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| author | Adam J. Stewart <ajstewart426@gmail.com> | 2019-10-28 20:27:54 -0500 |
|---|---|---|
| committer | GitHub <noreply@github.com> | 2019-10-28 20:27:54 -0500 |
| commit | 2264e30d99d8b9fbdec8fa69b594e53d8ced15a1 (patch) | |
| tree | b361d4d420ab2668be84cf27efb808d364a2abc1 | |
| parent | 4367e16740ccd39515ad75e86cce9f65ac46ca69 (diff) | |
| download | spack-2264e30d99d8b9fbdec8fa69b594e53d8ced15a1.tar.gz spack-2264e30d99d8b9fbdec8fa69b594e53d8ced15a1.tar.bz2 spack-2264e30d99d8b9fbdec8fa69b594e53d8ced15a1.tar.xz spack-2264e30d99d8b9fbdec8fa69b594e53d8ced15a1.zip | |
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
240 files changed, 773 insertions, 805 deletions
diff --git a/lib/spack/docs/getting_started.rst b/lib/spack/docs/getting_started.rst index b7ba386bb2..319d7f3c88 100644 --- a/lib/spack/docs/getting_started.rst +++ b/lib/spack/docs/getting_started.rst @@ -97,7 +97,7 @@ Check Installation With Spack installed, you should be able to run some basic Spack commands. For example: -.. command-output:: spack spec netcdf +.. command-output:: spack spec netcdf-c ^^^^^^^^^^^^^^^^^^^^^^^^^^ diff --git a/lib/spack/spack/cmd/url.py b/lib/spack/spack/cmd/url.py index a24fcc575c..3101f28f08 100644 --- a/lib/spack/spack/cmd/url.py +++ b/lib/spack/spack/cmd/url.py @@ -434,23 +434,10 @@ def name_parsed_correctly(pkg, name): Returns: bool: True if the name was correctly parsed, else False """ - pkg_name = pkg.name + pkg_name = remove_prefix(pkg.name) name = simplify_name(name) - # After determining a name, `spack create` determines a build system. - # Some build systems prepend a special string to the front of the name. - # Since this can't be guessed from the URL, it would be unfair to say - # that these names are incorrectly parsed, so we remove them. - if pkg_name.startswith('r-'): - pkg_name = pkg_name[2:] - elif pkg_name.startswith('py-'): - pkg_name = pkg_name[3:] - elif pkg_name.startswith('perl-'): - pkg_name = pkg_name[5:] - elif pkg_name.startswith('octave-'): - pkg_name = pkg_name[7:] - return name == pkg_name @@ -475,8 +462,32 @@ def version_parsed_correctly(pkg, version): return False +def remove_prefix(pkg_name): + """Remove build system prefix ('py-', 'perl-', etc.) from a package name. + + After determining a name, `spack create` determines a build system. + Some build systems prepend a special string to the front of the name. + Since this can't be guessed from the URL, it would be unfair to say + that these names are incorrectly parsed, so we remove them. + + Args: + pkg_name (str): the name of the package + + Returns: + str: the name of the package with any build system prefix removed + """ + prefixes = [ + 'r-', 'py-', 'tcl-', 'lua-', 'perl-', 'ruby-', 'llvm-', + 'intel-', 'votca-', 'octave-', 'gtkorvo-' + ] + + prefix = next((p for p in prefixes if pkg_name.startswith(p)), '') + + return pkg_name[len(prefix):] + + def remove_separators(version): - """Removes separator characters ('.', '_', and '-') from a version. + """Remove separator characters ('.', '_', and '-') from a version. A version like 1.2.3 may be displayed as 1_2_3 in the URL. Make sure 1.2.3, 1-2-3, 1_2_3, and 123 are considered equal. diff --git a/lib/spack/spack/test/url_parse.py b/lib/spack/spack/test/url_parse.py index c557f78405..7c292938d2 100644 --- a/lib/spack/spack/test/url_parse.py +++ b/lib/spack/spack/test/url_parse.py @@ -60,6 +60,8 @@ from spack.version import Version ('cppad-20170114.gpl', 'cppad-20170114'), # Arch ('pcraster-4.1.0_x86-64', 'pcraster-4.1.0'), + ('dislin-11.0.linux.i586_64', 'dislin-11.0'), + ('PAGIT.V1.01.64bit', 'PAGIT.V1.01'), # OS - linux ('astyle_2.04_linux', 'astyle_2.04'), # OS - unix @@ -85,20 +87,31 @@ from spack.version import Version # Combinations of multiple patterns - darwin ('ghc-7.0.4-x86_64-apple-darwin', 'ghc-7.0.4'), ('ghc-7.0.4-i386-apple-darwin', 'ghc-7.0.4'), + # Combinations of multiple patterns - centos + ('sratoolkit.2.8.2-1-centos_linux64', 'sratoolkit.2.8.2-1'), # Combinations of multiple patterns - arch ('VizGlow_v2.2alpha17-R21November2016-Linux-x86_64-Install', 'VizGlow_v2.2alpha17-R21November2016'), ('jdk-8u92-linux-x64', 'jdk-8u92'), ('cuda_6.5.14_linux_64.run', 'cuda_6.5.14'), + ('Mathematica_12.0.0_LINUX.sh', 'Mathematica_12.0.0'), + ('trf407b.linux64', 'trf407b'), # Combinations of multiple patterns - with ('mafft-7.221-with-extensions-src', 'mafft-7.221'), ('spark-2.0.0-bin-without-hadoop', 'spark-2.0.0'), + ('conduit-v0.3.0-src-with-blt', 'conduit-v0.3.0'), + # Combinations of multiple patterns - rock + ('bitlib-23-2.src.rock', 'bitlib-23-2'), # Combinations of multiple patterns - public ('dakota-6.3-public.src', 'dakota-6.3'), # Combinations of multiple patterns - universal ('synergy-1.3.6p2-MacOSX-Universal', 'synergy-1.3.6p2'), # Combinations of multiple patterns - dynamic ('snptest_v2.5.2_linux_x86_64_dynamic', 'snptest_v2.5.2'), + # Combinations of multiple patterns - other + ('alglib-3.11.0.cpp.gpl', 'alglib-3.11.0'), + ('hpcviewer-2019.08-linux.gtk.x86_64', 'hpcviewer-2019.08'), + ('apache-mxnet-src-1.3.0-incubating', 'apache-mxnet-src-1.3.0'), ]) def test_url_strip_version_suffixes(url, expected): stripped = strip_version_suffixes(url) @@ -109,24 +122,40 @@ def test_url_strip_version_suffixes(url, expected): # No suffix ('rgb-1.0.6', '1.0.6', 'rgb'), ('nauty26r7', '26r7', 'nauty'), + ('PAGIT.V1.01', '1.01', 'PAGIT'), + ('AmpliconNoiseV1.29', '1.29', 'AmpliconNoise'), # Download type - install ('converge_install_2.3.16', '2.3.16', 'converge'), # Download type - src ('jpegsrc.v9b', '9b', 'jpeg'), + ('blatSrc35', '35', 'blat'), + # Download type - open + ('RepeatMasker-open-4-0-7', '4-0-7', 'RepeatMasker'), # Download type - archive ('coinhsl-archive-2014.01.17', '2014.01.17', 'coinhsl'), # Download type - std ('ghostscript-fonts-std-8.11', '8.11', 'ghostscript-fonts'), + # Download type - bin + ('GapCloser-bin-v1.12-r6', '1.12-r6', 'GapCloser'), + # Download type - software + ('orthomclSoftware-v2.0.9', '2.0.9', 'orthomcl'), # Download version - release ('cbench_release_1.3.0.tar.gz', '1.3.0', 'cbench'), # Download version - snapshot ('gts-snapshot-121130', '121130', 'gts'), # Download version - distrib ('zoltan_distrib_v3.83', '3.83', 'zoltan'), + # Download version - latest + ('Platypus-latest', 'N/A', 'Platypus'), + # Download version - complex + ('qt-everywhere-opensource-src-5.7.0', '5.7.0', 'qt'), + # Arch + ('VESTA-x86_64', '3.4.6', 'VESTA'), # VCS - bazaar ('libvterm-0+bzr681', '681', 'libvterm'), # License - gpl - ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt-x11') + ('PyQt-x11-gpl-4.11.3', '4.11.3', 'PyQt'), + ('PyQt4_gpl_x11-4.12.3', '4.12.3', 'PyQt4'), ]) def test_url_strip_name_suffixes(url, version, expected): stripped = strip_name_suffixes(url, version) @@ -182,6 +211,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): @pytest.mark.parametrize('name,version,url', [ # Common Repositories - github downloads + # name/archive/ver.ver ('nco', '4.6.2', 'https://github.com/nco/nco/archive/4.6.2.tar.gz'), # name/archive/vver.ver ('vim', '8.0.0134', 'https://github.com/vim/vim/archive/v8.0.0134.tar.gz'), @@ -257,6 +287,15 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # Common Tarball Formats + # 1st Pass: Simplest case + # Assume name contains no digits and version contains no letters + + # name-ver.ver + ('libpng', '1.6.37', 'http://download.sourceforge.net/libpng/libpng-1.6.37.tar.gz'), + + # 2nd Pass: Version only + # Assume version contains no letters + # ver.ver ('eigen', '3.2.7', 'https://bitbucket.org/eigen/eigen/get/3.2.7.tar.bz2'), # ver.ver-ver @@ -266,10 +305,17 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # vver_ver ('luafilesystem', '1_6_3', 'https://github.com/keplerproject/luafilesystem/archive/v1_6_3.tar.gz'), - # No separators + # 3rd Pass: No separator characters are used + # Assume name contains no digits + + # namever ('turbolinux', '702', 'file://{0}/turbolinux702.tar.gz'.format(os.getcwd())), ('nauty', '26r7', 'http://pallini.di.uniroma1.it/nauty26r7.tar.gz'), - # Dashes only + + # 4th Pass: A single separator character is used + # Assume name contains no digits + + # name-name-ver-ver ('Trilinos', '12-10-1', 'https://github.com/trilinos/Trilinos/archive/trilinos-release-12-10-1.tar.gz'), ('panda', '2016-03-07', @@ -278,7 +324,7 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'http://gts.sourceforge.net/tarballs/gts-snapshot-121130.tar.gz'), ('cdd', '061a', 'http://www.cs.mcgill.ca/~fukuda/download/cdd/cdd-061a.tar.gz'), - # Only underscores + # name_name_ver_ver ('tinyxml', '2_6_2', 'https://sourceforge.net/projects/tinyxml/files/tinyxml/2.6.2/tinyxml_2_6_2.tar.gz'), ('boost', '1_55_0', @@ -287,9 +333,6 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): 'https://github.com/dhmunro/yorick/archive/y_2_2_04.tar.gz'), ('tbb', '44_20160413', 'https://www.threadingbuildingblocks.org/sites/default/files/software_releases/source/tbb44_20160413oss_src.tgz'), - - # Only dots - # name.name.ver.ver ('prank', '150803', 'http://wasabiapp.org/download/prank/prank.source.150803.tgz'), ('jpeg', '9b', 'http://www.ijg.org/files/jpegsrc.v9b.tar.gz'), @@ -302,61 +345,51 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): ('geant', '4.10.01.p03', 'http://geant4.cern.ch/support/source/geant4.10.01.p03.tar.gz'), ('tcl', '8.6.5', 'http://prdownloads.sourceforge.net/tcl/tcl8.6.5-src.tar.gz'), - # Dash and dots + # 5th Pass: Two separator characters are used + # Name may contain digits, version may contain letters # name-name-ver.ver - # digit in name ('m4', '1.4.17', 'https://ftp.gnu.org/gnu/m4/m4-1.4.17.tar.gz'), - # letter in version ('gmp', '6.0.0a', 'https://gmplib.org/download/gmp/gmp-6.0.0a.tar.bz2'), - # version starts with 'v' ('LaunchMON', '1.0.2', 'https://github.com/LLNL/LaunchMON/releases/download/v1.0.2/launchmon-v1.0.2.tar.gz'), # name-ver-ver.ver ('libedit', '20150325-3.1', 'http://thrysoee.dk/editline/libedit-20150325-3.1.tar.gz'), - - # Dash and unserscores - # name-name-ver_ver ('icu4c', '57_1', 'http://download.icu-project.org/files/icu4c/57.1/icu4c-57_1-src.tgz'), - - # Underscores and dots - # name_name_ver.ver ('superlu_dist', '4.1', 'http://crd-legacy.lbl.gov/~xiaoye/SuperLU/superlu_dist_4.1.tar.gz'), ('pexsi', '0.9.0', 'https://math.berkeley.edu/~linlin/pexsi/download/pexsi_v0.9.0.tar.gz'), # name_name.ver.ver ('fer', '696', 'ftp://ftp.pmel.noaa.gov/ferret/pub/source/fer_source.v696.tar.gz'), - - # Dash dot dah dot - + # name_name_ver-ver + ('Bridger', '2014-12-01', + 'https://downloads.sourceforge.net/project/rnaseqassembly/Bridger_r2014-12-01.tar.gz'), # name-name-ver.ver-ver.ver ('sowing', '1.1.23-p1', 'http://ftp.mcs.anl.gov/pub/petsc/externalpackages/sowing-1.1.23-p1.tar.gz'), ('bib2xhtml', '3.0-15-gf506', 'http://www.spinellis.gr/sw/textproc/bib2xhtml/bib2xhtml-v3.0-15-gf506.tar.gz'), # namever.ver-ver.ver ('go', '1.4-bootstrap-20161024', 'https://storage.googleapis.com/golang/go1.4-bootstrap-20161024.tar.gz'), - # Underscore dash dot + # 6th Pass: All three separator characters are used + # Name may contain digits, version may contain letters # name_name-ver.ver ('the_silver_searcher', '0.32.0', 'http://geoff.greer.fm/ag/releases/the_silver_searcher-0.32.0.tar.gz'), ('sphinx_rtd_theme', '0.1.10a0', 'https://pypi.python.org/packages/source/s/sphinx_rtd_theme/sphinx_rtd_theme-0.1.10a0.tar.gz'), - - # Dot underscore dot dash dot - # name.name_ver.ver-ver.ver ('TH.data', '1.0-8', 'https://cran.r-project.org/src/contrib/TH.data_1.0-8.tar.gz'), ('XML', '3.98-1.4', 'https://cran.r-project.org/src/contrib/XML_3.98-1.4.tar.gz'), - - # Dash dot underscore dot - # name-name-ver.ver_ver.ver ('pypar', '2.1.5_108', 'https://storage.googleapis.com/google-code-archive-downloads/v2/code.google.com/pypar/pypar-2.1.5_108.tgz'), # name-namever.ver_ver.ver ('STAR-CCM+', '11.06.010_02', 'file://{0}/STAR-CCM+11.06.010_02_linux-x86_64.tar.gz'.format(os.getcwd())), + # name-name_name-ver.ver + ('PerlIO-utf8_strict', '0.002', + 'http://search.cpan.org/CPAN/authors/id/L/LE/LEONT/PerlIO-utf8_strict-0.002.tar.gz'), # Various extensions # .tar.gz @@ -399,18 +432,61 @@ def test_url_parse_offset(name, noffset, ver, voffset, path): # .txz ('kim-api', '2.1.0', 'https://s3.openkim.org/kim-api/kim-api-2.1.0.txz'), - # Weird URLS + # 8th Pass: Query strings - # 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'), # suffix queries ('swiftsim', '0.3.0', 'http://gitlab.cosma.dur.ac.uk/swift/swiftsim/repository/archive.tar.gz?ref=v0.3.0'), - ('swiftsim', '0.3.0', 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), + ('swiftsim', '0.3.0', + 'https://gitlab.cosma.dur.ac.uk/api/v4/projects/swift%2Fswiftsim/repository/archive.tar.gz?sha=v0.3.0'), ('sionlib', '1.7.1', 'http://apps.fz-juelich.de/jsc/sionlib/download.php?version=1.7.1'), + ('jube2', '2.2.2', 'https://apps.fz-juelich.de/jsc/jube/jube2/download.php?version=2.2.2'), + ('archive', '1.0.0', 'https://code.ornl.gov/eck/papyrus/repository/archive.tar.bz2?ref=v1.0.0'), + ('VecGeom', '0.3.rc', + 'https://gitlab.cern.ch/api/v4/projects/VecGeom%2FVecGeom/repository/archive.tar.gz?sha=v0.3.rc'), + ('parsplice', '1.1', + 'https://gitlab.com/api/v4/projects/exaalt%2Fparsplice/repository/archive.tar.gz?sha=v1.1'), + ('busco', '2.0.1', 'https://gitlab.com/api/v4/projects/ezlab%2Fbusco/repository/archive.tar.gz?sha=2.0.1'), + ('libaec', '1.0.2', + 'https://gitlab.dkrz.de/api/v4/projects/k202009%2Flibaec/repository/archive.tar.gz?sha=v1.0.2'), + ('icet', '2.1.1', + 'https://gitlab.kitware.com/api/v4/projects/icet%2Ficet/repository/archive.tar.bz2?sha=IceT-2.1.1'), + ('vtk-m', '1.3.0', + 'https://gitlab.kitware.com/api/v4/projects/vtk%2Fvtk-m/repository/archive.tar.gz?sha=v1.3.0'), + ('GATK', '3.8-1-0-gf15c1c3ef', + 'https://software.broadinstitute.org/gatk/download/auth?package=GATK-archive&version=3.8-1-0-gf15c1c3ef'), # stem queries ('slepc', '3.6.2', 'http://slepc.upv.es/download/download.php?filename=slepc-3.6.2.tar.gz'), ('otf', '1.12.5salmon', 'http://wwwpub.zih.tu-dresden.de/%7Emlieber/dcount/dcount.php?package=otf&get=OTF-1.12.5salmon.tar.gz'), + ('eospac', '6.4.0beta.1', + 'http://laws-green.lanl.gov/projects/data/eos/get_file.php?package=eospac&filename=eospac_v6.4.0beta.1_r20171213193219.tgz'), + ('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 diff --git a/lib/spack/spack/url.py b/lib/spack/spack/url.py index 11b289a0b1..a298d44ea2 100644 --- a/lib/spack/spack/url.py +++ b/lib/spack/spack/url.py @@ -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), diff --git a/var/spack/repos/builtin/packages/adios/package.py b/var/spack/repos/builtin/packages/adios/package.py index 4b8e417a11..939ec797ab 100644 --- a/var/spack/repos/builtin/packages/adios/package.py +++ b/var/spack/repos/builtin/packages/adios/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/adios2/package.py b/var/spack/repos/builtin/packages/adios2/package.py index e5e10db996..29adcddaae 100644 --- a/var/spack/repos/builtin/packages/adios2/package.py +++ b/var/spack/repos/builtin/packages/adios2/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/adlbx/package.py b/var/spack/repos/builtin/packages/adlbx/package.py index e4e7c178f9..096a2cedd9 100644 --- a/var/spack/repos/builtin/packages/adlbx/package.py +++ b/var/spack/repos/builtin/packages/adlbx/package.py @@ -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): diff --git a/var/spack/repos/builtin/packages/alglib/package.py b/var/spack/repos/builtin/packages/alglib/package.py index 30a1c0b2c4..1f01fcc3f5 100644 --- a/var/spack/repos/builtin/packages/alglib/package.py +++ b/var/spack/repos/builtin/packages/alglib/package.py @@ -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): diff --git a/var/spack/repos/builtin/packages/allpaths-lg/package.py b/var/spack/repos/builtin/packages/allpaths-lg/package.py index c8d580d08e..dc2099948d 100644 --- a/var/spack/repos/builtin/packages/allpaths-lg/package.py +++ b/var/spack/repos/builtin/packages/allpaths-lg/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/amp/package.py b/var/spack/repos/builtin/packages/amp/package.py index 5410db4849..27bc465ffd 100644 --- a/var/spack/repos/builtin/packages/amp/package.py +++ b/var/spack/repos/builtin/packages/amp/package.py @@ -110,7 +110,7 @@ class Amp(CMakePackage): 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' % diff --git a/var/spack/repos/builtin/packages/aria2/package.py b/var/spack/repos/builtin/packages/aria2/package.py index 7cb7e3cfae..7518d3b488 100644 --- a/var/spack/repos/builtin/packages/aria2/package.py +++ b/var/spack/repos/builtin/packages/aria2/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/arm-forge/package.py b/var/spack/repos/builtin/packages/arm-forge/package.py index 94f853fef6..2434222796 100644 --- a/var/spack/repos/builtin/packages/arm-forge/package.py +++ b/var/spack/repos/builtin/packages/arm-forge/package.py @@ -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", ) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index de4c92c385..dd2576bb55 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/asagi/package.py b/var/spack/repos/builtin/packages/asagi/package.py index f24c83a68d..f99bad2f7e 100644 --- a/var/spack/repos/builtin/packages/asagi/package.py +++ b/var/spack/repos/builtin/packages/asagi/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/ascent/package.py b/var/spack/repos/builtin/packages/ascent/package.py index 8d8210edd1..4e31fa051e 100644 --- a/var/spack/repos/builtin/packages/ascent/package.py +++ b/var/spack/repos/builtin/packages/ascent/package.py @@ -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 @@ class Ascent(Package): 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 @@ class Ascent(Package): 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") diff --git a/var/spack/repos/builtin/packages/augustus/package.py b/var/spack/repos/builtin/packages/augustus/package.py index 18b30d29d4..c909ce102a 100644 --- a/var/spack/repos/builtin/packages/augustus/package.py +++ b/var/spack/repos/builtin/packages/augustus/package.py @@ -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 @@ class Augustus(MakefilePackage): 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')) diff --git a/var/spack/repos/builtin/packages/autofact/package.py b/var/spack/repos/builtin/packages/autofact/package.py index a22af26671..44bb89bff1 100644 --- a/var/spack/repos/builtin/packages/autofact/package.py +++ b/var/spack/repos/builtin/packages/autofact/package.py @@ -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 @@ class Autofact(Package): 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) diff --git a/var/spack/repos/builtin/packages/axl/package.py b/var/spack/repos/builtin/packages/axl/package.py index a524ca0643..85b5e0873d 100644 --- a/var/spack/repos/builtin/packages/axl/package.py +++ b/var/spack/repos/builtin/packages/axl/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/biopieces/package.py b/var/spack/repos/builtin/packages/biopieces/package.py index 2091f8508f..888ef18ccb 100644 --- a/var/spack/repos/builtin/packages/biopieces/package.py +++ b/var/spack/repos/builtin/packages/biopieces/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/breakdancer/package.py b/var/spack/repos/builtin/packages/breakdancer/package.py index 3ad2cdfc01..c943e88502 100644 --- a/var/spack/repos/builtin/packages/breakdancer/package.py +++ b/var/spack/repos/builtin/packages/breakdancer/package.py @@ -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 diff --git a/var/spack/repos/builtin/packages/bsseeker2/package.py b/var/spack/repos/builtin/packages/bsseeker2/package.py index 73fd8ca24b..5b78294250 100644 --- a/var/spack/repos/builtin/packages/bsseeker2/package.py +++ b/var/spack/repos/builtin/packages/bsseeker2/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/cares/package.py b/var/spack/repos/builtin/packages/c-ares/package.py index f3b35ee610..2311e4ac91 100644 --- a/var/spack/repos/builtin/packages/cares/package.py +++ b/var/spack/repos/builtin/packages/c-ares/package.py @@ -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" diff --git a/var/spack/repos/builtin/packages/c-blosc2/package.py b/var/spack/repos/builtin/packages/c-blosc2/package.py index 1596a9c1d5..450e93ed2c 100644 --- a/var/spack/repos/builtin/packages/c-blosc2/package.py +++ b/var/spack/repos/builtin/packages/c-blosc2/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/candle-benchmarks/package.py b/var/spack/repos/builtin/packages/candle-benchmarks/package.py index fb8401108d..5fcee8deeb 100644 --- a/var/spack/repos/builtin/packages/candle-benchmarks/package.py +++ b/var/spack/repos/builtin/packages/candle-benchmarks/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/catch/package.py b/var/spack/repos/builtin/packages/catch2/package.py index a9d8cb412b..939706c823 100644 --- a/var/spack/repos/builtin/packages/catch/package.py +++ b/var/spack/repos/builtin/packages/catch2/package.py @@ -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.') diff --git a/var/spack/repos/builtin/packages/cdo/package.py b/var/spack/repos/builtin/packages/cdo/package.py index 7711128186..0c0692852a 100644 --- a/var/spack/repos/builtin/packages/cdo/package.py +++ b/var/spack/repos/builtin/packages/cdo/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/ceed/README.md b/var/spack/repos/builtin/packages/ceed/README.md deleted file mode 100644 index 74bcae1d17..0000000000 --- a/var/spack/repos/builtin/packages/ceed/README.md +++ /dev/null @@ -1,3 +0,0 @@ -This is a bundle for the CEED software suite. - -See https://ceed.exascaleproject.org for details. diff --git a/var/spack/repos/builtin/packages/ceed/package.py b/var/spack/repos/builtin/packages/ceed/package.py index 4d598c03db..d594ac5544 100644 --- a/var/spack/repos/builtin/packages/ceed/package.py +++ b/var/spack/repos/builtin/packages/ceed/package.py @@ -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) diff --git a/var/spack/repos/builtin/packages/channelflow/package.py b/var/spack/repos/builtin/packages/channelflow/package.py index 4a22819678..fad8a1d018 100644 --- a/var/spack/repos/builtin/packages/channelflow/package.py +++ b/var/spack/repos/builtin/packages/channelflow/package.py @@ -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 @@ class Channelflow(CMakePackage): } 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 diff --git a/var/spack/repos/builtin/packages/check/package.py b/var/spack/repos/builtin/packages/check/package.py index ed7e933bc8..95076fdfc1 100644 --- a/var/spack/repos/builtin/packages/check/package.py +++ b/var/spack/repos/builtin/packages/check/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/clustalo/package.py b/var/spack/repos/builtin/packages/clustal-omega/package.py index 59b7606e6c..7c32f1f096 100644 --- a/var/spack/repos/builtin/packages/clustalo/package.py +++ b/var/spack/repos/builtin/packages/clustal-omega/package.py @@ -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/" diff --git a/var/spack/repos/builtin/packages/cmor/package.py b/var/spack/repos/builtin/packages/cmor/package.py index 31460e1645..ef8dd2f94b 100644 --- a/var/spack/repos/builtin/packages/cmor/package.py +++ b/var/spack/repos/builtin/packages/cmor/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/cppzmq/package.py b/var/spack/repos/builtin/packages/cppzmq/package.py index 0adaebf9c3..0a29b1b194 100644 --- a/var/spack/repos/builtin/packages/cppzmq/package.py +++ b/var/spack/repos/builtin/packages/cppzmq/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/cquery/package.py b/var/spack/repos/builtin/packages/cquery/package.py index 40edd13ce2..86ad88db71 100644 --- a/var/spack/repos/builtin/packages/cquery/package.py +++ b/var/spack/repos/builtin/packages/cquery/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/cub/package.py b/var/spack/repos/builtin/packages/cub/package.py index 9076ac78b1..17411dcddb 100644 --- a/var/spack/repos/builtin/packages/cub/package.py +++ b/var/spack/repos/builtin/packages/cub/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/czmq/package.py b/var/spack/repos/builtin/packages/czmq/package.py index b92de9106a..053d72aa2f 100644 --- a/var/spack/repos/builtin/packages/czmq/package.py +++ b/var/spack/repos/builtin/packages/czmq/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/damaris/package.py b/var/spack/repos/builtin/packages/damaris/package.py index 6c3ec891bd..6988973a7b 100644 --- a/var/spack/repos/builtin/packages/damaris/package.py +++ b/var/spack/repos/builtin/packages/damaris/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/davix/package.py b/var/spack/repos/builtin/packages/davix/package.py index 381251a62d..e1b66e6d39 100644 --- a/var/spack/repos/builtin/packages/davix/package.py +++ b/var/spack/repos/builtin/packages/davix/package.py @@ -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 diff --git a/var/spack/repos/builtin/packages/dbcsr/package.py b/var/spack/repos/builtin/packages/dbcsr/package.py index 0fef73b8fa..82a1cca300 100644 --- a/var/spack/repos/builtin/packages/dbcsr/package.py +++ b/var/spack/repos/builtin/packages/dbcsr/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 109b67da2d..9f1796f5b4 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -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 @@ class Dealii(CMakePackage, CudaPackage): # 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 @@ class Dealii(CMakePackage, CudaPackage): 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) diff --git a/var/spack/repos/builtin/packages/dislin/package.py b/var/spack/repos/builtin/packages/dislin/package.py index cfdffeb9ba..ca380ebb7a 100644 --- a/var/spack/repos/builtin/packages/dislin/package.py +++ b/var/spack/repos/builtin/packages/dislin/package.py @@ -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 @@ class Dislin(Package): 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') diff --git a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py index 5d9a3ef014..3a1b623ca0 100644 --- a/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py +++ b/var/spack/repos/builtin/packages/dotnet-core-sdk/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/eccodes/package.py b/var/spack/repos/builtin/packages/eccodes/package.py index 5bbc02f96b..8b8a4eceb7 100644 --- a/var/spack/repos/builtin/packages/eccodes/package.py +++ b/var/spack/repos/builtin/packages/eccodes/package.py @@ -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 @@ class Eccodes(CMakePackage): '-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') diff --git a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py index f86330613c..e099e2f1b1 100644 --- a/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py +++ b/var/spack/repos/builtin/packages/ecp-viz-sdk/package.py @@ -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): diff --git a/var/spack/repos/builtin/packages/elmer-fem/package.py b/var/spack/repos/builtin/packages/elmerfem/package.py index a22c1226f2..0fff28e817 100644 --- a/var/spack/repos/builtin/packages/elmer-fem/package.py +++ b/var/spack/repos/builtin/packages/elmerfem/package.py @@ -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 @@ class ElmerFem(CMakePackage): 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) diff --git a/var/spack/repos/builtin/packages/eqr/package.py b/var/spack/repos/builtin/packages/eq-r/package.py index e31f88bb39..76c10c82c5 100644 --- a/var/spack/repos/builtin/packages/eqr/package.py +++ b/var/spack/repos/builtin/packages/eq-r/package.py @@ -7,20 +7,18 @@ from spack import * 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] diff --git a/var/spack/repos/builtin/packages/er/package.py b/var/spack/repos/builtin/packages/er/package.py index 2edc201b97..0664b391e0 100644 --- a/var/spack/repos/builtin/packages/er/package.py +++ b/var/spack/repos/builtin/packages/er/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/es/package.py b/var/spack/repos/builtin/packages/es-shell/package.py index 99b846e96f..f8f745f488 100644 --- a/var/spack/repos/builtin/packages/es/package.py +++ b/var/spack/repos/builtin/packages/es-shell/package.py @@ -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 diff --git a/var/spack/repos/builtin/packages/esmf/package.py b/var/spack/repos/builtin/packages/esmf/package.py index bfe35d9f19..1f93eb372a 100644 --- a/var/spack/repos/builtin/packages/esmf/package.py +++ b/var/spack/repos/builtin/packages/esmf/package.py @@ -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 @@ class Esmf(MakefilePackage): 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. diff --git a/var/spack/repos/builtin/packages/exmcutils/package.py b/var/spack/repos/builtin/packages/exmcutils/package.py index 8d53b7a71a..bbd90d0ed0 100644 --- a/var/spack/repos/builtin/packages/exmcutils/package.py +++ b/var/spack/repos/builtin/packages/exmcutils/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/exodusii/package.py b/var/spack/repos/builtin/packages/exodusii/package.py index 6472b7b997..d4b38b19a6 100644 --- a/var/spack/repos/builtin/packages/exodusii/package.py +++ b/var/spack/repos/builtin/packages/exodusii/package.py @@ -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 @@ class Exodusii(CMakePackage): '-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'), diff --git a/var/spack/repos/builtin/packages/fastmath/package.py b/var/spack/repos/builtin/packages/fastmath/package.py index bc04da7237..463197cd97 100644 --- a/var/spack/repos/builtin/packages/fastmath/package.py +++ b/var/spack/repos/builtin/packages/fastmath/package.py @@ -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() diff --git a/var/spack/repos/builtin/packages/fastq-screen/package.py b/var/spack/repos/builtin/packages/fastq-screen/package.py index ef651a4c9d..7898ee31b4 100644 --- a/var/spack/repos/builtin/packages/fastq-screen/package.py +++ b/var/spack/repos/builtin/packages/fastq-screen/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/ferret/package.py b/var/spack/repos/builtin/packages/ferret/package.py index 0113dfba3a..47aff3cbf5 100644 --- a/var/spack/repos/builtin/packages/ferret/package.py +++ b/var/spack/repos/builtin/packages/ferret/package.py @@ -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 @@ class Ferret(Package): "-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, diff --git a/var/spack/repos/builtin/packages/flibcpp/package.py b/var/spack/repos/builtin/packages/flibcpp/package.py index b03fa79cbb..81d30b1568 100644 --- a/var/spack/repos/builtin/packages/flibcpp/package.py +++ b/var/spack/repos/builtin/packages/flibcpp/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/flux-core/package.py b/var/spack/repos/builtin/packages/flux-core/package.py index 11cb14d23c..e2b52f741c 100644 --- a/var/spack/repos/builtin/packages/flux-core/package.py +++ b/var/spack/repos/builtin/packages/flux-core/package.py @@ -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 @@ class FluxCore(AutotoolsPackage): 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'] diff --git a/var/spack/repos/builtin/packages/fpocket/package.py b/var/spack/repos/builtin/packages/fpocket/package.py index 5d5e92dc4d..a4516f0b10 100644 --- a/var/spack/repos/builtin/packages/fpocket/package.py +++ b/var/spack/repos/builtin/packages/fpocket/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/fstrack/package.py b/var/spack/repos/builtin/packages/fstrack/package.py index 297af6dbac..ffbb1714f5 100644 --- a/var/spack/repos/builtin/packages/fstrack/package.py +++ b/var/spack/repos/builtin/packages/fstrack/package.py @@ -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'): diff --git a/var/spack/repos/builtin/packages/funhpc/package.py b/var/spack/repos/builtin/packages/funhpc/package.py index ed69e4f88e..fe8adba18c 100644 --- a/var/spack/repos/builtin/packages/funhpc/package.py +++ b/var/spack/repos/builtin/packages/funhpc/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/gdal/package.py b/var/spack/repos/builtin/packages/gdal/package.py index 32e746472d..7e3fb6d8a0 100644 --- a/var/spack/repos/builtin/packages/gdal/package.py +++ b/var/spack/repos/builtin/packages/gdal/package.py @@ -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 @@ class Gdal(AutotoolsPackage): # 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') diff --git a/var/spack/repos/builtin/packages/gdl/package.py b/var/spack/repos/builtin/packages/gdl/package.py index eef7ada1c0..ab7a79c352 100644 --- a/var/spack/repos/builtin/packages/gdl/package.py +++ b/var/spack/repos/builtin/packages/gdl/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/ginkgo/package.py b/var/spack/repos/builtin/packages/ginkgo/package.py index 23d2b53495..bd94dbcab6 100644 --- a/var/spack/repos/builtin/packages/ginkgo/package.py +++ b/var/spack/repos/builtin/packages/ginkgo/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/gmsh/package.py b/var/spack/repos/builtin/packages/gmsh/package.py index 1e1d197295..3d3e3e4e53 100644 --- a/var/spack/repos/builtin/packages/gmsh/package.py +++ b/var/spack/repos/builtin/packages/gmsh/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/gmt/package.py b/var/spack/repos/builtin/packages/gmt/package.py index 045f4e11f6..c3dbbfc8e5 100644 --- a/var/spack/repos/builtin/packages/gmt/package.py +++ b/var/spack/repos/builtin/packages/gmt/package.py @@ -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 @@ class Gmt(Package): 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' ] diff --git a/var/spack/repos/builtin/packages/gnu-prolog/package.py b/var/spack/repos/builtin/packages/gprolog/package.py index d332711077..aa923deea8 100644 --- a/var/spack/repos/builtin/packages/gnu-prolog/package.py +++ b/var/spack/repos/builtin/packages/gprolog/package.py @@ -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" diff --git a/var/spack/repos/builtin/packages/grass/package.py b/var/spack/repos/builtin/packages/grass/package.py index f480d95fe3..ca070112a0 100644 --- a/var/spack/repos/builtin/packages/grass/package.py +++ b/var/spack/repos/builtin/packages/grass/package.py @@ -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 @@ class Grass(AutotoolsPackage): 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') diff --git a/var/spack/repos/builtin/packages/grib-api/package.py b/var/spack/repos/builtin/packages/grib-api/package.py index b54e909367..12978a4b75 100644 --- a/var/spack/repos/builtin/packages/grib-api/package.py +++ b/var/spack/repos/builtin/packages/grib-api/package.py @@ -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 @@ class GribApi(CMakePackage): '-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') diff --git a/var/spack/repos/builtin/packages/grpc/package.py b/var/spack/repos/builtin/packages/grpc/package.py index 20d09541ff..5c207d3358 100644 --- a/var/spack/repos/builtin/packages/grpc/package.py +++ b/var/spack/repos/builtin/packages/grpc/package.py @@ -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 = [ diff --git a/var/spack/repos/builtin/packages/guidance/package.py b/var/spack/repos/builtin/packages/guidance/package.py index ef4de4596c..32c75afeff 100644 --- a/var/spack/repos/builtin/packages/guidance/package.py +++ b/var/spack/repos/builtin/packages/guidance/package.py @@ -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 @@ class Guidance(MakefilePackage): 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) diff --git a/var/spack/repos/builtin/packages/hc/package.py b/var/spack/repos/builtin/packages/hc/package.py index 19fd4c6b4f..157b3ee6c7 100644 --- a/var/spack/repos/builtin/packages/hc/package.py +++ b/var/spack/repos/builtin/packages/hc/package.py @@ -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. diff --git a/var/spack/repos/builtin/packages/henson/package.py b/var/spack/repos/builtin/packages/henson/package.py index 11701e62d4..9e0b8d0ad7 100644 --- a/var/spack/repos/builtin/packages/henson/package.py +++ b/var/spack/repos/builtin/packages/henson/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/hisea/package.py b/var/spack/repos/builtin/packages/hisea/package.py index f934edbee5..6858452319 100644 --- a/var/spack/repos/builtin/packages/hisea/package.py +++ b/var/spack/repos/builtin/packages/hisea/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/homer/package.py b/var/spack/repos/builtin/packages/homer/package.py index bf190eb055..48063ce088 100644 --- a/var/spack/repos/builtin/packages/homer/package.py +++ b/var/spack/repos/builtin/packages/homer/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/hpgmg/package.py b/var/spack/repos/builtin/packages/hpgmg/package.py index 1805315130..9979fc4c6f 100644 --- a/var/spack/repos/builtin/packages/hpgmg/package.py +++ b/var/spack/repos/builtin/packages/hpgmg/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/hub/package.py b/var/spack/repos/builtin/packages/hub/package.py index 068e7b4a35..437c8b62a3 100644 --- a/var/spack/repos/builtin/packages/hub/package.py +++ b/var/spack/repos/builtin/packages/hub/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/ibmisc/package.py b/var/spack/repos/builtin/packages/ibmisc/package.py index 1e901220a3..3281301abf 100644 --- a/var/spack/repos/builtin/packages/ibmisc/package.py +++ b/var/spack/repos/builtin/packages/ibmisc/package.py @@ -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')) diff --git a/var/spack/repos/builtin/packages/image-magick/package.py b/var/spack/repos/builtin/packages/imagemagick/package.py index 2f9229c496..bbdc11213c 100644 --- a/var/spack/repos/builtin/packages/image-magick/package.py +++ b/var/spack/repos/builtin/packages/imagemagick/package.py @@ -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.""" diff --git a/var/spack/repos/builtin/packages/ioapi/package.py b/var/spack/repos/builtin/packages/ioapi/package.py index 2081d70754..0c66f4c51a 100644 --- a/var/spack/repos/builtin/packages/ioapi/package.py +++ b/var/spack/repos/builtin/packages/ioapi/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 7191faf234..655e5f4fee 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -237,7 +237,7 @@ class Julia(Package): 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( diff --git a/var/spack/repos/builtin/packages/kvtree/package.py b/var/spack/repos/builtin/packages/kvtree/package.py index 6f164b12d6..a9e2630ee3 100644 --- a/var/spack/repos/builtin/packages/kvtree/package.py +++ b/var/spack/repos/builtin/packages/kvtree/package.py @@ -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'] diff --git a/var/spack/repos/builtin/packages/lammps/package.py b/var/spack/repos/builtin/packages/lammps/package.py index 1b9e4c1fd8..413b8a924d 100644 --- a/var/spack/repos/builtin/packages/lammps/package.py +++ b/var/spack/repos/builtin/packages/lammps/package.py @@ -74,7 +74,7 @@ class Lammps(CMakePackage): 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') diff --git a/var/spack/repos/builtin/packages/libcheck/package.py b/var/spack/repos/builtin/packages/libcheck/package.py deleted file mode 100644 index 86886037f3..0000000000 --- a/var/spack/repos/builtin/packages/libcheck/package.py +++ /dev/null @@ -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') diff --git a/var/spack/repos/builtin/packages/libgit2/package.py b/var/spack/repos/builtin/packages/libgit2/package.py index 5ada427806..165ed6840a 100644 --- a/var/spack/repos/builtin/packages/libgit2/package.py +++ b/var/spack/repos/builtin/packages/libgit2/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/libgpuarray/package.py b/var/spack/repos/builtin/packages/libgpuarray/package.py index 1f26b75628..9ab2beba2b 100644 --- a/var/spack/repos/builtin/packages/libgpuarray/package.py +++ b/var/spack/repos/builtin/packages/libgpuarray/package.py @@ -25,4 +25,4 @@ class Libgpuarray(CMakePackage): depends_on('cuda') depends_on('cmake@3:', type='build') - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/libnrm/package.py b/var/spack/repos/builtin/packages/libnrm/package.py index ad79170f9e..178e4e7d34 100644 --- a/var/spack/repos/builtin/packages/libnrm/package.py +++ b/var/spack/repos/builtin/packages/libnrm/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/zeromq/package.py b/var/spack/repos/builtin/packages/libzmq/package.py index 7612bf5695..531d268f03 100644 --- a/var/spack/repos/builtin/packages/zeromq/package.py +++ b/var/spack/repos/builtin/packages/libzmq/package.py @@ -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/" diff --git a/var/spack/repos/builtin/packages/likwid/package.py b/var/spack/repos/builtin/packages/likwid/package.py index 411a6f8fe6..6e7c44ad99 100644 --- a/var/spack/repos/builtin/packages/likwid/package.py +++ b/var/spack/repos/builtin/packages/likwid/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/lsf/package.py b/var/spack/repos/builtin/packages/lsf/package.py index 7c8827c0bf..b257274c3a 100644 --- a/var/spack/repos/builtin/packages/lsf/package.py +++ b/var/spack/repos/builtin/packages/lsf/package.py @@ -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: diff --git a/var/spack/repos/builtin/packages/lua-bitlib/package.py b/var/spack/repos/builtin/packages/lua-bitlib/package.py index ca5d20764f..cf05980704 100644 --- a/var/spack/repos/builtin/packages/lua-bitlib/package.py +++ b/var/spack/repos/builtin/packages/lua-bitlib/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/lua-lpeg/package.py b/var/spack/repos/builtin/packages/lua-lpeg/package.py index 8d6d35d1ff..73f9d2e4c6 100644 --- a/var/spack/repos/builtin/packages/lua-lpeg/package.py +++ b/var/spack/repos/builtin/packages/lua-lpeg/package.py @@ -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") diff --git a/var/spack/repos/builtin/packages/lua-jit/package.py b/var/spack/repos/builtin/packages/lua-luajit/package.py index a0f8e2b88d..552096d716 100644 --- a/var/spack/repos/builtin/packages/lua-jit/package.py +++ b/var/spack/repos/builtin/packages/lua-luajit/package.py @@ -7,7 +7,7 @@ import os 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" diff --git a/var/spack/repos/builtin/packages/lua-mpack/package.py b/var/spack/repos/builtin/packages/lua-mpack/package.py index 777ff19e18..f332aba1e1 100644 --- a/var/spack/repos/builtin/packages/lua-mpack/package.py +++ b/var/spack/repos/builtin/packages/lua-mpack/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/macsio/package.py b/var/spack/repos/builtin/packages/macsio/package.py index d90aad340d..264e41590d 100644 --- a/var/spack/repos/builtin/packages/macsio/package.py +++ b/var/spack/repos/builtin/packages/macsio/package.py @@ -93,6 +93,6 @@ class Macsio(CMakePackage): .