{parskip.sty}{%
-    \usepackage{parskip}
-  }{% else
-    \setlength{\parindent}{0pt}
-    \setlength{\parskip}{6pt plus 2pt minus 1pt}}
-}{% if KOMA class
-  \KOMAoptions{parskip=half}}
-\makeatother
-$endif$
-$if(verbatim-in-note)$
-\usepackage{fancyvrb}
-$endif$
-\usepackage{xcolor}
-\IfFileExists{xurl.sty}{\usepackage{xurl}}{} % add URL line breaks if available
-\IfFileExists{bookmark.sty}{\usepackage{bookmark}}{\usepackage{hyperref}}
-\hypersetup{
-$if(title-meta)$
-  pdftitle={$title-meta$},
-$endif$
-$if(author-meta)$
-  pdfauthor={$author-meta$},
-$endif$
-$if(lang)$
-  pdflang={$lang$},
-$endif$
-$if(subject)$
-  pdfsubject={$subject$},
-$endif$
-$if(keywords)$
-  pdfkeywords={$for(keywords)$$keywords$$sep$, $endfor$},
-$endif$
-$if(colorlinks)$
-  colorlinks=true,
-  linkcolor=$if(linkcolor)$$linkcolor$$else$Maroon$endif$,
-  filecolor=$if(filecolor)$$filecolor$$else$Maroon$endif$,
-  citecolor=$if(citecolor)$$citecolor$$else$Blue$endif$,
-  urlcolor=$if(urlcolor)$$urlcolor$$else$Blue$endif$,
-$else$
-  hidelinks,
-$endif$
-  pdfcreator={LaTeX via pandoc}}
-\urlstyle{same} % disable monospaced font for URLs
-$if(verbatim-in-note)$
-\VerbatimFootnotes % allow verbatim text in footnotes
-$endif$
-$if(geometry)$
-\usepackage[$for(geometry)$$geometry$$sep$,$endfor$]{geometry}
-$endif$
-$if(listings)$
-\usepackage{listings}
-\newcommand{\passthrough}[1]{#1}
-\lstset{defaultdialect=[5.3]Lua}
-\lstset{defaultdialect=[x86masm]Assembler}
-$endif$
-$if(lhs)$
-\lstnewenvironment{code}{\lstset{language=Haskell,basicstyle=\small\ttfamily}}{}
-$endif$
-$if(highlighting-macros)$
-$highlighting-macros$
-$endif$
-$if(tables)$
-\usepackage{longtable,booktabs,array}
-\usepackage{calc} % for calculating minipage widths
-% Correct order of tables after \paragraph or \subparagraph
-\usepackage{etoolbox}
-\makeatletter
-\patchcmd\longtable{\par}{\if@noskipsec\mbox{}\fi\par}{}{}
-\makeatother
-% Allow footnotes in longtable head/foot
-\IfFileExists{footnotehyper.sty}{\usepackage{footnotehyper}}{\usepackage{footnote}}
-\makesavenoteenv{longtable}
-$endif$
-$if(graphics)$
-\usepackage{graphicx}
-\makeatletter
-\def\maxwidth{\ifdim\Gin@nat@width>\linewidth\linewidth\else\Gin@nat@width\fi}
-\def\maxheight{\ifdim\Gin@nat@height>\textheight\textheight\else\Gin@nat@height\fi}
-\makeatother
-% Scale images if necessary, so that they will not overflow the page
-% margins by default, and it is still possible to overwrite the defaults
-% using explicit options in \includegraphics[width, height, ...]{}
-\setkeys{Gin}{width=\maxwidth,height=\maxheight,keepaspectratio}
-% Set default figure placement to htbp
-\makeatletter
-\def\fps@figure{htbp}
-\makeatother
-$endif$
-$if(links-as-notes)$
-% Make links footnotes instead of hotlinks:
-\DeclareRobustCommand{\href}[2]{#2\footnote{\url{#1}}}
-$endif$
-$if(strikeout)$
-\usepackage[normalem]{ulem}
-% Avoid problems with \sout in headers with hyperref
-\pdfstringdefDisableCommands{\renewcommand{\sout}{}}
-$endif$
-\setlength{\emergencystretch}{3em} % prevent overfull lines
-\providecommand{\tightlist}{%
-  \setlength{\itemsep}{0pt}\setlength{\parskip}{0pt}}
-$if(numbersections)$
-\setcounter{secnumdepth}{$if(secnumdepth)$$secnumdepth$$else$5$endif$}
-$else$
-\setcounter{secnumdepth}{-\maxdimen} % remove section numbering
-$endif$
-$if(block-headings)$
-% Make \paragraph and \subparagraph free-standing
-\ifx\paragraph\undefined\else
-  \let\oldparagraph\paragraph
-  \renewcommand{\paragraph}[1]{\oldparagraph{#1}\mbox{}}
-\fi
-\ifx\subparagraph\undefined\else
-  \let\oldsubparagraph\subparagraph
-  \renewcommand{\subparagraph}[1]{\oldsubparagraph{#1}\mbox{}}
-\fi
-$endif$
-$if(pagestyle)$
-\pagestyle{$pagestyle$}
-$endif$
-$for(header-includes)$
-$header-includes$
-$endfor$
-$if(lang)$
-\ifxetex
-  % Load polyglossia as late as possible: uses bidi with RTL langages (e.g. Hebrew, Arabic)
-  \usepackage{polyglossia}
-  \setmainlanguage[$for(polyglossia-lang.options)$$polyglossia-lang.options$$sep$,$endfor$]{$polyglossia-lang.name$}
-$for(polyglossia-otherlangs)$
-  \setotherlanguage[$for(polyglossia-otherlangs.options)$$polyglossia-otherlangs.options$$sep$,$endfor$]{$polyglossia-otherlangs.name$}
-$endfor$
-\else
