Update URL parsing regexes and tests (#13411)
* Update URL parsing regexes and tests * Get rid of no longer used README * Merge py-udunits and py-cf-units * netcdf -> netcdf-c * setup_environment -> setup_*_environment * Fix doc tests * Few last minute fixes * Simplify prefix removal copypasta
This commit is contained in:
Adam J. Stewart
GitHub
parent
4367e16740
commit
2264e30d99
@ -97,7 +97,7 @@ Check Installation
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With Spack installed, you should be able to run some basic Spack
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commands. For example:
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.. command-output:: spack spec netcdf
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.. command-output:: spack spec netcdf-c
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^^^^^^^^^^^^^^^^^^^^^^^^^^
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@ -434,23 +434,10 @@ def name_parsed_correctly(pkg, name):
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Returns:
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bool: True if the name was correctly parsed, else False
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"""
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pkg_name = pkg.name
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pkg_name = remove_prefix(pkg.name)
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name = simplify_name(name)
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# After determining a name, `spack create` determines a build system.
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# Some build systems prepend a special string to the front of the name.
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# Since this can't be guessed from the URL, it would be unfair to say
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# that these names are incorrectly parsed, so we remove them.
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if pkg_name.startswith('r-'):
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pkg_name = pkg_name[2:]
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elif pkg_name.startswith('py-'):
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pkg_name = pkg_name[3:]
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elif pkg_name.startswith('perl-'):
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pkg_name = pkg_name[5:]
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elif pkg_name.startswith('octave-'):
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pkg_name = pkg_name[7:]
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return name == pkg_name
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@ -475,8 +462,32 @@ def version_parsed_correctly(pkg, version):
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return False
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def remove_prefix(pkg_name):
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"""Remove build system prefix ('py-', 'perl-', etc.) from a package name.
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After determining a name, `spack create` determines a build system.
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Some build systems prepend a special string to the front of the name.
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Since this can't be guessed from the URL, it would be unfair to say
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that these names are incorrectly parsed, so we remove them.
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Args:
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pkg_name (str): the name of the package
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Returns:
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str: the name of the package with any build system prefix removed
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"""
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prefixes = [
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'r-', 'py-', 'tcl-', 'lua-', 'perl-', 'ruby-', 'llvm-',
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'intel-', 'votca-', 'octave-', 'gtkorvo-'
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]
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prefix = next((p for p in prefixes if pkg_name.startswith(p)), '')
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return pkg_name[len(prefix):]
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def remove_separators(version):
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"""Removes separator characters ('.', '_', and '-') from a version.
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"""Remove separator characters ('.', '_', and '-') from a version.
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A version like 1.2.3 may be displayed as 1_2_3 in the URL.
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Make sure 1.2.3, 1-2-3, 1_2_3, and 123 are considered equal.
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@ -60,6 +60,8 @@
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('cppad-20170114.gpl', 'cppad-20170114'),
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# Arch
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('pcraster-4.1.0_x86-64', 'pcraster-4.1.0'),
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('dislin-11.0.linux.i586_64', 'dislin-11.0'),
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('PAGIT.V1.01.64bit', 'PAGIT.V1.01'),
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# OS - linux
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('astyle_2.04_linux', 'astyle_2.04'),
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# OS - unix
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@ -85,20 +87,31 @@
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# Combinations of multiple patterns - darwin
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('ghc-7.0.4-x86_64-apple-darwin', 'ghc-7.0.4'),
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('ghc-7.0.4-i386-apple-darwin', 'ghc-7.0.4'),
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# Combinations of multiple patterns - centos
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('sratoolkit.2.8.2-1-centos_linux64', 'sratoolkit.2.8.2-1'),
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# Combinations of multiple patterns - arch
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('VizGlow_v2.2alpha17-R21November2016-Linux-x86_64-Install',
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'VizGlow_v2.2alpha17-R21November2016'),
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('jdk-8u92-linux-x64', 'jdk-8u92'),
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('cuda_6.5.14_linux_64.run', 'cuda_6.5.14'),
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('Mathematica_12.0.0_LINUX.sh', 'Mathematica_12.0.0'),
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('trf407b.linux64', 'trf407b'),
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# Combinations of multiple patterns - with
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('mafft-7.221-with-extensions-src', 'mafft-7.221'),
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('spark-2.0.0-bin-without-hadoop', 'spark-2.0.0'),
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('conduit-v0.3.0-src-with-blt', 'conduit-v0.3.0'),
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# Combinations of multiple patterns - rock
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('bitlib-23-2.src.rock', 'bitlib-23-2'),
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# Combinations of multiple patterns - public
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('dakota-6.3-public.src', 'dakota-6.3'),
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# Combinations of multiple patterns - universal
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('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2'),
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# Combinations of multiple patterns - dynamic
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('snptest_v2.5.2_linux_x86_64_dynamic', 'snptest_v2.5.2'),
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# Combinations of multiple patterns - other
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('alglib-3.11.0.cpp.gpl', 'alglib-3.11.0'),
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('hpcviewer-2019.08-linux.gtk.x86_64', 'hpcviewer-2019.08'),
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('apache-mxnet-src-1.3.0-incubating', 'apache-mxnet-src-1.3.0'),
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])
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def test_url_strip_version_suffixes(url, expected):
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stripped = strip_version_suffixes(url)
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@ -109,24 +122,40 @@ def test_url_strip_version_suffixes(url, expected):
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# No suffix
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('rgb-1.0.6', '1.0.6', 'rgb'),
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('nauty26r7', '26r7', 'nauty'),
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('PAGIT.V1.01', '1.01', 'PAGIT'),
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('AmpliconNoiseV1.29', '1.29', 'AmpliconNoise'),
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# Download type - install
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('converge_install_2.3.16', '2.3.16', 'converge'),
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# Download type - src
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('jpegsrc.v9b', '9b', 'jpeg'),
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('blatSrc35', '35', 'blat'),
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# Download type - open
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('RepeatMasker-open-4-0-7', '4-0-7', 'RepeatMasker'),
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# Download type - archive
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('coinhsl-archive-2014.01.17', '2014.01.17', 'coinhsl'),
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# Download type - std
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('ghostscript-fonts-std-8.11', '8.11', 'ghostscript-fonts'),
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# Download type - bin
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('GapCloser-bin-v1.12-r6', '1.12-r6', 'GapCloser'),
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# Download type - software
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('orthomclSoftware-v2.0.9', '2.0.9', 'orthomcl'),
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# Download version - release
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('cbench_release_1.3.0.tar.gz', '1.3.0', 'cbench'),
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# Download version - snapshot
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('gts-snapshot-121130', '121130', 'gts'),
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# Download version - distrib
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('zoltan_distrib_v3.83', '3.83', 'zoltan'),
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# Download version - latest
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('Platypus-latest', 'N/A', 'Platypus'),
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# Download version - complex
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('qt-everywhere-opensource-src-5.7.0', '5.7.0', 'qt'),
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# Arch
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('VESTA-x86_64', '3.4.6', 'VESTA'),
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# VCS - bazaar
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('libvterm-0+bzr681', '681', 'libvterm'),
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# License - gpl
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('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt-x11')
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('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt'),
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('PyQt4_gpl_x11-4.12.3', '4.12.3', 'PyQt4'),
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])
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def test_url_strip_name_suffixes(url, version, expected):
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stripped = strip_name_suffixes(url, version)
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@ -182,6 +211,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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@pytest.mark.parametrize('name,version,url', [
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# Common Repositories - github downloads
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# name/archive/ver.ver
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('nco', '4.6.2', 'https://github.com/nco/nco/archive/4.6.2.tar.gz'),
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# name/archive/vver.ver
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('vim', '8.0.0134', 'https://github.com/vim/vim/archive/v8.0.0134.tar.gz'),
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@ -257,6 +287,15 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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# Common Tarball Formats
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# 1st Pass: Simplest case
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# Assume name contains no digits and version contains no letters
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# name-ver.ver
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('libpng', '1.6.37', 'http://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz'),
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# 2nd Pass: Version only
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# Assume version contains no letters
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# ver.ver
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('eigen', '3.2.7', 'https://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2'),
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# ver.ver-ver
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@ -266,10 +305,17 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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# vver_ver
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('luafilesystem', '1_6_3', 'https://github.com/keplerproject/luafilesystem/archive/v1_6_3.tar.gz'),
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# No separators
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# 3rd Pass: No separator characters are used
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# Assume name contains no digits
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# namever
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('turbolinux', '702', 'file://{0}/turbolinux702.tar.gz'.format(os.getcwd())),
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('nauty', '26r7', 'http://pallini.di.uniroma1.it/nauty26r7.tar.gz'),
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# Dashes only
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# 4th Pass: A single separator character is used
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# Assume name contains no digits
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# name-name-ver-ver
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('Trilinos', '12-10-1',
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'https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz'),
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('panda', '2016-03-07',
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@ -278,7 +324,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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'http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz'),
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('cdd', '061a',
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'http://www.cs.mcgill.ca/~fukuda/download/cdd/cdd-061a.tar.gz'),
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# Only underscores
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# name_name_ver_ver
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('tinyxml', '2_6_2',
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'https://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz'),
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('boost', '1_55_0',
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@ -287,9 +333,6 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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'https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz'),
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('tbb', '44_20160413',
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'https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz'),
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# Only dots
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# name.name.ver.ver
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('prank', '150803', 'http://wasabiapp.org/download/prank/prank.source.150803.tgz'),
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('jpeg', '9b', 'http://www.ijg.org/files/jpegsrc.v9b.tar.gz'),
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@ -302,61 +345,51 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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('geant', '4.10.01.p03', 'http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz'),
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('tcl', '8.6.5', 'http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz'),
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# Dash and dots
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# 5th Pass: Two separator characters are used
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# Name may contain digits, version may contain letters
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# name-name-ver.ver
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# digit in name
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('m4', '1.4.17', 'https://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz'),
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# letter in version