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 diff --git a/var/spack/repos/builtin/packages/maker/package.py b/var/spack/repos/builtin/packages/maker/package.py index 41363ec0a1..0528b3ed8f 100644 --- a/var/spack/repos/builtin/packages/maker/package.py +++ b/var/spack/repos/builtin/packages/maker/package.py @@ -55,7 +55,7 @@ class Maker(Package): 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') diff --git a/var/spack/repos/builtin/packages/mariadb/package.py b/var/spack/repos/builtin/packages/mariadb/package.py index 5990660d5d..774aeebf8c 100644 --- a/var/spack/repos/builtin/packages/mariadb/package.py +++ b/var/spack/repos/builtin/packages/mariadb/package.py @@ -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') diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py index a045e6d1ee..aeed3ed239 100644 --- a/var/spack/repos/builtin/packages/meme/package.py +++ b/var/spack/repos/builtin/packages/meme/package.py @@ -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): diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py index d8ff47d0b4..747fe707cd 100644 --- a/var/spack/repos/builtin/packages/mfem/package.py +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -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 @@ class Mfem(Package): 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: diff --git a/var/spack/repos/builtin/packages/moab/package.py b/var/spack/repos/builtin/packages/moab/package.py index 6ab1311309..b1b22cb281 100644 --- a/var/spack/repos/builtin/packages/moab/package.py +++ b/var/spack/repos/builtin/packages/moab/package.py @@ -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 @@ class Moab(AutotoolsPackage): 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') diff --git a/var/spack/repos/builtin/packages/libmongoc/package.py b/var/spack/repos/builtin/packages/mongo-c-driver/package.py index 0d3110a803..aeac6d31db 100644 --- a/var/spack/repos/builtin/packages/libmongoc/package.py +++ b/var/spack/repos/builtin/packages/mongo-c-driver/package.py @@ -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" diff --git a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py index 0f36e6174e..47732dcbb4 100644 --- a/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py +++ b/var/spack/repos/builtin/packages/mongo-cxx-driver/package.py @@ -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:') diff --git a/var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch b/var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch index 17e285b0bf..17e285b0bf 100644 --- a/var/spack/repos/builtin/packages/mpibash/mpibash-4.3.patch +++ b/var/spack/repos/builtin/packages/mpi-bash/mpibash-4.3.patch diff --git a/var/spack/repos/builtin/packages/mpibash/package.py b/var/spack/repos/builtin/packages/mpi-bash/package.py index 174109f6d9..5b3731fbbe 100644 --- a/var/spack/repos/builtin/packages/mpibash/package.py +++ b/var/spack/repos/builtin/packages/mpi-bash/package.py @@ -6,7 +6,7 @@ from spack import * -class Mpibash(AutotoolsPackage): +class MpiBash(AutotoolsPackage): """Parallel scripting right from the Bourne-Again Shell (Bash)""" homepage = "https://github.com/lanl/MPI-Bash" diff --git a/var/spack/repos/builtin/packages/mxnet/package.py b/var/spack/repos/builtin/packages/mxnet/package.py index 43796ab7d8..d261f60247 100644 --- a/var/spack/repos/builtin/packages/mxnet/package.py +++ b/var/spack/repos/builtin/packages/mxnet/package.py @@ -11,10 +11,9 @@ class Mxnet(MakefilePackage): designed for both efficiency and flexibility.""" homepage = "http://mxnet.io" - url = "https://github.com/apache/incubator-mxnet/archive/0.10.0.post2.tar.gz" + url = "https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz" - version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2', - url='https://github.com/apache/incubator-mxnet/releases/download/1.3.0/apache-mxnet-src-1.3.0-incubating.tar.gz') + version('1.3.0', sha256='c00d6fbb2947144ce36c835308e603f002c1eb90a9f4c5a62f4d398154eed4d2') variant('cuda', default=False, description='Enable CUDA support') variant('opencv', default=True, description='Enable OpenCV support') diff --git a/var/spack/repos/builtin/packages/nauty/package.py b/var/spack/repos/builtin/packages/nauty/package.py index 444629efd7..8e897c37d6 100644 --- a/var/spack/repos/builtin/packages/nauty/package.py +++ b/var/spack/repos/builtin/packages/nauty/package.py @@ -48,8 +48,8 @@ class Nauty(AutotoolsPackage): } # Iterate over patches for condition, urls in urls_for_patches.items(): - for url, sha256 in urls: - patch(url, when=condition, level=1, sha256=sha256) + for path, sha256 in urls: + patch(path, when=condition, level=1, sha256=sha256) depends_on('m4', type='build', when='@2.6r7') depends_on('autoconf', type='build', when='@2.6r7') diff --git a/var/spack/repos/builtin/packages/nccmp/package.py b/var/spack/repos/builtin/packages/nccmp/package.py index 6bf5fdb1b4..575b72a6ab 100644 --- a/var/spack/repos/builtin/packages/nccmp/package.py +++ b/var/spack/repos/builtin/packages/nccmp/package.py @@ -13,7 +13,7 @@ class Nccmp(Package): version('1.8.2.0', sha256='7f5dad4e8670568a71f79d2bcebb08d95b875506d3d5faefafe1a8b3afa14f18') - depends_on('netcdf') + depends_on('netcdf-c') def install(self, spec, prefix): # Configure says: F90 and F90FLAGS are replaced by FC and diff --git a/var/spack/repos/builtin/packages/ncl/package.py b/var/spack/repos/builtin/packages/ncl/package.py index c3940136c4..60e530bae9 100644 --- a/var/spack/repos/builtin/packages/ncl/package.py +++ b/var/spack/repos/builtin/packages/ncl/package.py @@ -42,7 +42,7 @@ class Ncl(Package): # Non-optional dependencies according to the manual: depends_on('jpeg') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('cairo+X+pdf') # Extra dependencies that may be missing from build system: @@ -65,7 +65,7 @@ class Ncl(Package): depends_on('bzip2') depends_on('freetype') - # In Spack, we do not have an option to compile netcdf without netcdf-4 + # In Spack, we do not have an option to compile netcdf-c without netcdf-4 # support, so we will tell the ncl configuration script that we want # support for netcdf-4, but the script assumes that hdf5 is compiled with # szip support. We introduce this restriction with the following dependency @@ -76,13 +76,13 @@ class Ncl(Package): # ESMF is only required at runtime (for ESMF_regridding.ncl) depends_on('esmf', type='run') - # In Spack, we also do not have an option to compile netcdf without DAP + # In Spack, we also do not have an option to compile netcdf-c without DAP # support, so we will tell the ncl configuration script that we have it. # Some of the optional dependencies according to the manual: depends_on('hdf', when='+hdf4') depends_on('gdal+proj@:2.4', when='+gdal') - depends_on('udunits2', when='+udunits2') + depends_on('udunits', when='+udunits2') # We need src files of triangle to appear in ncl's src tree if we want # triangle's features. @@ -123,8 +123,8 @@ class Ncl(Package): self.prepare_src_tree() make('Everything', parallel=False) - def setup_environment(self, spack_env, run_env): - run_env.set('NCARG_ROOT', self.spec.prefix) + def setup_run_environment(self, env): + env.set('NCARG_ROOT', self.spec.prefix) def prepare_site_config(self): fc_flags = [] diff --git a/var/spack/repos/builtin/packages/nco/package.py b/var/spack/repos/builtin/packages/nco/package.py index 951d6f5974..2fb78fcda2 100644 --- a/var/spack/repos/builtin/packages/nco/package.py +++ b/var/spack/repos/builtin/packages/nco/package.py @@ -30,10 +30,10 @@ class Nco(AutotoolsPackage): # See "Compilation Requirements" at: # http://nco.sourceforge.net/#bld - depends_on('netcdf') + depends_on('netcdf-c') depends_on('antlr@2.7.7+cxx') # required for ncap2 depends_on('gsl') # desirable for ncap2 - depends_on('udunits2') # allows dimensional unit transformations + depends_on('udunits') # allows dimensional unit transformations depends_on('flex', type='build') depends_on('bison', type='build') @@ -45,9 +45,9 @@ class Nco(AutotoolsPackage): spec = self.spec return ['--{0}-doc'.format('enable' if '+doc' in spec else 'disable')] - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec - spack_env.set('NETCDF_INC', spec['netcdf'].prefix.include) - spack_env.set('NETCDF_LIB', spec['netcdf'].prefix.lib) - spack_env.set('ANTLR_ROOT', spec['antlr'].prefix) - spack_env.set('UDUNITS2_PATH', spec['udunits2'].prefix) + env.set('NETCDF_INC', spec['netcdf-c'].prefix.include) + env.set('NETCDF_LIB', spec['netcdf-c'].prefix.lib) + env.set('ANTLR_ROOT', spec['antlr'].prefix) + env.set('UDUNITS2_PATH', spec['udunits'].prefix) diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index 3f1d6f4d8c..96666a29be 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -13,8 +13,8 @@ class Ncview(AutotoolsPackage): version('2.1.7', sha256='a14c2dddac0fc78dad9e4e7e35e2119562589738f4ded55ff6e0eca04d682c82') - depends_on('netcdf') - depends_on('udunits2') + depends_on('netcdf-c') + depends_on('udunits') depends_on('libpng') depends_on('libxaw') diff --git a/var/spack/repos/builtin/packages/netcdf/package.py b/var/spack/repos/builtin/packages/netcdf-c/package.py index 46a5695c58..e548848be0 100644 --- a/var/spack/repos/builtin/packages/netcdf/package.py +++ b/var/spack/repos/builtin/packages/netcdf-c/package.py @@ -16,13 +16,13 @@ def is_integral(x): return False -class Netcdf(AutotoolsPackage): - """NetCDF is a set of software libraries and self-describing, - machine-independent data formats that support the creation, access, - and sharing of array-oriented scientific data.""" +class NetcdfC(AutotoolsPackage): + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C distribution.""" homepage = "http://www.unidata.ucar.edu/software/netcdf" - git = "https://github.com/Unidata/netcdf-c" + git = "https://github.com/Unidata/netcdf-c.git" url = "https://www.gfd-dennou.org/arch/netcdf/unidata-mirror/netcdf-c-4.7.2.tar.gz" def url_for_version(self, version): @@ -45,7 +45,7 @@ class Netcdf(AutotoolsPackage): # Version 4.4.1.1 is having problems in tests # https://github.com/Unidata/netcdf-c/issues/343 version('4.4.1.1', sha256='4d44c6f4d02a8faf10ea619bfe1ba8224cd993024f4da12988c7465f663c8cae') - # netcdf@4.4.1 can crash on you (in real life and in tests). See: + # Version 4.4.1 can crash on you (in real life and in tests). See: # https://github.com/Unidata/netcdf-c/issues/282 version('4.4.1', sha256='8915cc69817f7af6165fbe69a8d1dfe21d5929d7cca9d10b10f568669ec6b342') version('4.4.0', sha256='0d40cb7845abd03c363abcd5f57f16e3c0685a0faf8badb2c59867452f6bcf78') @@ -121,20 +121,20 @@ class Netcdf(AutotoolsPackage): # Starting version 4.4.0, it became possible to disable parallel I/O even # if HDF5 supports it. For previous versions of the library we need # HDF5 without mpi support to disable parallel I/O. - # The following doesn't work if hdf5+mpi by default and netcdf~mpi is + # The following doesn't work if hdf5+mpi by default and netcdf-c~mpi is # specified in packages.yaml # depends_on('hdf5~mpi', when='@:4.3~mpi') # Thus, we have to introduce a conflict conflicts('~mpi', when='@:4.3^hdf5+mpi', - msg='netcdf@:4.3~mpi requires hdf5~mpi') + msg='netcdf-c@:4.3~mpi requires hdf5~mpi') # We need HDF5 with mpi support to enable parallel I/O. - # The following doesn't work if hdf5~mpi by default and netcdf+mpi is + # The following doesn't work if hdf5~mpi by default and netcdf-c+mpi is # specified in packages.yaml # depends_on('hdf5+mpi', when='+mpi') # Thus, we have to introduce a conflict conflicts('+mpi', when='^hdf5~mpi', - msg='netcdf+mpi requires hdf5+mpi') + msg='netcdf-c+mpi requires hdf5+mpi') # NetCDF 4.4.0 and prior have compatibility issues with HDF5 1.10 and later # https://github.com/Unidata/netcdf-c/issues/250 @@ -264,3 +264,10 @@ class Netcdf(AutotoolsPackage): def check(self): # h5_test fails when run in parallel make('check', parallel=False) + + @property + def libs(self): + shared = '+shared' in self.spec + return find_libraries( + 'libnetcdf', root=self.prefix, shared=shared, recursive=True + ) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx/package.py b/var/spack/repos/builtin/packages/netcdf-cxx/package.py index 94bb28412f..3c550e5669 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx/package.py @@ -17,7 +17,7 @@ class NetcdfCxx(AutotoolsPackage): version('4.2', sha256='95ed6ab49a0ee001255eac4e44aacb5ca4ea96ba850c08337a3e4c9a0872ccd1') - depends_on('netcdf') + depends_on('netcdf-c') variant( 'netcdf4', default=True, description='Compile with netCDF4 support') @@ -38,7 +38,7 @@ class NetcdfCxx(AutotoolsPackage): # Add these to LDFLAGS explicitly, so the linker doesn't accidentally # use system versions ldflags = [ - self.spec['netcdf'].libs.search_flags, + self.spec['netcdf-c'].libs.search_flags, self.spec['hdf5'].libs.search_flags, ] args.append('LDFLAGS=' + ' '.join(ldflags)) diff --git a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py index 938d74d6aa..b80b38be9e 100644 --- a/var/spack/repos/builtin/packages/netcdf-cxx4/package.py +++ b/var/spack/repos/builtin/packages/netcdf-cxx4/package.py @@ -7,7 +7,9 @@ from spack import * class NetcdfCxx4(AutotoolsPackage): - """C++ interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the C++ distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-cxx4-4.3.1.tar.gz" @@ -19,7 +21,7 @@ class NetcdfCxx4(AutotoolsPackage): # force its usage with this variant. variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('automake', type='build') depends_on('autoconf', type='build') @@ -32,7 +34,7 @@ class NetcdfCxx4(AutotoolsPackage): if name == 'cflags' and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append('-I' + self.spec['netcdf'].prefix.include) + flags.append('-I' + self.spec['netcdf-c'].prefix.include) return (None, None, flags) diff --git a/var/spack/repos/builtin/packages/netcdf-fortran/package.py b/var/spack/repos/builtin/packages/netcdf-fortran/package.py index d698ff1e8b..cfc4bc1018 100644 --- a/var/spack/repos/builtin/packages/netcdf-fortran/package.py +++ b/var/spack/repos/builtin/packages/netcdf-fortran/package.py @@ -7,7 +7,10 @@ from spack import * class NetcdfFortran(AutotoolsPackage): - """Fortran interface for NetCDF4""" + """NetCDF (network Common Data Form) is a set of software libraries and + machine-independent data formats that support the creation, access, and + sharing of array-oriented scientific data. This is the Fortran + distribution.""" homepage = "https://www.unidata.ucar.edu/software/netcdf" url = "https://www.unidata.ucar.edu/downloads/netcdf/ftp/netcdf-fortran-4.5.2.tar.gz" @@ -20,7 +23,7 @@ class NetcdfFortran(AutotoolsPackage): variant('pic', default=True, description='Produce position-independent code (for shared libs)') - depends_on('netcdf') + depends_on('netcdf-c') # The default libtool.m4 is too old to handle NAG compiler properly: # https://github.com/Unidata/netcdf-fortran/issues/94 @@ -30,14 +33,14 @@ class NetcdfFortran(AutotoolsPackage): if name in ['cflags', 'fflags'] and '+pic' in self.spec: flags.append(self.compiler.pic_flag) elif name == 'cppflags': - flags.append(self.spec['netcdf'].headers.cpp_flags) + flags.append(self.spec['netcdf-c'].headers.cpp_flags) elif name == 'ldflags': # We need to specify LDFLAGS to get correct dependency_libs # in libnetcdff.la, so packages that use libtool for linking # could correctly link to all the dependencies even when the # building takes place outside of Spack environment, i.e. # without Spack's compiler wrappers. - flags.append(self.spec['netcdf'].libs.search_flags) + flags.append(self.spec['netcdf-c'].libs.search_flags) return None, None, flags diff --git a/var/spack/repos/builtin/packages/nrm/package.py b/var/spack/repos/builtin/packages/nrm/package.py index b15bc11323..fa0b88201e 100644 --- a/var/spack/repos/builtin/packages/nrm/package.py +++ b/var/spack/repos/builtin/packages/nrm/package.py @@ -16,7 +16,7 @@ class Nrm(PythonPackage): depends_on('py-setuptools', type=('build')) depends_on('py-six', type=('build', 'run')) - depends_on('py-zmq@17.1.2', type=('build', 'run')) + depends_on('py-pyzmq@17.1.2', type=('build', 'run')) depends_on('py-pyyaml', type=('build', 'run')) depends_on('py-tornado@5.1.1', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/ntpoly/package.py b/var/spack/repos/builtin/packages/ntpoly/package.py index d390e19dba..75ba5a6890 100644 --- a/var/spack/repos/builtin/packages/ntpoly/package.py +++ b/var/spack/repos/builtin/packages/ntpoly/package.py @@ -16,7 +16,7 @@ class Ntpoly(CMakePackage): """ homepage = "https://william-dawson.github.io/NTPoly/" - url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1-alpha.tar.gz" + url = "https://github.com/william-dawson/NTPoly/archive/ntpoly-v2.3.1.tar.gz" version('2.3.1', sha256='af8c7690321607fbdee9671b9cb3acbed945148014e0541435858cf82bfd887e') diff --git a/var/spack/repos/builtin/packages/nut/package.py b/var/spack/repos/builtin/packages/nut/package.py index f159838c63..d5649fdaec 100644 --- a/var/spack/repos/builtin/packages/nut/package.py +++ b/var/spack/repos/builtin/packages/nut/package.py @@ -13,7 +13,7 @@ class Nut(CMakePackage): and performance issues.""" homepage = "https://github.com/lanl/NuT" - url = "https://github.com/lanl/NuT/archive/0.1.0.tar.gz" + url = "https://github.com/lanl/NuT/archive/0.1.1.tar.gz" git = "https://github.com/lanl/NuT.git" tags = ['proxy-app'] @@ -29,11 +29,11 @@ class Nut(CMakePackage): conflicts('%xl', when='@serial') conflicts('%nag', when='@serial') - def setup_environment(self, spack_env, run_env): - spack_env.set('RANDOM123_DIR', self.spec['random123'].prefix) - build_targets = ['VERBOSE=on'] + def setup_build_environment(self, env): + env.set('RANDOM123_DIR', self.spec['random123'].prefix) + def install(self, spec, prefix): install('README.md', prefix) mkdirp(prefix.bin) diff --git a/var/spack/repos/builtin/packages/octave/package.py b/var/spack/repos/builtin/packages/octave/package.py index cdfa076c73..f153ff839d 100644 --- a/var/spack/repos/builtin/packages/octave/package.py +++ b/var/spack/repos/builtin/packages/octave/package.py @@ -75,7 +75,7 @@ class Octave(AutotoolsPackage): depends_on('glpk', when='+glpk') depends_on('gl2ps', when='+gl2ps') depends_on('gnuplot', when='+gnuplot') - depends_on('image-magick', when='+magick') + depends_on('imagemagick', when='+magick') depends_on('hdf5', when='+hdf5') depends_on('java', when='+jdk') # TODO: requires Java 6 ? depends_on('llvm', when='+llvm') @@ -156,7 +156,7 @@ class Octave(AutotoolsPackage): if '+magick' in spec: config_args.append("--with-magick=%s" - % spec['image-magick'].prefix.lib) + % spec['imagemagick'].prefix.lib) else: config_args.append("--without-magick") diff --git a/var/spack/repos/builtin/packages/omega-h/package.py b/var/spack/repos/builtin/packages/omega-h/package.py index e459406164..0c9c323650 100644 --- a/var/spack/repos/builtin/packages/omega-h/package.py +++ b/var/spack/repos/builtin/packages/omega-h/package.py @@ -12,7 +12,7 @@ class OmegaH(CMakePackage): """ homepage = "https://github.com/SNLComputation/omega_h" - url = "https://github.com/SNLComputation/omega_h/archive/v9.13.4.tar.gz" + url = "https://github.com/SNLComputation/omega_h/archive/v9.29.0.tar.gz" git = "https://github.com/SNLComputation/omega_h.git" maintainers = ['ibaned'] diff --git a/var/spack/repos/builtin/packages/openldap/package.py b/var/spack/repos/builtin/packages/openldap/package.py index 3c8a9e453e..2bd92a41f4 100644 --- a/var/spack/repos/builtin/packages/openldap/package.py +++ b/var/spack/repos/builtin/packages/openldap/package.py @@ -17,7 +17,7 @@ class Openldap(AutotoolsPackage): """ homepage = "https://www.openldap.org/" - url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.9.tgz" + url = "ftp://ftp.openldap.org/pub/OpenLDAP/openldap-release/openldap-2.4.48.tgz" version('2.4.48', sha256='d9523ffcab5cd14b709fcf3cb4d04e8bc76bb8970113255f372bc74954c6074d') diff --git a/var/spack/repos/builtin/packages/openpmd-api/package.py b/var/spack/repos/builtin/packages/openpmd-api/package.py index fe9972776f..6dc7c89d78 100644 --- a/var/spack/repos/builtin/packages/openpmd-api/package.py +++ b/var/spack/repos/builtin/packages/openpmd-api/package.py @@ -33,7 +33,7 @@ class OpenpmdApi(CMakePackage): depends_on('cmake@3.11.0:', type='build') depends_on('mpark-variant@1.4.0:') - depends_on('catch@2.6.1: ~single_header', type='test') + depends_on('catch2@2.6.1: ~single_header', type='test') depends_on('mpi@2.3:', when='+mpi') # might become MPI 3.0+ depends_on('hdf5@1.8.13:', when='+hdf5') depends_on('hdf5@1.8.13: ~mpi', when='~mpi +hdf5') @@ -93,25 +93,24 @@ class OpenpmdApi(CMakePackage): return args - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec # pre-load dependent CMake-PUBLIC header-only libs - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) - run_env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpark-variant'].prefix) + env.prepend_path('CPATH', spec['mpark-variant'].prefix.include) # more deps searched in openPMDConfig.cmake if spec.satisfies("+mpi"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['mpi'].prefix) if spec.satisfies("+adios1"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios'].prefix) if spec.satisfies("+adios2"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['adios2'].prefix) if spec.satisfies("+hdf5"): - run_env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) + env.prepend_path('CMAKE_PREFIX_PATH', spec['hdf5'].prefix) - def setup_dependent_environment(self, spack_env, run_env, dependent_spec): + def setup_dependent_build_environment(self, env, dependent_spec): # pre-load dependent CMake-PUBLIC header-only libs - spack_env.prepend_path('CMAKE_PREFIX_PATH', - self.spec['mpark-variant'].prefix) - spack_env.prepend_path('CPATH', - self.spec['mpark-variant'].prefix.include) + env.prepend_path('CMAKE_PREFIX_PATH', + self.spec['mpark-variant'].prefix) + prepend_path('CPATH', self.spec['mpark-variant'].prefix.include) diff --git a/var/spack/repos/builtin/packages/pagit/package.py b/var/spack/repos/builtin/packages/pagit/package.py index 7cc1496b53..3bce58cd39 100644 --- a/var/spack/repos/builtin/packages/pagit/package.py +++ b/var/spack/repos/builtin/packages/pagit/package.py @@ -18,10 +18,6 @@ class Pagit(Package): depends_on('java', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - def url_for_version(self, version): - url = 'ftp://ftp.sanger.ac.uk/pub/resources/software/pagit/PAGIT.V{0}.64bit.tgz' - return url.format(version) - def install(self, spec, prefix): with working_dir('PAGIT'): install_tree('ABACAS', prefix.ABACAS) @@ -31,19 +27,18 @@ class Pagit(Package): install_tree('lib', prefix.lib) install_tree('RATT', prefix.RATT) - def setup_environment(self, spack_env, run_env): - run_env.set('PAGIT_HOME', self.prefix) - run_env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) - run_env.set('ICORN_HOME', self.prefix.icorn) - run_env.set('SNPOMATIC_HOME', self.prefix.bin) - run_env.set('RATT_HOME', self.prefix.RATT) - run_env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', - 'ssaha2')) - run_env.prepend_path('PATH', join_path(self.prefix.bin, - 'pileup_v0.5')) - run_env.prepend_path('PATH', self.prefix.IMAGE) - run_env.prepend_path('PATH', self.prefix.ABACAS) - run_env.prepend_path('PATH', self.prefix.ICORN) - run_env.prepend_path('PATH', self.prefix.RATT) - run_env.prepend_path('PERL5LIB', self.prefix.lib) + def setup_run_environment(self, env): + env.set('PAGIT_HOME', self.prefix) + env.set('PILEUP_HOME', join_path(self.prefix.bin, 'pileup_v0.5')) + env.set('ICORN_HOME', self.prefix.icorn) + env.set('SNPOMATIC_HOME', self.prefix.bin) + env.set('RATT_HOME', self.prefix.RATT) + env.set('RATT_CONFIG', join_path(self.prefix.RATT, 'RATT_config')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5', + 'ssaha2')) + env.prepend_path('PATH', join_path(self.prefix.bin, 'pileup_v0.5')) + env.prepend_path('PATH', self.prefix.IMAGE) + env.prepend_path('PATH', self.prefix.ABACAS) + env.prepend_path('PATH', self.prefix.ICORN) + env.prepend_path('PATH', self.prefix.RATT) + env.prepend_path('PERL5LIB', self.prefix.lib) diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index e19039caa5..0ca4ef375f 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -93,7 +93,7 @@ class Paraview(CMakePackage, CudaPackage): depends_on('libpng') depends_on('libtiff') depends_on('libxml2') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('expat') # depends_on('netcdf-cxx') # depends_on('protobuf') # version mismatches? @@ -127,7 +127,7 @@ class Paraview(CMakePackage, CudaPackage): """The paraview subdirectory name as paraview-major.minor""" return 'paraview-{0}'.format(self.spec.version.up_to(2)) - def setup_dependent_build_environment(self, env): + def setup_dependent_build_environment(self, env, dependent_spec): if os.path.isdir(self.prefix.lib64): lib_dir = self.prefix.lib64 else: diff --git a/var/spack/repos/builtin/packages/parquet/package.py b/var/spack/repos/builtin/packages/parquet-cpp/package.py index ac130b359f..de6559dc5e 100644 --- a/var/spack/repos/builtin/packages/parquet/package.py +++ b/var/spack/repos/builtin/packages/parquet-cpp/package.py @@ -6,7 +6,7 @@ from spack import * -class Parquet(CMakePackage): +class ParquetCpp(CMakePackage): """C++ bindings for the Apache Parquet columnar data format. """ diff --git a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py index 98c0a488d9..0c299e06b4 100644 --- a/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py +++ b/var/spack/repos/builtin/packages/perl-alien-libxml2/package.py @@ -10,7 +10,7 @@ class PerlAlienLibxml2(PerlPackage): """This module provides libxml2 for other modules to use.""" homepage = "https://metacpan.org/pod/Alien::Libxml2" - url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.09.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PL/PLICEASE/Alien-Libxml2-0.10_01.tar.gz" version('0.10_01', sha256='2f45b308b33503292f48bf46a75fe1e653d6b209ba5caf0628d8cc103f8d61ac') diff --git a/var/spack/repos/builtin/packages/perl-bio-perl/package.py b/var/spack/repos/builtin/packages/perl-bioperl/package.py index a8680d8b2e..8f585b376e 100644 --- a/var/spack/repos/builtin/packages/perl-bio-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-bioperl/package.py @@ -7,7 +7,7 @@ from spack import * import inspect -class PerlBioPerl(PerlPackage): +class PerlBioperl(PerlPackage): """BioPerl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. These objects not only do what they are @@ -36,8 +36,7 @@ class PerlBioPerl(PerlPackage): url = "https://cpan.metacpan.org/authors/id/C/CD/CDRAUG/BioPerl-1.7.6.tar.gz" version('1.7.6', sha256='df2a3efc991b9b5d7cc9d038a1452c6dac910c9ad2a0e47e408dd692c111688d') - version('1.7.2', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1', - url="http://search.cpan.org/CPAN/authors/id/C/CJ/CJFIELDS/BioPerl-1.007002.tar.gz") + version('1.007002', sha256='17aa3aaab2f381bbcaffdc370002eaf28f2c341b538068d6586b2276a76464a1') # According to cpandeps.grinnz.com Module-Build is both a build and run # time dependency for BioPerl diff --git a/var/spack/repos/builtin/packages/perl-dbfile/package.py b/var/spack/repos/builtin/packages/perl-db-file/package.py index 19cc9410c1..ff7263517f 100644 --- a/var/spack/repos/builtin/packages/perl-dbfile/package.py +++ b/var/spack/repos/builtin/packages/perl-db-file/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlDbfile(PerlPackage): +class PerlDbFile(PerlPackage): """DB_File is a module which allows Perl programs to make use of the facilities provided by Berkeley DB version 1.x (if you have a newer version of DB, see "Using DB_File with Berkeley DB version 2 or greater"). diff --git a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py index 9dfdc5ae98..386add30e4 100644 --- a/var/spack/repos/builtin/packages/perl-devel-symdump/package.py +++ b/var/spack/repos/builtin/packages/perl-devel-symdump/package.py @@ -10,6 +10,6 @@ class PerlDevelSymdump(PerlPackage): """Devel::Symdump - dump symbol names or the symbol table""" homepage = "https://metacpan.org/pod/Devel::Symdump" - url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.18.tar.gz" + url = "https://cpan.metacpan.org/authors/id/A/AN/ANDK/Devel-Symdump-2.0604.tar.gz" version('2.0604', sha256='1f9eaa557733f775ccaa852e846566274c017e6fee380aeb8d08e425cfa86d3e') diff --git a/var/spack/repos/builtin/packages/perl-file-chdir/package.py b/var/spack/repos/builtin/packages/perl-file-chdir/package.py index b628ca12e5..e26adb298f 100644 --- a/var/spack/repos/builtin/packages/perl-file-chdir/package.py +++ b/var/spack/repos/builtin/packages/perl-file-chdir/package.py @@ -18,6 +18,6 @@ class PerlFileChdir(PerlPackage): combine all the power of chdir(), File::Spec and Cwd.""" homepage = "https://metacpan.org/pod/File::chdir" - url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1010.tar.gz" + url = "https://cpan.metacpan.org/authors/id/D/DA/DAGOLDEN/File-chdir-0.1011.tar.gz" version('0.1011', sha256='31ebf912df48d5d681def74b9880d78b1f3aca4351a0ed1fe3570b8e03af6c79') diff --git a/var/spack/repos/builtin/packages/perl-gd-graph/package.py b/var/spack/repos/builtin/packages/perl-gdgraph/package.py index a4c83eefc4..98f015db35 100644 --- a/var/spack/repos/builtin/packages/perl-gd-graph/package.py +++ b/var/spack/repos/builtin/packages/perl-gdgraph/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlGdGraph(PerlPackage): +class PerlGdgraph(PerlPackage): """Graph Plotting Module for Perl 5""" homepage = "http://search.cpan.org/~bwarfield/GDGraph/Graph.pm" @@ -16,5 +16,5 @@ class PerlGdGraph(PerlPackage): depends_on('perl-capture-tiny', type=('build', 'run')) depends_on('perl-test-exception', type=('build', 'run')) - depends_on('perl-gd-text', type=('build', 'run')) + depends_on('perl-gdtextutil', type=('build', 'run')) depends_on('perl-gd', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-gd-text/package.py b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py index 1988eeaf70..929ac0e34e 100644 --- a/var/spack/repos/builtin/packages/perl-gd-text/package.py +++ b/var/spack/repos/builtin/packages/perl-gdtextutil/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlGdText(PerlPackage): +class PerlGdtextutil(PerlPackage): """Text utilities for use with GD""" homepage = "http://search.cpan.org/~mverb/GDTextUtil-0.86/Text.pm" diff --git a/var/spack/repos/builtin/packages/perl-io-prompt/package.py b/var/spack/repos/builtin/packages/perl-io-prompt/package.py index 2bf4144990..4734a3bc55 100644 --- a/var/spack/repos/builtin/packages/perl-io-prompt/package.py +++ b/var/spack/repos/builtin/packages/perl-io-prompt/package.py @@ -31,5 +31,5 @@ class PerlIoPrompt(PerlPackage): depends_on('perl-module-build', type='build') - depends_on('perl-term-readkey', type=('build', 'run')) + depends_on('perl-termreadkey', type=('build', 'run')) depends_on('perl-want', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-io-tty/package.py b/var/spack/repos/builtin/packages/perl-io-tty/package.py index 217b4fb71b..332a09e2f4 100644 --- a/var/spack/repos/builtin/packages/perl-io-tty/package.py +++ b/var/spack/repos/builtin/packages/perl-io-tty/package.py @@ -12,6 +12,6 @@ class PerlIoTty(PerlPackage): For a list of importable constants, see IO::Tty::Constant.""" homepage = "https://metacpan.org/pod/IO::Tty" - url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/T/TO/TODDR/IO-Tty-1.13_01.tar.gz" version('1.13_01', sha256='89798eba7c31d9c169ef2f38ff49490aa769b1d9a68033de365595cfaf9cc258') diff --git a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py index 63a36a0e65..b57ee53bbd 100644 --- a/var/spack/repos/builtin/packages/perl-libwww-perl/package.py +++ b/var/spack/repos/builtin/packages/perl-libwww-perl/package.py @@ -16,6 +16,7 @@ class PerlLibwwwPerl(PerlPackage): url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.33.tar.gz" version('6.33', sha256='97417386f11f007ae129fe155b82fd8969473ce396a971a664c8ae6850c69b99') + version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') depends_on('perl-encode-locale', type=('build', 'run')) depends_on('perl-file-listing', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py index ef7faad32c..9b1db2e856 100644 --- a/var/spack/repos/builtin/packages/perl-log-log4perl/package.py +++ b/var/spack/repos/builtin/packages/perl-log-log4perl/package.py @@ -10,6 +10,6 @@ class PerlLogLog4perl(PerlPackage): """Log4j implementation for Perl""" homepage = "http://search.cpan.org/~mschilli/Log-Log4perl-1.44/lib/Log/Log4perl.pm" - url = "https://github.com/mschilli/log4perl/archive/rel_146.tar.gz" + url = "https://cpan.metacpan.org/authors/id/M/MS/MSCHILLI/Log-Log4perl-1.46.tar.gz" - version('146', sha256='a361e483095795753b97f8a506b40c24c753cf73828bb8697665499ef8596402') + version('1.46', sha256='31011a17c04e78016e73eaa4865d0481d2ffc3dc22813c61065d90ad73c64e6f') diff --git a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py index 0974a00bc7..5567f6fbd2 100644 --- a/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py +++ b/var/spack/repos/builtin/packages/perl-lwp-protocol-https/package.py @@ -18,4 +18,4 @@ class PerlLwpProtocolHttps(PerlPackage): depends_on('perl-io-socket-ssl', type=('build', 'run')) depends_on('perl-net-http', type=('build', 'run')) depends_on('perl-mozilla-ca', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-lwp/package.py b/var/spack/repos/builtin/packages/perl-lwp/package.py deleted file mode 100644 index 4cbe00854e..0000000000 --- a/var/spack/repos/builtin/packages/perl-lwp/package.py +++ /dev/null @@ -1,26 +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 PerlLwp(PerlPackage): - """The World-Wide Web library for Perl""" - - homepage = "http://search.cpan.org/~oalders/libwww-perl-6.29/lib/LWP.pm" - url = "http://search.cpan.org/CPAN/authors/id/O/OA/OALDERS/libwww-perl-6.29.tar.gz" - - version('6.29', sha256='4c6f2697999d2d0e6436b584116b12b30dc39990ec0622751c1a6cec2c0e6662') - - depends_on('perl-test-requiresinternet', type=('build', 'run')) - depends_on('perl-http-message', type=('build', 'run')) - depends_on('perl-file-listing', type=('build', 'run')) - depends_on('perl-http-daemon', type=('build', 'run')) - depends_on('perl-html-parser', type=('build', 'run')) - depends_on('perl-http-cookies', type=('build', 'run')) - depends_on('perl-www-robotrules', type=('build', 'run')) - depends_on('perl-test-fatal', type=('build', 'run')) - depends_on('perl-http-negotiate', type=('build', 'run')) - depends_on('perl-net-http', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/perl-version/package.py b/var/spack/repos/builtin/packages/perl-perl-version/package.py index a1413c0c37..68155b87e8 100644 --- a/var/spack/repos/builtin/packages/perl-version/package.py +++ b/var/spack/repos/builtin/packages/perl-perl-version/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlVersion(PerlPackage): +class PerlPerlVersion(PerlPackage): """Parse and manipulate Perl version strings""" homepage = "http://search.cpan.org/~bdfoy/Perl-Version-1.013/lib/Perl/Version.pm" diff --git a/var/spack/repos/builtin/packages/perl-intervaltree/package.py b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py index 5f875cdd6e..96ed744908 100644 --- a/var/spack/repos/builtin/packages/perl-intervaltree/package.py +++ b/var/spack/repos/builtin/packages/perl-set-intervaltree/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlIntervaltree(PerlPackage): +class PerlSetIntervaltree(PerlPackage): """Set::IntervalTree uses Interval Trees to store and efficiently look up ranges using a range-based lookup.""" diff --git a/var/spack/repos/builtin/packages/perl-star-fusion/package.py b/var/spack/repos/builtin/packages/perl-star-fusion/package.py index ccab3095ad..625546c9c8 100644 --- a/var/spack/repos/builtin/packages/perl-star-fusion/package.py +++ b/var/spack/repos/builtin/packages/perl-star-fusion/package.py @@ -23,9 +23,9 @@ class PerlStarFusion(Package): depends_on('star', type=('build', 'run')) depends_on('perl', type=('build', 'run')) - depends_on('perl-intervaltree', type=('build', 'run')) + depends_on('perl-set-intervaltree', type=('build', 'run')) depends_on('perl-dbi', type=('build', 'run')) - depends_on('perl-dbfile', type=('build', 'run')) + depends_on('perl-db-file', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/perl-term-readkey/package.py b/var/spack/repos/builtin/packages/perl-termreadkey/package.py index 0e89420d33..f764964d29 100644 --- a/var/spack/repos/builtin/packages/perl-term-readkey/package.py +++ b/var/spack/repos/builtin/packages/perl-termreadkey/package.py @@ -6,7 +6,7 @@ from spack import * -class PerlTermReadkey(PerlPackage): +class PerlTermreadkey(PerlPackage): """Term::ReadKey is a compiled perl module dedicated to providing simple control over terminal driver modes (cbreak, raw, cooked, etc.,) support for non-blocking reads, if the architecture allows, and some generalized diff --git a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py index cb7e58bcd1..ef816a95e8 100644 --- a/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py +++ b/var/spack/repos/builtin/packages/perl-xml-namespacesupport/package.py @@ -12,6 +12,6 @@ class PerlXmlNamespacesupport(PerlPackage): prefix to namespace URI map, and provides a number of basic checks.""" homepage = "https://metacpan.org/pod/XML::NamespaceSupport" - url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12.tar.gz" + url = "https://cpan.metacpan.org/authors/id/P/PE/PERIGRIN/XML-NamespaceSupport-1.12_9.tar.gz" version('1.12_9', sha256='2e84a057f0a8c845a612d212742cb94fca4fc8a433150b5721bd448f77d1e4a9') diff --git a/var/spack/repos/builtin/packages/pism/package.py b/var/spack/repos/builtin/packages/pism/package.py index 10bc658dff..356b726cb4 100644 --- a/var/spack/repos/builtin/packages/pism/package.py +++ b/var/spack/repos/builtin/packages/pism/package.py @@ -10,7 +10,7 @@ class Pism(CMakePackage): """Parallel Ice Sheet Model""" homepage = "http://pism-docs.org/wiki/doku.php:=" - url = "https://github.com/pism/pism/archive/v0.7.3.tar.gz" + url = "https://github.com/pism/pism/archive/v1.1.4.tar.gz" git = "https://github.com/pism/pism.git" maintainers = ['citibeth'] @@ -73,9 +73,9 @@ class Pism(CMakePackage): depends_on('fftw') depends_on('gsl') depends_on('mpi') - depends_on('netcdf') # Only the C interface is used, no netcdf-cxx4 + depends_on('netcdf-c') # Only the C interface is used, no netcdf-cxx4 depends_on('petsc') - depends_on('udunits2') + depends_on('udunits') depends_on('proj@:4') depends_on('everytrace', when='+everytrace') @@ -116,7 +116,7 @@ class Pism(CMakePackage): '-DPism_USE_EVERYTRACE=%s' % ('YES' if '+everytrace' in spec else 'NO')] - def