-  \usepackage[$for(babel-otherlangs)$$babel-otherlangs$,$endfor$main=$babel-lang$]{babel}
-% get rid of language-specific shorthands (see #6817):
-\let\LanguageShortHands\languageshorthands
-\def\languageshorthands#1{}
-$if(babel-newcommands)$
-  $babel-newcommands$
-$endif$
-\fi
-$endif$
-\ifluatex
-  \usepackage{selnolig}  % disable illegal ligatures
-\fi
-$if(dir)$
-\ifxetex
-  % Load bidi as late as possible as it modifies e.g. graphicx
-  \usepackage{bidi}
-\fi
-\ifnum 0\ifxetex 1\fi\ifluatex 1\fi=0 % if pdftex
-  \TeXXeTstate=1
-  \newcommand{\RL}[1]{\beginR #1\endR}
-  \newcommand{\LR}[1]{\beginL #1\endL}
-  \newenvironment{RTL}{\beginR}{\endR}
-  \newenvironment{LTR}{\beginL}{\endL}
-\fi
-$endif$
-$if(csl-refs)$
-\newlength{\cslhangindent}
-\setlength{\cslhangindent}{1.5em}
-\newlength{\csllabelwidth}
-\setlength{\csllabelwidth}{3em}
-\newenvironment{CSLReferences}[2] % #1 hanging-ident, #2 entry spacing
- {% don't indent paragraphs
-  \setlength{\parindent}{0pt}
-  % turn on hanging indent if param 1 is 1
-  \ifodd #1 \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces\fi
-  % set entry spacing
-  \ifnum #2 > 0
-  \setlength{\parskip}{#2\baselineskip}
-  \fi
- }%
- {}
-\usepackage{calc}
-\newcommand{\CSLBlock}[1]{#1\hfill\break}
-\newcommand{\CSLLeftMargin}[1]{\parbox[t]{\csllabelwidth}{#1}}
-\newcommand{\CSLRightInline}[1]{\parbox[t]{\linewidth - \csllabelwidth}{#1}\break}
-\newcommand{\CSLIndent}[1]{\hspace{\cslhangindent}#1}
-% for compatibility with pandoc 2.10
-\newenvironment{cslreferences}%
-  {$if(csl-hanging-indent)$\setlength{\parindent}{0pt}%
-  \everypar{\setlength{\hangindent}{\cslhangindent}}\ignorespaces$endif$}%
-  {\par}
-$endif$
-
-$if(title)$
-\title{$title$$if(thanks)$\thanks{$thanks$}$endif$}
-$endif$
-$if(subtitle)$
-\usepackage{etoolbox}
-\makeatletter
-\providecommand{\subtitle}[1]{% add subtitle to \maketitle
-  \apptocmd{\@title}{\par {\large #1 \par}}{}{}
-}
-\makeatother
-\subtitle{$subtitle$}
-$endif$
-\usepackage{authblk}
-$for(author)$
-\author[$for(author.institute_indices)$%
-  $author.institute_indices$%
-  $sep$,$endfor$]{%
-  $author.name$%
-  $if(author.correspondence)$$if(author.email)$%
-  \textsuperscript{*\,}%
-  %$endif$$endif$%
-  $if(author.equal_contributor)$
-  \textsuperscript{$if(equal_contributor_symbol)$$equal_contributor_symbol$$else$\textdagger$endif$\,}%
-  $endif$%
-}
-$endfor$
-$for(institute)$
-\affil[$institute.index$]{$institute.name$}
-$endfor$
-\date{$date$}
-
-\makeatletter
-\def\@maketitle{%
-  \newpage \null \vskip 2em
-  \begin {center}%
-    \let \footnote \thanks
-         {\LARGE \@title \par}%
-         \vskip 1.5em%
-                {\large \lineskip .5em%
-                  \begin {tabular}[t]{c}%
-                    \@author
-                  \end {tabular}\par}%
-                $if(has_equal_contributors)$
-                \vskip 0.5em{\textsuperscript{$if(equal_contributor_symbol)$$equal_contributor_symbol$$else$\textdagger$endif$}\,%
-                  These authors contributed equally to this work.}
-                $endif$
-                $if(has_correspondence)$
-                \vskip 0.2em{\textsuperscript{*}\,Correspondence:
-                  $for(author)$$if(author.correspondence)$$if(author.email)$
-                  $author.name$ <$author.email$>\\
-                  $endif$$endif$$endfor$}%
-                %$endif$
-                \vskip 1em{\large \@date}%
-  \end {center}%
-  \par
-  \vskip 1.5em}
-\makeatother
-
-\begin{document}
-$if(has-frontmatter)$
-\frontmatter
-$endif$
-$if(title)$
-\maketitle
-$if(abstract)$
-\begin{abstract}
-$abstract$
-\end{abstract}
-$endif$
-$endif$
-
-$for(include-before)$
-$include-before$
-
-$endfor$
-$if(toc)$
-$if(toc-title)$
-\renewcommand*\contentsname{$toc-title$}
-$endif$
-{
-$if(colorlinks)$
-\hypersetup{linkcolor=$if(toccolor)$$toccolor$$else$$endif$}
-$endif$
-\setcounter{tocdepth}{$toc-depth$}
-\tableofcontents
-}
-$endif$
-$if(lot)$
-\listoftables
-$endif$
-$if(lof)$
-\listoffigures
-$endif$
-$if(linestretch)$
-\setstretch{$linestretch$}
-$endif$
-$if(has-frontmatter)$
-\mainmatter
-$endif$
-$body$
-
-$if(has-frontmatter)$
-\backmatter
-$endif$
-
-$for(include-after)$
-$include-after$
-
-$endfor$
-\end{document}