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('gmp', '6.0.0a', 'https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2'),
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# version starts with 'v'
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('LaunchMON', '1.0.2',
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'https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz'),
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# name-ver-ver.ver
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('libedit', '20150325-3.1', 'http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz'),
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# Dash and unserscores
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# name-name-ver_ver
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('icu4c', '57_1', 'http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz'),
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# Underscores and dots
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# name_name_ver.ver
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('superlu_dist', '4.1', 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz'),
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('pexsi', '0.9.0', 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'),
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# name_name.ver.ver
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('fer', '696', 'ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz'),
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# Dash dot dah dot
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# name_name_ver-ver
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('Bridger', '2014-12-01',
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'https://downloads.sourceforge.net/project/rnaseqassembly/Bridger_r2014-12-01.tar.gz'),
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# name-name-ver.ver-ver.ver
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('sowing', '1.1.23-p1', 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz'),
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('bib2xhtml', '3.0-15-gf506', 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'),
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# namever.ver-ver.ver
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('go', '1.4-bootstrap-20161024', 'https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz'),
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# Underscore dash dot
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# 6th Pass: All three separator characters are used
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# Name may contain digits, version may contain letters
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# name_name-ver.ver
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('the_silver_searcher', '0.32.0', 'http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz'),
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('sphinx_rtd_theme', '0.1.10a0',
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'https://pypi.python.org/packages/source/s/sphinx_rtd_theme/sphinx_rtd_theme-0.1.10a0.tar.gz'),
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# Dot underscore dot dash dot
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# name.name_ver.ver-ver.ver
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('TH.data', '1.0-8', 'https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz'),
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('XML', '3.98-1.4', 'https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz'),
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# Dash dot underscore dot
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# name-name-ver.ver_ver.ver
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('pypar', '2.1.5_108',
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'https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-2.1.5_108.tgz'),
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# name-namever.ver_ver.ver
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('STAR-CCM+', '11.06.010_02',
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'file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz'.format(os.getcwd())),
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# name-name_name-ver.ver
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('PerlIO-utf8_strict', '0.002',
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'http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz'),
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# Various extensions
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# .tar.gz
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@ -399,18 +432,61 @@ def test_url_parse_offset(name, noffset, ver, voffset, path):
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# .txz
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('kim-api', '2.1.0', 'https://s3.openkim.org/kim-api/kim-api-2.1.0.txz'),
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# Weird URLS
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# 8th Pass: Query strings
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# github.com/repo/name/releases/download/name-vver/name
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('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'),
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# suffix queries
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('swiftsim', '0.3.0', 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'),
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('swiftsim', '0.3.0', 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'),
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('swiftsim', '0.3.0',
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'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'),
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('sionlib', '1.7.1', 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'),
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('jube2', '2.2.2', 'https://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=2.2.2'),
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('archive', '1.0.0', 'https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0'),
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('VecGeom', '0.3.rc',
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'https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc'),
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||||
('parsplice', '1.1',
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'https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1'),
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||||
('busco', '2.0.1', 'https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1'),
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('libaec', '1.0.2',
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'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'),
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('icet', '2.1.1',
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'https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1'),
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('vtk-m', '1.3.0',
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'https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0'),
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||||
('GATK', '3.8-1-0-gf15c1c3ef',
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'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef'),
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# stem queries
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||||
('slepc', '3.6.2', 'http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz'),
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('otf', '1.12.5salmon',
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||||
'http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz'),
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||||
('eospac', '6.4.0beta.1',
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||||
'http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz'),
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('vampirtrace', '5.14.4',
|
||||
'http://wwwpub.zih.tu-dresden.de/~mlieber/dcount/dcount.php?package=vampirtrace&get=VampirTrace-5.14.4.tar.gz'),
|
||||
# (we don't actually look for these, they are picked up
|
||||
# during the preliminary stem parsing)
|
||||
('octopus', '6.0', 'http://octopus-code.org/down.php?file=6.0/octopus-6.0.tar.gz'),
|
||||
('cloog', '0.18.1', 'http://www.bastoul.net/cloog/pages/download/count.php3?url=./cloog-0.18.1.tar.gz'),
|
||||
('libxc', '2.2.2', 'http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz'),
|
||||
('cistem', '1.0.0-beta',
|
||||
'https://cistem.org/system/tdf/upload3/cistem-1.0.0-beta-source-code.tar.gz?file=1&type=cistem_details&id=37&force=0'),
|
||||
('Magics', '4.1.0',
|
||||
'https://confluence.ecmwf.int/download/attachments/3473464/Magics-4.1.0-Source.tar.gz?api=v2'),
|
||||
('grib_api', '1.17.0',
|
||||
'https://software.ecmwf.int/wiki/download/attachments/3473437/grib_api-1.17.0-Source.tar.gz?api=v2'),
|
||||
('eccodes', '2.2.0',
|
||||
'https://software.ecmwf.int/wiki/download/attachments/45757960/eccodes-2.2.0-Source.tar.gz?api=v2'),
|
||||
('SWFFT', '1.0',
|
||||
'https://xgitlab.cels.anl.gov/api/v4/projects/hacc%2FSWFFT/repository/archive.tar.gz?sha=v1.0'),
|
||||
|
||||
# 9th Pass: Version in path
|
||||
|
||||
# github.com/repo/name/releases/download/name-vver/name
|
||||
('nextflow', '0.20.1', 'https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow'),
|
||||
# ver/name
|
||||
('ncbi', '2.2.26', 'ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz'),
|
||||
|
||||
# Other tests for corner cases
|
||||
|
||||
# single character name
|
||||
('R', '3.3.2', 'https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz'),
|
||||
# name starts with digit
|
||||
|
||||
@ -153,13 +153,14 @@ def strip_version_suffixes(path):
|
||||
r'[Ii]nstall',
|
||||
r'all',
|
||||
r'code',
|
||||
r'src(_0)?',
|
||||
r'[Ss]ources?',
|
||||
r'file',
|
||||
r'full',
|
||||
r'single',
|
||||
r'public',
|
||||
r'with[a-zA-Z_-]+',
|
||||
r'rock',
|
||||
r'src(_0)?',
|
||||
r'public',
|
||||
r'bin',
|
||||
r'binary',
|
||||
r'run',
|
||||
@ -189,15 +190,24 @@ def strip_version_suffixes(path):
|
||||
r'ia32',
|
||||
r'intel',
|
||||
r'amd64',
|
||||
r'linux64',
|
||||
r'x64',
|
||||
r'64bit',
|
||||
r'x86[_-]64',
|
||||
r'i586_64',
|
||||
r'x86',
|
||||
r'i[36]86',
|
||||
r'ppc64(le)?',
|
||||
r'armv?(7l|6l|64)',
|
||||
|
||||
# Other
|
||||
r'cpp',
|
||||
r'gtk',
|
||||
r'incubating',
|
||||
|
||||
# OS
|
||||
r'[Ll]inux(_64)?',
|
||||
r'LINUX',
|
||||
r'[Uu]ni?x',
|
||||
r'[Ss]un[Oo][Ss]',
|
||||
r'[Mm]ac[Oo][Ss][Xx]?',
|
||||
@ -208,14 +218,18 @@ def strip_version_suffixes(path):
|
||||
r'[Ww]in(64|32)?',
|
||||
r'[Cc]ygwin(64|32)?',
|
||||
r'[Mm]ingw',
|
||||
r'centos',
|
||||
|
||||
# Arch
|
||||
# Needs to come before and after OS, appears in both orders
|
||||
r'ia32',
|
||||
r'intel',
|
||||
r'amd64',
|
||||
r'linux64',
|
||||
r'x64',
|
||||
r'64bit',
|
||||
r'x86[_-]64',
|
||||
r'i586_64',
|
||||
r'x86',
|
||||
r'i[36]86',
|
||||
r'ppc64(le)?',
|
||||
@ -270,31 +284,41 @@ def strip_name_suffixes(path, version):
|
||||
# name-ver
|
||||
# name_ver
|
||||
# name.ver
|
||||
r'[._-]v?' + str(version) + '.*',
|
||||
r'[._-][rvV]?' + str(version) + '.*',
|
||||
|
||||
# namever
|
||||
str(version) + '.*',
|
||||
r'V?' + str(version) + '.*',
|
||||
|
||||
# Download type
|
||||
r'install',
|
||||
r'src',
|
||||
r'[Ss]rc',
|
||||
r'(open)?[Ss]ources?',
|
||||
r'[._-]open',
|
||||
r'[._-]archive',
|
||||
r'[._-]std',
|
||||
r'[._-]bin',
|
||||
r'Software',
|
||||
|
||||
# Download version
|
||||
r'release',
|
||||
r'snapshot',
|
||||
r'distrib',
|
||||
r'everywhere',
|
||||
r'latest',
|
||||
|
||||
# Arch
|
||||
r'Linux64',
|
||||
r'Linux(64)?',
|
||||
r'x86_64',
|
||||
|
||||
# VCS
|
||||
r'0\+bzr',
|
||||
|
||||
# License
|
||||
r'gpl',
|
||||
|
||||
# Needs to come before and after gpl, appears in both orders
|
||||
r'[._-]x11',
|
||||
r'gpl',
|
||||
]
|
||||
|
||||
for regex in suffix_regexes:
|
||||
@ -407,7 +431,7 @@ def parse_version_offset(path):
|
||||
# 3. names can contain A-Z, a-z, 0-9, '+', separators
|
||||
# 4. versions can contain A-Z, a-z, 0-9, separators
|
||||
# 5. versions always start with a digit
|
||||
# 6. versions are often prefixed by a 'v' character
|
||||
# 6. versions are often prefixed by a 'v' or 'r' character
|
||||
# 7. separators are most reliable to determine name/version boundaries
|
||||
|
||||
# List of the following format:
|
||||
@ -450,7 +474,7 @@ def parse_version_offset(path):
|
||||
(r'^[a-zA-Z+-]*(\d[\da-zA-Z-]*)$', stem),
|
||||
|
||||
# name_name_ver_ver
|
||||
# e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128, v1_6_3
|
||||
# e.g. tinyxml_2_6_2, boost_1_55_0, tbb2017_20161128
|
||||
(r'^[a-zA-Z+_]*(\d[\da-zA-Z_]*)$', stem),
|
||||
|
||||
# name.name.ver.ver
|
||||
@ -476,6 +500,10 @@ def parse_version_offset(path):
|
||||
# e.g. fer_source.v696
|
||||
(r'^[a-zA-Z\d+_]+\.v?(\d[\da-zA-Z.]*)$', stem),
|
||||
|
||||
# name_ver-ver
|
||||
# e.g. Bridger_r2014-12-01
|
||||
(r'^[a-zA-Z\d+]+_r?(\d[\da-zA-Z-]*)$', stem),
|
||||
|
||||
# name-name-ver.ver-ver.ver
|
||||
# e.g. sowing-1.1.23-p1, bib2xhtml-v3.0-15-gf506, 4.6.3-alpha04
|
||||
(r'^(?:[a-zA-Z\d+-]+-)?v?(\d[\da-zA-Z.-]*)$', stem),
|
||||
@ -507,19 +535,17 @@ def parse_version_offset(path):
|
||||
# e.g. STAR-CCM+11.06.010_02
|
||||
(r'^[a-zA-Z+-]+(\d[\da-zA-Z._]*)$', stem),
|
||||
|
||||
# name-name_name-ver.ver
|
||||
# e.g. PerlIO-utf8_strict-0.002
|
||||
(r'^[a-zA-Z\d+_-]+-v?(\d[\da-zA-Z.]*)$', stem),
|
||||
|
||||
# 7th Pass: Specific VCS
|
||||
|
||||
# bazaar
|
||||
# e.g. libvterm-0+bzr681
|
||||
(r'bzr(\d[\da-zA-Z._-]*)$', stem),
|
||||
|
||||
# 8th Pass: Version in path
|
||||
|
||||
# github.com/repo/name/releases/download/vver/name
|
||||
# e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow
|
||||
(r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa
|
||||
|
||||
# 9th Pass: Query strings
|
||||
# 8th Pass: Query strings
|
||||
|
||||
# e.g. https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0
|
||||
(r'\?sha=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
|
||||
@ -528,13 +554,24 @@ def parse_version_offset(path):
|
||||
(r'\?ref=[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)$', suffix),
|
||||
|
||||
# e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1
|
||||
(r'\?version=v?(\d[\da-zA-Z._-]*)$', suffix),
|
||||
# e.g. https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef
|
||||
(r'[?&]version=v?(\d[\da-zA-Z._-]*)$', suffix),
|
||||
|
||||
# e.g. http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz
|
||||
(r'\?filename=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem),
|
||||
# e.g. http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz
|
||||
(r'[?&]filename=[a-zA-Z\d+-]+[_-]v?(\d[\da-zA-Z.]*)', stem),
|
||||
|
||||
# e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz
|
||||
(r'\?package=[a-zA-Z\d+-]+&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa
|
||||
(r'&get=[a-zA-Z\d+-]+-v?(\d[\da-zA-Z.]*)$', stem), # noqa
|
||||
|
||||
# 9th Pass: Version in path
|
||||
|
||||
# github.com/repo/name/releases/download/vver/name
|
||||
# e.g. https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow
|
||||
(r'github\.com/[^/]+/[^/]+/releases/download/[a-zA-Z+._-]*v?(\d[\da-zA-Z._-]*)/', path), # noqa
|
||||
|
||||
# e.g. ftp://ftp.ncbi.nlm.nih.gov/blast/executables/legacy.NOTSUPPORTED/2.2.26/ncbi.tar.gz
|
||||
(r'(\d[\da-zA-Z._-]*)/[^/]+$', path),
|
||||
]
|
||||
|
||||
for i, version_regex in enumerate(version_regexes):
|
||||
@ -662,6 +699,9 @@ def parse_name_offset(path, v=None):
|
||||
# e.g. http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz
|
||||
(r'\?package=([A-Za-z\d+-]+)', stem),
|
||||
|
||||
# ?package=name-version
|
||||
(r'\?package=([A-Za-z\d]+)', suffix),
|
||||
|
||||
# download.php
|
||||
# e.g. http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1
|
||||
(r'([^/]+)/download.php$', path),
|
||||
|
||||
@ -84,7 +84,7 @@ class Adios(AutotoolsPackage):
|
||||
depends_on('c-blosc@1.12.0:', when='+blosc')
|
||||
# optional transports & file converters
|
||||
depends_on('hdf5@1.8:+hl+mpi', when='+hdf5')
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('libevpath', when='staging=flexpath')
|
||||
depends_on('dataspaces+mpi', when='staging=dataspaces')
|
||||
|
||||
|
||||
@ -85,8 +85,8 @@ class Adios2(CMakePackage):
|
||||
# depends_on('flex', when='+sst') # optional in FFS, depends on BISON
|
||||
|
||||
depends_on('mpi', when='+mpi')
|
||||
depends_on('zeromq', when='+dataman')
|
||||
depends_on('zeromq', when='@2.4: +ssc')
|
||||
depends_on('libzmq', when='+dataman')
|
||||
depends_on('libzmq', when='@2.4: +ssc')
|
||||
depends_on('dataspaces@1.8.0:', when='+dataspaces')
|
||||
|
||||
depends_on('hdf5', when='+hdf5')
|
||||
|
||||
@ -11,7 +11,7 @@ class Adlbx(AutotoolsPackage):
|
||||
"""ADLB/X: Master-worker library + work stealing and data dependencies"""
|
||||
|
||||
homepage = 'http://swift-lang.org/Swift-T'
|
||||
url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.0.0.tar.gz'
|
||||
url = 'http://swift-lang.github.io/swift-t-downloads/spack/adlbx-0.9.2.tar.gz'
|
||||
git = "https://github.com/swift-lang/swift-t.git"
|
||||
|
||||
version('master', branch='master')
|
||||
@ -27,11 +27,11 @@ class Adlbx(AutotoolsPackage):
|
||||
depends_on('m4', type='build', when='@master')
|
||||
depends_on('mpi')
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
spec = self.spec
|
||||
spack_env.set('CC', spec['mpi'].mpicc)
|
||||
spack_env.set('CXX', spec['mpi'].mpicxx)
|
||||
spack_env.set('CXXLD', spec['mpi'].mpicxx)
|
||||
env.set('CC', spec['mpi'].mpicc)
|
||||
env.set('CXX', spec['mpi'].mpicxx)
|
||||
env.set('CXXLD', spec['mpi'].mpicxx)
|
||||
|
||||
@property
|
||||
def configure_directory(self):
|
||||
|
||||
@ -18,9 +18,6 @@ class Alglib(MakefilePackage):
|
||||
|
||||
version('3.11.0', sha256='34e391594aac89fb354bdaf58c42849489cd1199197398ba98bb69961f42bdb0')
|
||||
|
||||
def url_for_version(self, version):
|
||||
return 'http://www.alglib.net/translator/re/alglib-{0}.cpp.gpl.tgz'.format(version.dotted)
|
||||
|
||||
build_directory = 'src'
|
||||
|
||||
def edit(self, spec, prefix):
|
||||
|
||||
@ -11,7 +11,7 @@ class AllpathsLg(AutotoolsPackage):
|
||||
small and large (mammalian size) genomes."""
