Update

foss-2018b/ELIC-0.1-foss-2018b-Python-2.7.15.eb

@@ -47,7 +47,8 @@ exts_classmap = {
     'satellite': 'RPackage',
     'sf': 'RPackage',
     'svglite': 'RPackage',
-    'mapview': 'RPackage'
+    'mapview': 'RPackage',
+    'MuMIn': 'RPackage'
 }
 exts_list = [
     # Python deps, order is important!
@@ -420,6 +421,14 @@ exts_list = [
             'http://cran.freestatistics.org/src/contrib',
         ],
     }),
+    ('MuMIn', '1.43.6', {
+        'source_tmpl': '%(name)s_%(version)s.tar.gz',
+        'source_urls': [
+            'http://cran.r-project.org/src/contrib/Archive/MuMIn',
+            'http://cran.r-project.org/src/contrib/',
+            'http://cran.freestatistics.org/src/contrib',
+        ],
+    }),
 ]
 
 sanity_check_paths = {

foss-2018b/ELIC-0.1-foss-2018b-Python-3.6.6.eb

@@ -30,6 +30,7 @@ dependencies = [
     ('netCDF', '4.6.1'),
     ('GDAL', '2.2.3', versionsuffix),
     ('GTK+', '3.24.7', versionsuffix),
+    ('matplotlib', '3.0.3', versionsuffix),
     ('PyGObject', '3.28.3', versionsuffix),
     ('ecCodes', '2.8.2'),
     ('libmo_unpack', '3.1.2'),
@@ -48,7 +49,8 @@ exts_classmap = {
     'satellite': 'RPackage',
     'sf': 'RPackage',
     'svglite': 'RPackage',
-    'mapview': 'RPackage'
+    'mapview': 'RPackage',
+    'MuMIn': 'RPackage'
 }
 exts_list = [
     # Python deps, order is important!
@@ -113,10 +115,26 @@ exts_list = [
     ('dask', '1.1.4', {
         'source_urls': ['https://pypi.python.org/packages/source/d/dask/'],
     }),
-    ('PyKE', '1.1.1', {
-        'source_tmpl': 'pyke-1.1.1.zip',
-        'source_urls': ['http://download.sourceforge.net/pyke'],
-        'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'],
+    ('astropy', '3.1.2', {
+        'modulename': 'astropy',
+        'source_urls': ['https://pypi.python.org/packages/source/a/astropy/'],
+    }),
+    ('oktopus', '0.1.2', {
+        'modulename': 'oktopus',
+        'source_urls': ['https://pypi.python.org/packages/source/o/oktopus/'],
+    }),
+    ('bs4', '0.0.1', {
+        'modulename': 'bs4',
+        'source_urls': ['https://pypi.python.org/packages/source/b/bs4/'],
+    }),
+    ('tqdm', '4.31.1', {
+        'modulename': 'tqdm',
+        'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'],
+    }),
+    ('PyKE', '3.1.0', {
+        'modulename': 'pyke',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/KeplerGO/pyke/archive/'],
     }),
     ('cf-units', '2.1.1', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'],
@@ -150,25 +168,10 @@ exts_list = [
     ('tornado', '5.1.1', {
         'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'],
     }),
-    ('matplotlib', '2.2.4', {
-        'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'],
-    }),
     ('toolz', '0.9.0', {
         'source_urls': ['https://pypi.python.org/packages/source/t/toolz/'],
         'checksums': ['929f0a7ea7f61c178bd951bdae93920515d3fbdbafc8e6caf82d752b9b3b31c9'],
     }),
-    ('basemap', '1.1.0', {
-        'modulename': 'mpl_toolkits.basemap',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/matplotlib/basemap/archive'],
-        'checksums': ['6acdc3a08bfcebf0a1b52a05d73d51b7aa5e7240fedfa95537c92d16f2ef8778'],
-    }),
-    #('scitools-iris', '2.2.0', {
-    #    'modulename': 'iris',
-    #    'source_tmpl': 'v%(version)s.tar.gz',
-    #    'source_urls': ['https://github.com/SciTools/iris/archive/'],
-    #    'checksums': ['e4b52e43da16b72af9ccbcb4d53bc401'],
-    #}),
     ('patsy', '0.5.0', {
         'source_urls': ['https://pypi.python.org/packages/source/p/patsy/'],
         'checksums': ['e05f38d5c38c8d216f0cc2b765b1069b433c92d628b954fb2fee68d13e42883b'],
@@ -353,15 +356,30 @@ exts_list = [
         'modulename': 'skimage',
         'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image/'],
     }),
-    ################################
-    ('futures', '3.2.0', {
-        'modulename': '__future__',
-        'source_urls': ['https://pypi.python.org/packages/source/f/futures/'],
-    }),
     ('PyNaCl', '1.3.0', {
         'modulename': 'nacl',
         'source_urls': ['https://pypi.python.org/packages/source/p/PyNaCl/'],
     }),
+    ('descartes', '1.1.0', {
+        'modulename': 'descartes',
+        'source_urls': ['https://pypi.python.org/packages/source/d/descartes/'],
+        'checksums': ['135a502146af5ed6ff359975e2ebc5fa4b71b5432c355c2cafdc6dea1337035b'],
+    }),
+    ('salem', '0.2.4', {
+        'modulename': 'salem',
+        'source_urls': ['https://pypi.python.org/packages/source/s/salem/'],
+        'checksums': ['f29594c31124b9f1198ba3361850d57e180e3ea228bebe08080760195b96558c'],
+    }),
+    ('graphviz', '0.10.1', {
+        'modulename': 'graphviz',
+        'source_tmpl': '%(version)s.tar.gz',
+        'source_urls': ['https://github.com/xflr6/graphviz/archive/'],
+    }),
+    ('basemap', '1.2.0rel', {
+        'modulename': 'mpl_toolkits.basemap',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/matplotlib/basemap/archive'],
+    }),
     ################################
     # R extension
     ('ncdf4', '1.16', {
@@ -421,6 +439,14 @@ exts_list = [
             'http://cran.freestatistics.org/src/contrib',
         ],
     }),
+    ('MuMIn', '1.43.6', {
+        'source_tmpl': '%(name)s_%(version)s.tar.gz',
+        'source_urls': [
+            'http://cran.r-project.org/src/contrib/Archive/MuMIn',
+            'http://cran.r-project.org/src/contrib/',
+            'http://cran.freestatistics.org/src/contrib',
+        ],
+    }),
 ]
 