example/assets/pandoc-scholar/templates/styles/pandoc-scholar.css

@@ -1,478 +0,0 @@
-@import url(https://fonts.googleapis.com/css?family=Arvo:400,700,400italic);
-
-/* MeyerWeb Reset */
-
-html, body, div, span, applet, object, iframe,
-h1, h2, h3, h4, h5, h6, p, blockquote, pre,
-a, abbr, acronym, address, big, cite, code,
-del, dfn, em, img, ins, kbd, q, s, samp,
-small, strike, strong, sub, sup, tt, var,
-b, u, i, center,
-dl, dt, dd, ol, ul, li,
-fieldset, form, label, legend,
-table, caption, tbody, tfoot, thead, tr, th, td,
-article, aside, canvas, details, embed,
-figure, figcaption, footer, header, hgroup,
-article, menu, nav, output, ruby, section, summary,
-time, mark, audio, video {
-  margin: 0;
-  padding: 0;
-  border: 0;
-  font: inherit;
-  vertical-align: baseline;
-}
-
-
-/* Base text styles */
-
-body {
-  padding: 10px 50px 0 0;
-  font-family: "Helvetica Neue", Helvetica, Arial, sans-serif;
-  font-size: 15px;
-  color: #030303;
-  background-color: #FCFBF8;
-  margin: 0;
-  line-height: 1.8em;
-  -webkit-font-smoothing: antialiased;
-}
-
-h1, h2, h3, h4, h5, h6 {
-  color: #232323;
-  margin: 36px 0 10px;
-}
-
-p, ul, ol, table, dl {
-  margin: 0 0 22px;
-}
-
-sub, sup {
-  font-size: 80%;
-}
-
-sub {
-  vertical-align: sub;
-}
-
-sup {
-  vertical-align: sup;
-}
-
-.author-list {
-  margin:0 0 0px;
-  font-weight: 700;
-}
-
-.author-affiliations {
-  margin:0 0 0px;
-  font-style: italic;
-}
-
-.contact_email {
-  font-style: italic;
-}
-
-.abstract {
-  margin: 0% 1% 2%;
-  font-weight: 700;
-}
-
-h1, h2, h3 {
-  border-bottom: 1px solid #ccc;
-  font-family: Arvo, Monaco, serif;
-  font-weight: normal;
-  line-height: 1.3;
-  padding-bottom: 5px;
-}
-
-h1 {
-  font-size: 30px;
-}
-
-h2 {
-  font-size: 24px;
-}
-
-h3 {
-  font-size: 18px;
-}
-
-h4, h5 {
-  font-family: Arvo, Monaco, serif;
-  font-weight: 700;
-}
-
-h6 {
-  font-family: Arvo, Monaco, serif;
-  font-weight: 200;
-}
-
-a {
-  font-weight:200;
-  text-decoration:none;
-}
-
-a:hover {
-  text-decoration: underline;
-}
-
-a small {
-  font-size: 12px;
-}
-
-em {
-  font-style: italic;
-}
-
-strong {
-  font-weight:700;
-}
-
-sup {
-  vertical-align: super;
-  font-size: smaller;
-}
-
-ul {
-  list-style-position: inside;
-  list-style: disc;
-  padding-left: 25px;
-}
-
-ol {
-  list-style-position: inside;
-  list-style: decimal;
-  padding-left: 25px;
-}
-
-blockquote {
-  margin: 0;
-  padding: 0 0 0 20px;
-  font-style: italic;
-}
-
-dl, dt, dd, dl p {
-  font-color: #444;
-}
-
-dl dt {
-  font-weight: bold;
-}
-
-dl dd {
-  padding-left: 20px;
-  font-style: italic;
-}
-
-dl p {
-  padding-left: 20px;
-  font-style: italic;
-}
-
-hr {
-  border: 0;
-  background: #ccc;
-  height: 1px;
-  margin: 0 0 24px;
-}
-
-/* Images */
-
-img {
-  position: relative;
-  margin: 0 auto;
-  height: auto;
-  max-width: 100%;
-  padding: 0px;
-  margin: 0px 0 0px 0;
-  border: 0px solid #ccc;
-}
-
-p img {
-  display: inline;
-  margin: 0;
-  padding: 0;
-  vertical-align: middle;
-  text-align: center;
-  border: none;
-}
-
-figure {
-  border: 1px solid #ccc;
-  background: #FFFFFF;
-}
-
-figcaption {
-  font-size: 12px;
-  background: #FFFFFF;
-  line-height: 150%;
-  margin-right: 1%;
-  margin-left: 1%;
-}
-
-/* Code blocks */
-
-code, pre {
-  font-family: Monaco, "Bitstream Vera Sans Mono", "Lucida Console", Terminal, monospace;
-  color: #000;
-  background: #e7e7e7;
-  font-size: 12px;
-}
-
-pre {
-  padding: 4px 12px;
-  border-radius:4px;
-  border:1px solid #D7D8C8;
-  overflow: auto;
-  overflow-y: hidden;
-  margin-bottom: 32px;
-}
-
-
-/* Tables */
-
-table {
-  width: 100%;
-  border: 1px solid #ccc;
-  margin-bottom: 32px;
-  text-align: left;
- }
-
-table.figure_controls {
-  font-size: 12px;
-  line-height: 100%;
-  margin-bottom: 0px;
-}
-
-th {
-  background: #232323;
-  color: #FDFEFB;
-  font-family: 'Arvo', Helvetica, Arial, sans-serif;
-  font-size: 18px;
-  font-weight: normal;
-  padding: 10px;
-}
-
-td {
-  background: #eee;
-  padding: 0px;
-}
-
-
-/* Wrapper */
-.wrapper {
-  width:960px;
-}
-
-