|
||||
|
||||
homepage = "http://www.broadinstitute.org/software/allpaths-lg/blog/"
|
||||
url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/LATEST_VERSION.tar.gz"
|
||||
url = "ftp://ftp.broadinstitute.org/pub/crd/ALLPATHS/Release-LG/latest_source_code/allpathslg-52488.tar.gz"
|
||||
|
||||
version('52488', sha256='035b49cb21b871a6b111976757d7aee9c2513dd51af04678f33375e620998542')
|
||||
|
||||
|
||||
@ -110,7 +110,7 @@ def cmake_args(self):
|
||||
if '+netcdf' in spec:
|
||||
tpl_list = tpl_list + ";NETCDF"
|
||||
options.extend(['-DTPL_NETCDF_INSTALL_DIR=%s' %
|
||||
spec['netcdf'].prefix, ])
|
||||
spec['netcdf-c'].prefix, ])
|
||||
if '+hypre' in spec:
|
||||
tpl_list = tpl_list + ";HYPRE"
|
||||
options.extend(['-DTPL_HYPRE_INSTALL_DIR=%s' %
|
||||
|
||||
@ -19,5 +19,5 @@ class Aria2(AutotoolsPackage):
|
||||
depends_on('libssh2')
|
||||
depends_on('libgcrypt')
|
||||
depends_on('zlib')
|
||||
depends_on('cares')
|
||||
depends_on('c-ares')
|
||||
depends_on('sqlite')
|
||||
|
||||
@ -19,107 +19,107 @@ class ArmForge(Package):
|
||||
# versions (and checksums) based on the target platform shows up
|
||||
|
||||
version(
|
||||
"19.0.4-linux-rhel6-x86_64",
|
||||
"19.0.4-Redhat-6.0-x86_64",
|
||||
sha256="0b0b6ed5c3d6833bad46d5ea84346cd46f0e4b3020c31f2fd4318b75ddaf01aa",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-6.0-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-rhel7-x86_64",
|
||||
"19.0.4-Redhat-7.0-x86_64",
|
||||
sha256="de3c669f7cb4daf274aae603294c416a953fb558e101eb03bcccf0ef4291e079",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.0-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-sles11-x86_64",
|
||||
"19.0.4-Suse-11-x86_64",
|
||||
sha256="24a2c7761c2163f128e4f4b60e963c53774196809ddfa880131c5dde5eb454c2",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-11-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-sles12-x86_64",
|
||||
"19.0.4-Suse-12-x86_64",
|
||||
sha256="6688192291fe9696922a34371d07ea66f89bff9b976fd99796e5f9a6651f86e6",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-sles15-x86_64",
|
||||
"19.0.4-Suse-15-x86_64",
|
||||
sha256="dea60d93a157ab6952fd6887f40123ab9d633d5589ffe7824d53fb269294cf35",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-15-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-ubuntu16.04-x86_64",
|
||||
"19.0.4-19.0.4-Ubuntu-16.04-x86_64",
|
||||
sha256="240741beff96f6a0b3976bc98d90863fe475366d5c093af9b96b877a230d479c",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-ubuntu14.04-x86_64",
|
||||
"19.0.4-Ubuntu-14.04-x86_64",
|
||||
sha256="135903906111b61045ddd3e98f1d8e8fd02b5b6ef554a68dfbe6760c76ec65a2",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-14.04-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-rhel7-ppc64le",
|
||||
"19.0.4-Redhat-7.2-ppc64le",
|
||||
sha256="73cb9f4005278e8dd2106a871dcbb53edb8855faeeda75c7abd7936f85fcce56",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.2-ppc64le.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-rhel7-aarch64",
|
||||
"19.0.4-Redhat-7.4-aarch64",
|
||||
sha256="8d168e5665a158f65b72d7b996fd283f7f538efbff15648eff44cfb7371ecad7",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Redhat-7.4-aarch64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-sles12-aarch64",
|
||||
"19.0.4-Suse-12-aarch64",
|
||||
sha256="de3aa62c5b5d5181a7947dcd1dfa66df5d06fd482394044100147210c8182d75",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Suse-12-aarch64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.4-linux-ubuntu16.04-aarch64",
|
||||
"19.0.4-Ubuntu-16.04-aarch64",
|
||||
sha256="3910e320c635dd5c09af7f5696909c7c0ae25406910d2e592e522ed0233e0451",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.4-Ubuntu-16.04-aarch64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-rhel6-x86_64",
|
||||
"19.0.3-Redhat-6.0-x86_64",
|
||||
sha256="0ace88a1847d8f622f077cd38fa9dddf7f2d6dd6aad086be0e0a66e10fb8b64b",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-6.0-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-rhel7-x86_64",
|
||||
"19.0.3-Redhat-7.0-x86_64",
|
||||
sha256="35c7a9532aa19251343c37b8f5eb51ef04f7b6e8b42bea2bd932f4d83a1e8375",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.0-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-sles11-x86_64",
|
||||
"19.0.3-Suse-11-x86_64",
|
||||
sha256="48fe2b1b81a824909fedf5e02cd08d8a62033cce80440eca6efbea0ae8023e75",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-11-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-sles12-x86_64",
|
||||
"19.0.3-Suse-12-x86_64",
|
||||
sha256="b4d0f91780dc43544ea946f5117a50ba18750fd50ef811cae5b6b6771b4ebb77",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-ubuntu16.04-x86_64",
|
||||
"19.0.3-Ubuntu-16.04-x86_64",
|
||||
sha256="ed6726434a6d24d413ed6183756433d63438936dc671cb6a3567b407c8e233e1",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-ubuntu14.04-x86_64",
|
||||
"19.0.3-Ubuntu-14.04-x86_64",
|
||||
sha256="22350d068c4ef60d1aad330636d443f00269c0cc49bed4c05b80f93b9d9a9c66",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-14.04-x86_64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-rhel7-ppc64le",
|
||||
"19.0.3-Redhat-7.2-ppc64le",
|
||||
sha256="dc6ea53eead78f0d9ffd8fa74ffddb80e8bd3b4ab8a1edd6f8505ffbea9cea15",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.2-ppc64le.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-rhel7-aarch64",
|
||||
"19.0.3-Redhat-7.4-aarch64",
|
||||
sha256="4e19d4200e2936d542bf2b9dc79c7f8b00ccfb37b9191dfc90ac0787680a8b0c",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Redhat-7.4-aarch64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-sles12-aarch64",
|
||||
"19.0.3-Suse-12-aarch64",
|
||||
sha256="9b27b678d0228b4e51fd517ef0acd1df65b780a3a0b226caa6b6f1b7dccf31e6",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Suse-12-aarch64.tar",
|
||||
)
|
||||
version(
|
||||
"19.0.3-linux-ubuntu16.04-aarch64",
|
||||
"19.0.3-Ubuntu-16.04-aarch64",
|
||||
sha256="4470f7067d4a4e0369df8af28b6ca95f58fa0062bf8dffc49f0b7415112c0332",
|
||||
url="http://content.allinea.com/downloads/arm-forge-19.0.3-Ubuntu-16.04-aarch64.tar",
|
||||
)
|
||||
|
||||
@ -12,7 +12,7 @@ class Armadillo(CMakePackage):
|
||||
ease of use."""
|
||||
|
||||
homepage = "http://arma.sourceforge.net/"
|
||||
url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz"
|
||||
url = "http://sourceforge.net/projects/arma/files/armadillo-8.100.1.tar.xz"
|
||||
|
||||
version('8.100.1', sha256='54773f7d828bd3885c598f90122b530ded65d9b195c9034e082baea737cd138d')
|
||||
version('7.950.1', sha256='a32da32a0ea420b8397a53e4b40ed279c1a5fc791dd492a2ced81ffb14ad0d1b')
|
||||
|
||||
@ -46,8 +46,8 @@ class Asagi(CMakePackage):
|
||||
|
||||
depends_on('mpi', when="+mpi")
|
||||
depends_on('mpi@3:', when="+mpi3")
|
||||
depends_on('netcdf +mpi', when="+mpi")
|
||||
depends_on('netcdf ~mpi', when="~mpi")
|
||||
depends_on('netcdf-c +mpi', when="+mpi")
|
||||
depends_on('netcdf-c ~mpi', when="~mpi")
|
||||
depends_on('numactl', when="+numa")
|
||||
|
||||
conflicts('%gcc@5:', when='@:1.0.0')
|
||||
|
||||
@ -96,15 +96,17 @@ class Ascent(Package):
|
||||
# TPLs for Runtime Features
|
||||
#############################
|
||||
|
||||
depends_on("vtkh@develop", when="+vtkh")
|
||||
depends_on("vtkh@develop~openmp", when="+vtkh~openmp")
|
||||
depends_on("vtkh@develop+cuda+openmp", when="+vtkh+cuda+openmp")
|
||||
depends_on("vtkh@develop+cuda~openmp", when="+vtkh+cuda~openmp")
|
||||
depends_on("vtk-m", when="+vtkh")
|
||||
|
||||
depends_on("vtkh@develop~shared", when="~shared+vtkh")
|
||||
depends_on("vtkh@develop~shared~openmp", when="~shared+vtkh~openmp")
|
||||
depends_on("vtkh@develop~shared+cuda", when="~shared+vtkh+cuda")
|
||||
depends_on("vtkh@develop~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp")
|
||||
depends_on("vtk-h@develop", when="+vtkh")
|
||||
depends_on("vtk-h@develop~openmp", when="+vtkh~openmp")
|
||||
depends_on("vtk-h@develop+cuda+openmp", when="+vtkh+cuda+openmp")
|
||||
depends_on("vtk-h@develop+cuda~openmp", when="+vtkh+cuda~openmp")
|
||||
|
||||
depends_on("vtk-h@develop~shared", when="~shared+vtkh")
|
||||
depends_on("vtk-h@develop~shared~openmp", when="~shared+vtkh~openmp")
|
||||
depends_on("vtk-h@develop~shared+cuda", when="~shared+vtkh+cuda")
|
||||
depends_on("vtk-h@develop~shared+cuda~openmp", when="~shared+vtkh+cuda~openmp")
|
||||
|
||||
# mfem
|
||||
depends_on("mfem+shared+mpi+conduit", when="+shared+mfem+mpi")
|
||||
@ -178,8 +180,8 @@ def check_install(self):
|
||||
create=True):
|
||||
cmake_args = ["-DASCENT_DIR={0}".format(install_prefix),
|
||||
"-DCONDUIT_DIR={0}".format(spec['conduit'].prefix),
|
||||
"-DVTKM_DIR={0}".format(spec['vtkm'].prefix),
|
||||
"-DVTKH_DIR={0}".format(spec['vtkh'].prefix),
|
||||
"-DVTKM_DIR={0}".format(spec['vtk-m'].prefix),
|
||||
"-DVTKH_DIR={0}".format(spec['vtk-h'].prefix),
|
||||
example_src_dir]
|
||||
cmake(*cmake_args)
|
||||
make()
|
||||
@ -405,10 +407,10 @@ def create_host_config(self, spec, prefix, py_site_pkgs_dir=None):
|
||||
|
||||
if "+vtkh" in spec:
|
||||
cfg.write("# vtk-m from spack\n")
|
||||
cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtkm'].prefix))
|
||||
cfg.write(cmake_cache_entry("VTKM_DIR", spec['vtk-m'].prefix))
|
||||
|
||||
cfg.write("# vtk-h from spack\n")
|
||||
cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtkh'].prefix))
|
||||
cfg.write(cmake_cache_entry("VTKH_DIR", spec['vtk-h'].prefix))
|
||||
|
||||
else:
|
||||
cfg.write("# vtk-h not built by spack \n")
|
||||
|
||||
@ -16,7 +16,7 @@ class Augustus(MakefilePackage):
|
||||
# Releases have moved to github
|
||||
|
||||
version('3.3.2', sha256='d09f972cfd88deb34b19b69878eb8af3bbbe4f1cde1434b69cedc2aa6247a0f2')
|
||||
version('3.3.1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
|
||||
version('3.3.1-tag1', sha256='011379606f381ee21b9716f83e8a1a57b2aaa01aefeebd2748104efa08c47cab',
|
||||
url='https://github.com/Gaius-Augustus/Augustus/archive/v3.3.1-tag1.tar.gz')
|
||||
version('3.3', sha256='b5eb811a4c33a2cc3bbd16355e19d530eeac6d1ac923e59f48d7a79f396234ee',
|
||||
url='http://bioinf.uni-greifswald.de/augustus/binaries/old/augustus-3.3.tar.gz')
|
||||
@ -98,7 +98,7 @@ def filter_sbang(self):
|
||||
for file in files:
|
||||
filter_file(pattern, repl, *files, backup=False)
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
run_env.set('AUGUSTUS_CONFIG_PATH', join_path(
|
||||
def setup_run_environment(self, env):
|
||||
env.set('AUGUSTUS_CONFIG_PATH', join_path(
|
||||
self.prefix, 'config'))
|
||||
run_env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
|
||||
env.prepend_path('PATH', join_path(self.prefix, 'scripts'))
|
||||
|
||||
@ -16,9 +16,9 @@ class Autofact(Package):
|
||||
version('3_4', sha256='1465d263b19adb42f01f6e636ac40ef1c2e3dbd63461f977b89da9493fe9c6f4')
|
||||
|
||||
depends_on('perl', type='run')
|
||||
depends_on('perl-bio-perl', type='run')
|
||||
depends_on('perl-bioperl', type='run')
|
||||
depends_on('perl-io-string', type='run')
|
||||
depends_on('perl-lwp', type='run')
|
||||
depends_on('perl-libwww-perl', type='run')
|
||||
depends_on('blast-legacy', type='run')
|
||||
|
||||
def patch(self):
|
||||
@ -31,6 +31,6 @@ def patch(self):
|
||||
def install(self, spec, prefix):
|
||||
install_tree(self.stage.source_path, prefix)
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
run_env.prepend_path('PATH', self.prefix.scripts)
|
||||
run_env.set('PATH2AUTOFACT', self.prefix)
|
||||
def setup_run_environment(self, env):
|
||||
env.prepend_path('PATH', self.prefix.scripts)
|
||||
env.set('PATH2AUTOFACT', self.prefix)
|
||||
|
||||
@ -20,7 +20,7 @@ class Axl(CMakePackage):
|
||||
"""Asynchronous transfer library"""
|
||||
|
||||
homepage = "https://github.com/ECP-VeloC/AXL"
|
||||
url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.0.zip"
|
||||
url = "https://github.com/ECP-VeloC/AXL/archive/v0.1.1.zip"
|
||||
git = "https://github.com/ecp-veloc/axl.git"
|
||||
|
||||
tags = ['ecp']
|
||||
|
||||
@ -21,21 +21,21 @@ class Biopieces(Package):
|
||||
depends_on('perl-module-build', type=('build', 'run'))
|
||||
depends_on('perl-bit-vector', type=('build', 'run'))
|
||||
depends_on('perl-svg', type=('build', 'run'))
|
||||
depends_on('perl-term-readkey', type=('build', 'run'))
|
||||
depends_on('perl-termreadkey', type=('build', 'run'))
|
||||
depends_on('perl-time-hires', type=('build', 'run'))
|
||||
depends_on('perl-dbi', type=('build', 'run'))
|
||||
depends_on('perl-xml-parser', type=('build', 'run'))
|
||||
depends_on('perl-carp-clan', type=('build', 'run'))
|
||||
depends_on('perl-class-inspector', type=('build', 'run'))
|
||||
depends_on('perl-html-parser', type=('build', 'run'))
|
||||
depends_on('perl-lwp', type=('build', 'run'))
|
||||
depends_on('perl-libwww-perl', type=('build', 'run'))
|
||||
depends_on('perl-soap-lite', type=('build', 'run'))
|
||||
depends_on('perl-uri', type=('build', 'run'))
|
||||
depends_on('perl-inline', type=('build', 'run'))
|
||||
depends_on('perl-inline-c', type=('build', 'run'))
|
||||
depends_on('perl-parse-recdescent', type=('build', 'run'))
|
||||
depends_on('perl-version', type=('build', 'run'))
|
||||
depends_on('perl-dbfile', type=('build', 'run'))
|
||||
depends_on('perl-perl-version', type=('build', 'run'))
|
||||
depends_on('perl-db-file', type=('build', 'run'))
|
||||
depends_on('perl-dbd-mysql', type=('build', 'run'))
|
||||
|
||||
depends_on('ruby@1.9:')
|
||||
@ -61,10 +61,10 @@ class Biopieces(Package):
|
||||
def install(self, spec, prefix):
|
||||
install_tree('.', prefix)
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_run_environment(self, env):
