ESMValTools

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

@@ -30,6 +30,7 @@ dependencies = [
     ('PyGTK', '2.24.0', versionsuffix),
     ('ecCodes', '2.8.2'),
     ('libmo_unpack', '3.1.2'),
+    ('numba', '0.43.0', versionsuffix),
 ]
 
 exts_defaultclass = 'PythonPackage'
@@ -117,15 +118,20 @@ exts_list = [
     ('pyugrid', '0.3.1', {
         'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'],
         'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'],
-    }), 
+    }),
+    ('mo_pack', '0.2.0', {
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/SciTools/mo_pack/archive/'],
+        'checksums': ['4aa70e1f846b666670843bc2514435dedf7393203e88abaf74d48f8f2717a726'],
+    }),
     ('cycler', '0.10.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cycler/'],
         'checksums': ['cd7b2d1018258d7247a71425e9f26463dfb444d411c39569972f4ce586b0c9d8'],
-    }), 
+    }),
     ('singledispatch', '3.4.0.3', {
         'source_urls': ['https://pypi.python.org/packages/source/s/singledispatch/'],
         'checksums': ['5b06af87df13818d14f08a028e42f566640aef80805c3b50c5056b086e3c2b9c'],
-    }), 
+    }),
     ('backports_abc', '0.5', {
         'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'],
         'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'],
@@ -152,7 +158,34 @@ exts_list = [
         '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'],
+    }),
+    ('statsmodels', '0.9.0', {
+        'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'],
+        'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'],
+    }),
+    ('nc-time-axis', '1.1.0', {
+        'modulename': 'nc_time_axis',
+        'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'],
+        'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'],
+    }),
+    ('yamale', '1.10.0', {
+        'modulename': 'yamale',
+        'source_urls': ['https://pypi.python.org/packages/source/y/yamale/'],
+    }),
+    ('stratify', '0.2', {
+        'modulename': 'stratify',
+        'source_tmpl': 'master.zip',
+        'source_urls': ['https://github.com/SciTools-incubator/python-stratify/archive/'],
+    }),
+    ('psutil', '5.6.1', {
+        'modulename': 'psutil',
+        'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'],
+        'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'],
+    }),
+    ################################
     ################################
     # R extension
     ('ncdf4', '1.16', {

foss-2018b/ESMValTool-2.0a1-foss-2018b-Python-2.7.15.eb

@@ -31,10 +31,14 @@ dependencies = [
     ('PROJ', '5.0.0'),
     ('netCDF', '4.6.1'),
     ('GDAL', '2.2.3', versionsuffix),
-    ('libmo_unpack', '3.1.2'),
+    ('PyGTK', '2.24.0', versionsuffix),
     ('ecCodes', '2.8.2'),
+    ('libmo_unpack', '3.1.2'),
+    ('numba', '0.43.0', versionsuffix),
 ]
 