-/* Header */
-
-.page-header {
-  background-color: #474747;
-  border-bottom-right-radius: 4px;
-  border-top-right-radius: 4px;
-  border: 1px solid #000;
-  color: #FDFDFB;
-  float: left;
-  margin: 30px 25px 0 0;
-  padding: 34px 25px 22px 50px;
-  position: fixed;
-  width: 170px;
-  -webkit-font-smoothing: antialiased;
-}
-
-.subtitle {
-  font-size: 16px;
-}
-
-.page-header h1 {
-  font-family: Arvo, sans-serif;
-  font-size: 30px;
-  font-weight: 300;
-  line-height: 1.3em;
-  border-bottom: none;
-  margin-top: 0;
-}
-
-
-.page-header h1,
-.page-header a {
-  color: #fff;
-}
-
-.page-header a {
-  text-decoration: underline;
-}
-
-a.name {
-  white-space: nowrap;
-}
-
-.page-header ul {
-  list-style:none;
-  padding:0;
-}
-
-.page-header li {
-  list-style-type: none;
-  width: 135px;
-  height: 15px;
-  margin-bottom: 12px;
-  line-height: 1em;
-  padding: 6px 6px 6px 7px;
-  background: #1100AF;
-  background: -moz-linear-gradient(top, #1100AF 0%, #110082 100%);
-  background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,#f8f8f8), color-stop(100%, #dddddd));
-  background: -webkit-linear-gradient(top, #1100AF 0%,#110082 100%);
-  background: -o-linear-gradient(top, #1100AF 0%,#110082 100%);
-  background: -ms-linear-gradient(top, #1100AF 0%,#110082 100%);
-  background: linear-gradient(top, #1100AF 0%,#110082 100%);
-  border-radius:4px;
-  border:1px solid #0D0D0D;
-  -webkit-box-shadow: inset 0px 1px 1px 0 rgba(38,2,233, 1);
-  box-shadow: inset 0px 1px 1px 0 rgba(38,2,233, 1);
-}
-
-.page-header li:hover {
-  background: #1D00C3;
-  background: -moz-linear-gradient(top, #1D00C3 0%, #190195 100%);
-  background: -webkit-gradient(linear, left top, left bottom, color-stop(0%,#f8f8f8), color-stop(100%,#dddddd));
-  background: -webkit-linear-gradient(top, #1D00C3 0%,#190195 100%);
-  background: -o-linear-gradient(top, #1D00C3 0%,#190195 100%);
-  background: -ms-linear-gradient(top, #1D00C3 0%,#190195 100%);
-  background: linear-gradient(top, #1D00C3 0%,#190195 100%);
-}
-
-.buttons {
-  -webkit-font-smoothing: antialiased;
-  background: url(../images/arrow-down.png) no-repeat;
-  font-weight: normal;
-  height: 30px;
-  padding: 2px 2px 2px 22px;
-  text-shadow: rgba(0, 0, 0, 0.4) 0 -1px 0;
-}
-
-a.buttons {
-  text-decoration: none;
-}
-
-.buttons.github {
-  background: url(../images/octocat-small.png) no-repeat 1px;
-}
-
-.buttons.pdf {
-  background: url(../images/pdf.png) no-repeat 1px;
-}
-
-.buttons:hover {
-  color: #fff;
-  text-decoration: none;
-}
-
-
-/* Article - for main page content */
-
-article {
-  width: 650px;
-  float: right;
-  padding-bottom: 50px;
-}
-
-
-/* Footer */
-
-footer {
-  width: 170px;
-  float: left;
-  position: fixed;
-  bottom: 10px;
-  padding-left: 50px;
-}
-
-@media print, screen and (max-width: 960px) {
-  div.wrapper {
-    width: auto;
-    margin: 0;
-  }
-
-  .page-header, article, footer {
-    float: none;
-    position: static;
-    width: auto;
-  }
-
-  footer {
-    border-top: 1px solid #ccc;
-    margin: 0 84px 0 50px;
-    padding: 0;
-  }
-
-  .page-header {
-    padding-right: 320px;
-  }
-
-  article {
-    padding: 20px 84px 20px 50px;
-    margin: 0 0 20px;
-  }
-
-  .page-header a small {
-    display: inline;
-  }
-
-  .page-header ul {
-    position: absolute;
-    right: 130px;
-    top: 84px;
-  }
-}
-
-@media print, screen and (max-width: 720px) {
-  body {
-    word-wrap:break-word;
-  }
-
-  .page-header {
-    padding: 10px 20px 0;
-    margin-right: 0;
-  }
-
-  article {
-    margin: 0 0 30px;
-    padding: 10px 0 10px 20px;
-  }
-
-  footer {
-    margin: 0 0 0 30px;
-  }
-
-  .page-header ul, .page-header p.view {
-    position: static;
-  }
-}
-
-@media print, screen and (max-width: 480px) {
-  .page-header ul li.download {
-    display: none;
-  }
-
-  footer {
-    margin: 0 0 0 20px;
-  }
-
-  footer a {
-    display:block;
-  }
-}
-
-@media print {
-  body {
-    padding:0.4in;
-    font-size:12pt;
-    color:#444;
-  }
-}
-
-.onlyprint {display: none;}
-@media print {
-  .onlyprint {display: block;}
-}