|
||||
# Note: user will need to set environment variables on their own,
|
||||
# dependent on where they will want data to be located:
|
||||
# BP_DATA - Contains genomic data etc.
|
||||
# BP_TMP - Required temporary directory
|
||||
# BP_LOG - Required log directory
|
||||
run_env.prepend_path('BP_DIR', prefix)
|
||||
env.prepend_path('BP_DIR', self.prefix)
|
||||
|
||||
@ -32,7 +32,7 @@ class Breakdancer(CMakePackage):
|
||||
|
||||
depends_on('perl-statistics-descriptive', type='run')
|
||||
depends_on('perl-math-cdf', type='run')
|
||||
depends_on('perl-gd-graph', type='run')
|
||||
depends_on('perl-gdgraph', type='run')
|
||||
depends_on('perl-gdgraph-histogram', type='run')
|
||||
depends_on('perl-list-moreutils', type='run')
|
||||
depends_on('perl-exporter-tiny', type='run')
|
||||
@ -41,9 +41,9 @@ class Breakdancer(CMakePackage):
|
||||
|
||||
parallel = False
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_run_environment(self, env):
|
||||
# get the perl tools in the path
|
||||
run_env.prepend_path('PATH', self.prefix.lib)
|
||||
env.prepend_path('PATH', self.prefix.lib)
|
||||
|
||||
def edit(self, spec, prefix):
|
||||
# perl tools end up in a silly lib subdirectory, fixing that
|
||||
|
||||
@ -13,7 +13,7 @@ class Bsseeker2(Package):
|
||||
url = "https://github.com/BSSeeker/BSseeker2/archive/BSseeker2-v2.1.8.tar.gz"
|
||||
|
||||
version('2.1.8', sha256='34ebedce36a0fca9e22405d4c2c20bc978439d4a34d1d543657fbc53ff847934')
|
||||
version('2.1.5', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a',
|
||||
version('2.1.7', sha256='ac90fb4ad8853ee920f1ffea2b1a8cfffcdb1508ff34be0091d5a9c90ac8c74a',
|
||||
url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.7.tar.gz')
|
||||
version('2.1.2', sha256='08055dd314f85a9b74c259c2cb894ea2affdab2c7a120af3589c649e1900c5c6',
|
||||
url='https://github.com/BSSeeker/BSseeker2/archive/v2.1.2.tar.gz')
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Cares(CMakePackage):
|
||||
class CAres(CMakePackage):
|
||||
"""c-ares: A C library for asynchronous DNS requests"""
|
||||
|
||||
homepage = "https://c-ares.haxx.se"
|
||||
@ -11,7 +11,6 @@ class CBlosc2(CMakePackage):
|
||||
other bells and whistles"""
|
||||
|
||||
homepage = "http://www.blosc.org"
|
||||
url = "https://github.com/Blosc/c-blosc2/archive/v2.0.0-beta.1.tar.gz"
|
||||
git = "https://github.com/Blosc/c-blosc2.git"
|
||||
|
||||
maintainers = ['ax3l']
|
||||
|
||||
@ -10,7 +10,7 @@ class CandleBenchmarks(Package):
|
||||
"""ECP-CANDLE Benchmarks"""
|
||||
|
||||
homepage = "https://github.com/ECP-CANDLE/Benchmarks"
|
||||
url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v1.0.tar.gz"
|
||||
url = "https://github.com/ECP-CANDLE/Benchmarks/archive/v0.1.tar.gz"
|
||||
|
||||
tags = ['proxy-app', 'ecp-proxy-app']
|
||||
|
||||
|
||||
@ -6,11 +6,12 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Catch(CMakePackage):
|
||||
"""Catch tests"""
|
||||
class Catch2(CMakePackage):
|
||||
"""Catch2 is a multi-paradigm test framework for C++, which also
|
||||
supports Objective-C (and maybe C)."""
|
||||
|
||||
homepage = "https://github.com/catchorg/Catch2"
|
||||
url = "https://github.com/catchorg/Catch2/archive/v1.3.0.tar.gz"
|
||||
url = "https://github.com/catchorg/Catch2/archive/v2.9.1.tar.gz"
|
||||
|
||||
variant('single_header', default=True,
|
||||
description='Install a single header only.')
|
||||
@ -51,7 +51,7 @@ class Cdo(AutotoolsPackage):
|
||||
|
||||
depends_on('pkgconfig', type='build')
|
||||
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
# In this case CDO does not depend on hdf5 directly but we need the backend
|
||||
# of netcdf to be thread safe.
|
||||
depends_on('hdf5+threadsafe', when='+netcdf')
|
||||
@ -63,7 +63,7 @@ class Cdo(AutotoolsPackage):
|
||||
|
||||
depends_on('hdf5+threadsafe', when='+hdf5')
|
||||
|
||||
depends_on('udunits2', when='+udunits2')
|
||||
depends_on('udunits', when='+udunits2')
|
||||
depends_on('libxml2', when='+libxml2')
|
||||
depends_on('proj@:5', when='+proj')
|
||||
depends_on('curl', when='+curl')
|
||||
|
||||
@ -1,3 +0,0 @@
|
||||
This is a bundle for the CEED software suite.
|
||||
|
||||
See https://ceed.exascaleproject.org for details.
|
||||
@ -4,10 +4,9 @@
|
||||
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
||||
|
||||
from spack import *
|
||||
import os
|
||||
|
||||
|
||||
class Ceed(Package):
|
||||
class Ceed(BundlePackage):
|
||||
"""Ceed is a collection of benchmarks, miniapps, software libraries and
|
||||
APIs for efficient high-order finite element and spectral element
|
||||
discretizations for exascale applications developed in the Department of
|
||||
@ -17,12 +16,6 @@ class Ceed(Package):
|
||||
|
||||
homepage = "https://ceed.exascaleproject.org"
|
||||
|
||||
url = 'file://' + os.path.dirname(__file__) + '/README.md'
|
||||
sha256 = '418c4b6b6a098648e25befdc28cdf9c351ecea9deaa660c0d9a674f8c6917122'
|
||||
|
||||
version('2.0.0', sha256, expand=False)
|
||||
version('1.0.0', sha256, expand=False)
|
||||
|
||||
variant('cuda', default=False,
|
||||
description='Build MAGMA; enable CUDA support in libCEED and OCCA')
|
||||
variant('mfem', default=True, description='Build MFEM and Laghos')
|
||||
@ -139,7 +132,3 @@ class Ceed(Package):
|
||||
|
||||
# If using gcc version <= 4.8 build suite-sparse version <= 5.1.0
|
||||
depends_on('suite-sparse@:5.1.0', when='@1.0.0%gcc@:4.8+mfem+petsc')
|
||||
|
||||
# Dummy install
|
||||
def install(self, spec, prefix):
|
||||
install('README.md', prefix)
|
||||
|
||||
@ -12,13 +12,9 @@ class Channelflow(CMakePackage):
|
||||
"""
|
||||
|
||||
homepage = 'https://github.com/epfl-ecps/channelflow'
|
||||
url = 'https://github.com/epfl-ecps/channelflow.git'
|
||||
git = 'https://github.com/epfl-ecps/channelflow.git'
|
||||
|
||||
version(
|
||||
'develop',
|
||||
git='https://github.com/epfl-ecps/channelflow.git',
|
||||
branch='master'
|
||||
)
|
||||
version('master', branch='master')
|
||||
|
||||
variant('shared', default=True, description='Build shared libs')
|
||||
variant('mpi', default=True, description='Enable MPI parallelism')
|
||||
@ -38,8 +34,8 @@ class Channelflow(CMakePackage):
|
||||
|
||||
# Support for different I/O formats
|
||||
depends_on('hdf5+cxx', when='+hdf5')
|
||||
depends_on('netcdf', when='netcdf=serial')
|
||||
depends_on('netcdf+mpi', when='netcdf=parallel')
|
||||
depends_on('netcdf-c', when='netcdf=serial')
|
||||
depends_on('netcdf-c+mpi', when='netcdf=parallel')
|
||||
|
||||
# Python bindings
|
||||
depends_on('boost+python', when='+python')
|
||||
@ -73,7 +69,7 @@ def cmake_args(self):
|
||||
}
|
||||
|
||||
args.append('-DWITH_NETCDF:STRING={0}'.format(
|
||||
netcdf_str[spec.variants['netcdf'].value]
|
||||
netcdf_str[spec.variants['netcdf-c'].value]
|
||||
))
|
||||
|
||||
# Set an MPI compiler for parallel builds
|
||||
|
||||
@ -15,6 +15,8 @@ class Check(AutotoolsPackage):
|
||||
logging format."""
|
||||
|
||||
homepage = "https://libcheck.github.io/check/index.html"
|
||||
url = "https://downloads.sourceforge.net/project/check/check/0.10.0/check-0.10.0.tar.gz"
|
||||
url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz"
|
||||
|
||||
version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234')
|
||||
version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616')
|
||||
version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052')
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Clustalo(AutotoolsPackage):
|
||||
class ClustalOmega(AutotoolsPackage):
|
||||
"""Clustal Omega: the last alignment program you'll ever need."""