+exts_download_dep_fail = True
+
 exts_defaultclass = 'PythonPackage'
 exts_default_options = {
     'source_tmpl': '%(name)s-%(version)s.tar.gz',
@@ -61,36 +65,25 @@ exts_list = [
         'source_urls': ['https://pypi.python.org/packages/source/p/pyproj/'],
         'checksums': ['53fa54c8fa8a1dfcd6af4bf09ce1aae5d4d949da63b90570ac5ec849efaf3ea8'],
     }),
-    ('pyshp', '1.2.12', {
+    ('pyshp', '2.1.0', {
         'modulename': 'shapefile',
         'source_urls': ['https://pypi.python.org/packages/source/p/pyshp/'],
-        'checksums': ['8dcd65e0aa2aa2951527ddb7339ea6e69023543d8a20a73fc51e2829b9ed6179'],
     }),
     ('chardet', '3.0.4', {
         'source_urls': ['https://pypi.python.org/packages/source/c/chardet/'],
         'checksums': ['84ab92ed1c4d4f16916e05906b6b75a6c0fb5db821cc65e70cbd64a3e2a5eaae'],
     }),
-    ('urllib3', '1.22', {
+    ('urllib3', '1.24.1', {
         'source_urls': ['https://pypi.python.org/packages/source/u/urllib3/'],
-        'checksums': ['cc44da8e1145637334317feebd728bd869a35285b93cbb4cca2577da7e62db4f'],
     }),
-    ('certifi', '2018.4.16', {
+    ('certifi', '2019.3.9', {
         'source_urls': ['https://pypi.python.org/packages/source/c/certifi/'],
-        'checksums': ['13e698f54293db9f89122b0581843a782ad0934a4fe0172d2a980ba77fc61bb7'],
     }),
-    ('requests', '2.18.4', {
+    ('requests', '2.21.0', {
         'source_urls': ['https://pypi.python.org/packages/source/r/requests/'],
-        'checksums': ['9c443e7324ba5b85070c4a818ade28bfabedf16ea10206da1132edaa6dda237e'],
     }),
-    ('OWSLib', '0.16.0', {
+    ('OWSLib', '0.17.1', {
         'source_urls': ['https://pypi.python.org/packages/source/o/OWSLib/'],
-        'checksums': ['ec95a5e93c145a5d84b0074b9ea27570943486552a669151140debf08a100554'],
-    }),
-    ('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'],
     }),
     ('netCDF4', '1.3.1', {
         'modulename': 'netCDF4',
@@ -105,27 +98,28 @@ exts_list = [
         'source_urls': ['https://pypi.python.org/packages/source/c/cdo/'],
         'checksums': ['b167efbbac7d0a6cbf74f5d211255705c73245f7c2590b6d9eb634347d8b2c1f'],
     }),
-    ('Shapely', '1.6.4.post1', {
+    ('Shapely', '1.6.4.post2', {
         'source_urls': ['https://pypi.python.org/packages/source/s/Shapely/'],
-        'checksums': ['30df7572d311514802df8dc0e229d1660bc4cbdcf027a8281e79c5fc2fcf02f2'],
     }),
-    ('Cartopy', '0.16.0', {
+    ('Cartopy', '0.17.0', {
         'source_urls': ['https://pypi.python.org/packages/source/c/Cartopy/'],
-        'checksums': ['f23dffa101f43dd91e866a49ebb5f5048be2a24ab8a921a5c07edabde746d9a4'],
     }),
-    ('dask', '0.17.4', {
+    ('dask', '1.1.4', {
         'source_urls': ['https://pypi.python.org/packages/source/d/dask/'],
-        'checksums': ['c111475a3d1f8cba41c8094e1fb1831c65015390dcef0308042a11a9606a2f6d'],
     }),
     ('PyKE', '1.1.1', {
         'source_tmpl': 'pyke-1.1.1.zip',
         'source_urls': ['http://download.sourceforge.net/pyke'],
         'checksums': ['b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae'],
     }),
-    ('cf_units', '1.2.0', {
+    ('cf-units', '2.1.1', {
         'source_urls': ['https://pypi.python.org/packages/source/c/cf_units/'],
-        'checksums': ['abdd2a0937b958322f7ff7ec6866e80f08603c60aa06cef5766b6512c750028a'],
-    }),
+    }), 
+    ('cftime', '1.0.3.4rel', {
+        'modulename': 'cftime',
+        'source_tmpl': 'v%(version)s.tar.gz',
+        'source_urls': ['https://github.com/Unidata/cftime/archive/'],
+    }), 
     ('pyugrid', '0.3.1', {
         'source_urls': ['https://pypi.python.org/packages/source/p/pyugrid/'],
         'checksums': ['eddadc1e88c0e801f780b1e6f636fbfc00e3d14cdab82b43300fde0918310053'],
@@ -146,19 +140,23 @@ exts_list = [
     ('backports_abc', '0.5', {
         'source_urls': ['https://pypi.python.org/packages/source/b/backports_abc/'],
         'checksums': ['033be54514a03e255df75c5aee8f9e672f663f93abb723444caec8fe43437bde'],
-    }),
-    ('tornado', '4.5.3', {
+    }), 
+    ('tornado', '5.1.1', {
         'source_urls': ['https://pypi.python.org/packages/source/t/tornado/'],
-        'checksums': ['6d14e47eab0e15799cf3cdcc86b0b98279da68522caace2bd7ce644287685f0a'],
     }),
-    ('matplotlib', '1.5.3', {
+    ('matplotlib', '2.2.4', {
         'source_urls': ['https://pypi.python.org/packages/source/m/matplotlib/'],
-        'checksums': ['a0a5dc39f785014f2088fed2c6d2d129f0444f71afbb9c44f7bdf1b14d86ebbc'],
     }),
     ('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',
@@ -179,15 +177,25 @@ exts_list = [
         'source_urls': ['https://pypi.python.org/packages/source/s/statsmodels/'],
         'checksums': ['6461f93a842c649922c2c9a9bc9d9c4834110b89de8c4af196a791ab8f42ba3b'],
     }),
-    ('cftime', '1.0.0', {
-        'source_urls': ['https://pypi.python.org/packages/source/c/cftime/'],
-        'checksums': ['f62fe79ed2ad38f4211477e59f6f045c91278351f4ce7578e33ddf52fb121ea8'],
-    }),
     ('nc-time-axis', '1.1.0', {
         'modulename': 'nc_time_axis',
         'source_urls': ['https://pypi.python.org/packages/source/n/nc-time-axis/'],
         'checksums': ['ea9d4f7f9e9189c96f7d320235ac6c4be7f63dc5aa256b3ee5d5cca5845e6e26'],
     }),
+    ('yamale', '1.10.0', {
+        'modulename': 'yamale',
+        'source_urls': ['https://pypi.python.org/packages/source/y/yamale/'],
+    }),
+    ('stratify', '0.2', {
+        'modulename': 'stratify',
+        'source_tmpl': 'master.zip',
+        'source_urls': ['https://github.com/SciTools-incubator/python-stratify/archive/'],
+    }),
+    ('psutil', '5.6.1', {
+        'modulename': 'psutil',
+        'source_urls': ['https://pypi.python.org/packages/source/p/psutil/'],
+        'checksums': ['fa0a570e0a30b9dd618bffbece590ae15726b47f9f1eaf7518dfb35f4d7dcd21'],
+    }),
     # R extension
     ('ncdf4', '1.16', {
         'source_tmpl': '%(name)s_%(version)s.tar.gz',
@@ -200,14 +208,23 @@ exts_list = [
     }),
 ]
 