example/assets/pandoc-scholar/writers/jsonld.lua

@@ -1,14 +0,0 @@
---
--- jsonld.lua
---
--- Copyright (c) 2017 Albert Krewinkel, Robert Winkler
---
--- This program is free software; you can redistribute it and/or modify it
--- under the terms of the GNU public license version 2 or later.
--- See the LICENSE file for details.
-
-function Doc (body, meta, variables)
-  return meta.jsonld
-end
-
-setmetatable(_G, {__index = function () return function () return '' end end})

example/assets/pd-chem-filter.lua

@@ -1,19 +0,0 @@
--- This pandoc lua filter helps with latex chemical formulas with \ce
---      In the case of markdown, it is re-escaped for math mode
---      In the case of docx, the \ce is fully removed
-
-if FORMAT:match 'markdown' then
-
-    function Math(elem)
-        elem.text = elem.text:gsub("%\\\\ce", "\\ce")
-        return elem
-    end
-
-elseif FORMAT:match 'docx' then
-
-    function Math(elem)
-        elem.text = elem.text:gsub("%\\ce", "")
-        return elem
-    end
-
-end

example/assets/pd-image-filter.lua

@@ -1,21 +0,0 @@
-if FORMAT:match 'markdown' then
-
-  function Image(elem)
-    -- Make sure extension is .png
-    elem.src = elem.src:gsub("%.pdf", ".png")
-
-    -- Prepend figure directory
-    elem.src = "figs/" .. elem.src
-    return elem
-  end
-
-end
-
--- Filter images with this function if the target format is HTML
-if FORMAT:match 'html' then
-  function Image(elem)
-    elem.attributes.style = 'cursor:pointer'
-    elem.attributes.onclick = 'onClickImage(this)'
-    return elem
-  end
-end

example/assets/pd-meta.py

@@ -1,109 +0,0 @@
-import argparse
-import pathlib
-import re
-
-NEWCOMAND_RE = re.compile(r"\\newcommand{[^}]*}{[^}]*}")  # a user new command
-ARGUMENT_RE = re.compile(r"(?<={)[^}]*(?=})")  # latex arguments
-
-meta_types = {
-    r"\pubtitle": "title",
-    r"\pubauth": "author",
-    r"\eqcontrib": "contribution",
-    r"\pubaffil": "affil",
-    r"\authemail": "email",
-    r"\orcid": "orcid",
-    r"\pubaddr": "institute",
-    r"\pubemail": "contact",
-}
-
-
-def repl_input(inp_section):
-
-    input_text = inp_section.group()
-    filename = ARGUMENT_RE.search(input_text)
-    print(filename)
-
-
-def read_meta(metafile):
-
-    metadata = {t: {} for t in meta_types.values()}
-    metadata['contact'] = []
-
-    with open(metafile, encoding="utf8") as f:
-        lines = f.readlines()
-
-    lines = [l.strip() for l in lines]
-    lines = [l for l in lines if l and not l.startswith("%")]
-    text = "".join(lines).replace("%", "")
-
-    for meta in NEWCOMAND_RE.findall(text):
-
-        m_typeno, m_val = ARGUMENT_RE.findall(meta)
-        m_type = next(
-            iter(t for t in meta_types if m_typeno.startswith(t)), None
-        )
-        if not m_type:
-            continue
-        elif m_type in [r"\pubemail", r"\contribution"]:
-            metadata[meta_types[m_type]].append(m_val[-1].lower())
-        elif m_type == r"\pubtitle":
-            metadata[meta_types[m_type]] = m_val
-        elif m_type == r"\pubaffil":
-            metadata[meta_types[m_type]][m_no] = m_val.replace(" ",
-                                                               "").split(",")
-        else:
-            m_no = m_typeno[-1].lower()
-            metadata[meta_types[m_type]][m_no] = m_val
-
-    return metadata
-
-
-def write_meta(meta, metafile):
-
-    with open("templates/pandoc/meta-base.yaml", encoding="utf8") as f:
-        base = f.read()
-
-    with open(metafile, 'w', encoding='utf8') as f:
-        f.write("---\n")
-        f.write(f"title: \"{meta['title']}\"\n")
-        f.write("author:\n")
-        for a in meta['author']:
-            f.write(f"  - {meta['author'][a]}:\n")
-            f.write("      institute:\n")
-            for aff in meta['affil'][a]:
-                f.write(f"        - {aff}\n")
-            if meta['orcid'].get(a, None):
-                f.write(f"      orcid: {meta['orcid'][a]}\n")
-            if meta['email'].get(a, None):
-                f.write(f"      email: {meta['email'][a]}\n")
-            if a in meta['contact']:
-                f.write("      correspondence: \"yes\"\n")
-            if a in meta['contribution']:
-                f.write("      equal_contributor: \"yes\"\n")
-
-        f.write("institute:\n")
-        for i in meta['institute']:
-            f.write(f"  - {i}:\n")
-            f.write(f"      name: {meta['institute'][i]}\n")
-        f.write(base)
-        f.write("\n---\n")
-
-
-if __name__ == "__main__":
-
-    parser = argparse.ArgumentParser(description='Write metadata files.')
-    parser.add_argument(
-        '--tex',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'templates' /
-        'metadata.tex'
-    )
-    parser.add_argument(
-        '--yaml',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'templates' /
-        'metadata-pd.yaml'
-    )
-    args = parser.parse_args()
-    meta = read_meta(args.tex)
-    write_meta(meta, args.yaml)

