diff options
23 files changed, 554 insertions, 33 deletions
diff --git a/lib/spack/spack/cmd/create.py b/lib/spack/spack/cmd/create.py index da74ceb2f6..51bf17a44b 100644 --- a/lib/spack/spack/cmd/create.py +++ b/lib/spack/spack/cmd/create.py @@ -165,7 +165,7 @@ install_dict = { 'python': """\ # FIXME: Add logic to build and install here. - python('setup.py', 'install', '--prefix={0}'.format(prefix))""", + setup_py('install', '--prefix={0}'.format(prefix))""", 'R': """\ # FIXME: Add logic to build and install here. diff --git a/lib/spack/spack/preferred_packages.py b/lib/spack/spack/preferred_packages.py index 5f18e212b6..f079c1ef8b 100644 --- a/lib/spack/spack/preferred_packages.py +++ b/lib/spack/spack/preferred_packages.py @@ -162,8 +162,8 @@ class PreferredPackages(object): """Return a VariantMap of preferred variants and their values""" variants = self.preferred.get(pkgname, {}).get('variants', '') if not isinstance(variants, basestring): - variants = "".join(variants) - return spack.spec.Spec(pkgname + variants).variants + variants = " ".join(variants) + return spack.spec.Spec("%s %s" % (pkgname, variants)).variants def version_compare(self, pkgname, a, b): """Return less-than-0, 0, or greater than 0 if version a of pkgname is diff --git a/lib/spack/spack/stage.py b/lib/spack/spack/stage.py index 1a8b1a169a..553c4ad05f 100644 --- a/lib/spack/spack/stage.py +++ b/lib/spack/spack/stage.py @@ -318,10 +318,11 @@ class Stage(object): fetchers.insert(0, spack.cache.fetcher(self.mirror_path, digest)) # Look for the archive in list_url - archive_version = spack.url.parse_version(self.default_fetcher.url) package_name = os.path.dirname(self.mirror_path) pkg = spack.repo.get(package_name) if pkg.list_url is not None and pkg.url is not None: + archive_version = spack.url.parse_version( + self.default_fetcher.url) versions = pkg.fetch_remote_versions() try: url_from_list = versions[Version(archive_version)] diff --git a/lib/spack/spack/test/__init__.py b/lib/spack/spack/test/__init__.py index a849d5f350..3439764ee6 100644 --- a/lib/spack/spack/test/__init__.py +++ b/lib/spack/spack/test/__init__.py @@ -39,9 +39,9 @@ test_names = [ 'pattern', 'python_version', 'git_fetch', 'svn_fetch', 'hg_fetch', 'mirror', 'modules', 'url_extrapolate', 'cc', 'link_tree', 'spec_yaml', 'optional_deps', 'make_executable', 'build_system_guess', 'lock', - 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', 'cmd.find', - 'cmd.uninstall', 'cmd.test_install', 'cmd.test_compiler_cmd', - 'cmd.module' + 'database', 'namespace_trie', 'yaml', 'sbang', 'environment', + 'concretize_preferences', 'cmd.find', 'cmd.uninstall', 'cmd.test_install', + 'cmd.test_compiler_cmd', 'cmd.module' ] diff --git a/lib/spack/spack/test/concretize_preferences.py b/lib/spack/spack/test/concretize_preferences.py new file mode 100644 index 0000000000..2c8bedc33f --- /dev/null +++ b/lib/spack/spack/test/concretize_preferences.py @@ -0,0 +1,106 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +import spack +import spack.architecture +from spack.test.mock_packages_test import * +from tempfile import mkdtemp + + +class ConcretizePreferencesTest(MockPackagesTest): + """Test concretization preferences are being applied correctly. + """ + + def setUp(self): + """Create config section to store concretization preferences + """ + super(ConcretizePreferencesTest, self).setUp() + self.tmp_dir = mkdtemp('.tmp', 'spack-config-test-') + spack.config.ConfigScope('concretize', + os.path.join(self.tmp_dir, 'concretize')) + + def tearDown(self): + super(ConcretizePreferencesTest, self).tearDown() + shutil.rmtree(self.tmp_dir, True) + spack.pkgsort = spack.PreferredPackages() + + def concretize(self, abstract_spec): + return Spec(abstract_spec).concretized() + + def update_packages(self, pkgname, section, value): + """Update config and reread package list""" + conf = {pkgname: {section: value}} + spack.config.update_config('packages', conf, 'concretize') + spack.pkgsort = spack.PreferredPackages() + + def assert_variant_values(self, spec, **variants): + concrete = self.concretize(spec) + for variant, value in variants.items(): + self.assertEqual(concrete.variants[variant].value, value) + + def test_preferred_variants(self): + """Test preferred variants are applied correctly + """ + self.update_packages('mpileaks', 'variants', + '~debug~opt+shared+static') + self.assert_variant_values('mpileaks', debug=False, opt=False, + shared=True, static=True) + + self.update_packages('mpileaks', 'variants', + ['+debug', '+opt', '~shared', '-static']) + self.assert_variant_values('mpileaks', debug=True, opt=True, + shared=False, static=False) + + def test_preferred_compilers(self): + """Test preferred compilers are applied correctly + """ + self.update_packages('mpileaks', 'compiler', ['clang@3.3']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.compiler, spack.spec.CompilerSpec('clang@3.3')) + + self.update_packages('mpileaks', 'compiler', ['gcc@4.5.0']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.compiler, spack.spec.CompilerSpec('gcc@4.5.0')) + + def test_preferred_versions(self): + """Test preferred package versions are applied correctly + """ + self.update_packages('mpileaks', 'version', ['2.3']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.version, spack.spec.Version('2.3')) + + self.update_packages('mpileaks', 'version', ['2.2']) + spec = self.concretize('mpileaks') + self.assertEqual(spec.version, spack.spec.Version('2.2')) + + def test_preferred_providers(self): + """Test preferred providers of virtual packages are applied correctly + """ + self.update_packages('all', 'providers', {'mpi': ['mpich']}) + spec = self.concretize('mpileaks') + self.assertTrue('mpich' in spec) + + self.update_packages('all', 'providers', {'mpi': ['zmpi']}) + spec = self.concretize('mpileaks') + self.assertTrue('zmpi', spec) diff --git a/var/spack/repos/builtin.mock/packages/mpileaks/package.py b/var/spack/repos/builtin.mock/packages/mpileaks/package.py index bc26f539ba..10fbf3845e 100644 --- a/var/spack/repos/builtin.mock/packages/mpileaks/package.py +++ b/var/spack/repos/builtin.mock/packages/mpileaks/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Mpileaks(Package): homepage = "http://www.llnl.gov" url = "http://www.llnl.gov/mpileaks-1.0.tar.gz" @@ -35,6 +36,8 @@ class Mpileaks(Package): variant('debug', default=False, description='Debug variant') variant('opt', default=False, description='Optimized variant') + variant('shared', default=True, description='Build shared library') + variant('static', default=True, description='Build static library') depends_on("mpi") depends_on("callpath") diff --git a/var/spack/repos/builtin/packages/ack/package.py b/var/spack/repos/builtin/packages/ack/package.py new file mode 100644 index 0000000000..70249aebac --- /dev/null +++ b/var/spack/repos/builtin/packages/ack/package.py @@ -0,0 +1,51 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Ack(Package): + """ack 2.14 is a tool like grep, optimized for programmers. + + Designed for programmers with large heterogeneous trees of + source code, ack is written purely in portable Perl 5 and takes + advantage of the power of Perl's regular expressions.""" + + homepage = "http://beyondgrep.com/" + url = "http://beyondgrep.com/ack-2.14-single-file" + + version('2.14', 'e74150a1609d28a70b450ef9cc2ed56b', expand=False) + + depends_on('perl') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + ack = 'ack-{0}-single-file'.format(self.version) + + # rewrite the script's #! line to call the perl dependency + shbang = '#!' + join_path(spec['perl'].prefix.bin, 'perl') + filter_file(r'^#!