+skipsteps = ['sanitycheck']
+
+postinstallcmds = [
+    "cd %(installdir)s && " +
+    "tar xzf ESMValTool-%(version)s.tar.gz && " +
+    "cd ESMValTool-%(version)s && " +
+    'PYTHONPATH="%(installdir)s/lib/python%(pyshortver)s/site-packages":"${PYTHONPATH}" && python setup.py install --prefix=%(installdir)s && ' +
+    "cd esmvaltool  && " +
+    "cp -r cmor diag_scripts interface_scripts preprocessor recipes utils %(installdir)s/lib/python%(pyshortver)s/site-packages/ESMValTool-%(version)s-py2.7.egg/esmvaltool && " +
+    "cp config-developer.yml config-logging.yml config-references.yml config-user.yml %(installdir)s/lib/python%(pyshortver)s/site-packages/ESMValTool-%(version)s-py2.7.egg/esmvaltool && " +
+    "cd %(installdir)s && " +
+    "rm -rf ESMValTool-%(version)s ESMValTool-%(version)s.tar.gz"
+]
+
 modextrapaths = {
     'PYTHONPATH': 'lib/python%(pyshortver)s/site-packages',
     'R_LIBS': '',
 }
 
-modloadmsg = (
-    "To install ESMValTool in your directory execute: "
-    "tar zxf $EBROOTESMVALTOOL/ESMValTool-%(version)s.tar.gz\n"
-)
-
 moduleclass = 'geo'

foss-2018b/Mesa-18.1.1-foss-2018b.eb

@@ -48,7 +48,7 @@ dependencies = [
     ('zlib', '1.2.11'),
     ('nettle', '3.4'),
     ('libdrm', '2.4.92'),
-    ('LLVM', '6.0.0'),
+    ('LLVM', '7.0.0'),
     ('X11', '20180604'),
 ]
 

foss-2018b/llvmlite-0.28.0_fix-ffi-Makefile.patch

@@ -0,0 +1,13 @@
+make sure easybuild flags and libs are used for llvmlite
+March 25th 2019 by PY Barriat (ELIC - UCL)
+--- llvmlite-0.28.0/ffi/Makefile.linux.orig 2019-03-25 16:43:28.855604493 +0100
++++ llvmlite-0.28.0/ffi/Makefile.linux      2019-03-25 16:45:52.698599613 +0100
+@@ -2,7 +2,7 @@
+ CXX ?= g++
+
+ # -flto and --exclude-libs allow us to remove those parts of LLVM we don't use
+-CXX_FLTO_FLAGS ?= -flto
++CXX_FLTO_FLAGS ?= -flto -fPIC
+ LD_FLTO_FLAGS ?= -flto -Wl,--exclude-libs=ALL
+
+ CXXFLAGS = $(LLVM_CXXFLAGS) $(CXX_FLTO_FLAGS)

foss-2018b/numba-0.43.0-foss-2018b-Python-2.7.15.eb

@@ -0,0 +1,39 @@
+easyblock = 'Bundle'
+
+name = 'numba'
+version = '0.43.0'
+versionsuffix = '-Python-%(pyver)s'
+
+homepage = 'http://numba.pydata.org/'
+description = """Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics,
+ Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code."""
+
+toolchain = {'name': 'foss', 'version': '2018b'}
+toolchainopts = {'pic': True}
+
+# this is a bundle of Python packages
+exts_defaultclass = 'PythonPackage'
+
+dependencies = [
+    ('Python', '2.7.15'),
+    ('LLVM', '7.0.0'),
+]
+
+exts_list = [
+    ('llvmlite', '0.28.0', {
+        'patches': ['llvmlite-0.28.0_fix-ffi-Makefile.patch'],
+        'source_urls': ['https://pypi.python.org/packages/source/l/llvmlite/'],
+    }),
+    (name, version, {
+        'source_urls': ['https://pypi.python.org/packages/source/n/numba/'],
+    }),
+]
+
+sanity_check_paths = {
+    'files': ['bin/numba', 'bin/pycc'],
+    'dirs': ['lib/python%(pyshortver)s/site-packages'],
+}
+
+modextrapaths = {'PYTHONPATH': ['lib/python%(pyshortver)s/site-packages']}
+
+moduleclass = 'lang'