example/assets/pd-ref-filter.lua

@@ -1,54 +0,0 @@
--- Generate string
-local function split_prepend_ref(inputstr)
-  local t = '['
-  for str in inputstr:gmatch('([^,]+)') do
-    if t ~= '[' then
-      t = t..';'
-    end
-    t = t..'@'..str:gsub('^%s*', ''):gsub('%s*$', '')
-  end
-  t = t..']'
-  return t
-end
-
-if FORMAT:match 'markdown' then
-  function Link(elem)
-    if elem.attributes.reference then
-        return pandoc.RawInline('markdown', split_prepend_ref(elem.attributes.reference))
-        -- return pandoc.RawInline('markdown', '{+@' ..elem.attributes.reference .. '}')
-    else
-        return elem
-    end
-  end
-end
-
-if FORMAT:match 'markdown' then
-  function Math(elem)
-    if elem.mathtype == "DisplayMath" then
-      if elem.text:find("\\label") then
-        for label in elem.text:gmatch("\\label{(.-)}") do
-          elem.text = elem.text:gsub("\\label{"..label.."}", "")
-          return pandoc.RawInline('markdown', "$$"..elem.text.."$$".." {#"..label.."}")
-        end
-      end
-    end
-    -- tprint(elem, 4)
-  end
-end
-
--- Print contents of `tbl`, with indentation.
--- `indent` sets the initial level of indentation.
-function tprint(tbl, indent)
-  if not indent then indent = 0 end
-  for k, v in pairs(tbl) do
-    formatting = string.rep("  ", indent) .. k .. ": "
-    if type(v) == "table" then
-      print(formatting)
-      tprint(v, indent+1)
-    elseif type(v) == 'boolean' then
-      print(formatting .. tostring(v))      
-    else
-      print(formatting .. v)
-    end
-  end
-end

example/assets/submit-clean.py

@@ -1,28 +0,0 @@
-"""Clean processed folder.
-
-Usage: clean [--output_dir=<output_dir>] [<directory>]
-"""
-
-import argparse
-import pathlib
-import shutil
-import os
-
-
-def main(source_dir):
-    if source_dir.exists():
-        shutil.rmtree(source_dir)
-    zip_path = source_dir.parent / "manuscript.zip"
-    if zip_path.exists():
-        os.remove(zip_path)
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='Clean processed folder.')
-    parser.add_argument(
-        '--dir',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'condensed'
-    )
-    args = parser.parse_args()
-    main(args.dir)