|
||||
|
||||
homepage = "http://www.clustal.org/omega/"
|
||||
@ -24,8 +24,8 @@ class Cmor(AutotoolsPackage):
|
||||
variant('python', default=False, description='Enable PYTHON support')
|
||||
|
||||
depends_on('uuid')
|
||||
depends_on('netcdf')
|
||||
depends_on('udunits2')
|
||||
depends_on('netcdf-c')
|
||||
depends_on('udunits')
|
||||
depends_on('hdf5@:1.8.19')
|
||||
|
||||
extends('python', when='+python')
|
||||
|
||||
@ -18,5 +18,5 @@ class Cppzmq(CMakePackage):
|
||||
version('4.2.2', sha256='3ef50070ac5877c06c6bb25091028465020e181bbfd08f110294ed6bc419737d')
|
||||
|
||||
depends_on('cmake@3.0.0:', type='build')
|
||||
depends_on('zeromq@4.2.5', when='@4.3.0')
|
||||
depends_on('zeromq@4.2.2', when='@4.2.2')
|
||||
depends_on('libzmq@4.2.5', when='@4.3.0')
|
||||
depends_on('libzmq@4.2.2', when='@4.2.2')
|
||||
|
||||
@ -11,10 +11,10 @@ class Cquery(CMakePackage):
|
||||
"""
|
||||
|
||||
homepage = "https://github.com/cquery-project/cquery"
|
||||
url = "https://github.com/cquery-project/cquery/archive/v20180718.tar.gz"
|
||||
git = "https://github.com/cquery-project/cquery.git"
|
||||
|
||||
version('v20180823', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07',
|
||||
submodules=True, git='https://github.com/cquery-project/cquery')
|
||||
version('2018-08-23', commit='70c755b2e390d3edfb594a84a7531beb26b2bc07',
|
||||
submodules=True)
|
||||
|
||||
depends_on('llvm')
|
||||
|
||||
|
||||
@ -11,7 +11,7 @@ class Cub(Package):
|
||||
and other utilities for CUDA kernel programming."""
|
||||
|
||||
homepage = "https://nvlabs.github.com/cub"
|
||||
url = "https://github.com/NVlabs/cub/archive/1.6.4.zip"
|
||||
url = "https://github.com/NVlabs/cub/archive/1.7.1.zip"
|
||||
|
||||
version('1.7.1', sha256='50b8777b83093fdfdab429a61fccdbfbbb991b3bbc08385118e5ad58e8f62e1d')
|
||||
|
||||
|
||||
@ -19,8 +19,8 @@ class Czmq(AutotoolsPackage):
|
||||
depends_on('automake', type='build')
|
||||
depends_on('autoconf', type='build')
|
||||
depends_on('pkgconfig', type='build')
|
||||
depends_on("libuuid")
|
||||
depends_on('zeromq')
|
||||
depends_on('libuuid')
|
||||
depends_on('libzmq')
|
||||
|
||||
def autoreconf(self, spec, prefix):
|
||||
autogen = Executable('./autogen.sh')
|
||||
|
||||
@ -12,10 +12,10 @@ class Damaris(CMakePackage):
|
||||
targeting large-scale, MPI-based HPC simulations."""
|
||||
|
||||
homepage = "https://project.inria.fr/damaris/"
|
||||
url = "https://gitlab.inria.fr/Damaris/damaris"
|
||||
git = "https://gitlab.inria.fr/Damaris/damaris.git"
|
||||
|
||||
version('master', git='https://gitlab.inria.fr/Damaris/damaris.git')
|
||||
version('1.3.1', git='https://gitlab.inria.fr/Damaris/damaris.git', tag='v1.3.1', preferred=True)
|
||||
version('master', branch='master')
|
||||
version('1.3.1', tag='v1.3.1')
|
||||
|
||||
variant('fortran', default=True, description='Enables Fortran support')
|
||||
variant('hdf5', default=False, description='Enables the HDF5 storage plugin')
|
||||
|
||||
@ -10,7 +10,7 @@ class Davix(CMakePackage):
|
||||
"""High-performance file management over WebDAV/HTTP."""
|
||||
|
||||
homepage = "https://dmc.web.cern.ch/projects/davix"
|
||||
url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.7/davix-0.6.7.tar.gz"
|
||||
url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/0.6.8/davix-0.6.8.tar.gz"
|
||||
list_url = "http://grid-deployment.web.cern.ch/grid-deployment/dms/lcgutil/tar/davix/"
|
||||
list_depth = 1
|
||||
|
||||
|
||||
@ -10,9 +10,9 @@ class Dbcsr(CMakePackage):
|
||||
"""Distributed Block Compressed Sparse Row matrix library."""
|
||||
|
||||
homepage = "https://github.com/cp2k/dbcsr"
|
||||
url = "https://github.com/cp2k/dbcsr/archive/v1.0.0-rc.0.tar.gz"
|
||||
git = "https://github.com/cp2k/dbcsr.git"
|
||||
|
||||
version('develop', git='https://github.com/cp2k/dbcsr.git', branch='develop')
|
||||
version('develop', branch='develop')
|
||||
|
||||
variant('mpi', default=True, description='Compile with MPI')
|
||||
variant('openmp', default=False, description='Build with OpenMP support')
|
||||
|
||||
@ -137,7 +137,7 @@ class Dealii(CMakePackage, CudaPackage):
|
||||
depends_on('metis@5:~int64', when='+metis~int64')
|
||||
depends_on('muparser', when='+muparser')
|
||||
depends_on('nanoflann', when='@9.0:+nanoflann')
|
||||
depends_on('netcdf+mpi', when='+netcdf+mpi')
|
||||
depends_on('netcdf-c+mpi', when='+netcdf+mpi')
|
||||
depends_on('netcdf-cxx', when='+netcdf+mpi')
|
||||
depends_on('oce', when='+oce')
|
||||
depends_on('p4est', when='+p4est+mpi')
|
||||
@ -393,13 +393,13 @@ def cmake_args(self):
|
||||
|
||||
# since Netcdf is spread among two, need to do it by hand:
|
||||
if '+netcdf' in spec and '+mpi' in spec:
|
||||
netcdf = spec['netcdf-cxx'].libs + spec['netcdf'].libs
|
||||
netcdf = spec['netcdf-cxx'].libs + spec['netcdf-c'].libs
|
||||
options.extend([
|
||||
'-DNETCDF_FOUND=true',
|
||||
'-DNETCDF_LIBRARIES=%s' % netcdf.joined(';'),
|
||||
'-DNETCDF_INCLUDE_DIRS=%s;%s' % (
|
||||
spec['netcdf-cxx'].prefix.include,
|
||||
spec['netcdf'].prefix.include),
|
||||
spec['netcdf-c'].prefix.include),
|
||||
])
|
||||
else:
|
||||
options.extend([
|
||||
@ -447,5 +447,5 @@ def cmake_args(self):
|
||||
|
||||
return options
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
run_env.set('DEAL_II_DIR', self.prefix)
|
||||
def setup_run_environment(self, env):
|
||||
env.set('DEAL_II_DIR', self.prefix)
|
||||
|
||||
@ -14,7 +14,7 @@ class Dislin(Package):
|
||||
homepage = "http://www.mps.mpg.de/dislin"
|
||||
url = "ftp://ftp.gwdg.de/pub/grafik/dislin/linux/i586_64/dislin-11.0.linux.i586_64.tar.gz"
|
||||
|
||||
version('11.2.linux.i586_64', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10')
|
||||
version('11.0', sha256='13d28188924e0b0b803d72aa4b48be4067e98e890701b0aa6f54a11c7d34dd10')
|
||||
|
||||
depends_on('motif')
|
||||
depends_on('gl')
|
||||
@ -39,16 +39,18 @@ def libs(self):
|
||||
libraries, root=self.prefix, shared=True, recursive=True
|
||||
)
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
spack_env.set('DISLIN', self.prefix)
|
||||
run_env.set('DISLIN', self.prefix)
|
||||
run_env.prepend_path('PATH', self.prefix)
|
||||
run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
|
||||
run_env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib)
|
||||
run_env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib)
|
||||
def setup_build_environment(self, env):
|
||||
env.set('DISLIN', self.prefix)
|
||||
|
||||
def setup_dependent_environment(self, spack_env, run_env, dependent_spec):
|
||||
run_env.prepend_path('LD_LIBRARY_PATH', self.prefix)
|
||||
def setup_run_environment(self, env):
|
||||
env.set('DISLIN', self.prefix)
|
||||
env.prepend_path('PATH', self.prefix)
|
||||
env.prepend_path('LD_LIBRARY_PATH', self.prefix)
|
||||
env.prepend_path('LD_LIBRARY_PATH', self.spec['motif'].prefix.lib)
|
||||
env.prepend_path('LD_LIBRARY_PATH', self.spec['mesa'].prefix.lib)
|
||||
|
||||
def setup_dependent_run_environment(self, env, dependent_spec):
|
||||
env.prepend_path('LD_LIBRARY_PATH', self.prefix)
|
||||
|
||||
def install(self, spec, prefix):
|
||||
install = Executable('./INSTALL')
|
||||
|
||||
@ -12,19 +12,17 @@ class DotnetCoreSdk(Package):
|
||||
applications for all types of infrastructure."""
|
||||
|
||||
homepage = "https://www.microsoft.com/net/"
|
||||
url = "https://github.com/dotnet/core/"
|
||||
|
||||
version('2.1.300',
|
||||
url='https://download.microsoft.com/download/8/8/5/88544F33-836A'
|
||||
'-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz',
|
||||
url='https://download.microsoft.com/download/8/8/5/88544F33-836A-49A5-8B67-451C24709A8F/dotnet-sdk-2.1.300-linux-x64.tar.gz',
|
||||
sha256='fabca4c8825182ff18e5a2f82dfe75aecd10260ee9e7c85a8c4b3d108e5d8e1b')
|
||||
|
||||
variant('telemetry', default=False,
|
||||
description='allow collection of telemetry data')
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
if '-telemetry' in self.spec:
|
||||
spack_env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1)
|
||||
env.set('DOTNET_CLI_TELEMETRY_OPTOUT', 1)
|
||||
|
||||
def install(self, spec, prefix):
|
||||
mkdirp('bin')
|
||||
|
||||
@ -49,7 +49,7 @@ class Eccodes(CMakePackage):
|
||||
# tests are enabled but the testing scripts don't use it.
|
||||
# depends_on('valgrind', type='test', when='+test')
|
||||
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('openjpeg@1.5.0:1.5.999,2.1.0:2.1.999', when='jp2k=openjpeg')
|
||||
depends_on('jasper', when='jp2k=jasper')
|
||||
depends_on('libpng', when='+png')
|
||||
@ -100,7 +100,7 @@ def cmake_args(self):
|
||||
'-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
|
||||
# Prevent possible overriding by environment variables
|
||||
# NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
|
||||
'-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
|
||||
'-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix])
|
||||
else:
|
||||
args.append('-DENABLE_NETCDF=OFF')
|
||||
|
||||
|
||||
@ -37,7 +37,7 @@ class EcpVizSdk(CMakePackage):
|
||||
depends_on('paraview', when='+paraview')
|
||||
depends_on('sz', when='+sz')
|
||||
depends_on('visit', when='+visit')
|
||||
depends_on('vtkm', when='+vtkm')
|
||||
depends_on('vtk-m', when='+vtkm')
|
||||
depends_on('zfp', when='+zfp')
|
||||
|
||||
def cmake_args(self):
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class ElmerFem(CMakePackage):
|
||||
class Elmerfem(CMakePackage):
|
||||
"""Elmer is an open source multiphysical simulation software. It
|
||||
includes physical models of fluid dynamics, structural mechanics,
|
||||
electromagnetics, heat transfer and acoustics."""
|
||||
@ -83,5 +83,5 @@ def cmake_args(self):
|
||||
|
||||
return args
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
run_env.set('ELMER_HOME', self.prefix)
|
||||
def setup_run_environment(self, env):
|
||||
env.set('ELMER_HOME', self.prefix)
|
||||
@ -7,20 +7,18 @@
|
||||
import os
|
||||
|
||||
|
||||
class Eqr(AutotoolsPackage):
|
||||
class EqR(AutotoolsPackage):
|
||||
"""
|
||||
EMEWS Queues for R (EQ/R)
|
||||
Installs EQ/R.