setup_environment(self, spack_env, env): + def setup_run_environment(self, env): env.set('PISM_PREFIX', self.prefix) env.set('PISM_BIN', self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/prank/package.py b/var/spack/repos/builtin/packages/prank/package.py index 0eb0050d34..d45eadb028 100644 --- a/var/spack/repos/builtin/packages/prank/package.py +++ b/var/spack/repos/builtin/packages/prank/package.py @@ -10,7 +10,7 @@ class Prank(Package): """A powerful multiple sequence alignment browser.""" homepage = "http://wasabiapp.org/software/prank/" - url = "http://wasabiapp.org/download/prank/prank.source.150803.tgz" + url = "http://wasabiapp.org/download/prank/prank.source.170427.tgz" version('170427', sha256='623eb5e9b5cb0be1f49c3bf715e5fabceb1059b21168437264bdcd5c587a8859') diff --git a/var/spack/repos/builtin/packages/ps-lite/package.py b/var/spack/repos/builtin/packages/ps-lite/package.py index 92a0b7ff88..9d20d09d55 100644 --- a/var/spack/repos/builtin/packages/ps-lite/package.py +++ b/var/spack/repos/builtin/packages/ps-lite/package.py @@ -17,6 +17,6 @@ class PsLite(CMakePackage): version('20170328', commit='acdb698fa3bb80929ef83bb37c705f025e119b82') depends_on('protobuf@3:') - depends_on('zeromq') + depends_on('libzmq') patch('cmake.patch') diff --git a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py index 029745dec1..5d949c053a 100644 --- a/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py +++ b/var/spack/repos/builtin/packages/py-avro-json-serializer/package.py @@ -10,9 +10,9 @@ class PyAvroJsonSerializer(PythonPackage): """Serializes data into a JSON format using AVRO schema.""" homepage = "https://github.com/linkedin/python-avro-json-serializer" - url = "https://github.com/linkedin/python-avro-json-serializer/archive/0.4.tar.gz" + url = "https://pypi.io/packages/source/a/avro_json_serializer/avro_json_serializer-0.4.tar.gz" - version('0.4', sha256='58df57e6c85b1b453668eb0bff2b049efcfd83d6e5dfa72cee1df220f330820d') + version('0.4', sha256='f9dac2dac92036c5dd5aba8c716545fc0a0630cc365a51ab15bc2ac47eac28f1') depends_on('py-setuptools', type='build') depends_on('py-simplejson', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-brian2/package.py b/var/spack/repos/builtin/packages/py-brian2/package.py index 5ebb9f85bc..0d79bb5c5e 100644 --- a/var/spack/repos/builtin/packages/py-brian2/package.py +++ b/var/spack/repos/builtin/packages/py-brian2/package.py @@ -24,6 +24,6 @@ class PyBrian2(PythonPackage): depends_on('py-sympy@0.7.6:', type=('build', 'run')) depends_on('py-pyparsing', type=('build', 'run')) depends_on('py-jinja2@2.7:', type=('build', 'run')) - depends_on('py-cpuinfo@0.1.6:', type=('build', 'run')) + depends_on('py-py-cpuinfo@0.1.6:', type=('build', 'run')) depends_on('py-sphinx@1.4.2:', type=('build', 'run'), when='+docs') depends_on('py-nosetests@1.0:', type='test') diff --git a/var/spack/repos/builtin/packages/py-cdat-lite/package.py b/var/spack/repos/builtin/packages/py-cdat-lite/package.py index facb14a43f..19614e5cba 100644 --- a/var/spack/repos/builtin/packages/py-cdat-lite/package.py +++ b/var/spack/repos/builtin/packages/py-cdat-lite/package.py @@ -17,7 +17,7 @@ class PyCdatLite(PythonPackage): version('6.0.1', sha256='092ae4ff1fb03dee00096e8dd595b769b422759ce972d96525950adf8e1c9374') - depends_on("netcdf") + depends_on("netcdf-c") depends_on("python@2.5:2.8", type=('build', 'run')) depends_on("py-numpy", type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-cf-units/package.py b/var/spack/repos/builtin/packages/py-cf-units/package.py index aaa2505d10..ea7634afbb 100644 --- a/var/spack/repos/builtin/packages/py-cf-units/package.py +++ b/var/spack/repos/builtin/packages/py-cf-units/package.py @@ -26,4 +26,4 @@ class PyCfUnits(PythonPackage): depends_on('py-numpy', type=('build', 'run')) depends_on('py-antlr4-python3-runtime', type=('build', 'run')) depends_on('py-pytest-runner', type=('build')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/py-espressopp/package.py b/var/spack/repos/builtin/packages/py-espressopp/package.py index 95bf54a8e9..8111ba1e80 100644 --- a/var/spack/repos/builtin/packages/py-espressopp/package.py +++ b/var/spack/repos/builtin/packages/py-espressopp/package.py @@ -14,7 +14,7 @@ class PyEspressopp(CMakePackage): atomistic or bead-spring models as they are used in soft matter research """ homepage = "https://espressopp.github.io" - url = "https://github.com/espressopp/espressopp/tarball/v1.9.4.1" + url = "https://github.com/espressopp/espressopp/tarball/v2.0.2" git = "https://github.com/espressopp/espressopp.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/py-exodus/package.py b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py index 5794a146a6..42cf282cdf 100644 --- a/var/spack/repos/builtin/packages/py-exodus/package.py +++ b/var/spack/repos/builtin/packages/py-exodus-bundler/package.py @@ -6,7 +6,7 @@ from spack import * -class PyExodus(PythonPackage): +class PyExodusBundler(PythonPackage): """Exodus is a tool that makes it easy to successfully relocate Linux ELF binaries from one system to another.""" diff --git a/var/spack/repos/builtin/packages/py-filelock/package.py b/var/spack/repos/builtin/packages/py-filelock/package.py index b82459a256..89d0a7b37c 100644 --- a/var/spack/repos/builtin/packages/py-filelock/package.py +++ b/var/spack/repos/builtin/packages/py-filelock/package.py @@ -12,15 +12,14 @@ class PyFilelock(PythonPackage): inter-process communication""" homepage = "https://github.com/benediktschmitt/py-filelock" - url = "https://github.com/benediktschmitt/py-filelock/archive/v3.0.4.tar.gz" + url = "https://pypi.io/packages/source/f/filelock/filelock-3.0.4.tar.gz" - version('3.0.4', sha256='8521523f3eafb7bbbdd0a5a7a15ddb8076ea6f106385bbfc4c9d055db2585214') - version('3.0.3', sha256='8e1b1ad91de70e091de381ab8705b37e41d240c211d8d888dcf1d0e31d6274bb') - version('3.0.1', sha256='533107ab60de691030b7e90105ab38c8b0d60d52de382fe5302819cba95561f8') - version('3.0.0', sha256='f41bed24b280b2fd11b2f12fecdfd2a21e5f9babc4e89929b316946288fa195c') - version('2.0.13', sha256='85e2a001693c2995854e42783a8c11994d143f8ba9c92d31f573476a22a5b3b3') - version('2.0.12', sha256='3b67cddd8c405c27b9118a1383d5257b5b6e066d3a9a30ab03d42b4dc6828cbb') - version('2.0.11', sha256='97c36de6e0c2eaed6638a9575a96d176e4ec2820b888f3da3194bbb852f86c5e') - version('2.0.10', sha256='f15d99cfa3e89072d7709bf3b5d354cf1c9096cffdb1127c4dbff1ca4a89cb84') - version('2.0.9', sha256='86d8e95afe77bc92a94c2e0db2b452c067b453b017fd78edfbb679b199dadbd5') - version('2.0.8', sha256='4f69474338ebf6ead2e0c2e91c5f94a25af8125d307f539db10886a19e2e2628') + version('3.0.4', sha256='011327d4ed939693a5b28c0fdf2fd9bda1f68614c1d6d0643a89382ce9843a71') + version('3.0.3', sha256='7d8a86350736aa0efea0730e6a7f774195cbb1c2d61134c15f6be576399e87ff') + version('3.0.0', sha256='b3ad481724adfb2280773edd95ce501e497e88fa4489c6e41e637ab3fd9a456c') + version('2.0.13', sha256='d05079e7d7cae7576e192749d3461999ca6b0843d35b0f79f1fa956b0f6fc7d8') + version('2.0.12', sha256='eb4314a9a032707a914b037433ce866d4ed363fce8605d45f0c9d2cd6ac52f98') + version('2.0.11', sha256='e9e370efe86c30b19a2c8c36dd9fcce8e5ce294ef4ed6ac86664b666eaf852ca') + version('2.0.10', sha256='c73bf706d8a0c5722de0b745495fed9cda0e46c0eabb44eb18ee3f00520fa85f') + version('2.0.9', sha256='0f91dce339c9f25d6f2e0733a17e4f9a47b139dffda52619a0e61e013e5c6782') + version('2.0.8', sha256='7e48e4906de3c9a5d64d8f235eb3ae1050dfefa63fd65eaf318cc915c935212b') diff --git a/var/spack/repos/builtin/packages/py-fn/package.py b/var/spack/repos/builtin/packages/py-fn-py/package.py index 95cf3d4adf..0d4888be3a 100644 --- a/var/spack/repos/builtin/packages/py-fn/package.py +++ b/var/spack/repos/builtin/packages/py-fn-py/package.py @@ -6,7 +6,7 @@ from spack import * -class PyFn(PythonPackage): +class PyFnPy(PythonPackage): """Functional programming in Python: implementation of missing features to enjoy FP.""" diff --git a/var/spack/repos/builtin/packages/py-fsspec/package.py b/var/spack/repos/builtin/packages/py-fsspec/package.py index 7d7372f66a..4e774360f0 100644 --- a/var/spack/repos/builtin/packages/py-fsspec/package.py +++ b/var/spack/repos/builtin/packages/py-fsspec/package.py @@ -10,9 +10,9 @@ class PyFsspec(PythonPackage): """A specification for pythonic filesystems.""" homepage = "https://github.com/intake/filesystem_spec" - url = "https://github.com/intake/filesystem_spec/archive/0.4.4.tar.gz" + url = "https://pypi.io/packages/source/f/fsspec/fsspec-0.4.4.tar.gz" - version('0.4.4', sha256='27dfc3dab37d5c037683c7a3eaf7acd8b24ee56e4ce3edb14af54bdb43973d43') + version('0.4.4', sha256='97697a46e8bf8be34461c2520d6fc4bfca0ed749b22bb2b7c21939fd450a7d63') depends_on('python@3.5:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-hpccm/package.py b/var/spack/repos/builtin/packages/py-hpccm/package.py index fee945d1ed..31d8074470 100644 --- a/var/spack/repos/builtin/packages/py-hpccm/package.py +++ b/var/spack/repos/builtin/packages/py-hpccm/package.py @@ -11,9 +11,9 @@ class PyHpccm(PythonPackage): tool to make it easier to generate container specification files.""" homepage = "https://github.com/NVIDIA/hpc-container-maker" - url = "https://github.com/NVIDIA/hpc-container-maker/archive/v19.2.0.tar.gz" + url = "https://pypi.io/packages/source/h/hpccm/hpccm-19.2.0.tar.gz" - version('19.2.0', sha256='99eb0f48cfbdfb29815aed8bcd0fa8c5a857fd912a2bb9658b217b0712ca4af5') + version('19.2.0', sha256='c60eec914a802b0a76596cfd5fdf7122d3f8665fcef06ef928323f5dfb5219a6') depends_on('py-setuptools', type=('build', 'run')) depends_on('py-enum34', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jpype/package.py b/var/spack/repos/builtin/packages/py-jpype1/package.py index f8292f4132..0d8ccd7e97 100644 --- a/var/spack/repos/builtin/packages/py-jpype/package.py +++ b/var/spack/repos/builtin/packages/py-jpype1/package.py @@ -6,7 +6,7 @@ from spack import * -class PyJpype(PythonPackage): +class PyJpype1(PythonPackage): """JPype is an effort to allow python programs full access to java class libraries.""" diff --git a/var/spack/repos/builtin/packages/py-jsonpatch/package.py b/var/spack/repos/builtin/packages/py-jsonpatch/package.py index b9e60c9a88..6c374ac169 100644 --- a/var/spack/repos/builtin/packages/py-jsonpatch/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpatch/package.py @@ -10,9 +10,9 @@ class PyJsonpatch(PythonPackage): """Library to apply JSON Patches according to RFC 6902""" homepage = "https://github.com/stefankoegl/python-json-patch" - url = "https://github.com/stefankoegl/python-json-patch/archive/v1.23.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpatch/jsonpatch-1.23.tar.gz" - version('1.23', sha256='0af03651204ea3049bc4aedaa42b591e134a4ee16e421f9c5f3ac4e9092885ad') + version('1.23', sha256='49f29cab70e9068db3b1dc6b656cbe2ee4edf7dfe9bf5a0055f17a4b6804a4b9') depends_on('py-setuptools', type='build') depends_on('py-jsonpointer@1.9', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jsonpointer/package.py b/var/spack/repos/builtin/packages/py-jsonpointer/package.py index 9e33b53b0d..99bd34913b 100644 --- a/var/spack/repos/builtin/packages/py-jsonpointer/package.py +++ b/var/spack/repos/builtin/packages/py-jsonpointer/package.py @@ -10,8 +10,8 @@ class PyJsonpointer(PythonPackage): """Library to resolve JSON Pointers according to RFC 6901""" homepage = "https://github.com/stefankoegl/python-json-pointer" - url = "https://github.com/stefankoegl/python-json-pointer/archive/v2.0.tar.gz" + url = "https://pypi.io/packages/source/j/jsonpointer/jsonpointer-2.0.tar.gz" - version('2.0', sha256='9594b7574a3216c9994181e9db7566a5cafb4ab24956e554f2dba1bb39edecb2') + version('2.0', sha256='c192ba86648e05fdae4f08a17ec25180a9aef5008d973407b581798a83975362') depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-jupyter-client/package.py b/var/spack/repos/builtin/packages/py-jupyter-client/package.py index 1b69aa1e4e..ef66494661 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-client/package.py +++ b/var/spack/repos/builtin/packages/py-jupyter-client/package.py @@ -24,4 +24,4 @@ class PyJupyterClient(PythonPackage): depends_on('python@2.7:2.8,3.3:') depends_on('py-traitlets', type=('build', 'run')) depends_on('py-jupyter-core', type=('build', 'run')) - depends_on('py-zmq@13:', type=('build', 'run')) + depends_on('py-pyzmq@13:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-jupyterhub/package.py b/var/spack/repos/builtin/packages/py-jupyterhub/package.py index 2b3e39a389..0ada619352 100644 --- a/var/spack/repos/builtin/packages/py-jupyterhub/package.py +++ b/var/spack/repos/builtin/packages/py-jupyterhub/package.py @@ -31,5 +31,5 @@ class PyJupyterhub(PythonPackage): depends_on('py-oauthlib@3.0:', when='@1.0.0:', type=('build', 'run')) depends_on('py-python-oauth2@1.0:', when='@:9.4', type=('build', 'run')) depends_on('py-pamela', type=('build', 'run')) - depends_on('py-jupyter-notebook', type=('build', 'run')) + depends_on('py-notebook', type=('build', 'run')) depends_on('py-prometheus-client@0.0.21:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-lrudict/package.py b/var/spack/repos/builtin/packages/py-lru-dict/package.py index 79c3550219..a3bd6c023f 100644 --- a/var/spack/repos/builtin/packages/py-lrudict/package.py +++ b/var/spack/repos/builtin/packages/py-lru-dict/package.py @@ -7,13 +7,13 @@ from spack import * -class PyLrudict(PythonPackage): - """ A fast LRU cache""" +class PyLruDict(PythonPackage): + """A fast LRU cache""" homepage = "https://github.com/amitdev/lru-dict" url = "https://pypi.io/packages/source/l/lru-dict/lru-dict-1.1.6.tar.gz" version('1.1.6', sha256='365457660e3d05b76f1aba3e0f7fedbfcd6528e97c5115a351ddd0db488354cc') - depends_on('python@2.7:') + depends_on('python@2.7:', type=('build', 'run')) depends_on('py-setuptools', type=('build')) diff --git a/var/spack/repos/builtin/packages/py-macholib/package.py b/var/spack/repos/builtin/packages/py-macholib/package.py index 4f730733c8..368aba2ec1 100644 --- a/var/spack/repos/builtin/packages/py-macholib/package.py +++ b/var/spack/repos/builtin/packages/py-macholib/package.py @@ -10,7 +10,7 @@ class PyMacholib(PythonPackage): """Python package for Mach-O header analysis and editing""" homepage = "https://pypi.python.org/pypi/macholib" - url = "https://pypi.io/packages/source/m/macholib/macholib-1.8.tar.gz" + url = "https://pypi.io/packages/source/m/macholib/macholib-1.11.tar.gz" version('1.11', 'c4180ffc6f909bf8db6cd81cff4b6f601d575568f4d5dee148c830e9851eb9db') diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index a53c2c892b..dfefbf0175 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -113,7 +113,7 @@ class PyMatplotlib(PythonPackage): # Optional dependencies depends_on('ffmpeg', when='+movies') # depends_on('libav', when='+movies') - depends_on('image-magick', when='+animation') + depends_on('imagemagick', when='+animation') depends_on('py-pillow@3.4:', when='+image', type=('build', 'run')) depends_on('texlive', when='+latex', type='run') depends_on('ghostscript@0.9:', when='+latex', type='run') diff --git a/var/spack/repos/builtin/packages/py-methylcode/package.py b/var/spack/repos/builtin/packages/py-methylcode/package.py index 512d1f2d01..53b9292edf 100644 --- a/var/spack/repos/builtin/packages/py-methylcode/package.py +++ b/var/spack/repos/builtin/packages/py-methylcode/package.py @@ -11,15 +11,13 @@ class PyMethylcode(PythonPackage): reads and outputs per-base methylation data. """ homepage = "https://github.com/brentp/methylcode" - url = "https://github.com/brentp/methylcode/archive/master.zip" + git = "https://github.com/brentp/methylcode.git" - version('1.0.0', sha256='30f707a690a887e3161c8debba3c322bd313865df40212275b02203c52a416ae') + version('master', branch='master') - depends_on('python@2.7.0:2.7.999') - depends_on('py-six') - depends_on('py-setuptools') + depends_on('python@2.6:2.8', type=('build', 'run')) + depends_on('py-setuptools', type='build') depends_on('py-numpy') - depends_on('py-pyparsing') depends_on('py-pyfasta') depends_on('py-bsddb3') depends_on('bowtie') diff --git a/var/spack/repos/builtin/packages/py-mongo/package.py b/var/spack/repos/builtin/packages/py-mongo/package.py deleted file mode 100644 index 117c59cf70..0000000000 --- a/var/spack/repos/builtin/packages/py-mongo/package.py +++ /dev/null @@ -1,20 +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 PyMongo(PythonPackage): - """Python driver for MongoDB <http://www.mongodb.org>""" - - homepage = "http://github.com/mongodb/mongo-python-driver" - url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.6.0.tar.gz" - - version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') - version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') - - depends_on('python@2.6:2.8,3.3:') - - depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/package.py b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py index e3e04280c4..07000af952 100644 --- a/var/spack/repos/builtin/packages/py-mysql-connector/package.py +++ b/var/spack/repos/builtin/packages/py-mysql-connector-python/package.py @@ -6,7 +6,7 @@ from spack import * -class PyMysqlConnector(PythonPackage): +class PyMysqlConnectorPython(PythonPackage): """MySQL Connector/Python is implementing the MySQL Client/Server protocol completely in Python. No MySQL libraries are needed, and no compilation is necessary to run this Python DB API v2.0 diff --git a/var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch b/var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch index 27cf5e5d22..27cf5e5d22 100644 --- a/var/spack/repos/builtin/packages/py-mysql-connector/single-version.patch +++ b/var/spack/repos/builtin/packages/py-mysql-connector-python/single-version.patch diff --git a/var/spack/repos/builtin/packages/py-netcdf4/package.py b/var/spack/repos/builtin/packages/py-netcdf4/package.py index ef9bbafad1..f76b6067b6 100644 --- a/var/spack/repos/builtin/packages/py-netcdf4/package.py +++ b/var/spack/repos/builtin/packages/py-netcdf4/package.py @@ -22,15 +22,15 @@ class PyNetcdf4(PythonPackage): depends_on('py-numpy@1.7:', type=('build', 'run')) depends_on('py-cftime', type=('build', 'run')) - depends_on('netcdf') + depends_on('netcdf-c') depends_on('hdf5@1.8.0:+hl') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """Ensure installed netcdf and hdf5 libraries are used""" # Explicitly set these variables so setup.py won't erroneously pick up # system versions - spack_env.set('USE_SETUPCFG', '0') - spack_env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) - spack_env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) - spack_env.set('NETCDF4_INCDIR', self.spec['netcdf'].prefix.include) - spack_env.set('NETCDF4_LIBDIR', self.spec['netcdf'].prefix.lib) + env.set('USE_SETUPCFG', '0') + env.set('HDF5_INCDIR', self.spec['hdf5'].prefix.include) + env.set('HDF5_LIBDIR', self.spec['hdf5'].prefix.lib) + env.set('NETCDF4_INCDIR', self.spec['netcdf-c'].prefix.include) + env.set('NETCDF4_LIBDIR', self.spec['netcdf-c'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py b/var/spack/repos/builtin/packages/py-notebook/package.py index 55c2f0f256..4eb62b3ac8 100644 --- a/var/spack/repos/builtin/packages/py-jupyter-notebook/package.py +++ b/var/spack/repos/builtin/packages/py-notebook/package.py @@ -6,7 +6,7 @@ from spack import * -class PyJupyterNotebook(PythonPackage): +class PyNotebook(PythonPackage): """Jupyter Interactive Notebook""" homepage = "https://github.com/jupyter/notebook" diff --git a/var/spack/repos/builtin/packages/py-opentuner/package.py b/var/spack/repos/builtin/packages/py-opentuner/package.py index 5c34fbfab7..f8f2347692 100644 --- a/var/spack/repos/builtin/packages/py-opentuner/package.py +++ b/var/spack/repos/builtin/packages/py-opentuner/package.py @@ -18,7 +18,7 @@ class PyOpentuner(PythonPackage): depends_on('python@2.7:2.8', type=('build', 'run')) depends_on('py-argparse@1.2.1:', type=('build', 'run')) - depends_on('py-fn@0.2.12:', type=('build', 'run')) + depends_on('py-fn-py@0.2.12:', type=('build', 'run')) depends_on('py-numpy@1.8.0:', type=('build', 'run')) depends_on('py-pysqlite@2.6.