example/assets/submit-condense.py

@@ -1,311 +0,0 @@
-"""Condense manuscript into single files, often preferred by journals.
-
-Usage: condense [--output_dir=<output_dir>] [<directory>]
-"""
-
-import argparse
-import pathlib
-import shutil
-import re
-
-STYLE_RE = re.compile(r"\\def\\style{\d}\s")  # style statement + newline
-INPUT_RE = re.compile(r"\\input{.*}")  # an input statement
-ARGUMENT_RE = re.compile(r"(?<={)[\s\S]*(?=})")  # any latex argument
-IF_RE = re.compile(r"\\if[^def][\s\S]*?\\fi")  # any if/fi section not ifdef
-ELSE_RE = re.compile(r"\\else[\s\S]*?\\fi")  # any else/fi section
-IF_ARG_RE = re.compile(r"(?<=\\if\\style)\d")  # the style if comparator
-IF_ARG_STRIP = re.compile(r"\\if\\\w*\s*|\\fi")  # the if/fi edges
-ELSE_ARG_STRIP = re.compile(r"\\else|\\fi")  # the else/fi edges
-META_RE = re.compile(r"% !TEX .*")  # tex meta commands
-
-IFDEF_RE = re.compile(r"\\ifdef")  # any ifdefined/fi section
-NEWCOMM_RE = re.compile(r"\\newcommand")  # any ifdefined/fi section
-
-style_d = {
-    '0': 'pi',
-    '1': 'els',
-    '2': 'rsc',
-    '3': 'acs',
-}
-
-
-def check(directory, filename):
-    for path in directory.iterdir():
-        if path.name == filename:
-            return True
-    return False
-
-
-def get_style(text):
-    """Figure out style, then remove from file."""
-    style_match = STYLE_RE.search(text)
-    if not style_match:
-        return None, text
-    style = ARGUMENT_RE.search(style_match.group()).group()
-    text = STYLE_RE.sub("", text)
-
-    return style, text
-
-
-def find_close_bracket(string):
-    """finds the closing of a scope, taking into account nesting"""
-    nest = 1
-    for ind, char in enumerate(string):
-        if char == '{':
-            nest += 1
-        elif char == '}':
-            nest -= 1
-        if nest == 0:
-            return ind
-
-
-def sort_style_ifs(text, style):
-    r"""
-    Deal with any if/else/fi flags.
-    The if/else types to replace are only '\if\style'
-    """
-    def repl_ifs(if_section):
-        if_text = if_section.group()
-        if_style = IF_ARG_RE.search(if_text)  # find if in group
-        if not if_style:
-            raise Exception(if_text)
-        else_match = ELSE_RE.search(if_text)
-        if else_match:
-            if_text = if_text[0:else_match.start()]
-            else_text = else_match.group()
-        if style == if_style.group():
-            return IF_ARG_STRIP.sub("", if_text)
-        else:
-            if else_match:
-                return ELSE_ARG_STRIP.sub("", else_text)
-            return ""
-
-    return IF_RE.sub(repl_ifs, text)
-
-
-def sort_other_ifs(text):
-    r"""
-    Deal with other if flags.
-    # The types to replace are either \ifdef or \if@switch
-    """
-    def repl_ifswitch(if_section):
-        if_text = if_section.group()
-        if if_text.startswith("\\if@switch"):
-            if text.startswith("% Master SI"):
-                return ""
-            else_match = ELSE_RE.search(if_text)
-            if_text = if_text[0:else_match.start()]
-            else_text = else_match.group()
-            return ELSE_ARG_STRIP.sub("", else_text)
-        else:
-            raise Exception
-
-    text = IF_RE.sub(repl_ifswitch, text)
-
-    hit = IFDEF_RE.search(text)
-    while hit:
-        arg1_o = hit.end() + 1
-        arg1_e = arg1_o + find_close_bracket(text[arg1_o:])
-        arg2_o = arg1_e + 2
-        arg2_e = arg2_o + find_close_bracket(text[arg2_o:])
-        arg3_o = arg2_e + 2
-        arg3_e = arg3_o + find_close_bracket(text[arg3_o:])
-
-        if text.find(f"\\newcommand{{{text[arg1_o:arg1_e]}}}") != -1:
-            text = text[:hit.start()] + text[arg2_o:arg2_e] + text[arg3_e + 1:]
-        else:
-            text = text[:hit.start()] + text[arg3_o:arg3_e] + text[arg3_e + 1:]
-        hit = IFDEF_RE.search(text)
-
-    return text
-
-
-def expand(text):
-    def repl_input(inp_section):
-
-        input_text = inp_section.group()
-        filename = ARGUMENT_RE.search(input_text)
-        if not filename:
-            raise Exception
-        filepath = pathlib.Path("./" + filename.group() + '.tex')
-        with open(filepath, 'r', encoding="utf-8") as file:
-            return file.read()
-
-    return INPUT_RE.subn(repl_input, text)
-
-
-def expand_meta(text):
-
-    replaced = [
-        r'\pubauth',
-        r'\pubaffil',
-        r'\pubaddr',
-        r'\orcid',
-        r'\pubkeywords',
-        r'\pubSI',
-        r'\pubtitle',
-        r'\dg',
-        r'\eqcontrib',
-        r'\authemail',
-        r'\pubemail',
-    ]
-
-    for r in replaced:
-        replaced_vals = []
-        for hit in NEWCOMM_RE.finditer(text):
-            arg1_o = hit.end() + 1
-            arg1_e = arg1_o + find_close_bracket(text[arg1_o:])
-            if text[arg1_e + 1] == "{":
-                arg2_o = arg1_e + 2
-                arg2_e = arg2_o + find_close_bracket(text[arg2_o:])
-
-            command = text[arg1_o:arg1_e]
-            value = text[arg2_o:arg2_e]
-
-            if command.startswith(r):
-                replaced_vals.append([command, value, hit.start(), arg2_e + 1])
-
-        text = ''.join([
-            chr for idx, chr in enumerate(text, 1) if not any(
-                strt_idx <= idx <= end_idx
-                for _, _, strt_idx, end_idx in replaced_vals
-            )
-        ])
-        for val in replaced_vals:
-            text = text.replace(val[0], val[1])
-
-    return text
-
-
-def clean(text, style):
-
-    # remove meta commands
-    text = META_RE.sub("", text)
-
-    # remove advanced tex lines
-    text = re.sub(r"\\makeatletter", r'', text)
-    text = re.sub(r"\\makeatother", r'', text)
-
-    # pandoc unnecessary commands
-    text = text.replace(
-        r"\newenvironment{widefigure}{\begin{figure*}}{\end{figure*}}", ""
-    )
-    text = text.replace("widefigure", "figure*")
-    text = text.replace(
-        r"\newenvironment{widetable}{\begin{table*}}{\end{table*}}", ""
-    )
-    text = text.replace("widetable", "table*")
-
-    # remove comment lines
-    text = re.sub(r'(?<!\\)%.*', r'', text)
-
-    # remove superfluous newlines
-    text = re.sub(r'\n\s*\n', r'\n\n', text)
-
-    # update references
-    text = re.sub(r"(?<=\\bibliography{)refs/biblio(?=})", r'biblio', text)
-
-    if style == '0' or style is None:
-        text = re.sub(r"templates/pi/", r'', text)
-    elif style == '2':
-        text = re.sub(r"templates/rsc/", r'', text)
-
-    return text
-
-
-def process_tex(target):
-    """Process a tex file to return it to a simple 'one file' format."""
-    with target.open() as file:
-
-        # get file contents
-        filetext = file.read()
-
-        # get style
-        style, filetext = get_style(filetext)
-
-        # style if/else processing
-        if style:
-            filetext = sort_style_ifs(filetext, style)
-
-        # input expansion
-        expansions = 1
-        while expansions > 0:
-            filetext, expansions = expand(filetext)
-
-        # second if/else processing
-        filetext = sort_other_ifs(filetext)
-
-        # replace metadata commands
-        filetext = expand_meta(filetext)
-
-        # cleaning
-        filetext = clean(filetext, style)
-
-        return filetext, style
-
-
-def copy_files(source, target, style):
-    shutil.copy((source / 'refs' / 'biblio.bib'), (target / 'biblio.bib'))
-    shutil.copy((source / 'manuscript-SI.aux'), (target / 'manuscript-SI.aux'))
-    shutil.copy((source / 'manuscript-SI.pdf'), (target / 'manuscript-SI.pdf'))
-    shutil.copytree((source / 'figs'), (target / 'figs'),
-                    ignore=shutil.ignore_patterns('*.md', '*.txt'))
-    if style == '0':
-        shutil.copy((source / 'templates' / 'pi' / 'pi-article.cls'),
-                    (target / 'pi-article.cls'))
-        shutil.copy((source / 'templates' / 'pi' / 'pi-bib.bst'),
-                    (target / 'pi-bib.bst'))
-    elif style == '2':
-        shutil.copy((source / 'templates' / 'rsc' / 'rsc.bst'),
-                    (target / 'rsc.bst'))
-        shutil.copytree((source / 'templates' / 'rsc' / 'head_foot'),
-                        (target / 'head_foot'))
-
-
-def main(source_dir, output_dir='./condensed/'):
-
-    # define source and output dirs
-    source_dir = pathlib.Path(source_dir)
-    output_dir = pathlib.Path(output_dir)
-
-    # create and clean output dir
-    if output_dir.exists():
-        shutil.rmtree(output_dir)
-    output_dir.mkdir(parents=True, exist_ok=True)
-
-    # the manuscript style (own, RCS, etc)
-    man_style = None
-
-    # condense the manuscript files
-    files = [
-        'manuscript.tex',
-        'manuscript-SI.tex',
-    ]
-    for filename in files:
-        if check(source_dir, filename):
-            target_in = source_dir / filename
-            target_out = output_dir / filename
-            processed, style = process_tex(target_in)
-            if style:
-                man_style = style
-            with open(target_out, "w", encoding="utf-8") as file:
-                file.write(processed)
-
-    # copy over other required data
-    copy_files(source_dir, output_dir, man_style)
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(
-        description='Condense manuscript to a single file.'
-    )
-    parser.add_argument(
-        '--source', type=str, default=pathlib.Path(__file__).parent.parent
-    )
-    parser.add_argument(
-        '--dest',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'condensed'
-    )
-    args = parser.parse_args()
-    main(args.source, args.dest)