 sanity_check_paths = {

foss-2018b/ELIC-0.2-foss-2018b-Python-3.6.6.eb

@@ -23,264 +23,56 @@ exts_default_options = {
     'source_tmpl': '%(name)s-%(version)s.tar.gz',
 }
 
-exts_classmap = {
-    'ncdf4': 'RPackage',
-    'gdtools': 'RPackage',
-    'leaflet': 'RPackage',
-    'satellite': 'RPackage',
-    'sf': 'RPackage',
-    'svglite': 'RPackage',
-    'mapview': 'RPackage'
-}
+#exts_classmap = {
+#    'sf': 'RPackage',
+#}
 exts_list = [
     # Python deps, order is important!
-    ('matplotlib', '3.0.3', {
-        'modulename': 'matplotlib',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/matplotlib/matplotlib/archive/'],
-    }),
-    ('astropy', '3.1.2', {
-        'modulename': 'skimage',
-        'source_urls': ['https://pypi.python.org/packages/source/a/astropy/'],
-    }),
-    ('oktopus', '0.1.2', {
-        'modulename': 'skimage',
-        'source_urls': ['https://pypi.python.org/packages/source/o/oktopus/'],
-    }),
-    ('bs4', '0.0.1', {
-        'modulename': 'skimage',
-        'source_urls': ['https://pypi.python.org/packages/source/b/bs4/'],
-    }),
-    ('tqdm', '4.31.1', {
-        'modulename': 'skimage',
-        'source_urls': ['https://pypi.python.org/packages/source/t/tqdm/'],
-    }),
-    ('PyKE', '3.1.0', {
-        'modulename': 'pyke',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/KeplerGO/pyke/archive/'],
+    #('traitlets', '4.3.2', {
+    #    'modulename': 'traitlets',
+    #    'source_urls': ['https://pypi.python.org/packages/source/t/traitlets/'],
+    #}),
+    #('Pygments', '2.3.1', {
+    #    'modulename': 'Pygments',
+    #    'source_urls': ['https://pypi.python.org/packages/source/p/pygments/'],
+    #}),
+    #('ipython', '7.4.0', {
+    #    'modulename': 'IPython',
+    #    'source_urls': ['https://pypi.python.org/packages/source/i/ipython/'],
+    #    'checksums': ['b038baa489c38f6d853a3cfc4c635b0cda66f2864d136fe8f40c1a6e334e2a6b'],
+    #}),
+    ('typelib', '0.0.10', {
+        'modulename': 'typelib',
+        'source_urls': ['https://pypi.python.org/packages/source/t/typelib/'],
     }),
+    ################################
     ('scitools-iris', '2.2.0', {
         'modulename': 'iris',
         'source_tmpl': 'v%(version)s.tar.gz',
         'source_urls': ['https://github.com/SciTools/iris/archive/'],
         'checksums': ['e4b52e43da16b72af9ccbcb4d53bc401'],
     }),
-    ('basemap', '1.2.0rel', {
-        'modulename': 'mpl_toolkits.basemap',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/matplotlib/basemap/archive'],
-    }),
-    ###############################################################"
-    ('scipy', '1.2.1', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/scipy/'],
-    }),            
-    ('six', '1.12.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/six/'],
-    }),
-    ('virtualenv', '16.4.3', {
-        'source_urls': ['https://pypi.python.org/packages/source/x/virtualenv/'],
-    }),
-    ('xlrd', '1.2.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/x/xlrd/'],
-    }),
-    ('affine', '2.2.2', {
-        'source_urls': ['https://pypi.python.org/packages/source/a/affine/'],
-    }),          
-    ('atomicwrites', '1.3.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/a/atomicwrites/'],
-    }),
-    ('boto3', '1.9.116', {
-        'source_urls': ['https://pypi.python.org/packages/source/b/boto3/'],
-    }),
-    ('botocore', '1.12.116', {
-        'source_urls': ['https://pypi.python.org/packages/source/b/botocore/'],
-    }),          
-    ('bottleneck', '1.2.1', {
-        'modulename': 'bottleneck',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/kwgoodman/bottleneck/archive/'],
-    }),
-     ('click', '7.0', {
-        'modulename': 'click',
-        'source_tmpl': '%(version)s.tar.gz',
-        'source_urls': ['https://github.com/pallets/click/archive/'],
-    }),      
-    ('click-plugins', '1.0.4', {
-        'source_urls': ['https://pypi.python.org/packages/source/c/click-plugins/'],
-    }),
-    ('cligj', '0.5.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/c/cligj/'],
-    }),          
-    ('cloudpickle', '0.8.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/c/cloudpickle/'],
-    }),
-    ('configobj', '5.0.6', {
-        'source_urls': ['https://pypi.python.org/packages/source/c/configobj/'],
-    }), 
-    ('docutils', '0.14', {
-        'source_urls': ['https://pypi.python.org/packages/source/d/docutils/'],
-    }),          
-    ('fiona', '1.8.6', {
-        'modulename': 'fiona',
-        'source_tmpl': '%(version)s.tar.gz',
-        'source_urls': ['https://github.com/Toblerity/Fiona/archive/'],
-    }),
-    ('geopandas', '0.4.1', {