|
||||
"""
|
||||
|
||||
git = "https://github.com/emews/EQ-R"
|
||||
|
||||
version('develop', branch='master')
|
||||
|
||||
configure_directory = 'src'
|
||||
|
||||
homepage = "http://emews.org"
|
||||
url = "https://github.com/emews/EQ-R/archive/1.0.tar.gz"
|
||||
git = "https://github.com/emews/EQ-R.git"
|
||||
|
||||
version('master', branch='master')
|
||||
|
||||
version('1.0', sha256='68047cb0edf088eaaefc5e36cefda9818292e5c832593e10a1dd9c73c27661b6')
|
||||
|
||||
depends_on('autoconf', type='build')
|
||||
@ -34,11 +32,13 @@ class Eqr(AutotoolsPackage):
|
||||
depends_on('tcl')
|
||||
depends_on('swig')
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
configure_directory = 'src'
|
||||
|
||||
def setup_build_environment(self, env):
|
||||
spec = self.spec
|
||||
spack_env.set('CC', spec['mpi'].mpicc)
|
||||
spack_env.set('CXX', spec['mpi'].mpicxx)
|
||||
spack_env.set('CXXLD', spec['mpi'].mpicxx)
|
||||
env.set('CC', spec['mpi'].mpicc)
|
||||
env.set('CXX', spec['mpi'].mpicxx)
|
||||
env.set('CXXLD', spec['mpi'].mpicxx)
|
||||
|
||||
def configure_args(self):
|
||||
args = ['--with-tcl=' + self.spec['tcl'].prefix]
|
||||
@ -10,7 +10,7 @@ class Er(CMakePackage):
|
||||
"""Encoding and redundancy on a file set"""
|
||||
|
||||
homepage = "https://github.com/ECP-VeloC/er"
|
||||
url = "https://github.com/ECP-VeloC/er/archive/v0.0.2.zip"
|
||||
url = "https://github.com/ECP-VeloC/er/archive/v0.0.3.zip"
|
||||
git = "https://github.com/ecp-veloc/er.git"
|
||||
|
||||
tags = ['ecp']
|
||||
|
||||
@ -6,8 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Es(AutotoolsPackage):
|
||||
|
||||
class EsShell(AutotoolsPackage):
|
||||
"""Es is an extensible shell. The language was derived from the Plan 9
|
||||
shell, rc, and was influenced by functional programming languages,
|
||||
such as Scheme, and the Tcl embeddable programming language. This
|
||||
@ -34,7 +34,7 @@ class Esmf(MakefilePackage):
|
||||
# Optional dependencies
|
||||
depends_on('mpi', when='+mpi')
|
||||
depends_on('lapack@3:', when='+lapack')
|
||||
depends_on('netcdf@3.6:', when='+netcdf')
|
||||
depends_on('netcdf-c@3.6:', when='+netcdf')
|
||||
depends_on('netcdf-fortran@3.6:', when='+netcdf')
|
||||
depends_on('parallel-netcdf@1.2.0:', when='+pnetcdf')
|
||||
depends_on('xerces-c@3.1.0:', when='+xerces')
|
||||
@ -200,7 +200,7 @@ def edit(self, spec, prefix):
|
||||
if '+netcdf' in spec:
|
||||
# ESMF provides the ability to read Grid and Mesh data in
|
||||
# NetCDF format.
|
||||
if spec.satisfies('^netcdf@4.2:'):
|
||||
if spec.satisfies('^netcdf-c@4.2:'):
|
||||
# ESMF_NETCDF_LIBS will be set to "-lnetcdff -lnetcdf".
|
||||
# This option is useful for systems which have the Fortran
|
||||
# and C bindings archived in seperate library files.
|
||||
|
||||
@ -11,7 +11,7 @@ class Exmcutils(AutotoolsPackage):
|
||||
"""ExM C-Utils: Generic C utility library for ADLB/X and Swift/T"""
|
||||
|
||||
homepage = 'http://swift-lang.org/Swift-T'
|
||||
url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.0.0.tar.gz'
|
||||
url = 'http://swift-lang.github.io/swift-t-downloads/spack/exmcutils-0.5.7.tar.gz'
|
||||
git = "https://github.com/swift-lang/swift-t.git"
|
||||
|
||||
version('master', branch='master')
|
||||
|
||||
@ -30,8 +30,8 @@ class Exodusii(CMakePackage):
|
||||
depends_on('mpi', when='+mpi')
|
||||
|
||||
# https://github.com/gsjaardema/seacas/blob/master/NetCDF-Mapping.md
|
||||
depends_on('netcdf@4.6.1:+mpi', when='+mpi')
|
||||
depends_on('netcdf@4.6.1:~mpi', when='~mpi')
|
||||
depends_on('netcdf-c@4.6.1:+mpi', when='+mpi')
|
||||
depends_on('netcdf-c@4.6.1:~mpi', when='~mpi')
|
||||
|
||||
def cmake_args(self):
|
||||
spec = self.spec
|
||||
@ -49,7 +49,7 @@ def cmake_args(self):
|
||||
'-DSEACASProj_SKIP_FORTRANCINTERFACE_VERIFY_TEST:BOOL=ON',
|
||||
'-DSEACASProj_ENABLE_CXX11:BOOL=OFF',
|
||||
'-DSEACASProj_ENABLE_Zoltan:BOOL=OFF',
|
||||
'-DNetCDF_DIR:PATH={0}'.format(spec['netcdf'].prefix),
|
||||
'-DNetCDF_DIR:PATH={0}'.format(spec['netcdf-c'].prefix),
|
||||
|
||||
# MPI Flags #
|
||||
'-DTPL_ENABLE_MPI={0}'.format('ON' if '+mpi' in spec else 'OFF'),
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Fastmath(Package):
|
||||
class Fastmath(BundlePackage):
|
||||
"""FASTMath is a suite of ~15 numerical libraries frequently used together
|
||||
in various SciDAC and CSE applications. The suite includes discretization
|
||||
libraries for structured, AMR and unstructured grids as well as solver
|
||||
@ -14,16 +14,12 @@ class Fastmath(Package):
|
||||
Solvers."""
|
||||
|
||||
homepage = "www.fastmath-scidac.org/"
|
||||
url = "https://github.com/citibeth/dummy/tarball/v1.0"
|
||||
|
||||
version('1.0', sha256='402a2198e40b7e9022a99ab88ba6f0ee1c04b103fc15589b22c892859f14b60a')
|
||||
|
||||
# BundlePackage
|
||||
depends_on('amrex') # default is 3 dimensions
|
||||
depends_on('chombo@3.2')
|
||||
depends_on('hypre~internal-superlu')
|
||||
# depends_on('ml-trilinos') # hoping for stripped down install of just ml
|
||||
# depends_on('nox-trilinos') # hoping for stripped down install of just nox
|
||||
# depends_on('ml-trilinos') # hoping for stripped down install of just ml
|
||||
# depends_on('nox-trilinos') # hoping for stripped down install of just nox
|
||||
depends_on('mpi')
|
||||
depends_on('arpack-ng')
|
||||
depends_on('petsc')
|
||||
@ -33,12 +29,3 @@ class Fastmath(Package):
|
||||
depends_on('superlu-dist')
|
||||
depends_on('trilinos')
|
||||
depends_on('zoltan')
|
||||
|
||||
# Dummy install for now, will be removed when metapackage is available
|
||||
def install(self, spec, prefix):
|
||||
# Prevent the error message
|
||||
# ==> Error: Install failed for fastmath. Nothing was installed!
|
||||
# ==> Error: Installation process had nonzero exit code : 256
|
||||
with open(join_path(spec.prefix, 'bundle-package.txt'), 'w') as out:
|
||||
out.write('This is a bundle\n')
|
||||
out.close()
|
||||
|
||||
@ -17,7 +17,7 @@ class FastqScreen(Package):
|
||||
version('0.11.2', sha256='a179df1f5803b42bbbb2b50af05ea18ae6fefcbf7020ca2feeb0d3c598a65207')
|
||||
|
||||
depends_on('perl', type='run')
|
||||
depends_on('perl-gd-graph', type='run')
|
||||
depends_on('perl-gdgraph', type='run')
|
||||
depends_on('bowtie')
|
||||
depends_on('bowtie2')
|
||||
depends_on('bwa')
|
||||
|
||||
@ -19,7 +19,7 @@ class Ferret(Package):
|
||||
version('6.96', sha256='7eb87156aa586cfe838ab83f08b2102598f9ab62062d540a5da8c9123816331a')
|
||||
|
||||
depends_on("hdf5+hl")
|
||||
depends_on("netcdf")
|
||||
depends_on("netcdf-c")
|
||||
depends_on("netcdf-fortran")
|
||||
depends_on("readline")
|
||||
depends_on("zlib")
|
||||
@ -63,7 +63,7 @@ def patch(self):
|
||||
"-L%s -lnetcdff" % self.spec['netcdf-fortran'].prefix.lib,
|
||||
'FERRET/platform_specific.mk.x86_64-linux')
|
||||
filter_file(r'\$\(NETCDF4_DIR\)/lib64/libnetcdf.a',
|
||||
"-L%s -lnetcdf" % self.spec['netcdf'].prefix.lib,
|
||||
"-L%s -lnetcdf" % self.spec['netcdf-c'].prefix.lib,
|
||||
'FERRET/platform_specific.mk.x86_64-linux')
|
||||
filter_file(r'\$\(HDF5_DIR\)/lib64/libhdf5_hl.a',
|
||||
"-L%s -lhdf5_hl" % self.spec['hdf5'].prefix.lib,
|
||||
|
||||
@ -12,7 +12,7 @@ class Flibcpp(CMakePackage):
|
||||
|
||||
homepage = "https://flibcpp.readthedocs.io/en/latest"
|
||||
git = "https://github.com/swig-fortran/flibcpp.git"
|
||||
url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.0.tar.gz"
|
||||
url = "https://github.com/swig-fortran/flibcpp/archive/v0.3.1.tar.gz"
|
||||
|
||||
version('master', branch='master')
|
||||
version('0.3.1', sha256='871570124122c18018478275d5040b4b787d1966e50ee95b634b0b5e0cd27e91')
|
||||
|
||||
@ -27,7 +27,7 @@ class FluxCore(AutotoolsPackage):
|
||||
variant('docs', default=False, description='Build flux manpages')
|
||||
variant('cuda', default=False, description='Build dependencies with support for CUDA')
|
||||
|
||||
depends_on("zeromq@4.0.4:")
|
||||
depends_on("libzmq@4.0.4:")
|
||||
depends_on("czmq")
|
||||
depends_on("czmq@2.2:3.99", when="@0.1:0.6.99")
|
||||
depends_on("czmq@3.0.1:", when="@0.7:,master")
|
||||
@ -95,28 +95,29 @@ def lua_share_dir(self):
|
||||
def lua_lib_dir(self):
|
||||
return os.path.join('lib', 'lua', str(self.lua_version))
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
# Ensure ./fluxometer.lua can be found during flux's make check
|
||||
spack_env.append_path('LUA_PATH', './?.lua', separator=';')
|
||||
|
||||
run_env.prepend_path(
|
||||
def setup_run_environment(self, env):
|
||||
env.prepend_path(
|
||||
'LUA_PATH',
|
||||
os.path.join(self.spec.prefix, self.lua_share_dir, '?.lua'),
|
||||
separator=';')
|
||||
run_env.prepend_path(
|
||||
env.prepend_path(
|
||||
'LUA_CPATH',
|
||||
os.path.join(self.spec.prefix, self.lua_lib_dir, '?.so'),
|
||||
separator=';')
|
||||
run_env.prepend_path(
|
||||
env.prepend_path(
|
||||
'PYTHONPATH',
|
||||
os.path.join(
|
||||
self.spec.prefix.lib,
|
||||
"python{0}".format(self.spec['python'].version.up_to(2)),
|
||||
"site-packages"),
|
||||
)
|
||||
run_env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
|
||||
run_env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
|
||||
run_env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux)
|
||||
env.prepend_path('FLUX_MODULE_PATH', self.prefix.lib.flux.modules)
|
||||
env.prepend_path('FLUX_EXEC_PATH', self.prefix.libexec.flux.cmd)
|
||||
env.prepend_path('FLUX_RC_PATH', self.prefix.etc.flux)
|
||||
|
||||
def configure_args(self):
|
||||
args = ['--enable-pylint=no']
|
||||
|
||||
@ -14,11 +14,11 @@ class Fpocket(MakefilePackage):
|
||||
version('master', branch='master',
|
||||
git='https://github.com/Discngine/fpocket.git')
|
||||
|
||||
depends_on("netcdf")
|
||||
depends_on("netcdf-c")
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
if self.compiler.name == 'gcc':
|
||||
spack_env.set('CXX', 'g++')
|
||||
env.set('CXX', 'g++')
|
||||
|
||||
def edit(self):
|
||||
makefile = FileFilter('makefile')
|
||||
|
||||
@ -20,25 +20,25 @@ class Fstrack(MakefilePackage):
|
||||
variant('flow', default=True, description='Build the flow tracker')
|
||||
|
||||
depends_on('gmt@4.0:4.999', when='+flow')
|
||||
depends_on('netcdf', when='+flow')
|
||||
depends_on('netcdf-c', when='+flow')
|
||||
|
||||
parallel = False
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
# Compilers
|
||||
spack_env.set('F90', spack_fc)
|
||||
env.set('F90', spack_fc)
|
||||
|
||||
# Compiler flags (assumes GCC)
|
||||
spack_env.set('CFLAGS', '-O2')
|
||||
spack_env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2')
|
||||
spack_env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input')
|
||||
spack_env.set('F90FLAGS', '-O2 -x f95-cpp-input')
|
||||
spack_env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input')
|
||||
spack_env.set('LDFLAGS', '-lm')
|
||||
env.set('CFLAGS', '-O2')
|
||||
env.set('FFLAGS', '-ffixed-line-length-132 -x f77-cpp-input -O2')
|
||||
env.set('FFLAGS_DEBUG', '-g -x f77-cpp-input')
|
||||
env.set('F90FLAGS', '-O2 -x f95-cpp-input')
|
||||
env.set('F90FLAGS_DEBUG', '-g -x f95-cpp-input')
|
||||
env.set('LDFLAGS', '-lm')
|
||||
|
||||
if '+flow' in self.spec:
|
||||
spack_env.set('GMTHOME', self.spec['gmt'].prefix)
|
||||
spack_env.set('NETCDFDIR', self.spec['netcdf'].prefix)
|
||||
env.set('GMTHOME', self.spec['gmt'].prefix)
|
||||
env.set('NETCDFDIR', self.spec['netcdf-c'].prefix)
|
||||
|
||||
def build(self, spec, prefix):
|
||||
with working_dir('eispack'):
|
||||
|
||||
@ -11,7 +11,7 @@ class Funhpc(CMakePackage):
|
||||
"""FunHPC: Functional HPC Programming"""
|
||||
|
||||
homepage = "https://github.com/eschnett/FunHPC.cxx"
|
||||
url = "https://github.com/eschnett/FunHPC.cxx/archive/version/0.1.0.tar.gz"
|
||||
url = "https://github.com/eschnett/FunHPC.cxx/archive/version/1.3.0.tar.gz"
|
||||
git = "https://github.com/eschnett/FunHPC.cxx.git"
|
||||
|
||||
version('develop', branch='master')
|
||||
|
||||
@ -114,7 +114,7 @@ class Gdal(AutotoolsPackage):
|
||||
depends_on('hdf', when='+hdf4')
|
||||
depends_on('hdf5', when='+hdf5')
|
||||
depends_on('kealib', when='+kea @2:')
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('jasper@1.900.1', patches='uuid.patch', when='+jasper')
|
||||
depends_on('openjpeg', when='+openjpeg')
|
||||
depends_on('xerces-c', when='+xerces')
|
||||
@ -157,12 +157,12 @@ class Gdal(AutotoolsPackage):
|
||||
|
||||
conflicts('+mdb', when='~java', msg='MDB driver requires Java')
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
def setup_build_environment(self, env):