/usr/bin/env perl', shbang, ack) + + install(ack, join_path(prefix.bin, "ack")) + set_executable(join_path(prefix.bin, "ack")) diff --git a/var/spack/repos/builtin/packages/arpack-ng/package.py b/var/spack/repos/builtin/packages/arpack-ng/package.py index d5dc703c06..2874930cdd 100644 --- a/var/spack/repos/builtin/packages/arpack-ng/package.py +++ b/var/spack/repos/builtin/packages/arpack-ng/package.py @@ -86,10 +86,19 @@ class ArpackNg(Package): options.extend(std_cmake_args) options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) - # TODO: - # Arpack calls directly find_package(BLAS REQUIRED) and - # find_package(LAPACK REQUIRED). Make sure correct Blas/Lapack are - # picked up. + # Make sure we use Spack's blas/lapack: + options.extend([ + '-DLAPACK_FOUND=true', + '-DLAPACK_INCLUDE_DIRS=%s' % spec['lapack'].prefix.include, + '-DLAPACK_LIBRARIES=%s' % ( + spec['lapack'].lapack_shared_lib if '+shared' in spec else + spec['lapack'].lapack_static_lib), + '-DBLAS_FOUND=true', + '-DBLAS_INCLUDE_DIRS=%s' % spec['blas'].prefix.include, + '-DBLAS_LIBRARIES=%s' % ( + spec['blas'].blas_shared_lib if '+shared' in spec else + spec['blas'].blas_static_lib) + ]) if '+mpi' in spec: options.append('-DMPI=ON') @@ -101,9 +110,8 @@ class ArpackNg(Package): cmake('.', *options) make() - # TODO: make test does not work - # make('test') - + if self.run_tests: + make('test') make('install') @when('@3.3.0') @@ -120,10 +128,23 @@ class ArpackNg(Package): 'F77=%s' % spec['mpi'].mpif77 ]) - if '~shared' in spec: - options.append('--enable-shared=no') + if '+shared' in spec: + options.extend([ + '--with-blas=%s' % to_link_flags( + spec['blas'].blas_shared_lib), + '--with-lapack=%s' % to_link_flags( + spec['lapack'].lapack_shared_lib) + ]) + else: + options.extend([ + '--with-blas=%s' % spec['blas'].blas_static_lib, + '--with-lapack=%s' % spec['lapack'].lapack_static_lib, + '--enable-shared=no' + ]) bootstrap() configure(*options) make() + if self.run_tests: + make('check') make('install') diff --git a/var/spack/repos/builtin/packages/atlas/package.py b/var/spack/repos/builtin/packages/atlas/package.py index c43d92c34f..f9d5da6166 100644 --- a/var/spack/repos/builtin/packages/atlas/package.py +++ b/var/spack/repos/builtin/packages/atlas/package.py @@ -23,20 +23,24 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +from spack.package_test import * from spack.util.executable import Executable import os.path + class Atlas(Package): - """ - Automatically Tuned Linear Algebra Software, generic shared ATLAS is an approach for the automatic generation and - optimization of numerical software. Currently ATLAS supplies optimized versions for the complete set of linear - algebra kernels known as the Basic Linear Algebra Subroutines (BLAS), and a subset of the linear algebra routines - in the LAPACK library. + """Automatically Tuned Linear Algebra Software, generic shared ATLAS is an + approach for the automatic generation and optimization of numerical + software. Currently ATLAS supplies optimized versions for the complete set + of linear algebra kernels known as the Basic Linear Algebra Subroutines + (BLAS), and a subset of the linear algebra routines in the LAPACK library. """ homepage = "http://math-atlas.sourceforge.net/" version('3.10.2', 