-        'source_urls': ['https://pypi.python.org/packages/source/g/geopandas/'],
-    }),
-    ('jmespath', '0.9.4', {
-        'source_urls': ['https://pypi.python.org/packages/source/j/jmespath/'],
-    }),          
-    ('more-itertools', '5.0.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/m/more-itertools/'],
-    }),
-    ('motionless', '1.3.2', {
-        'source_urls': ['https://pypi.python.org/packages/source/m/motionless/'],
-    }),     
-    ('munch', '2.3.2', {
-        'source_urls': ['https://pypi.python.org/packages/source/m/munch/'],
-    }),
-    ('networkx', '2.2', {
-        'modulename': 'networkx',
-        'source_tmpl': 'networkx-%(version)s.tar.gz',
-        'source_urls': ['https://github.com/networkx/networkx/archive/'],
-    }),          
-    ('pathlib2', '2.3.3', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/pathlib2/'],
-    }),
-    ('pluggy', '0.9.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/pluggy/'],
-    }),   
-    ('py', '1.8.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/py/'],
-    }),           
-    ('pytest', '4.3.1', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/pytest/'],
-    }),   
-    ('python-utils', '2.3.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/p/python-utils/'],
-    }),
-    ('rasterio', '1.0.21', {
-        'source_urls': ['https://pypi.python.org/packages/source/r/rasterio/'],
-    }), 
-    ('s3transfer', '0.2.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/s3transfer/'],
-    }),   
-    ('scandir', '1.10.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/scandir/'],
-    }),
-    ('snuggs', '1.4.3', {
-        'source_urls': ['https://pypi.python.org/packages/source/s/snuggs/'],
-    }),
-    ('xarray', '0.11.3', {
-        'source_urls': ['https://pypi.python.org/packages/source/x/xarray/'],
-    }),
-    ('py-expression-eval', '0.3.6', {
-        'modulename': 'py_expression_eval',
-        'source_tmpl': 'v%(version)s.tar.gz',
-        'source_urls': ['https://github.com/Axiacore/py-expression-eval/archive/'],
-    }),
-    ('PyWavelets', '1.0.2', {
-        'modulename': 'pywt',
-        'source_urls': ['https://pypi.python.org/packages/source/p/PyWavelets/'],
-    }),
-    ('attrs', '19.1.0', {
-        'modulename': 'attr',
-        'source_urls': ['https://pypi.python.org/packages/source/a/attrs/'],
-    }),
-    ('progressbar2', '3.39.3', {
-        'modulename': 'progressbar',
-        'source_urls': ['https://pypi.python.org/packages/source/p/progressbar2/'],
-    }),
-    ('scikit-image', '0.14.2', {
-        'modulename': 'skimage',
-        'source_urls': ['https://pypi.python.org/packages/source/s/scikit-image/'],
-    }),
-    ################################
-    ('futures', '3.2.0', {
-        'modulename': '__future__',
-        'source_urls': ['https://pypi.python.org/packages/source/f/futures/'],
-    }),
-    ('PyNaCl', '1.3.0', {
-        'modulename': 'nacl',
-        'source_urls': ['https://pypi.python.org/packages/source/p/PyNaCl/'],
-    }),
     ################################
     # R extension
-    ('ncdf4', '1.16', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/ncdf4',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-        'checksums': ['edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253'],
-    }),
-    ('gdtools', '0.1.7', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/gdtools',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
-    ('leaflet', '2.0.2', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/leaflet',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
-    ('satellite', '1.0.1', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/satellite',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
-    ('sf', '0.7-3', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/sf',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
-    ('svglite', '1.2.1', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/svglite',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
-    ('mapview', '2.6.3', {
-        'source_tmpl': '%(name)s_%(version)s.tar.gz',
-        'source_urls': [
-            'http://cran.r-project.org/src/contrib/Archive/mapview',
-            'http://cran.r-project.org/src/contrib/',
-            'http://cran.freestatistics.org/src/contrib',
-        ],
-    }),
+    #('sf', '0.7-3', {
+    #    'source_tmpl': '%(name)s_%(version)s.tar.gz',
+    #    'source_urls': [
+    #        'http://cran.r-project.org/src/contrib/Archive/sf',
+    #        'http://cran.r-project.org/src/contrib/',
+    #        'http://cran.freestatistics.org/src/contrib',
+    #    ],
+    #}),
 ]
 