example/assets/submit-zip.py

@@ -1,68 +0,0 @@
-"""Zip manuscript folder.
-
-Usage: zip [--source=<output_dir>] [--dest=<destination_dir>]
-"""
-
-import argparse
-import pathlib
-import shutil
-
-EXCLUDE_EXTS = (
-    '*.pdf',
-    '*.gz',
-    '*.aux',
-    '*.bbl',
-    '*.blg',
-    '*.fdb_latexmk',
-    '*.fls',
-    '*.log',
-    '*.out',
-)
-
-
-def clean(source_dir):
-
-    source_temp = source_dir.parent / 'condensed_temp'
-    if source_temp.exists():
-        shutil.rmtree(source_temp)
-
-    # create temp files
-    shutil.copytree(
-        source_dir, source_temp, ignore=shutil.ignore_patterns(*EXCLUDE_EXTS)
-    )
-    shutil.copy(
-        source_dir / "manuscript-SI.aux", source_temp / "manuscript-SI.aux"
-    )
-
-    return source_temp
-
-
-def main(source_dir, output_file='./manuscript'):
-
-    source_dir = pathlib.Path(source_dir)
-
-    # clean from source dir
-    cleaned_source_dir = clean(source_dir)
-
-    # archive source dir
-    shutil.make_archive(output_file, format='zip', root_dir=cleaned_source_dir)
-
-    # delete temp files
-    shutil.rmtree(cleaned_source_dir)
-
-
-if __name__ == "__main__":
-    parser = argparse.ArgumentParser(description='Zip submission files.')
-    parser.add_argument(
-        '--source',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'condensed'
-    )
-    parser.add_argument(
-        '--dest',
-        type=str,
-        default=pathlib.Path(__file__).parent.parent / 'condensed' /
-        'manuscript'
-    )
-    args = parser.parse_args()
-    main(args.source, args.dest)

example/blank_article.md

@@ -71,7 +71,7 @@ Table: A table legend; values are mean ± SD Markdown
 
 \clearpage
 
-![Figure caption.](img/figure1.png){ width=16cm }
+![Figure caption.](assets/example-image.png){ width=16cm }
 
 \clearpage
 

example/blank_article.yaml

@@ -0,0 +1,32 @@
+---
+# References and Reference Style
+csl: assets/journal-of-neurophysiology.csl
+bibliography: assets/references.bib
+citeproc: true # required in pandoc 2.14
+
+# Names of Input and Output Files
+input-file: blank_article.md
+output-file: blank_article.pdf  # Change to .docx to make a Word file
+
+# Addition to LaTeX Template
+include-in-header: tex_templates/header.tex # Change margin and line spacing
+include-before-body: tex_templates/before_body.tex
+include-after-body: tex_templates/after_body.tex
+
+# LaTeX Specifications
+pdf-engine: xelatex
+variables:
+  documentclass: article
+  mainfont: "DejaVu Serif"
+  sansfont: Ubuntu
+  classoption:
+    - 10pt # 11pt, 12pt
+
+# To have numbered sections, uncomment the following line.
+# But we don't want our Title or Abstract to be numbered,
+# so we will add {.unnumbered} next to our Title and Abstract
+# headers, separated by one space.
+# Example: # Abstract {.unnumbered}
+
+number-sections: false
+...