|
||||
# Needed to install Python bindings to GDAL installation
|
||||
# prefix instead of Python installation prefix.
|
||||
# See swig/python/GNUmakefile for more details.
|
||||
spack_env.set('PREFIX', self.prefix)
|
||||
spack_env.set('DESTDIR', '/')
|
||||
env.set('PREFIX', self.prefix)
|
||||
env.set('DESTDIR', '/')
|
||||
|
||||
# https://trac.osgeo.org/gdal/wiki/BuildHints
|
||||
def configure_args(self):
|
||||
@ -299,7 +299,7 @@ def configure_args(self):
|
||||
|
||||
# https://trac.osgeo.org/gdal/wiki/NetCDF
|
||||
if '+netcdf' in spec:
|
||||
args.append('--with-netcdf={0}'.format(spec['netcdf'].prefix))
|
||||
args.append('--with-netcdf={0}'.format(spec['netcdf-c'].prefix))
|
||||
else:
|
||||
args.append('--with-netcdf=no')
|
||||
|
||||
|
||||
@ -57,7 +57,7 @@ class Gdl(CMakePackage):
|
||||
depends_on('libsm')
|
||||
depends_on('libxinerama')
|
||||
depends_on('libxxf86vm')
|
||||
depends_on('netcdf')
|
||||
depends_on('netcdf-c')
|
||||
depends_on('pslib')
|
||||
depends_on('readline')
|
||||
|
||||
|
||||
@ -12,7 +12,6 @@ class Ginkgo(CMakePackage, CudaPackage):
|
||||
with a focus on sparse solution of linear systems."""
|
||||
|
||||
homepage = "https://ginkgo-project.github.io/"
|
||||
url = "https://github.com/ginkgo-project/ginkgo.git"
|
||||
git = "https://github.com/ginkgo-project/ginkgo.git"
|
||||
|
||||
maintainers = ['tcojean', 'hartwiganzt']
|
||||
|
||||
@ -17,7 +17,7 @@ class Gmsh(CMakePackage):
|
||||
"""
|
||||
|
||||
homepage = 'http://gmsh.info'
|
||||
url = 'http://gmsh.info/src/gmsh-2.11.0-source.tgz'
|
||||
url = 'http://gmsh.info/src/gmsh-4.4.1-source.tgz'
|
||||
|
||||
version('4.4.1', sha256='853c6438fc4e4b765206e66a514b09182c56377bb4b73f1d0d26eda7eb8af0dc')
|
||||
version('4.2.2', sha256='e9ee9f5c606bbec5f2adbb8c3d6023c4e2577f487fa4e4ecfcfc94a241cc8dcc')
|
||||
|
||||
@ -33,7 +33,7 @@ class Gmt(Package):
|
||||
depends_on('ghostscript')
|
||||
depends_on('subversion')
|
||||
depends_on('cmake@2.8.5:', type='build', when='@5:')
|
||||
depends_on('netcdf@4:')
|
||||
depends_on('netcdf-c@4:')
|
||||
depends_on('curl', when='@5.4:')
|
||||
|
||||
# Optional dependencies
|
||||
@ -58,7 +58,7 @@ def install(self, spec, prefix):
|
||||
def install(self, spec, prefix):
|
||||
args = [
|
||||
'--prefix={0}'.format(prefix),
|
||||
'--enable-netcdf={0}'.format(spec['netcdf'].prefix),
|
||||
'--enable-netcdf={0}'.format(spec['netcdf-c'].prefix),
|
||||
'--enable-shared',
|
||||
'--without-x'
|
||||
]
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class GnuProlog(Package):
|
||||
class Gprolog(Package):
|
||||
"""A free Prolog compiler with constraint solving over finite domains."""
|
||||
homepage = "http://www.gprolog.org/"
|
||||
url = "http://www.gprolog.org/gprolog-1.4.5.tar.gz"
|
||||
@ -69,7 +69,7 @@ class Grass(AutotoolsPackage):
|
||||
depends_on('readline', when='+readline')
|
||||
depends_on('opencl', when='+opencl')
|
||||
depends_on('bzip2', when='+bzlib')
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('geos', when='+geos')
|
||||
|
||||
def url_for_version(self, version):
|
||||
@ -184,7 +184,7 @@ def configure_args(self):
|
||||
|
||||
if '+netcdf' in spec:
|
||||
args.append('--with-netcdf={0}/bin/nc-config'.format(
|
||||
spec['netcdf'].prefix))
|
||||
spec['netcdf-c'].prefix))
|
||||
else:
|
||||
args.append('--without-netcdf')
|
||||
|
||||
|
||||
@ -50,7 +50,7 @@ class GribApi(CMakePackage):
|
||||
# tests are enabled but the testing scripts don't use it.
|
||||
# depends_on('valgrind', type='test', when='+test')
|
||||
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('openjpeg@1.5.0:1.5.999', when='jp2k=openjpeg')
|
||||
depends_on('jasper', when='jp2k=jasper')
|
||||
depends_on('libpng', when='+png')
|
||||
@ -100,7 +100,7 @@ def cmake_args(self):
|
||||
'-DHDF5_ROOT=' + self.spec['hdf5'].prefix,
|
||||
# Prevent possible overriding by environment variables
|
||||
# NETCDF_ROOT, NETCDF_DIR, and NETCDF_PATH.
|
||||
'-DNETCDF_PATH=' + self.spec['netcdf'].prefix])
|
||||
'-DNETCDF_PATH=' + self.spec['netcdf-c'].prefix])
|
||||
else:
|
||||
args.append('-DENABLE_NETCDF=OFF')
|
||||
|
||||
|
||||
@ -20,7 +20,7 @@ class Grpc(CMakePackage):
|
||||
depends_on('protobuf')
|
||||
depends_on('openssl')
|
||||
depends_on('zlib')
|
||||
depends_on('cares')
|
||||
depends_on('c-ares')
|
||||
|
||||
def cmake_args(self):
|
||||
args = [
|
||||
|
||||
@ -17,7 +17,7 @@ class Guidance(MakefilePackage):
|
||||
version('2.02', sha256='825e105dde526759fb5bda1cd539b24db0b90b8b586f26b1df74d9c5abaa7844')
|
||||
|
||||
depends_on('perl', type=('build', 'run'))
|
||||
depends_on('perl-bio-perl', type=('build', 'run'))
|
||||
depends_on('perl-bioperl', type=('build', 'run'))
|
||||
depends_on('ruby')
|
||||
depends_on('prank')
|
||||
depends_on('clustalw')
|
||||
@ -43,5 +43,5 @@ def install(self, spac, prefix):
|
||||
install('guidance.pl', join_path(prefix.bin.www.Guidance,
|
||||
'guidance'))
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
run_env.prepend_path('PATH', prefix.bin.www.Guidance)
|
||||
def setup_run_environment(self, env):
|
||||
env.prepend_path('PATH', prefix.bin.www.Guidance)
|
||||
|
||||
@ -17,7 +17,7 @@ class Hc(MakefilePackage):
|
||||
version('1.0.7', sha256='7499ea76ac4739a9c0941bd57d124fb681fd387c8d716ebb358e6af3395103ed')
|
||||
|
||||
depends_on('gmt@4.2.1:4.999')
|
||||
depends_on('netcdf')
|
||||
depends_on('netcdf-c')
|
||||
|
||||
# Build phase fails in parallel with the following error messages:
|
||||
# /usr/bin/ld: cannot find -lrick
|
||||
@ -25,11 +25,11 @@ class Hc(MakefilePackage):
|
||||
# /usr/bin/ld: cannot find -lggrd
|
||||
parallel = False
|
||||
|
||||
def setup_environment(self, spack_env, run_env):
|
||||
spack_env.set('GMTHOME', self.spec['gmt'].prefix)
|
||||
spack_env.set('NETCDFHOME', self.spec['netcdf'].prefix)
|
||||
spack_env.set('HC_HOME', self.prefix)
|
||||
spack_env.unset('ARCH')
|
||||
def setup_build_environment(self, env):
|
||||
env.set('GMTHOME', self.spec['gmt'].prefix)
|
||||
env.set('NETCDFHOME', self.spec['netcdf-c'].prefix)
|
||||
env.set('HC_HOME', self.prefix)
|
||||
env.unset('ARCH')
|
||||
|
||||
def install(self, spec, prefix):
|
||||
# Most files are installed during the build stage.
|
||||
|
||||
@ -10,10 +10,9 @@ class Henson(CMakePackage):
|
||||
"""Cooperative multitasking for in situ processing."""
|
||||
|
||||
homepage = "https://github.com/henson-insitu/henson"
|
||||
url = "https://github.com/henson-insitu/henson"
|
||||
git = "https://github.com/henson-insitu/henson.git"
|
||||
|
||||
version('develop', branch='master')
|
||||
version('master', branch='master')
|
||||
|
||||
depends_on('mpi')
|
||||
|
||||
|
||||
@ -12,7 +12,6 @@ class Hisea(MakefilePackage):
|
||||
among others."""
|
||||
|
||||
homepage = "https://doi.org/10.1186/s12859-017-1953-9"
|
||||
url = "https://github.com/lucian-ilie/HISEA"
|
||||
|
||||
version('2017.12.26', sha256='3c6ddfb8490a327cc5f9e45f64cd4312abc6ef5719661ce8892db8a20a1e9c5e',
|
||||
url='https://github.com/lucian-ilie/HISEA/tarball/39e01e98caa0f2101da806ca59306296effe789c')
|
||||
|
||||
@ -11,7 +11,7 @@ class Homer(Package):
|
||||
"""Software for motif discovery and next generation sequencing analysis"""
|
||||
|
||||
homepage = "http://homer.ucsd.edu/homer"
|
||||
url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.zip"
|
||||
url = "http://homer.ucsd.edu/homer/data/software/homer.v4.9.1.zip"
|
||||
|
||||
version('4.9.1', sha256='ad1303b0b0400dc8a88dbeae1ee03a94631977b751a3d335326c4febf0eec3a9')
|
||||
|
||||
|
||||
@ -17,7 +17,7 @@ class Hpgmg(Package):
|
||||
"""
|
||||
|
||||
homepage = "https://bitbucket.org/hpgmg/hpgmg"
|
||||
url = "https://hpgmg.org/static/hpgmg-0.tar.gz"
|
||||
url = "https://hpgmg.org/static/hpgmg-0.4.tar.gz"
|
||||
git = "https://bitbucket.org/hpgmg/hpgmg.git"
|
||||
|
||||
tags = ['proxy-app']
|
||||
|
||||
@ -11,10 +11,10 @@ class Hub(Package):
|
||||
"""The github git wrapper"""
|
||||
|
||||
homepage = "https://github.com/github/hub"
|
||||
url = "https://github.com/github/hub/archive/v2.2.3.tar.gz"
|
||||
url = "https://github.com/github/hub/archive/v2.2.2.tar.gz"
|
||||
git = "https://github.com/github/hub.git"
|
||||
|
||||
version('head', branch='master')
|
||||
version('master', branch='master')
|
||||
version('2.2.2', sha256='610572ee903aea1fa8622c16ab7ddef2bd1bfec9f4854447ab8e0fbdbe6a0cae')
|
||||
version('2.2.1', sha256='9350aba6a8e3da9d26b7258a4020bf84491af69595f7484f922d75fc8b86dc10')
|
||||
version('2.2.0', sha256='2da1351197eb5696c207f22c69a5422af052d74277b73d0b8661efb9ec1d0eb1')
|
||||
|
||||
@ -40,7 +40,7 @@ class Ibmisc(CMakePackage):
|
||||
depends_on('proj@:4', when='+proj')
|
||||
depends_on('blitz', when='+blitz')
|
||||
depends_on('netcdf-cxx4', when='+netcdf')
|
||||
depends_on('udunits2', when='+udunits2')
|
||||
depends_on('udunits', when='+udunits2')
|
||||
depends_on('googletest', when='+googletest', type='build')
|
||||
depends_on('py-cython', when='+python', type=('build', 'run'))
|
||||
depends_on('py-numpy', when='+python', type=('build', 'run'))
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class ImageMagick(AutotoolsPackage):
|
||||
class Imagemagick(AutotoolsPackage):
|
||||
"""ImageMagick is a software suite to create, edit, compose,
|
||||
or convert bitmap images."""