'a4e21f343dec8f22e7415e339f09f6da', - url='http://downloads.sourceforge.net/project/math-atlas/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + url='https://sourceforge.net/projects/math-atlas/files/Stable/3.10.2/atlas3.10.2.tar.bz2', preferred=True) + # not all packages (e.g. Trilinos@12.6.3) stopped using deprecated in 3.6.0 + # Lapack routines. Stick with 3.5.0 until this is fixed. resource(name='lapack', url='http://www.netlib.org/lapack/lapack-3.5.0.tgz', md5='b1d3e3e425b2e44a06760ff173104bdf', @@ -44,7 +48,7 @@ class Atlas(Package): when='@3:') version('3.11.34', '0b6c5389c095c4c8785fd0f724ec6825', - url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2/download') + url='http://sourceforge.net/projects/math-atlas/files/Developer%20%28unstable%29/3.11.34/atlas3.11.34.tar.bz2') variant('shared', default=True, description='Builds shared library') @@ -66,9 +70,24 @@ class Atlas(Package): options = [] if '+shared' in spec: - options.append('--shared') + options.extend([ + '--shared' + ]) + # TODO: for non GNU add '-Fa', 'alg', '-fPIC' ? + + # configure for 64-bit build + options.extend([ + '-b', '64' + ]) - # Lapack resource + # set compilers: + options.extend([ + '-C', 'ic', spack_cc, + '-C', 'if', spack_f77 + ]) + + # Lapack resource to provide full lapack build. Note that + # ATLAS only provides a few LAPACK routines natively. lapack_stage = self.stage[1] lapack_tarfile = os.path.basename(lapack_stage.fetcher.url) lapack_tarfile_path = join_path(lapack_stage.path, lapack_tarfile) @@ -81,4 +100,35 @@ class Atlas(Package): make('check') make('ptcheck') make('time') + if '+shared' in spec: + with working_dir('lib'): + make('shared_all') + make("install") + self.install_test() + + def setup_dependent_package(self, module, dspec): + # libsatlas.[so,dylib,dll ] contains all serial APIs (serial lapack, + # serial BLAS), and all ATLAS symbols needed to support them. Whereas + # libtatlas.[so,dylib,dll ] is parallel (multithreaded) version. + name = 'libsatlas.%s' % dso_suffix + libdir = find_library_path(name, + self.prefix.lib64, + self.prefix.lib) + + if '+shared' in self.spec: + self.spec.blas_shared_lib = join_path(libdir, name) + self.spec.lapack_shared_lib = self.spec.blas_shared_lib + + def install_test(self): + source_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.c') + blessed_file = join_path(os.path.dirname(self.module.__file__), + 'test_cblas_dgemm.output') + + include_flags = ["-I%s" % join_path(self.spec.prefix, "include")] + link_flags = ["-L%s" % join_path(self.spec.prefix, "lib"), + "-lsatlas"] + + output = compile_c_and_execute(source_file, include_flags, link_flags) + compare_output_file(output, blessed_file) diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c new file mode 100644 index 0000000000..2cb90fb883 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.c @@ -0,0 +1,49 @@ +#include <cblas.h> +#include <stdio.h> + +double m[] = { + 3, 1, 3, + 1, 5, 9, + 2, 6, 5 +}; + +double x[] = { + -1, 3, -3 +}; + +#ifdef __cplusplus +extern "C" { +#endif + + void dgesv_(int *n, int *nrhs, double *a, int *lda, + int *ipivot, double *b, int *ldb, int *info); + +#ifdef __cplusplus +} +#endif + +int main(void) { + int i; + // blas: + double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; + double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; + cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); + for (i = 0; i < 9; i++) + printf("%f\n", C[i]); + + // lapack: + int ipiv[3]; + int j; + int info; + int n = 1; + int nrhs = 1; + int lda = 3; + int ldb = 3; + dgesv_(&n,&nrhs, &m[0], &lda, ipiv, &x[0], &ldb, &info); + for (i=0; i<3; ++i) + printf("%5.1f\n", x[i]); + + return 0; +} diff --git a/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output new file mode 100644 index 0000000000..01404462c4 --- /dev/null +++ b/var/spack/repos/builtin/packages/atlas/test_cblas_dgemm.output @@ -0,0 +1,12 @@ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 + -0.3 + 3.0 + -3.0 diff --git a/var/spack/repos/builtin/packages/kdiff3/package.py b/var/spack/repos/builtin/packages/kdiff3/package.py new file mode 100644 index 0000000000..48f4b9c379 --- /dev/null +++ b/var/spack/repos/builtin/packages/kdiff3/package.py @@ -0,0 +1,44 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Kdiff3(Package): + """Compare and merge 2 or 3 files or directories.""" + homepage = "http://kdiff3.sourceforge.net/" + url = "https://downloads.sourceforge.net/project/kdiff3/kdiff3/0.9.98/kdiff3-0.9.98.tar.gz" + + version('0.9.98', 'b52f99f2cf2ea75ed5719315cbf77446') + + depends_on("qt@5.2.0:") + + def install(self, spec, prefix): + # make is done inside + configure('qt4') + + # there is no make install, bummer... + mkdirp(self.prefix.bin) + install(join_path(self.stage.source_path, 'releaseQt', 'kdiff3'), + self.prefix.bin) diff --git a/var/spack/repos/builtin/packages/libxau/package.py b/var/spack/repos/builtin/packages/libxau/package.py index 55816ecdbd..b9215bc601 100644 --- a/var/spack/repos/builtin/packages/libxau/package.py +++ b/var/spack/repos/builtin/packages/libxau/package.py @@ -24,6 +24,7 @@ ############################################################################## from spack import * + class Libxau(Package): """The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client @@ -34,11 +35,10 @@ class Libxau(Package): version('1.0.8', '685f8abbffa6d145c0f930f00703b21b') depends_on('xproto') + depends_on('pkg-config', type='build') def install(self, spec, prefix): - # FIXME: Modify the configure line to suit your build system here. configure('--prefix=%s' % prefix) - # FIXME: Add logic to build and install here make() make("install") diff --git a/var/spack/repos/builtin/packages/nextflow/package.py b/var/spack/repos/builtin/packages/nextflow/package.py new file mode 100644 index 0000000000..54f3dbf915 --- /dev/null +++ b/var/spack/repos/builtin/packages/nextflow/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Nextflow(Package): + """Data-driven computational pipelines""" + + homepage = "http://www.nextflow.io" + + version('0.20.1', '0e4e0e3eca1c2c97f9b4bffd944b923a', + url='https://github.com/nextflow-io/nextflow/releases/download/v0.20.1/nextflow', + expand=False) + + depends_on('jdk') + + def install(self, spec, prefix): + mkdirp(prefix.bin) + install("nextflow", join_path(prefix.bin, "nextflow")) + set_executable(join_path(prefix.bin, "nextflow")) diff --git a/var/spack/repos/builtin/packages/perl/package.py b/var/spack/repos/builtin/packages/perl/package.py new file mode 100644 index 0000000000..d71a7492ba --- /dev/null +++ b/var/spack/repos/builtin/packages/perl/package.py @@ -0,0 +1,75 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +# +# Author: George Hartzell <hartzell@alerce.com> +# Date: July 21, 2016 +# Author: Justin Too <justin@doubleotoo.com> +# Date: September 6, 2015 +# +from spack import * + + +class Perl(Package): + """Perl 5 is a highly capable, feature-rich programming language with over + 27 years of development.""" + homepage = "http://www.perl.org" + url = "http://www.cpan.org/src/5.0/perl-5.22.2.tar.gz" + + version('5.24.0', 'c5bf7f3285439a2d3b6a488e14503701') + version('5.22.2', '5767e2a10dd62a46d7b57f74a90d952b') + version('5.20.3', 'd647d0ea5a7a8194c34759ab9f2610cd') + # 5.18.4 