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-performance/package.py b/var/spack/repos/builtin/packages/py-performance/package.py index 9abc3c4d48..0be0b0b5ba 100644 --- a/var/spack/repos/builtin/packages/py-performance/package.py +++ b/var/spack/repos/builtin/packages/py-performance/package.py @@ -22,4 +22,4 @@ class PyPerformance(PythonPackage): depends_on('py-setuptools', type=('build', 'run')) depends_on('py-six', type=('build', 'run')) - depends_on('py-perf', type=('build', 'run')) + depends_on('py-pyperf', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-plotly/package.py b/var/spack/repos/builtin/packages/py-plotly/package.py index cd315180ed..6bf5ea9da0 100644 --- a/var/spack/repos/builtin/packages/py-plotly/package.py +++ b/var/spack/repos/builtin/packages/py-plotly/package.py @@ -10,9 +10,9 @@ class PyPlotly(PythonPackage): """An interactive, browser-based graphing library for Python""" homepage = "https://plot.ly/python/" - url = "https://github.com/plotly/plotly.py/archive/v2.2.0.tar.gz" + url = "https://pypi.io/packages/source/p/plotly/plotly-2.2.0.tar.gz" - version('2.2.0', sha256='dad2a49fe355dddb6ae159e96c10ac22413a33cbac513b4dbf3791e63ec33c1f') + version('2.2.0', sha256='ca668911ffb4d11fed6d7fbb12236f8ecc6a7209db192326bcb64bdb41451a58') depends_on('py-setuptools', type='build') depends_on('py-requests@2.3.0', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-cpuinfo/package.py b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py index e9f4db3142..c4278bf678 100644 --- a/var/spack/repos/builtin/packages/py-cpuinfo/package.py +++ b/var/spack/repos/builtin/packages/py-py-cpuinfo/package.py @@ -6,7 +6,7 @@ from spack import * -class PyCpuinfo(PythonPackage): +class PyPyCpuinfo(PythonPackage): """Get CPU info with pure Python 2 & 3""" homepage = "https://github.com/workhorsy/py-cpuinfo" diff --git a/var/spack/repos/builtin/packages/py-git2/package.py b/var/spack/repos/builtin/packages/py-pygit2/package.py index a4c6404ef1..216c61a74f 100644 --- a/var/spack/repos/builtin/packages/py-git2/package.py +++ b/var/spack/repos/builtin/packages/py-pygit2/package.py @@ -6,7 +6,7 @@ from spack import * -class PyGit2(PythonPackage): +class PyPygit2(PythonPackage): """Pygit2 is a set of Python bindings to the libgit2 shared library, libgit2 implements the core of Git. """ @@ -24,8 +24,8 @@ class PyGit2(PythonPackage): depends_on('py-six', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): spec = self.spec # http://www.pygit2.org/install.html - spack_env.set('LIBGIT2', spec['libgit2'].prefix) - spack_env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) + env.set('LIBGIT2', spec['libgit2'].prefix) + env.set('LIBGIT2_LIB', spec['libgit2'].prefix.lib) diff --git a/var/spack/repos/builtin/packages/py-pygpu/package.py b/var/spack/repos/builtin/packages/py-pygpu/package.py index 3675482b08..84182e5a43 100644 --- a/var/spack/repos/builtin/packages/py-pygpu/package.py +++ b/var/spack/repos/builtin/packages/py-pygpu/package.py @@ -28,4 +28,4 @@ class PyPygpu(PythonPackage): depends_on('py-nose', type=('build', 'run')) depends_on('py-numpy', type=('build', 'run')) depends_on('py-mako', type=('build', 'run')) - depends_on('libcheck') + depends_on('check') diff --git a/var/spack/repos/builtin/packages/py-pyke/package.py b/var/spack/repos/builtin/packages/py-pyke/package.py index e003dbc981..c2fdbe69f1 100644 --- a/var/spack/repos/builtin/packages/py-pyke/package.py +++ b/var/spack/repos/builtin/packages/py-pyke/package.py @@ -13,8 +13,8 @@ class PyPyke(PythonPackage): """ homepage = "http://sourceforge.net/projects/pyke" - url = "https://downloads.sourceforge.net/pyke/pyke3-1.1.1.zip" + url = "https://sourceforge.net/projects/pyke/files/pyke/1.1.1/pyke-1.1.1.zip" - version('1.1.1', sha256='b877b390e70a2eacc01d97c3a992fde947276afc2798ca3ac6c6f74c796cb6dc') + version('1.1.1', sha256='b0b294f435c6e6d2d4a80badf57d92cb66814dfe21e644a521901209e6a3f8ae') - depends_on('python@3:') + depends_on('python@3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-pymongo/package.py b/var/spack/repos/builtin/packages/py-pymongo/package.py index 8e28001e4c..3f52238dfd 100644 --- a/var/spack/repos/builtin/packages/py-pymongo/package.py +++ b/var/spack/repos/builtin/packages/py-pymongo/package.py @@ -19,6 +19,8 @@ class PyPymongo(PythonPackage): url = "https://pypi.io/packages/source/p/pymongo/pymongo-3.9.0.tar.gz" version('3.9.0', sha256='4249c6ba45587b959292a727532826c5032d59171f923f7f823788f413c2a5a3') + version('3.6.0', sha256='c6de26d1e171cdc449745b82f1addbc873d105b8e7335097da991c0fc664a4a8') + version('3.3.0', sha256='3d45302fc2622fabf34356ba274c69df41285bac71bbd229f1587283b851b91e') depends_on('python@2.7:2.8,3.4:', type=('build', 'run')) depends_on('py-setuptools', type='build') diff --git a/var/spack/repos/builtin/packages/py-pynio/package.py b/var/spack/repos/builtin/packages/py-pynio/package.py index d6d4076554..d1d489a1ba 100644 --- a/var/spack/repos/builtin/packages/py-pynio/package.py +++ b/var/spack/repos/builtin/packages/py-pynio/package.py @@ -27,7 +27,7 @@ class PyPynio(PythonPackage): # Spack does not currently have netcdf below 4.x, and 3.x is a # fundamentally different format. So, currently this is only providing # support for netcdf4. - depends_on('netcdf@3.6.0:') + depends_on('netcdf-c@3.6.0:') # Turning on the hdf (i.e. hdf4) dependency causes it not to build, with # compile errors that (weirdly) relate to the declarations of HDF5. @@ -50,22 +50,22 @@ class PyPynio(PythonPackage): depends_on('py-numpy', type=('build', 'run')) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): """ These environment variables are how the setup.py knows which options to turn on, and how to find them. """ - spack_env.set('F2CLIBS', 'gfortran') - spack_env.set('HAS_NETCDF4', '1') - spack_env.set('NETCDF4_PREFIX', self.spec['netcdf'].prefix) + env.set('F2CLIBS', 'gfortran') + env.set('HAS_NETCDF4', '1') + env.set('NETCDF4_PREFIX', self.spec['netcdf-c'].prefix) if '+hdf5' in self.spec: - spack_env.set('HAS_HDF5', '1') - spack_env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) + env.set('HAS_HDF5', '1') + env.set('HDF5_PREFIX', self.spec['hdf5'].prefix) if '+gdal' in self.spec: - spack_env.set('HAS_GDAL', '1') - spack_env.set('GDAL_PREFIX', self.spec['gdal'].prefix) + env.set('HAS_GDAL', '1') + env.set('GDAL_PREFIX', self.spec['gdal'].prefix) # This one is trouble - see comments above. # if '+hdf4' in self.spec: -# spack_env.set('HAS_HDF4', '1') -# spack_env.set('HDF4_PREFIX', self.spec['hdf'].prefix) +# env.set('HAS_HDF4', '1') +# env.set('HDF4_PREFIX', self.spec['hdf'].prefix) diff --git a/var/spack/repos/builtin/packages/py-perf/package.py b/var/spack/repos/builtin/packages/py-pyperf/package.py index 2d2c025691..53106bb468 100644 --- a/var/spack/repos/builtin/packages/py-perf/package.py +++ b/var/spack/repos/builtin/packages/py-pyperf/package.py @@ -6,7 +6,7 @@ from spack import * -class PyPerf(PythonPackage): +class PyPyperf(PythonPackage): """The Python perf module is a toolkit to write, run and analyze benchmarks. """ diff --git a/var/spack/repos/builtin/packages/py-igraph/package.py b/var/spack/repos/builtin/packages/py-python-igraph/package.py index e6f6ccdf20..7812983c21 100644 --- a/var/spack/repos/builtin/packages/py-igraph/package.py +++ b/var/spack/repos/builtin/packages/py-python-igraph/package.py @@ -6,7 +6,7 @@ from spack import * -class PyIgraph(PythonPackage): +class PyPythonIgraph(PythonPackage): """igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use.""" diff --git a/var/spack/repos/builtin/packages/py-meep/package.py b/var/spack/repos/builtin/packages/py-python-meep/package.py index 81a219145f..4eedd1ef17 100644 --- a/var/spack/repos/builtin/packages/py-meep/package.py +++ b/var/spack/repos/builtin/packages/py-python-meep/package.py @@ -6,7 +6,7 @@ from spack import * -class PyMeep(PythonPackage): +class PyPythonMeep(PythonPackage): """Python-meep is a wrapper around libmeep. It allows the scripting of Meep-simulations with Python""" diff --git a/var/spack/repos/builtin/packages/py-pyyaml/package.py b/var/spack/repos/builtin/packages/py-pyyaml/package.py index 980d5fae51..39b5b7f516 100644 --- a/var/spack/repos/builtin/packages/py-pyyaml/package.py +++ b/var/spack/repos/builtin/packages/py-pyyaml/package.py @@ -8,8 +8,9 @@ from spack import * class PyPyyaml(PythonPackage): """PyYAML is a YAML parser and emitter for Python.""" + homepage = "http://pyyaml.org/wiki/PyYAML" - url = "http://pyyaml.org/download/pyyaml/PyYAML-5.1.2.tar.gz" + url = "https://pypi.io/packages/source/P/PyYAML/PyYAML-5.1.2.tar.gz" version('5.1.2', sha256='01adf0b6c6f61bd11af6e10ca52b7d4057dd0be0343eb9283c878cf3af56aee4') version('3.13', sha256='3ef3092145e9b70e3ddd2c7ad59bdd0252a94dfe3949721633e41344de00a6bf') diff --git a/var/spack/repos/builtin/packages/py-zmq/package.py b/var/spack/repos/builtin/packages/py-pyzmq/package.py index 7d2d783a7a..e3e3944e2d 100644 --- a/var/spack/repos/builtin/packages/py-zmq/package.py +++ b/var/spack/repos/builtin/packages/py-pyzmq/package.py @@ -6,7 +6,7 @@ from spack import * -class PyZmq(PythonPackage): +class PyPyzmq(PythonPackage): """PyZMQ: Python bindings for zeromq.""" homepage = "https://github.com/zeromq/pyzmq" url = "https://github.com/zeromq/pyzmq/archive/v14.7.0.tar.gz" @@ -18,4 +18,4 @@ class PyZmq(PythonPackage): depends_on('py-cython@0.16:', type=('build', 'run')) depends_on('py-py', type=('build', 'run')) depends_on('py-cffi', type=('build', 'run')) - depends_on('zeromq') + depends_on('libzmq') diff --git a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py index c6e25d373e..875563f260 100644 --- a/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py +++ b/var/spack/repos/builtin/packages/py-requests-toolbelt/package.py @@ -11,10 +11,10 @@ class PyRequestsToolbelt(PythonPackage): python-requests""" homepage = "https://toolbelt.readthedocs.org/" - url = "https://github.com/requests/toolbelt/archive/0.9.1.tar.gz" + url = "https://pypi.io/packages/source/r/requests-toolbelt/requests-toolbelt-0.9.1.tar.gz" - version('0.9.1', sha256='c8e68e537e87ae088e3a0eb6d80ed5b7cf5d6df503d0e843e0a5e47283db487b') - version('0.8.0', sha256='f151c07e88148dc05b6f31cc75dfb7a6770968e4a5c8e6690325eed4e79160a1') + version('0.9.1', sha256='968089d4584ad4ad7c171454f0a5c6dac23971e9472521ea3b6d49d610aa6fc0') + version('0.8.0', sha256='f6a531936c6fa4c6cfce1b9c10d5c4f498d16528d2a54a22ca00011205a187b5') depends_on('py-setuptools', type='build') depends_on('py-requests@2.0.1:2.999', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-scoop/package.py b/var/spack/repos/builtin/packages/py-scoop/package.py index b26140c384..0c9cf81e3e 100644 --- a/var/spack/repos/builtin/packages/py-scoop/package.py +++ b/var/spack/repos/builtin/packages/py-scoop/package.py @@ -19,4 +19,4 @@ class PyScoop(PythonPackage): depends_on('py-setuptools', type='build') depends_on('py-greenlet@0.3.4:', type=('build', 'run')) - depends_on('py-zmq@13.1.0:', type=('build', 'run')) + depends_on('py-pyzmq@13.1.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py index 0781ea59f3..34100e15d6 100644 --- a/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py +++ b/var/spack/repos/builtin/packages/py-sphinxautomodapi/package.py @@ -10,9 +10,9 @@ class PySphinxautomodapi(PythonPackage): """Provides Sphinx directives to autogenerate API documentation pages""" homepage = "https://sphinx-automodapi.readthedocs.io/en/latest/" - url = "https://github.com/astropy/sphinx-automodapi/archive/v0.9.tar.gz" + url = "https://pypi.io/packages/source/s/sphinx-automodapi/sphinx-automodapi-0.9.tar.gz" - version('0.9', sha256='017817812e9266319fdcfcc89ddfbe570935ca87a3bda62d61c8507cf1337aa8') + version('0.9', sha256='71a69e1a7ab8d849f416d7431db854d7b1925f749ba6345bc7d88f288892871d') depends_on('py-setuptools', type='build') depends_on('py-sphinx@1.3:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-spyder/package.py b/var/spack/repos/builtin/packages/py-spyder/package.py index 607a52393b..c8e48ec2a7 100644 --- a/var/spack/repos/builtin/packages/py-spyder/package.py +++ b/var/spack/repos/builtin/packages/py-spyder/package.py @@ -39,6 +39,6 @@ class PySpyder(PythonPackage): # to pick up webkit, but this is the easier solution (see #9207) depends_on('qt+webkit', type=('build', 'run')) depends_on('py-pickleshare', type=('build', 'run')) - depends_on('py-zmq', type=('build', 'run')) + depends_on('py-pyzmq', type=('build', 'run')) depends_on('py-chardet@2.0.0:', type=('build', 'run')) depends_on('py-numpydoc', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-symengine/package.py b/var/spack/repos/builtin/packages/py-symengine/package.py index 3e3664f075..33953c4b9e 100644 --- a/var/spack/repos/builtin/packages/py-symengine/package.py +++ b/var/spack/repos/builtin/packages/py-symengine/package.py @@ -10,14 +10,14 @@ class PySymengine(PythonPackage): """Python wrappers for SymEngine, a symbolic manipulation library.""" homepage = "https://github.com/symengine/symengine.py" - url = "https://github.com/symengine/symengine.py/archive/v0.2.0.tar.gz" + url = "https://pypi.io/packages/source/s/symengine/symengine-0.2.0.tar.gz" git = "https://github.com/symengine/symengine.py.git" version('develop', branch='master') - version('0.2.0', sha256='8f6468137baa7f799e047dd0b9149c4017d8d32e755f1e0329209680879c1f8f') + version('0.2.0', sha256='78a14aea7aad5e7cbfb5cabe141581f9bba30e3c319690e5db8ad99fdf2d8885') # Build dependencies - depends_on('python@2.7:2.8,3.3:') + depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-setuptools', type='build') depends_on('py-cython@0.19.1:', type='build') depends_on('cmake@2.8.7:', type='build') diff --git a/var/spack/repos/builtin/packages/py-tables/package.py b/var/spack/repos/builtin/packages/py-tables/package.py index 2fcb494c6c..c6476692d8 100644 --- a/var/spack/repos/builtin/packages/py-tables/package.py +++ b/var/spack/repos/builtin/packages/py-tables/package.py @@ -11,18 +11,17 @@ class PyTables(PythonPackage): efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" - url = "https://github.com/PyTables/PyTables/archive/v3.6.0.tar.gz" + url = "https://pypi.io/packages/source/t/tables/tables-3.6.0.tar.gz" import_modules = [ 'tables', 'tables.misc', 'tables.nodes', 'tables.scripts' ] - version('3.6.0', sha256='2dcd077f42b195f48aa00f5a720b79189ea92fba0d16ad35e2881e403ba6914e') - version('3.5.2', sha256='e4fc6f1194f02a8b10ff923e77364fb70710592f620d7de35f4d4e064dc70e91') - version('3.4.4', sha256='c9682c0f35d8175e12bbd38d925bdb606d47b7c8e358ba056a9dbf3b1f183114') - version('3.3.0', sha256='dceb15fef556a2775121bcc695561df4ff0e09248e0ce3a2d58f5244a9f61421') - version('3.2.2', sha256='2626e874caa6b3fcf2bfc28b9dd6a40a3f859c72e19ce0764a60a6d77e350008', - url='https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz') + version('3.6.0', sha256='db3488214864fb313a611fca68bf1c9019afe4e7877be54d0e61c84416603d4d') + version('3.5.2', sha256='b220e32262bab320aa41d33125a7851ff898be97c0de30b456247508e2cc33c2') + version('3.4.4', sha256='bdc5c073712af2a43babd139c4855fc99496bb2c3f3f5d1b4770a985e6f9ce29') + version('3.3.0', sha256='8383ccf02e041a5d55494a09fc5514140b4653055a2732c981b5fd0f7408822c') + version('3.2.2', sha256='3564b351a71ec1737b503b001eb7ceae1f65d5d6e3ffe1ea75aafba10f37fa84') variant('zlib', default=True, description='Support for zlib compression') variant('bzip2', default=False, description='Support for bzip2 compression') diff --git a/var/spack/repos/builtin/packages/py-tappy/package.py b/var/spack/repos/builtin/packages/py-tap-py/package.py index 1c97e7a763..c0ece59fd6 100644 --- a/var/spack/repos/builtin/packages/py-tappy/package.py +++ b/var/spack/repos/builtin/packages/py-tap-py/package.py @@ -6,10 +6,10 @@ from spack import * -class PyTappy(PythonPackage): +class PyTapPy(PythonPackage): """Python TAP interface module for unit tests""" + homepage = "https://github.com/mblayman/tappy" - # base https://pypi.python.org/pypi/cffi url = "https://pypi.io/packages/source/t/tap.py/tap.py-1.6.tar.gz" version('1.6', sha256='3ee315567cd1cf444501c405b7f7146ffdb2e630bac58d0840d378a3b9a0dbe4') diff --git a/var/spack/repos/builtin/packages/py-udunits/package.py b/var/spack/repos/builtin/packages/py-udunits/package.py deleted file mode 100644 index b7fb343439..0000000000 --- a/var/spack/repos/builtin/packages/py-udunits/package.py +++ /dev/null @@ -1,50 +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 * -import os - - -class PyUdunits(PythonPackage): - """The MetOffice cf_units Python interface to the UDUNITS-2 Library.""" - homepage = "https://github.com/SciTools/cf_units" - url = "https://github.com/SciTools/cf_units/archive/v1.1.3.tar.gz" - - version('1.1.3', sha256='cc27f4f06c99d242c36beb8dc5c517e1b1124a8c65ca3f76f372b9674aa320ba') - - maintainers = ['citibeth'] - - depends_on('py-setuptools', type='build') - depends_on('py-six', type=('build', 'run')) - depends_on('py-netcdf4', type=('build', 'run')) - depends_on('udunits2') - - # See: https://github.com/SciTools/cf_units/blob/master/cf_units/etc/site.cfg.template - # udunits2_path = /path/to/libudunits2.so - # udunits2_xml_path = /path/to/udunits2.xml - site_cfg_template = """[System] -udunits2_path = %s -udunits2_xml_path = %s -""" - - @run_after('install') - def configure_template(self): - spec = self.spec - - cfg_templates = find(spec.prefix, ['site.cfg.template']) - if len(cfg_templates) != 1: - tty.die( - 'Found %d instances of site.cfg.template, wanted 1' % - len(cfg_templates)) - cfg_template = cfg_templates[0] - - cfg = os.path.join(os.path.split(cfg_template)[0], 'site.cfg') - - udunits2_xml_path = os.path.join( - spec['udunits2'].prefix, 'share', 'udunits', 'udunits2.xml') - - with open(cfg, 'w') as fout: - fout.write(self.site_cfg_template % - (spec['udunits2'].libs, udunits2_xml_path)) diff --git a/var/spack/repos/builtin/packages/py-wand/package.py b/var/spack/repos/builtin/packages/py-wand/package.py index ac4f82fd5b..fcecd5e663 100644 --- a/var/spack/repos/builtin/packages/py-wand/package.py +++ b/var/spack/repos/builtin/packages/py-wand/package.py @@ -20,7 +20,7 @@ class PyWand(PythonPackage): depends_on('py-setuptools', type='build') # provides libmagickwand - depends_on('image-magick') + depends_on('imagemagick') depends_on('python@2.7:2.8,3.3:', type=('build', 'run')) depends_on('py-sphinx@1:', type='build', when='+docs') diff --git a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py index 589e733c77..9ce05b1c35 100644 --- a/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py +++ b/var/spack/repos/builtin/packages/py-widgetsnbextension/package.py @@ -16,4 +16,4 @@ class PyWidgetsnbextension(PythonPackage): depends_on('py-setuptools', type='build') depends_on('python@2.7:2.8,3.3:') - depends_on('py-jupyter-notebook@4.2.0:', type=('build', 'run')) + depends_on('py-notebook@4.2.0:', type=('build', 'run')) diff --git a/var/spack/repos/builtin/packages/py-xdot/package.py b/var/spack/repos/builtin/packages/py-xdot/package.py index ecdc47e494..3f09fc6b32 100644 --- a/var/spack/repos/builtin/packages/py-xdot/package.py +++ b/var/spack/repos/builtin/packages/py-xdot/package.py @@ -11,12 +11,12 @@ class PyXdot(PythonPackage): dot language.""" homepage = "https://github.com/jrfonseca/xdot.py" - url = "https://github.com/jrfonseca/xdot.py/archive/0.9.tar.gz" + url = "https://pypi.io/packages/source/x/xdot/xdot-1.0.tar.gz" git = "https://github.com/jrfonseca/xdot.py.git" - version('master', branch="master") - version('1.0', sha256='a8594f94f43f938e01e42ff6015c7e00e3ee1a00c7f06d6287d8c939ffa94f76') - version('0.9', sha256='df7790db573d7a5512e6fa618d9051508c43cf64ca432d97c2207c87b6f20dbd') + version('master', branch='master') + version('1.0', sha256='7e067896d729af82f1fd0758e265f129944d469c30f550e3f15dbdb751cc42a1') + version('0.9', sha256='a33701664ecfefe7c7313a120a587e87334f3a566409bc451538fcde5edd6907') # setuptools is required at runtime to avoid: # No module named 'pkg_resources' @@ -46,17 +46,17 @@ class PyXdot(PythonPackage): python3 = spec['python'].command python3('-m', 'compileall', dst) - def setup_environment(self, spack_env, run_env): + def setup_run_environment(self, env): spec = self.spec - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['pango'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['atk'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gdk-pixbuf'].prefix.lib, - 'girepository-1.0')) - run_env.prepend_path('GI_TYPELIB_PATH', - join_path(spec['gtkplus'].prefix.lib, - 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['pango'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['atk'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gdk-pixbuf'].prefix.lib, + 'girepository-1.0')) + env.prepend_path('GI_TYPELIB_PATH', + join_path(spec['gtkplus'].prefix.lib, + 'girepository-1.0')) diff --git a/var/spack/repos/builtin/packages/qt-creator/package.py b/var/spack/repos/builtin/packages/qt-creator/package.py index 9b23300a65..1aae1353b6 100644 --- a/var/spack/repos/builtin/packages/qt-creator/package.py +++ b/var/spack/repos/builtin/packages/qt-creator/package.py @@ -9,7 +9,7 @@ from spack import * class QtCreator(QMakePackage): """The Qt Creator IDE.""" homepage = 'https://www.qt.io/ide/' - url = 'http://download.qt.io/official_releases/qtcreator/4.3/4.3.1/qt-creator-opensource-src-4.3.1.tar.gz' + url = 'http://download.qt.io/official_releases/qtcreator/4.8/4.8.0/qt-creator-opensource-src-4.8.0.tar.gz' list_url = 'http://download.qt.io/official_releases/qtcreator/' list_depth = 2 @@ -32,8 +32,8 @@ class QtCreator(QMakePackage): url = 'http://download.qt.io/official_releases/qtcreator/{0}/{1}/qt-creator-opensource-src-{1}.tar.gz' return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): - spack_env.set('INSTALL_ROOT', self.prefix) + def setup_build_environment(self, env): + env.set('INSTALL_ROOT', self.prefix) def qmake_args(self): return ['-r'] diff --git a/var/spack/repos/builtin/packages/r-animation/package.py b/var/spack/repos/builtin/packages/r-animation/package.py index 69426a1cd7..7883e4c8e3 100644 --- a/var/spack/repos/builtin/packages/r-animation/package.py +++ b/var/spack/repos/builtin/packages/r-animation/package.py @@ -22,7 +22,7 @@ class RAnimation(RPackage): depends_on('r@2.14:', type=('build', 'run')) depends_on('r-magick', when='@2.6:', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') depends_on('ffmpeg') depends_on('swftools') depends_on('texlive') diff --git a/var/spack/repos/builtin/packages/r-checkpoint/package.py b/var/spack/repos/builtin/packages/r-checkpoint/package.py index c212794956..08656458f4 100644 --- a/var/spack/repos/builtin/packages/r-checkpoint/package.py +++ b/var/spack/repos/builtin/packages/r-checkpoint/package.py @@ -13,7 +13,7 @@ class RCheckpoint(RPackage): date as if you had a CRAN time machine.""" homepage = "https://cloud.r-project.org/package=checkpoint" - url = "https://cloud.r-project.org/src/contrib/checkpoint_0.3.18.tar.gz" + url = "https://cloud.r-project.org/src/contrib/checkpoint_0.4.6.