|
||||
|
||||
@ -15,7 +15,7 @@ class Ioapi(MakefilePackage):
|
||||
homepage = "https://www.cmascenter.org/ioapi/"
|
||||
url = "https://www.cmascenter.org/ioapi/download/ioapi-3.2.tar.gz"
|
||||
version('3.2', sha256='56771ff0053d47f2445e00ff369bca7bfc484325a2816b2c648744e523134fe9')
|
||||
depends_on('netcdf@4:')
|
||||
depends_on('netcdf-c@4:')
|
||||
depends_on('netcdf-fortran@4:')
|
||||
depends_on('sed', type='build')
|
||||
|
||||
|
||||
@ -237,7 +237,7 @@ def install(self, spec, prefix):
|
||||
if "+plot" in spec:
|
||||
julia("-e", pkgstart + 'Pkg.add("PyPlot"); using PyPlot')
|
||||
julia("-e", pkgstart + 'Pkg.add("Colors"); using Colors')
|
||||
# These require maybe gtk and image-magick
|
||||
# These require maybe gtk and imagemagick
|
||||
julia("-e", pkgstart + 'Pkg.add("Plots"); using Plots')
|
||||
julia("-e", pkgstart + 'Pkg.add("PlotRecipes"); using PlotRecipes')
|
||||
julia(
|
||||
|
||||
@ -11,7 +11,7 @@ class Kvtree(CMakePackage):
|
||||
hashes."""
|
||||
|
||||
homepage = "https://github.com/ECP-VeloC/KVTree"
|
||||
url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.1.zip"
|
||||
url = "https://github.com/ECP-VeloC/KVTree/archive/v1.0.2.zip"
|
||||
git = "https://github.com/ecp-veloc/kvtree.git"
|
||||
|
||||
tags = ['ecp']
|
||||
|
||||
@ -74,7 +74,7 @@ def url_for_version(self, version):
|
||||
depends_on('mpi', when='+mpiio')
|
||||
depends_on('fftw', when='+kspace')
|
||||
depends_on('voropp+pic', when='+voronoi')
|
||||
depends_on('netcdf+mpi', when='+user-netcdf')
|
||||
depends_on('netcdf-c+mpi', when='+user-netcdf')
|
||||
depends_on('blas', when='+user-atc')
|
||||
depends_on('lapack', when='+user-atc')
|
||||
depends_on('latte@1.0.1', when='@:20180222+latte')
|
||||
|
||||
@ -1,17 +0,0 @@
|
||||
# Copyright 2013-2019 Lawrence Livermore National Security, LLC and other
|
||||
# Spack Project Developers. See the top-level COPYRIGHT file for details.
|
||||
#
|
||||
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
|
||||
|
||||
from spack import *
|
||||
|
||||
|
||||
class Libcheck(CMakePackage):
|
||||
"""A unit testing framework for C."""
|
||||
|
||||
homepage = "https://libcheck.github.io/check/index.html"
|
||||
url = "https://github.com/libcheck/check/releases/download/0.12.0/check-0.12.0.tar.gz"
|
||||
|
||||
version('0.12.0', sha256='464201098bee00e90f5c4bdfa94a5d3ead8d641f9025b560a27755a83b824234')
|
||||
version('0.11.0', sha256='24f7a48aae6b74755bcbe964ce8bc7240f6ced2141f8d9cf480bc3b3de0d5616')
|
||||
version('0.10.0', sha256='f5f50766aa6f8fe5a2df752666ca01a950add45079aa06416b83765b1cf71052')
|
||||
@ -14,7 +14,7 @@ class Libgit2(CMakePackage):
|
||||
"""
|
||||
|
||||
homepage = "https://libgit2.github.com/"
|
||||
url = "https://github.com/libgit2/libgit2/archive/v0.24.2.tar.gz"
|
||||
url = "https://github.com/libgit2/libgit2/archive/v0.26.0.tar.gz"
|
||||
|
||||
version('0.26.0', sha256='6a62393e0ceb37d02fe0d5707713f504e7acac9006ef33da1e88960bd78b6eac')
|
||||
|
||||
|
||||
@ -25,4 +25,4 @@ class Libgpuarray(CMakePackage):
|
||||
|
||||
depends_on('cuda')
|
||||
depends_on('cmake@3:', type='build')
|
||||
depends_on('libcheck')
|
||||
depends_on('check')
|
||||
|
||||
@ -19,5 +19,5 @@ class Libnrm(AutotoolsPackage):
|
||||
depends_on('automake', type='build')
|
||||
depends_on('libtool', type='build')
|
||||
|
||||
depends_on('zeromq')
|
||||
depends_on('libzmq')
|
||||
depends_on('mpich')
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Zeromq(AutotoolsPackage):
|
||||
class Libzmq(AutotoolsPackage):
|
||||
"""The ZMQ networking/concurrency library and core API"""
|
||||
|
||||
homepage = "http://zguide.zeromq.org/"
|
||||
@ -17,7 +17,7 @@ class Likwid(Package):
|
||||
for information."""
|
||||
|
||||
homepage = "https://github.com/RRZE-HPC/likwid"
|
||||
url = "https://github.com/RRZE-HPC/likwid/archive/4.1.2.tar.gz"
|
||||
url = "https://github.com/RRZE-HPC/likwid/archive/4.3.4.tar.gz"
|
||||
|
||||
version('4.3.4', sha256='5c0d1c66b25dac8292a02232f06454067f031a238f010c62f40ef913c6609a83')
|
||||
version('4.3.3', sha256='a681378cd66c1679ca840fb5fac3136bfec93c01b3d78cc1d00a641db325a9a3')
|
||||
|
||||
@ -11,7 +11,6 @@ class Lsf(Package):
|
||||
"""IBM Platform LSF is a batch scheduler for HPC environments"""
|
||||
|
||||
homepage = "https://www.ibm.com/marketplace/hpc-workload-management"
|
||||
url = "https://www.ibm.com/marketplace/hpc-workload-management"
|
||||
|
||||
# LSF needs to be added as an external package to SPACK. For this, the
|
||||
# config file packages.yaml needs to be adjusted:
|
||||
|
||||
@ -14,8 +14,7 @@ class LuaBitlib(Package):
|
||||
homepage = "http://luaforge.net/projects/bitlib"
|
||||
url = "https://luarocks.org/bitlib-23-2.src.rock"
|
||||
|
||||
version('23', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34',
|
||||
url="https://luarocks.org/bitlib-23-2.src.rock",
|
||||
version('23-2', sha256='fe226edc2808162e67418e6b2c98befc0ed25a489ecffc6974fa153f951c0c34',
|
||||
expand=False)
|
||||
|
||||
extends('lua')
|
||||
|
||||
@ -13,8 +13,7 @@ class LuaLpeg(Package):
|
||||
homepage = "http://www.inf.puc-rio.br/~roberto/lpeg/"
|
||||
url = "https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock"
|
||||
|
||||
version('0.12.1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a',
|
||||
url='https://luarocks.org/manifests/luarocks/lpeg-0.12-1.src.rock',
|
||||
version('0.12-1', sha256='3962e8d695d0f9095c9453f2a42f9f1a89fb94db9b0c3bf22934c1e8a3b0ef5a',
|
||||
expand=False)
|
||||
|
||||
extends("lua")
|
||||
|
||||
@ -7,7 +7,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class LuaJit(Package):
|
||||
class LuaLuajit(Package):
|
||||
"""Flast flexible JITed lua"""
|
||||
homepage = "http://www.luajit.org"
|
||||
url = "http://luajit.org/download/LuaJIT-2.0.4.tar.gz"
|
||||
@ -15,8 +15,7 @@ class LuaMpack(Package):
|
||||
|
||||
depends_on('msgpack-c')
|
||||
|
||||
version('1.0.0-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f',
|
||||
url='https://luarocks.org/manifests/tarruda/mpack-1.0.6-0.src.rock',
|
||||
version('1.0.6-0', sha256='9068d9d3f407c72a7ea18bc270b0fa90aad60a2f3099fa23d5902dd71ea4cd5f',
|
||||
expand=False)
|
||||
|
||||
extends('lua')
|
||||
|
||||
@ -93,6 +93,6 @@ def cmake_args(self):
|
||||
.format(spec['exodusii'].prefix))
|
||||
# exodus requires netcdf
|
||||
cmake_args.append("-DWITH_NETCDF_PREFIX={0}"
|
||||
.format(spec['netcdf'].prefix))
|
||||
.format(spec['netcdf-c'].prefix))
|
||||
|
||||
return cmake_args
|
||||
|
||||
@ -55,7 +55,7 @@ def url_for_version(self, version):
|
||||
depends_on('perl-inline-c', type=('build', 'run'))
|
||||
depends_on('perl-io-all', type=('build', 'run'))
|
||||
depends_on('perl-io-prompt', type=('build', 'run'))
|
||||
depends_on('perl-bio-perl', type=('build', 'run'))
|
||||
depends_on('perl-bioperl', type=('build', 'run'))
|
||||
depends_on('blast-plus')
|
||||
depends_on('snap-korf')
|
||||
depends_on('repeatmasker')
|
||||
|
||||
@ -45,7 +45,7 @@ class Mariadb(CMakePackage):
|
||||
depends_on('curl')
|
||||
depends_on('libxml2')
|
||||
depends_on('lz4')
|
||||
depends_on('zeromq')
|
||||
depends_on('libzmq')
|
||||
depends_on('msgpack-c')
|
||||
depends_on('openssl')
|
||||
depends_on('openssl@:1.0', when='@:10.1')
|
||||
|
||||
@ -25,7 +25,7 @@ class Meme(AutotoolsPackage):
|
||||
depends_on('perl', type=('build', 'run'))
|
||||
depends_on('python@2.7:', type=('build', 'run'))
|
||||
depends_on('mpi', when='+mpi')
|
||||
depends_on('image-magick', type=('build', 'run'), when='+image-magick')
|
||||
depends_on('imagemagick', type=('build', 'run'), when='+image-magick')
|
||||
depends_on('perl-xml-parser', type=('build', 'run'))
|
||||
|
||||
def configure_args(self):
|
||||
|
||||
@ -189,7 +189,7 @@ class Mfem(Package):
|
||||
# depends_on('petsc@3.8:+mpi+double+hypre+suite-sparse+mumps',
|
||||
# when='+petsc')
|
||||
depends_on('mpfr', when='+mpfr')
|
||||
depends_on('netcdf@4.1.3:', when='+netcdf')
|
||||
depends_on('netcdf-c@4.1.3:', when='+netcdf')
|
||||
depends_on('unwind', when='+libunwind')
|
||||
depends_on('zlib', when='+gzstream')
|
||||
depends_on('gnutls', when='+gnutls')
|
||||
@ -368,9 +368,9 @@ def find_optional_library(name, prefix):
|
||||
|
||||
if '+netcdf' in spec:
|
||||
options += [
|
||||
'NETCDF_OPT=-I%s' % spec['netcdf'].prefix.include,
|
||||
'NETCDF_OPT=-I%s' % spec['netcdf-c'].prefix.include,
|
||||
'NETCDF_LIB=%s' %
|
||||
ld_flags_from_dirs([spec['netcdf'].prefix.lib], ['netcdf'])]
|
||||
ld_flags_from_dirs([spec['netcdf-c'].prefix.lib], ['netcdf'])]
|
||||
|
||||
if '+gzstream' in spec:
|
||||
if "@:3.3.2" in spec:
|
||||
|
||||
@ -39,8 +39,6 @@ class Moab(AutotoolsPackage):
|
||||
description='Required to enable the ExodusII reader/writer.')
|
||||
variant('pnetcdf', default=False,
|
||||
description='Enable pnetcdf (AKA parallel-netcdf) support')
|
||||
variant('netcdf', default=False,
|
||||
description='Required to enable the ExodusII reader/writer.')
|
||||
variant('zoltan', default=False, description='Enable zoltan support')
|
||||
variant('cgm', default=False, description='Enable common geometric module')
|
||||
variant('metis', default=True, description='Enable metis link')
|
||||
@ -77,7 +75,7 @@ class Moab(AutotoolsPackage):
|
||||
depends_on('mpi', when='+mpi')
|
||||
depends_on('hdf5', when='+hdf5')
|
||||
depends_on('hdf5+mpi', when='+hdf5+mpi')
|
||||
depends_on('netcdf', when='+netcdf')
|
||||
depends_on('netcdf-c', when='+netcdf')
|
||||
depends_on('parallel-netcdf', when='+pnetcdf')
|
||||
depends_on('cgm', when='+cgm')
|
||||
depends_on('metis', when='+metis')
|
||||
@ -129,7 +127,7 @@ def configure_args(self):
|
||||
options.append('--without-hdf5')
|
||||
|
||||
if '+netcdf' in spec:
|
||||
options.append('--with-netcdf=%s' % spec['netcdf'].prefix)
|
||||
options.append('--with-netcdf=%s' % spec['netcdf-c'].prefix)
|
||||
else:
|
||||
options.append('--without-netcdf')
|
||||
|
||||
|
||||
@ -6,7 +6,7 @@
|
||||
from spack import *
|
||||
|
||||
|
||||
class Libmongoc(AutotoolsPackage):
|
||||
class MongoCDriver(AutotoolsPackage):
|
||||
"""libmongoc is a client library written in C for MongoDB."""
|
||||
|
||||
homepage = "https://github.com/mongodb/mongo-c-driver"
|
||||
@ -15,4 +15,4 @@ class MongoCxxDriver(CMakePackage):
|
||||
|
||||
version('3.2.0', sha256='e26edd44cf20bd6be91907403b6d63a065ce95df4c61565770147a46716aad8c')
|
||||
|
||||
depends_on('libmongoc@1.9.2:')
|
||||
depends_on('mongo-c-driver@1.9.2:')
|
||||
|
||||
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Loading…
Reference in New Issue
Block a user