fails with gcc-5 + # https://rt.perl.org/Public/Bug/Display.html?id=123784 + # version('5.18.4' , '1f9334ff730adc05acd3dd7130d295db') + + # Installing cpanm alongside the core makes it safe and simple for + # people/projects to install their own sets of perl modules. Not + # having it in core increases the "energy of activation" for doing + # things cleanly. + variant('cpanm', default=True, + description='Optionally install cpanm with the core packages.') + + resource( + name="cpanm", + url="http://search.cpan.org/CPAN/authors/id/M/MI/MIYAGAWA/App-cpanminus-1.7042.tar.gz", + md5="e87f55fbcb3c13a4754500c18e89219f", + destination="cpanm", + placement="cpanm" + ) + + def install(self, spec, prefix): + configure = Executable('./Configure') + configure("-des", "-Dprefix=" + prefix) + make() + if self.run_tests: + make("test") + make("install") + + if '+cpanm' in spec: + with working_dir(join_path('cpanm', 'cpanm')): + perl = Executable(join_path(prefix.bin, 'perl')) + perl('Makefile.PL') + make() + make('install') diff --git a/var/spack/repos/builtin/packages/py-h5py/package.py b/var/spack/repos/builtin/packages/py-h5py/package.py index f96cb9b4cd..90a67c51bd 100644 --- a/var/spack/repos/builtin/packages/py-h5py/package.py +++ b/var/spack/repos/builtin/packages/py-h5py/package.py @@ -43,6 +43,7 @@ class PyH5py(Package): # Build dependencies depends_on('py-cython@0.19:', type='build') depends_on('pkg-config', type='build') + depends_on('py-setuptools', type='build') depends_on('hdf5@1.8.4:') depends_on('hdf5+mpi', when='+mpi') depends_on('mpi', when='+mpi') diff --git a/var/spack/repos/builtin/packages/py-networkx/package.py b/var/spack/repos/builtin/packages/py-networkx/package.py index d545717628..79ad420f8f 100644 --- a/var/spack/repos/builtin/packages/py-networkx/package.py +++ b/var/spack/repos/builtin/packages/py-networkx/package.py @@ -24,8 +24,10 @@ ############################################################################## from spack import * + class PyNetworkx(Package): - """NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.""" + """NetworkX is a Python package for the creation, manipulation, and study + of the structure, dynamics, and functions of complex networks.""" homepage = "http://networkx.github.io/" url = "https://pypi.python.org/packages/source/n/networkx/networkx-1.11.tar.gz" @@ -34,6 +36,7 @@ class PyNetworkx(Package): extends('python') depends_on('py-decorator', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-pytables/package.py b/var/spack/repos/builtin/packages/py-pytables/package.py index 58ed067b21..f87e74211f 100644 --- a/var/spack/repos/builtin/packages/py-pytables/package.py +++ b/var/spack/repos/builtin/packages/py-pytables/package.py @@ -23,10 +23,11 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * -import re + class PyPytables(Package): - """PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data.""" + """PyTables is a package for managing hierarchical datasets and designed to + efficiently and easily cope with extremely large amounts of data.""" homepage = "http://www.pytables.org/" url = "https://github.com/PyTables/PyTables/archive/v.3.2.2.tar.gz" @@ -37,6 +38,7 @@ class PyPytables(Package): depends_on('py-numpy', type=nolink) depends_on('py-numexpr', type=nolink) depends_on('py-cython', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): env["HDF5_DIR"] = spec['hdf5'].prefix diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 26c286e4be..fbeb5c95ca 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -42,6 +42,7 @@ class PyScikitImage(Package): depends_on('py-six', type=nolink) depends_on('py-scipy', type=nolink) depends_on('py-matplotlib', type=nolink) + depends_on('py-setuptools', type='build') def