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/checkpoint" version('0.4.6', sha256='fd1a5edb5cb1a40d7ed26bb196de566110fe2ef62e70b4e947c003576a03ebb2') diff --git a/var/spack/repos/builtin/packages/r-magick/package.py b/var/spack/repos/builtin/packages/r-magick/package.py index 66ae049615..858b92174f 100644 --- a/var/spack/repos/builtin/packages/r-magick/package.py +++ b/var/spack/repos/builtin/packages/r-magick/package.py @@ -27,4 +27,4 @@ class RMagick(RPackage): depends_on('r-rcpp@0.12.12:', type=('build', 'run')) depends_on('r-magrittr', type=('build', 'run')) depends_on('r-curl', type=('build', 'run')) - depends_on('image-magick') + depends_on('imagemagick') diff --git a/var/spack/repos/builtin/packages/r-mzr/package.py b/var/spack/repos/builtin/packages/r-mzr/package.py index 5ccf4dd6cd..4ff0958eea 100644 --- a/var/spack/repos/builtin/packages/r-mzr/package.py +++ b/var/spack/repos/builtin/packages/r-mzr/package.py @@ -24,5 +24,5 @@ class RMzr(RPackage): depends_on('r-protgenerics', type=('build', 'run')) depends_on('r-rcpp', type=('build', 'run')) depends_on('r-zlibbioc', type=('build', 'run')) - depends_on('netcdf') + depends_on('netcdf-c') depends_on('r@3.4.0:3.4.9', when='@2.10.0') diff --git a/var/spack/repos/builtin/packages/r-ncdf4/package.py b/var/spack/repos/builtin/packages/r-ncdf4/package.py index 14e1273381..1a837ded21 100644 --- a/var/spack/repos/builtin/packages/r-ncdf4/package.py +++ b/var/spack/repos/builtin/packages/r-ncdf4/package.py @@ -30,4 +30,4 @@ class RNcdf4(RPackage): version('1.16', sha256='edd5731a805bbece3a8f6132c87c356deafc272351e1dd07256ca00574949253') version('1.15', sha256='d58298f4317c6c80a041a70216126492fd09ba8ecde9da09d5145ae26f324d4d') - depends_on('netcdf@4.1:') + depends_on('netcdf-c@4.1:') diff --git a/var/spack/repos/builtin/packages/r-nmf/package.py b/var/spack/repos/builtin/packages/r-nmf/package.py index 95346b8290..d89d20ef02 100644 --- a/var/spack/repos/builtin/packages/r-nmf/package.py +++ b/var/spack/repos/builtin/packages/r-nmf/package.py @@ -15,7 +15,7 @@ class RNmf(RPackage): computations on multicore machines..""" homepage = "http://renozao.github.io/NMF" - url = "https://cloud.r-project.org/src/contrib/NMF_0.20.6.tar.gz" + url = "https://cloud.r-project.org/src/contrib/NMF_0.21.0.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/NMF" version('0.21.0', sha256='3b30c81c66066fab4a63c5611a0313418b840d8b63414db31ef0e932872d02e3') diff --git a/var/spack/repos/builtin/packages/r-pbdzmq/package.py b/var/spack/repos/builtin/packages/r-pbdzmq/package.py index 4ec6ee9055..7e44f3b9e8 100644 --- a/var/spack/repos/builtin/packages/r-pbdzmq/package.py +++ b/var/spack/repos/builtin/packages/r-pbdzmq/package.py @@ -27,4 +27,4 @@ class RPbdzmq(RPackage): depends_on('r@3.0.0:', when='@:0.2-5', type=('build', 'run')) depends_on('r@3.2.0:', when='@0.2-6:', type=('build', 'run')) depends_on('r-r6', when='@:0.2-6', type=('build', 'run')) - depends_on('zeromq@4.0.4:') + depends_on('libzmq@4.0.4:') diff --git a/var/spack/repos/builtin/packages/r-pkgmaker/package.py b/var/spack/repos/builtin/packages/r-pkgmaker/package.py index e400f1228f..d2c2843f3a 100644 --- a/var/spack/repos/builtin/packages/r-pkgmaker/package.py +++ b/var/spack/repos/builtin/packages/r-pkgmaker/package.py @@ -16,7 +16,7 @@ class RPkgmaker(RPackage): changes in the interface(s) are more than likely to happen.""" homepage = "https://renozao.github.io/pkgmaker" - url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.22.tar.gz" + url = "https://cloud.r-project.org/src/contrib/pkgmaker_0.27.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/pkgmaker" version('0.27', sha256='17a289d8f596ba5637b07077b3bff22411a2c2263c0b7de59fe848666555ec6a') diff --git a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py index f8420eebb0..f3d5e951f9 100644 --- a/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py +++ b/var/spack/repos/builtin/packages/r-randomfieldsutils/package.py @@ -13,7 +13,7 @@ class RRandomfieldsutils(RPackage): Furthermore, it includes the Struve functions.""" homepage = "https://cloud.r-project.org/package=RandomFieldsUtils" - url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.3.25.tar.gz" + url = "https://cloud.r-project.org/src/contrib/RandomFieldsUtils_0.5.3.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/RandomFieldsUtils" version('0.5.3', sha256='ea823cba2e254a9f534efb4b772c0aeef2039ee9ef99744e077b969a87f8031d') diff --git a/var/spack/repos/builtin/packages/r-rngtools/package.py b/var/spack/repos/builtin/packages/r-rngtools/package.py index c4b52c3437..30762d7464 100644 --- a/var/spack/repos/builtin/packages/r-rngtools/package.py +++ b/var/spack/repos/builtin/packages/r-rngtools/package.py @@ -14,7 +14,7 @@ class RRngtools(RPackage): the way current RNG settings can be changed.""" homepage = "https://renozao.github.io/rngtools" - url = "https://cloud.r-project.org/src/contrib/rngtools_1.2.4.tar.gz" + url = "https://cloud.r-project.org/src/contrib/rngtools_1.4.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/rngtools" version('1.4', sha256='3aa92366e5d0500537964302f5754a750aff6b169a27611725e7d84552913bce') diff --git a/var/spack/repos/builtin/packages/r-rzmq/package.py b/var/spack/repos/builtin/packages/r-rzmq/package.py index aeaa990a45..862ebcf066 100644 --- a/var/spack/repos/builtin/packages/r-rzmq/package.py +++ b/var/spack/repos/builtin/packages/r-rzmq/package.py @@ -19,4 +19,4 @@ class RRzmq(RPackage): version('0.7.7', sha256='bdbaf77a0e04c5b6d6ce79ab2747848a5044355eed2e2c4d39c4ba16f97dc83d') depends_on('r@3.1.0:', when='@0.9.0:', type=('build', 'run')) - depends_on('zeromq@3.0.0:') + depends_on('libzmq@3.0.0:') diff --git a/var/spack/repos/builtin/packages/r-udunits2/package.py b/var/spack/repos/builtin/packages/r-udunits2/package.py index 551455471f..120895ec77 100644 --- a/var/spack/repos/builtin/packages/r-udunits2/package.py +++ b/var/spack/repos/builtin/packages/r-udunits2/package.py @@ -16,4 +16,4 @@ class RUdunits2(RPackage): version('0.13', sha256='d155d3c07f6202b65dec4075ffd1e1c3f4f35f5fdece8cfb319d39256a3e5b79') depends_on('r@2.10.0:', type=('build', 'run')) - depends_on('udunits2') + depends_on('udunits') diff --git a/var/spack/repos/builtin/packages/r-units/package.py b/var/spack/repos/builtin/packages/r-units/package.py index c6b4ce8f19..936a4a695c 100644 --- a/var/spack/repos/builtin/packages/r-units/package.py +++ b/var/spack/repos/builtin/packages/r-units/package.py @@ -25,4 +25,4 @@ class RUnits(RPackage): depends_on('r@3.0.2:', type=('build', 'run')) depends_on('r-udunits2@0.13:', when='@:0.5-1', type=('build', 'run')) depends_on('r-rcpp@0.12.10:', type=('build', 'run')) - depends_on('udunits2', when='@0.6-0:') + depends_on('udunits', when='@0.6-0:') diff --git a/var/spack/repos/builtin/packages/r-wgcna/package.py b/var/spack/repos/builtin/packages/r-wgcna/package.py index 7b21e756ed..426116c677 100644 --- a/var/spack/repos/builtin/packages/r-wgcna/package.py +++ b/var/spack/repos/builtin/packages/r-wgcna/package.py @@ -10,7 +10,7 @@ class RWgcna(RPackage): """WGCNA: Weighted Correlation Network Analysis""" homepage = "https://cloud.r-project.org/package=WGCNA" - url = "https://cloud.r-project.org/src/contrib/WGCNA_1.66.tar.gz" + url = "https://cloud.r-project.org/src/contrib/WGCNA_1.68.tar.gz" list_url = "https://cloud.r-project.org/src/contrib/Archive/WGCNA/" version('1.68', sha256='0a04f15a20817f9260ae1896eda3be83a7f4855a27a348df85c7f4d376f1efe8') diff --git a/var/spack/repos/builtin/packages/r-xlsx/package.py b/var/spack/repos/builtin/packages/r-xlsx/package.py index ee0f934447..2f575b9cfa 100644 --- a/var/spack/repos/builtin/packages/r-xlsx/package.py +++ b/var/spack/repos/builtin/packages/r-xlsx/package.py @@ -11,7 +11,7 @@ class RXlsx(RPackage): 97/2000/XP/2003 file formats.""" homepage = "http://code.google.com/p/rexcel/" - url = "https://cloud.r-project.org/src/contrib/xlsx_0.5.7.tar.gz" + url = "https://cloud.r-project.org/src/contrib/xlsx_0.6.1.tar.gz" listurl = "https://cloud.r-project.org/src/contrib/Archive/xlsx" version('0.6.1', sha256='a580bd16b5477c1c185bf681c12c1ffff4088089f97b6a37997913d93ec5a8b4') diff --git a/var/spack/repos/builtin/packages/r3d/package.py b/var/spack/repos/builtin/packages/r3d/package.py index 6e2984253c..6704e05419 100644 --- a/var/spack/repos/builtin/packages/r3d/package.py +++ b/var/spack/repos/builtin/packages/r3d/package.py @@ -11,11 +11,11 @@ class R3d(MakefilePackage): conservative voxelization.""" homepage = "https://github.com/devonmpowell/r3d" - url = "https://github.com/devonmpowell/r3d.git" + git = "https://github.com/devonmpowell/r3d.git" - version('2019-04-24', git=url, commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') - version('2018-12-19', git=url, commit='47308f68c782ed3227d3dab1eff24d41f6421f21') - version('2018-01-07', git=url, commit='d6799a582256a120ef3bd7e18959e96cba0e5495') + version('2019-04-24', commit='86cea79c124c6a8edd8c8cdea61e3e923acb0b22') + version('2018-12-19', commit='47308f68c782ed3227d3dab1eff24d41f6421f21') + version('2018-01-07', commit='d6799a582256a120ef3bd7e18959e96cba0e5495') variant("test", default=False, description="Build R3D regression tests") diff --git a/var/spack/repos/builtin/packages/rankstr/package.py b/var/spack/repos/builtin/packages/rankstr/package.py index c72c46b54a..d56b9211ad 100644 --- a/var/spack/repos/builtin/packages/rankstr/package.py +++ b/var/spack/repos/builtin/packages/rankstr/package.py @@ -10,7 +10,7 @@ class Rankstr(CMakePackage): """Assign one-to-one mapping of MPI ranks to strings""" homepage = "https://github.com/ECP-VeloC/rankstr" - url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.1.zip" + url = "https://github.com/ECP-VeloC/rankstr/archive/v0.0.2.zip" git = "https://github.com/ecp-veloc/rankstr.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/redset/package.py b/var/spack/repos/builtin/packages/redset/package.py index d875c1ddfc..c439bdd10e 100644 --- a/var/spack/repos/builtin/packages/redset/package.py +++ b/var/spack/repos/builtin/packages/redset/package.py @@ -10,7 +10,7 @@ class Redset(CMakePackage): """Create MPI communicators for disparate redundancy sets""" homepage = "https://github.com/ECP-VeloC/redset" - url = "https://github.com/ECP-VeloC/redset/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/redset/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/redset.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/regcm/package.py b/var/spack/repos/builtin/packages/regcm/package.py index fc80deb4d0..136c270359 100644 --- a/var/spack/repos/builtin/packages/regcm/package.py +++ b/var/spack/repos/builtin/packages/regcm/package.py @@ -45,11 +45,11 @@ class Regcm(AutotoolsPackage): description='Build NetCDF using the high performance parallel ' 'NetCDF implementation.') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('hdf5') depends_on('mpi') - depends_on('netcdf +parallel-netcdf', when='+pnetcdf') + depends_on('netcdf-c +parallel-netcdf', when='+pnetcdf') intel_msg = ('Intel compiler not working with this specific version of ' 'RegCM (generates a bug at runtime): please install a newer ' diff --git a/var/spack/repos/builtin/packages/repeatmodeler/package.py b/var/spack/repos/builtin/packages/repeatmodeler/package.py index fa395f4109..f068fb2600 100644 --- a/var/spack/repos/builtin/packages/repeatmodeler/package.py +++ b/var/spack/repos/builtin/packages/repeatmodeler/package.py @@ -18,7 +18,7 @@ class Repeatmodeler(Package): depends_on('perl', type=('build', 'run')) depends_on('perl-json', type=('build', 'run')) depends_on('perl-uri', type=('build', 'run')) - depends_on('perl-lwp', type=('build', 'run')) + depends_on('perl-libwww-perl', type=('build', 'run')) depends_on('repeatmasker', type='run') depends_on('recon+repeatmasker', type='run') diff --git a/var/spack/repos/builtin/packages/rose/package.py b/var/spack/repos/builtin/packages/rose/package.py index 23b497a2e7..90b6d0d6dd 100644 --- a/var/spack/repos/builtin/packages/rose/package.py +++ b/var/spack/repos/builtin/packages/rose/package.py @@ -16,8 +16,7 @@ class Rose(AutotoolsPackage): (Developed at Lawrence Livermore National Lab)""" homepage = "http://rosecompiler.org/" - # url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.7.0.tar.gz" - url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.9.104.zip" + url = "https://github.com/rose-compiler/rose-develop/archive/v0.9.10.0.zip" git = "https://github.com/rose-compiler/rose-develop.git" # -------------------------------------------------------------------------- @@ -212,9 +211,9 @@ class Rose(AutotoolsPackage): return args - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if "+codethorn" in self.spec: - spack_env.set("CXXFLAGS", "-std=c++11") + env.set("CXXFLAGS", "-std=c++11") def build(self, spec, prefix): # Spack will automatically pass ncpus as the number of make jobs. diff --git a/var/spack/repos/builtin/packages/seacas/package.py b/var/spack/repos/builtin/packages/seacas/package.py index f02cb9b09e..f4c145d243 100644 --- a/var/spack/repos/builtin/packages/seacas/package.py +++ b/var/spack/repos/builtin/packages/seacas/package.py @@ -71,8 +71,8 @@ class Seacas(CMakePackage): # Everything should be compiled position independent (-fpic) - depends_on('netcdf@4.6.2:+mpi+parallel-netcdf', when='+mpi') - depends_on('netcdf@4.6.2:~mpi', when='~mpi') + depends_on('netcdf-c@4.6.2:+mpi+parallel-netcdf', when='+mpi') + depends_on('netcdf-c@4.6.2:~mpi', when='~mpi') depends_on('cgns@develop+mpi+scoping', when='+cgns +mpi') depends_on('cgns@develop~mpi+scoping', when='+cgns ~mpi') depends_on('adios2@develop~mpi', when='+adios2 ~mpi') @@ -198,10 +198,10 @@ class Seacas(CMakePackage): ]) # ##################### Dependencies ########################## - # Always need NetCDF + # Always need NetCDF-C options.extend([ '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, ]) if '+metis' in spec: diff --git a/var/spack/repos/builtin/packages/shuffile/package.py b/var/spack/repos/builtin/packages/shuffile/package.py index 13ba8b96b4..bfd6defb23 100644 --- a/var/spack/repos/builtin/packages/shuffile/package.py +++ b/var/spack/repos/builtin/packages/shuffile/package.py @@ -10,7 +10,7 @@ class Shuffile(CMakePackage): """Shuffle files between MPI ranks""" homepage = "https://github.com/ECP-VeloC/shuffile" - url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.2.zip" + url = "https://github.com/ECP-VeloC/shuffile/archive/v0.0.3.zip" git = "https://github.com/ecp-veloc/shuffile.git" tags = ['ecp'] diff --git a/var/spack/repos/builtin/packages/siesta/package.py b/var/spack/repos/builtin/packages/siesta/package.py index 70d52a2607..1733585274 100644 --- a/var/spack/repos/builtin/packages/siesta/package.py +++ b/var/spack/repos/builtin/packages/siesta/package.py @@ -23,7 +23,7 @@ class Siesta(Package): depends_on('blas') depends_on('lapack') depends_on('scalapack') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') phases = ['configure', 'build', 'install'] @@ -40,7 +40,7 @@ class Siesta(Package): spec['blas'].libs), '--with-scalapack=%s' % spec['scalapack'].libs, '--with-netcdf=%s' % (spec['netcdf-fortran'].libs + - spec['netcdf'].libs), + spec['netcdf-c'].libs), # need to specify MPIFC explicitly below, otherwise # Intel's mpiifort is not found 'MPIFC=%s' % spec['mpi'].mpifc diff --git a/var/spack/repos/builtin/packages/simulationio/package.py b/var/spack/repos/builtin/packages/simulationio/package.py index 51b43719d8..d209f702f7 100644 --- a/var/spack/repos/builtin/packages/simulationio/package.py +++ b/var/spack/repos/builtin/packages/simulationio/package.py @@ -11,7 +11,7 @@ class Simulationio(CMakePackage): """SimulationIO: Efficient and convenient I/O for large PDE simulations""" homepage = "https://github.com/eschnett/SimulationIO" - url = "https://github.com/eschnett/SimulationIO/archive/version/0.1.0.tar.gz" + url = "https://github.com/eschnett/SimulationIO/archive/version/9.0.1.tar.gz" git = "https://github.com/eschnett/SimulationIO.git" version('develop', branch='master') diff --git a/var/spack/repos/builtin/packages/squid/package.py b/var/spack/repos/builtin/packages/squid/package.py index a039bbedc5..bce6f19590 100644 --- a/var/spack/repos/builtin/packages/squid/package.py +++ b/var/spack/repos/builtin/packages/squid/package.py @@ -10,5 +10,6 @@ class Squid(AutotoolsPackage): """C function library for sequence analysis.""" homepage = "http://eddylab.org/software.html" + url = "http://eddylab.org/software/squid/squid-1.9g.tar.gz" - version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7', url='http://eddylab.org/software/squid/squid.tar.gz') + version('1.9g', sha256='302f42e8794aa4dbcfa0996c14fb7a70a7c4397fc45c2bbd2748055460d8dca7') diff --git a/var/spack/repos/builtin/packages/sra-toolkit/package.py b/var/spack/repos/builtin/packages/sratoolkit/package.py index 972f4d8a70..a8cf5d9b6c 100644 --- a/var/spack/repos/builtin/packages/sra-toolkit/package.py +++ b/var/spack/repos/builtin/packages/sratoolkit/package.py @@ -6,7 +6,7 @@ from spack import * -class SraToolkit(Package): +class Sratoolkit(Package): """The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.""" @@ -18,10 +18,6 @@ class SraToolkit(Package): version('2.9.2', sha256='17dbe13aa1ed7955d31e1e76e8b62786e80a77e9ed9d396631162dc3ad8b716d') version('2.8.2-1', sha256='b053061aae7c6d00162fe0f514be4128a60365b4b2b5b36e7f4798b348b55cf5') - def url_for_version(self, version): - url = 'https://ftp-trace.ncbi.nlm.nih.gov/sra/sdk/{0}/sratoolkit.{0}-centos_linux64.