-sanity_check_paths = {
-    'files': ['sf/libs/sf.so'],
-    'dirs': [],
-}
-
-postinstallcmds = [
-    "cd %(installdir)s/bin && " +
-    'chmod 755 pip'
-]
+#sanity_check_paths = {
+#    'files': ['sf/libs/sf.so'],
+#    'dirs': [],
+#}
 
 modextrapaths = {
     'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
     'PYTHONUSERBASE': '',
-    'R_LIBS': '',
+    #'R_LIBS': '',
 }
 
 moduleclass = 'numlib'

foss-2018b/matplotlib-3.0.3-foss-2018b-Python-3.6.6.eb

@@ -0,0 +1,63 @@
+easyblock = 'Bundle'
+
+name = 'matplotlib'
+version = '3.0.3'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://matplotlib.org'
+description = """matplotlib is a python 2D plotting library which produces publication quality figures in a variety of
+ hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python
+ and ipython shell, web application servers, and six graphical user interface toolkits."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+exts_default_options = {
+    'download_dep_fail': True,
+    'use_pip': True,
+}
+
+builddependencies = [
+    ('pkg-config', '0.29.2'),
+]
+
+dependencies = [
+    ('Python', '3.6.6'),
+    ('libpng', '1.6.34'),
+    ('freetype', '2.9.1'),
+    ('Tkinter', '%(pyver)s', versionsuffix),
+]
+
+exts_list = [
+    ('Cycler', '0.10.0', {
+        'modulename': 'cycler',
+        'source_tmpl': 'cycler-%(version)s.tar.gz',
+        'source_urls': ['https://pypi.python.org/packages/source/C/Cycler'],
+        'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'],
+    }),
+    ('kiwisolver', '1.0.1', {
+        'source_urls': ['https://pypi.python.org/packages/source/k/kiwisolver'],
+        'checksums': ['ce3be5d520b4d2c3e5eeb4cd2ef62b9b9ab8ac6b6fedbaa0e39cdb6f50644278'],
+    }),
+    (name, version, {
+        'prebuildopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'preinstallopts': "export CPLUS_INCLUDE_PATH=$EBROOTFREETYPE/include/freetype2:${CPLUS_INCLUDE_PATH} && ",
+        'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib'],
+        'checksums': ['e1d33589e32f482d0a7d1957bf473d43341115d40d33f578dad44432e47df7b7'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': [],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+sanity_check_commands = ["""python -c 'import matplotlib; matplotlib.use("TkAgg"); import matplotlib.pyplot' """]
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+# see https://matplotlib.org/tutorials/introductory/usage.html#what-is-a-backend
+modextravars = {'MPLBACKEND': 'TkAgg'}
+
+moduleclass = 'vis'