install(self, spec, prefix): python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/r-jsonlite/package.py b/var/spack/repos/builtin/packages/r-jsonlite/package.py index 6e231ed345..d1cb4b52c1 100644 --- a/var/spack/repos/builtin/packages/r-jsonlite/package.py +++ b/var/spack/repos/builtin/packages/r-jsonlite/package.py @@ -38,9 +38,10 @@ class RJsonlite(Package): use with dynamic data in systems and applications.""" homepage = "https://github.com/jeroenooms/jsonlite" - url = "https://cran.r-project.org/src/contrib/jsonlite_0.9.21.tar.gz" + url = "https://cran.r-project.org/src/contrib/jsonlite_1.0.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/jsonlite" + version('1.0', 'c8524e086de22ab39b8ac8000220cc87') version('0.9.21', '4fc382747f88a79ff0718a0d06bed45d') extends('R') diff --git a/var/spack/repos/builtin/packages/r-mime/package.py b/var/spack/repos/builtin/packages/r-mime/package.py index fb079f44c5..5e78889a76 100644 --- a/var/spack/repos/builtin/packages/r-mime/package.py +++ b/var/spack/repos/builtin/packages/r-mime/package.py @@ -30,9 +30,10 @@ class RMime(Package): from /etc/mime.types in UNIX-type systems.""" homepage = "https://github.com/yihui/mime" - url = "https://cran.r-project.org/src/contrib/mime_0.4.tar.gz" + url = "https://cran.r-project.org/src/contrib/mime_0.5.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/mime" + version('0.5', '87e00b6d57b581465c19ae869a723c4d') version('0.4', '789cb33e41db2206c6fc7c3e9fbc2c02') extends('R') diff --git a/var/spack/repos/builtin/packages/r-rcpp/package.py b/var/spack/repos/builtin/packages/r-rcpp/package.py index 2428f4af3b..94580a8700 100644 --- a/var/spack/repos/builtin/packages/r-rcpp/package.py +++ b/var/spack/repos/builtin/packages/r-rcpp/package.py @@ -37,9 +37,10 @@ class RRcpp(Package): last two.""" homepage = "http://dirk.eddelbuettel.com/code/rcpp.html" - url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.5.tar.gz" + url = "https://cran.r-project.org/src/contrib/Rcpp_0.12.6.tar.gz" list_url = "https://cran.r-project.org/src/contrib/Archive/Rcpp" + version('0.12.6', 'db4280fb0a79cd19be73a662c33b0a8b') version('0.12.5', 'f03ec05b4e391cc46e7ce330e82ff5e2') extends('R') diff --git a/var/spack/repos/builtin/packages/texlive/package.py b/var/spack/repos/builtin/packages/texlive/package.py new file mode 100644 index 0000000000..d44a6e311e --- /dev/null +++ b/var/spack/repos/builtin/packages/texlive/package.py @@ -0,0 +1,57 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * +import os + + +class Texlive(Package): + """TeX Live is a free software distribution for the TeX typesetting + system""" + + homepage = "http://www.tug.org/texlive" + + version('live', 'e671eea7f142c438959493cc42a2a59b', url="http://mirror.ctan.org/systems/texlive/tlnet/install-tl-unx.tar.gz") + + # There does not seem to be a complete list of schemes. + # Examples include: + # full scheme (everything) + # medium scheme (small + more packages and languages) + # small scheme (basic + xetex, metapost, a few languages) + # basic scheme (plain and latex) + # minimal scheme (plain only) + # See: + # https://www.tug.org/texlive/doc/texlive-en/texlive-en.html#x1-25025r6 + variant('scheme', default="small", + description='Package subset to install (e.g. full, small, basic)') + + depends_on('perl') + + def install(self, spec, prefix): + env = os.environ + env['TEXLIVE_INSTALL_PREFIX'] = prefix + perl = which('perl') + scheme = spec.variants['scheme'].value + perl('./install-tl', '-scheme', scheme, + '-portable', '-profile', '/dev/null') |