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree('bin', prefix.bin, symlinks=True) install_tree('example', prefix.example) diff --git a/var/spack/repos/builtin/packages/stc/package.py b/var/spack/repos/builtin/packages/stc/package.py index ce52a418f2..631d7647e7 100644 --- a/var/spack/repos/builtin/packages/stc/package.py +++ b/var/spack/repos/builtin/packages/stc/package.py @@ -11,7 +11,7 @@ class Stc(AutotoolsPackage): """STC: The Swift-Turbine Compiler""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/stc-0.8.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" version('master', branch='master') diff --git a/var/spack/repos/builtin/packages/subversion/package.py b/var/spack/repos/builtin/packages/subversion/package.py index de26e0dece..ba621061fd 100644 --- a/var/spack/repos/builtin/packages/subversion/package.py +++ b/var/spack/repos/builtin/packages/subversion/package.py @@ -34,7 +34,7 @@ class Subversion(AutotoolsPackage): extends('perl', when='+perl') depends_on('swig@1.3.24:3.0.0', when='+perl') - depends_on('perl-term-readkey', when='+perl') + depends_on('perl-termreadkey', when='+perl') # Installation has race cases. parallel = False diff --git a/var/spack/repos/builtin/packages/thrift/package.py b/var/spack/repos/builtin/packages/thrift/package.py index 0644ed1fea..098de9bacd 100644 --- a/var/spack/repos/builtin/packages/thrift/package.py +++ b/var/spack/repos/builtin/packages/thrift/package.py @@ -17,7 +17,7 @@ class Thrift(Package): """ homepage = "http://thrift.apache.org" - url = "http://apache.mirrors.ionfish.org/thrift/0.9.2/thrift-0.9.2.tar.gz" + url = "http://apache.mirrors.ionfish.org/thrift/0.11.0/thrift-0.11.0.tar.gz" version('0.11.0', sha256='c4ad38b6cb4a3498310d405a91fef37b9a8e79a50cd0968148ee2524d2fa60c2') version('0.10.0', sha256='2289d02de6e8db04cbbabb921aeb62bfe3098c4c83f36eec6c31194301efa10b') @@ -47,10 +47,10 @@ class Thrift(Package): depends_on('zlib', when='+c') depends_on('libevent', when='+c') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): if '+pic' in self.spec: - spack_env.append_flags('CFLAGS', self.compiler.pic_flag) - spack_env.append_flags('CXXFLAGS', self.compiler.pic_flag) + env.append_flags('CFLAGS', self.compiler.pic_flag) + env.append_flags('CXXFLAGS', self.compiler.pic_flag) def install(self, spec, prefix): env['PY_PREFIX'] = prefix diff --git a/var/spack/repos/builtin/packages/transabyss/package.py b/var/spack/repos/builtin/packages/transabyss/package.py index 85cf56bd85..a77fcbd621 100644 --- a/var/spack/repos/builtin/packages/transabyss/package.py +++ b/var/spack/repos/builtin/packages/transabyss/package.py @@ -16,7 +16,7 @@ class Transabyss(Package): depends_on('abyss@1.5.2') depends_on('python@2.7.6:', type=('build', 'run')) - depends_on('py-igraph@0.7.0:', type=('build', 'run')) + depends_on('py-python-igraph@0.7.0:', type=('build', 'run')) depends_on('blat') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py index f1bc186dcf..0826b8d00c 100644 --- a/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py +++ b/var/spack/repos/builtin/packages/trilinos-catalyst-ioss-adapter/package.py @@ -10,7 +10,6 @@ class TrilinosCatalystIossAdapter(CMakePackage): """Adapter for Trilinos Seacas Ioss and Paraview Catalyst""" homepage = "https://trilinos.org/" - url = "https://github.com/trilinos/Trilinos/archive/trilinos-release-12-12-1.tar.gz" git = "https://github.com/trilinos/Trilinos.git" version('develop', branch='develop') @@ -20,17 +19,17 @@ class TrilinosCatalystIossAdapter(CMakePackage): depends_on('flex', type='build') depends_on('paraview+mpi+python+osmesa') depends_on('py-numpy', type=('build', 'run')) - # Here we avoid paraview trying to use netcdf~parallel-netcdf - # which is netcdf's default, even though paraview depends on 'netcdf' + # Here we avoid paraview trying to use netcdf-c~parallel-netcdf + # which is netcdf-c's default, even though paraview depends on 'netcdf-c' # without any variants. Concretizer bug? - depends_on('netcdf+parallel-netcdf') + depends_on('netcdf-c+parallel-netcdf') root_cmakelists_dir = join_path('packages', 'seacas', 'libraries', 'ioss', 'src', 'visualization', 'ParaViewCatalystIossAdapter') - def setup_environment(self, spack_env, run_env): - run_env.prepend_path('PYTHONPATH', self.prefix.python) + def setup_run_environment(self, env): + env.prepend_path('PYTHONPATH', self.prefix.python) def cmake_args(self): spec = self.spec diff --git a/var/spack/repos/builtin/packages/trilinos/package.py b/var/spack/repos/builtin/packages/trilinos/package.py index 47e1fb1936..db6621ed6b 100644 --- a/var/spack/repos/builtin/packages/trilinos/package.py +++ b/var/spack/repos/builtin/packages/trilinos/package.py @@ -297,8 +297,8 @@ class Trilinos(CMakePackage): # MPI related dependencies depends_on('mpi') - depends_on('netcdf+mpi', when="~pnetcdf") - depends_on('netcdf+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") + depends_on('netcdf-c+mpi', when="~pnetcdf") + depends_on('netcdf-c+mpi+parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parallel-netcdf', when="+pnetcdf@master,12.12.1:") depends_on('parmetis', when='+metis') depends_on('cgns', when='+cgns') @@ -505,7 +505,7 @@ class Trilinos(CMakePackage): '-DLAPACK_LIBRARY_NAMES=%s' % ';'.join(lapack.names), '-DLAPACK_LIBRARY_DIRS=%s' % ';'.join(lapack.directories), '-DTPL_ENABLE_Netcdf:BOOL=ON', - '-DNetCDF_ROOT:PATH=%s' % spec['netcdf'].prefix, + '-DNetCDF_ROOT:PATH=%s' % spec['netcdf-c'].prefix, '-DTPL_ENABLE_X11:BOOL=%s' % ( 'ON' if '+x11' in spec else 'OFF'), '-DTrilinos_ENABLE_Gtest:BOOL=%s' % ( diff --git a/var/spack/repos/builtin/packages/trinity/package.py b/var/spack/repos/builtin/packages/trinity/package.py index 997e36c0ef..68b8c7b98c 100644 --- a/var/spack/repos/builtin/packages/trinity/package.py +++ b/var/spack/repos/builtin/packages/trinity/package.py @@ -52,7 +52,7 @@ class Trinity(MakefilePackage): depends_on("samtools", type="run") depends_on("py-numpy", type="run") depends_on("express", type="run") - depends_on("perl-dbfile", type="run") + depends_on("perl-db-file", type="run") depends_on("perl-uri", type="run") depends_on("r-fastcluster", type="run") depends_on("r-ctc", type="run") @@ -85,7 +85,9 @@ class Trinity(MakefilePackage): force_remove(join_path(prefix.bin, 'trinity-plugins', 'slclust', 'bin', '.hidden')) - def setup_environment(self, spack_env, run_env): - run_env.set('TRINITY_HOME', self.prefix.bin) - run_env.prepend_path('PATH', self.prefix.bin.util) - spack_env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + def setup_build_environment(self, env): + env.append_flags('CXXFLAGS', self.compiler.openmp_flag) + + def setup_run_environment(self, env): + env.set('TRINITY_HOME', self.prefix.bin) + env.prepend_path('PATH', self.prefix.bin.util) diff --git a/var/spack/repos/builtin/packages/turbine/package.py b/var/spack/repos/builtin/packages/turbine/package.py index 4788efd070..902cae7a94 100644 --- a/var/spack/repos/builtin/packages/turbine/package.py +++ b/var/spack/repos/builtin/packages/turbine/package.py @@ -13,7 +13,7 @@ class Turbine(AutotoolsPackage): """Turbine: The Swift/T runtime""" homepage = 'http://swift-lang.org/Swift-T' - url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-0.0.0.tar.gz' + url = 'http://swift-lang.github.io/swift-t-downloads/spack/turbine-1.2.3.tar.gz' git = "https://github.com/swift-lang/swift-t.git" configure_directory = 'turbine/code' @@ -44,12 +44,12 @@ class Turbine(AutotoolsPackage): depends_on('libtool', type='build', when='@master') depends_on('m4', type=('build', 'run')) - 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): diff --git a/var/spack/repos/builtin/packages/udunits2/package.py b/var/spack/repos/builtin/packages/udunits/package.py index c5704d6a5e..e3e31bee5c 100644 --- a/var/spack/repos/builtin/packages/udunits2/package.py +++ b/var/spack/repos/builtin/packages/udunits/package.py @@ -6,7 +6,7 @@ from spack import * -class Udunits2(AutotoolsPackage): +class Udunits(AutotoolsPackage): """Automated units conversion""" homepage = "http://www.unidata.ucar.edu/software/udunits" diff --git a/var/spack/repos/builtin/packages/vmatch/package.py b/var/spack/repos/builtin/packages/vmatch/package.py index 3cedce4ede..b4433f6174 100644 --- a/var/spack/repos/builtin/packages/vmatch/package.py +++ b/var/spack/repos/builtin/packages/vmatch/package.py @@ -15,9 +15,5 @@ class Vmatch(Package): version('2.3.0', sha256='5e18d0dddf04e86dad193fcdde6e48f3901365932634125602d8808f35acf979') - def url_for_version(self, version): - url = 'http://www.vmatch.de/distributions/vmatch-{0}-Linux_x86_64-64bit.tar.gz' - return url.format(version) - def install(self, spec, prefix): install_tree(self.stage.source_path, prefix.bin) diff --git a/var/spack/repos/builtin/packages/vtkh/package.py b/var/spack/repos/builtin/packages/vtk-h/package.py index 3d60ee9a50..e3c1bd4031 100644 --- a/var/spack/repos/builtin/packages/vtkh/package.py +++ b/var/spack/repos/builtin/packages/vtk-h/package.py @@ -28,7 +28,7 @@ def cmake_cache_entry(name, value, vtype=None): return 'set({0} "{1}" CACHE {2} "")\n\n'.format(name, value, vtype) -class Vtkh(Package): +class VtkH(Package): """VTK-h is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-h brings together several projects like VTK-m and DIY2 to provide a toolkit with hybrid parallel capabilities.""" @@ -53,29 +53,29 @@ class Vtkh(Package): depends_on("intel-tbb", when="@0.1.0+tbb") depends_on("cuda", when="+cuda") - depends_on("vtkm@1.2.0", when="@0.1.0") - depends_on("vtkm@1.2.0+tbb", when="@0.1.0+tbb") - depends_on("vtkm@1.2.0+cuda", when="@0.1.0+cuda") - depends_on("vtkm@1.2.0~shared", when="@0.1.0~shared") + depends_on("vtk-m@1.2.0", when="@0.1.0") + depends_on("vtk-m@1.2.0+tbb", when="@0.1.0+tbb") + depends_on("vtk-m@1.2.0+cuda", when="@0.1.0+cuda") + depends_on("vtk-m@1.2.0~shared", when="@0.1.0~shared") - depends_on("vtkm@master~tbb+openmp", when="@develop+openmp") - depends_on("vtkm@master~tbb~openmp", when="@develop~openmp") + depends_on("vtk-m@master~tbb+openmp", when="@develop+openmp") + depends_on("vtk-m@master~tbb~openmp", when="@develop~openmp") - depends_on("vtkm@master+cuda~tbb+openmp", when="@develop+cuda+openmp") - depends_on("vtkm@master+cuda~tbb~openmp", when="@develop+cuda~openmp") + depends_on("vtk-m@master+cuda~tbb+openmp", when="@develop+cuda+openmp") + depends_on("vtk-m@master+cuda~tbb~openmp", when="@develop+cuda~openmp") - depends_on("vtkm@master~tbb+openmp~shared", when="@develop+openmp~shared") - depends_on("vtkm@master~tbb~openmp~shared", when="@develop~openmp~shared") + depends_on("vtk-m@master~tbb+openmp~shared", when="@develop+openmp~shared") + depends_on("vtk-m@master~tbb~openmp~shared", when="@develop~openmp~shared") - depends_on("vtkm@master+cuda~tbb+openmp~shared", when="@develop+cuda+openmp~shared") - depends_on("vtkm@master+cuda~tbb~openmp~shared", when="@develop+cuda~openmp~shared") + depends_on("vtk-m@master+cuda~tbb+openmp~shared", when="@develop+cuda+openmp~shared") + depends_on("vtk-m@master+cuda~tbb~openmp~shared", when="@develop+cuda~openmp~shared") patch('vtkm_lagrange_cuda_fix.patch') def install(self, spec, prefix): with working_dir('spack-build', create=True): cmake_args = ["../src", - "-DVTKM_DIR={0}".format(spec["vtkm"].prefix), + "-DVTKM_DIR={0}".format(spec["vtk-m"].prefix), "-DENABLE_TESTS=OFF", "-DBUILD_TESTING=OFF"] @@ -203,7 +203,7 @@ class Vtkh(Package): cfg.write(cmake_cache_entry("ENABLE_OPENMP", "ON")) 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)) ####################################################################### # Optional Dependencies diff --git a/var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch b/var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch index 2f90477e76..2f90477e76 100644 --- a/var/spack/repos/builtin/packages/vtkh/vtkm_lagrange_cuda_fix.patch +++ b/var/spack/repos/builtin/packages/vtk-h/vtkm_lagrange_cuda_fix.patch diff --git a/var/spack/repos/builtin/packages/vtkm/package.py b/var/spack/repos/builtin/packages/vtk-m/package.py index eee37bf9af..317343bc82 100644 --- a/var/spack/repos/builtin/packages/vtkm/package.py +++ b/var/spack/repos/builtin/packages/vtk-m/package.py @@ -9,7 +9,7 @@ import os import sys -class Vtkm(CMakePackage, CudaPackage): +class VtkM(CMakePackage, CudaPackage): """VTK-m is a toolkit of scientific visualization algorithms for emerging processor architectures. VTK-m supports the fine-grained concurrency for data analysis and visualization algorithms required to drive extreme scale @@ -90,8 +90,7 @@ class Vtkm(CMakePackage, CudaPackage): # logging support if "+logging" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('logging is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_LOGGING:BOOL=ON") @@ -100,8 +99,7 @@ class Vtkm(CMakePackage, CudaPackage): # mpi support if "+mpi" in spec: - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('mpi is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_MPI:BOOL=ON") @@ -111,8 +109,7 @@ class Vtkm(CMakePackage, CudaPackage): # openmp support if "+openmp" in spec: # openmp is added since version 1.3.0 - if spec.satisfies('@:1.2.0') and \ - spec['vtkm'].version.string != 'master': + if spec.satisfies('@:1.2.0'): raise InstallError('OpenMP is not supported for\ vtkm version lower than 1.3') options.append("-DVTKm_ENABLE_OPENMP:BOOL=ON") diff --git a/var/spack/repos/builtin/packages/vtk/package.py b/var/spack/repos/builtin/packages/vtk/package.py index 3d9d108ae4..8ed305c53f 100644 --- a/var/spack/repos/builtin/packages/vtk/package.py +++ b/var/spack/repos/builtin/packages/vtk/package.py @@ -86,7 +86,7 @@ class Vtk(CMakePackage): depends_on('jsoncpp') depends_on('libxml2') depends_on('lz4') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-cxx') depends_on('libpng') depends_on('libtiff') @@ -96,10 +96,10 @@ class Vtk(CMakePackage): url = "http://www.vtk.org/files/release/{0}/VTK-{1}.tar.gz" return url.format(version.up_to(2), version) - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # VTK has some trouble finding freetype unless it is set in # the environment - spack_env.set('FREETYPE_DIR', self.spec['freetype'].prefix) + env.set('FREETYPE_DIR', self.spec['freetype'].prefix) def cmake_args(self): spec = self.spec @@ -120,8 +120,8 @@ class Vtk(CMakePackage): '-DVTK_USE_SYSTEM_LIBPROJ4:BOOL=OFF', '-DVTK_USE_SYSTEM_OGGTHEORA:BOOL=OFF', - '-DNETCDF_DIR={0}'.format(spec['netcdf'].prefix), - '-DNETCDF_C_ROOT={0}'.format(spec['netcdf'].prefix), + '-DNETCDF_DIR={0}'.format(spec['netcdf-c'].prefix), + '-DNETCDF_C_ROOT={0}'.format(spec['netcdf-c'].prefix), '-DNETCDF_CXX_ROOT={0}'.format(spec['netcdf-cxx'].prefix), # Allow downstream codes (e.g. VisIt) to override VTK's classes diff --git a/var/spack/repos/builtin/packages/warpx/package.py b/var/spack/repos/builtin/packages/warpx/package.py index 015c38406b..89c0117d2e 100644 --- a/var/spack/repos/builtin/packages/warpx/package.py +++ b/var/spack/repos/builtin/packages/warpx/package.py @@ -16,10 +16,10 @@ class Warpx(MakefilePackage): """ homepage = "https://ecp-warpx.github.io/index.html" - url = "https://github.com/ECP-WarpX/WarpX" + git = "https://github.com/ECP-WarpX/WarpX.git" - version('master', git='https://github.com/ECP-WarpX/WarpX.git', tag='master') - version('dev', git='https://github.com/ECP-WarpX/WarpX.git', tag='dev') + version('master', tag='master') + version('dev', tag='dev') depends_on('mpi') @@ -94,11 +94,11 @@ class Warpx(MakefilePackage): 'TINY_PROFILE = {0}'.format(torf('+tprof'))) makefile.filter('EBASE .*', 'EBASE = warpx') - def setup_environment(self, spack_env, run_env): + def setup_build_environment(self, env): # --- Fool the compiler into using the "unknown" configuration. # --- With this, it will use the spack provided mpi. - spack_env.set('HOSTNAME', 'unknown') - spack_env.set('NERSC_HOST', 'unknown') + env.set('HOSTNAME', 'unknown') + env.set('NERSC_HOST', 'unknown') def install(self, spec, prefix): make('WarpxBinDir = {0}'.format(prefix.bin), 'all') diff --git a/var/spack/repos/builtin/packages/wireshark/package.py b/var/spack/repos/builtin/packages/wireshark/package.py index 5df47d773b..cd334ed76e 100644 --- a/var/spack/repos/builtin/packages/wireshark/package.py +++ b/var/spack/repos/builtin/packages/wireshark/package.py @@ -24,7 +24,7 @@ class Wireshark(CMakePackage): variant('headers', default=True, description='Install headers') depends_on('bison', type='build') - depends_on('cares') + depends_on('c-ares') depends_on('doxygen', type='build') depends_on('flex', type='build') depends_on('git', type='build') diff --git a/var/spack/repos/builtin/packages/xdmf3/package.py b/var/spack/repos/builtin/packages/xdmf3/package.py index 772135846c..8a245ddc2d 100644 --- a/var/spack/repos/builtin/packages/xdmf3/package.py +++ b/var/spack/repos/builtin/packages/xdmf3/package.py @@ -13,7 +13,6 @@ class Xdmf3(CMakePackage): """ homepage = "http://xdmf.org" - url = "https://gitlab.kitware.com/xdmf/xdmf/-/archive/master/xdmf-master.tar.bz2" git = "https://gitlab.kitware.com/xdmf/xdmf.git" # There is no official release of XDMF and development has largely ceased, diff --git a/var/spack/repos/builtin/packages/xeus/package.py b/var/spack/repos/builtin/packages/xeus/package.py index d67d32d188..1cca2c2cf5 100644 --- a/var/spack/repos/builtin/packages/xeus/package.py +++ b/var/spack/repos/builtin/packages/xeus/package.py @@ -23,7 +23,7 @@ class Xeus(CMakePackage): conflicts('%clang@:3.6') conflicts('%intel@:17') - depends_on('zeromq@4.2.5:-libsodium') + depends_on('libzmq@4.2.5:-libsodium') depends_on('cppzmq@4.3.0:') depends_on('cryptopp@7.0.0:') depends_on('xtl@0.4.0:') diff --git a/var/spack/repos/builtin/packages/xios/package.py b/var/spack/repos/builtin/packages/xios/package.py index 799bdc03d7..997e54ec57 100644 --- a/var/spack/repos/builtin/packages/xios/package.py +++ b/var/spack/repos/builtin/packages/xios/package.py @@ -21,7 +21,7 @@ class Xios(Package): description='Build for debugging, development or production') # NOTE: oasis coupler could be supported with a variant - # Use spack versions of blitz and netcdf for compatibility + # Use spack versions of blitz and netcdf-c for compatibility # with recent compilers and optimised platform libraries: patch('bld_extern_1.0.patch', when='@:1.0') patch('bld_extern_1.x.patch', when='@1.1:') @@ -30,7 +30,7 @@ class Xios(Package): # followed by a character is broken (e.g. duration '1d'): patch('llvm_bug_17782.patch', when='@1.1: %clang') - depends_on('netcdf+mpi') + depends_on('netcdf-c+mpi') depends_on('netcdf-fortran') depends_on('hdf5+mpi') depends_on('mpi') @@ -60,8 +60,8 @@ class Xios(Package): def xios_path(self): file = join_path('arch', 'arch-SPACK.path') spec = self.spec - paths = {'NETCDF_INC_DIR': spec['netcdf'].prefix.include, - 'NETCDF_LIB_DIR': spec['netcdf'].prefix.lib, + paths = {'NETCDF_INC_DIR': spec['netcdf-c'].prefix.include, + 'NETCDF_LIB_DIR': spec['netcdf-c'].prefix.lib, 'HDF5_INC_DIR': spec['hdf5'].prefix.include, 'HDF5_LIB_DIR': spec['hdf5'].prefix.lib} text = r""" diff --git a/var/spack/repos/builtin/packages/yambo/package.py b/var/spack/repos/builtin/packages/yambo/package.py index 29d84a20b7..e4c07cf679 100644 --- a/var/spack/repos/builtin/packages/yambo/package.py +++ b/var/spack/repos/builtin/packages/yambo/package.py @@ -45,20 +45,20 @@ class Yambo(AutotoolsPackage): # MPI dependencies are forced, until we have proper forwarding of variants # # Note that yambo is used as an application, and not linked as a library, - # thus there will be no case where another package pulls-in e.g. netcdf+mpi - # and wants to depend on yambo~mpi. + # thus there will be no case where another package pulls-in e.g. + # netcdf-c+mpi and wants to depend on yambo~mpi. depends_on('mpi', when='+mpi') - depends_on('netcdf+mpi', when='+mpi') + depends_on('netcdf-c+mpi', when='+mpi') depends_on('hdf5+mpi', when='+mpi') depends_on('fftw+mpi', when='+mpi') depends_on('scalapack', when='+mpi') - depends_on('netcdf~mpi', when='~mpi') + depends_on('netcdf-c~mpi', when='~mpi') depends_on('hdf5~mpi', when='~mpi') depends_on('fftw~mpi', when='~mpi') depends_on('hdf5+fortran') - depends_on('netcdf') + depends_on('netcdf-c') depends_on('netcdf-fortran') depends_on('libxc@2.0.3:') @@ -124,7 +124,7 @@ class Yambo(AutotoolsPackage): '--enable-netcdf-hdf5', '--enable-hdf5-compression', '--with-hdf5-libs={0}'.format(spec['hdf5'].libs), - '--with-netcdf-path={0}'.format(spec['netcdf'].prefix), + '--with-netcdf-path={0}'.format(spec['netcdf-c'].prefix), '--with-netcdff-path={0}'.format(spec['netcdf-fortran'].prefix) ]) |