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Commit 1c0b3c12 authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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update packages from Spack v0.19.2 upstream

parent 2760b0e9
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2 merge requests!330create new experimental release,!320use Spack v0.19.2
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    packages/py-deap/package.py
    + 6
    − 7
    View file @ 1c0b3c12
    # (this package was adapted from the spack develop upstream as a dependency of py-bluepyopt)
    # this package was backported from the spack develop upstream to support newer setuptools
    # Copyright 2013-2023 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 *
    from spack.package import *
    class PyDeap(PythonPackage):
    ......@@ -15,10 +14,10 @@ class PyDeap(PythonPackage):
    homepage = "https://deap.readthedocs.org/"
    pypi = "deap/deap-1.3.1.tar.gz"
    maintainers = ["hjorth", "elmath"]
    version("1.3.3", sha256="8772f1b0fff042d5e516b0aebac2c706243045aa7d0de8e0b8658f380181cf31")
    version("1.3.1", sha256="11f54493ceb54aae10dde676577ef59fc52d52f82729d5a12c90b0813c857a2f")
    depends_on("py-setuptools@:57", type=("build"))
    depends_on("py-numpy", type=("build", "run"))
    depends_on("py-setuptools", type="build")
    # uses 2to3
    depends_on("py-setuptools@:57", type="build", when="@1.3.1")
    depends_on("py-numpy", type=("build", "run"))
    packages/py-ipycanvas/package.py
    + 15
    − 13
    View file @ 1c0b3c12
    # this package was adapted from Spack upstream v0.19.2, to add version 0.12.0
    # Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
    # Spack Project Developers. See the top-level COPYRIGHT file for details.
    #
    ......@@ -10,20 +12,20 @@ class PyIpycanvas(PythonPackage):
    """Interactive Canvas in Jupyter."""
    homepage = "https://github.com/martinRenou/ipycanvas"
    pypi = "ipycanvas/ipycanvas-0.9.0.tar.gz"
    pypi = "ipycanvas/ipycanvas-0.9.0.tar.gz"
    version('0.12.0', sha256='3984339cef0c15674e347dd65ffb0cd1edc62e37869cbb5efea46f3259e976f3')
    version('0.10.2', sha256='a02c494834cb3c60509801172e7429beae837b3cb6c61d3becf8b586c5a66004')
    version('0.9.0', sha256='f29e56b93fe765ceace0676c3e75d44e02a3ff6c806f3b7e5b869279f470cc43')
    version("0.12.0", sha256="3984339cef0c15674e347dd65ffb0cd1edc62e37869cbb5efea46f3259e976f3")
    version("0.10.2", sha256="a02c494834cb3c60509801172e7429beae837b3cb6c61d3becf8b586c5a66004")
    version("0.9.0", sha256="f29e56b93fe765ceace0676c3e75d44e02a3ff6c806f3b7e5b869279f470cc43")
    depends_on('python@3.5:', type=('build', 'run'))
    depends_on('python@3.6:', when='@10:', type=('build', 'run'))
    depends_on('python@3.7:', when='@11:', type=('build', 'run'))
    depends_on('py-setuptools@40.8:', type='build')
    depends_on("python@3.5:", type=("build", "run"))
    depends_on("python@3.6:", when="@10:", type=("build", "run"))
    depends_on("python@3.7:", when="@11:", type=("build", "run"))
    depends_on("py-setuptools@40.8:", type="build")
    # TODO: replace this after concretizer learns how to concretize separate build deps
    depends_on('py-jupyter-packaging7', type='build')
    depends_on("py-jupyter-packaging7", type="build")
    # depends_on('py-jupyter-packaging@0.7.0:0.7', type='build')
    depends_on('py-jupyterlab@3.0:3', type='build')
    depends_on('py-ipywidgets@7.6:', type=('build', 'run'))
    depends_on('pil@6:', type=('build', 'run'))
    depends_on('py-numpy', type=('build', 'run'))
    depends_on("py-jupyterlab@3.0:3", type="build")
    depends_on("py-ipywidgets@7.6:", type=("build", "run"))
    depends_on("pil@6:", type=("build", "run"))
    depends_on("py-numpy", type=("build", "run"))
    packages/py-nilearn/package.py
    + 1
    − 1
    View file @ 1c0b3c12
    # this package was added from spack develop:
    # https://github.com/spack/spack/blob/c10b84f08d1febce6d1f64a5f8b9cbff73e461d9/var/spack/repos/builtin/packages/py-nilearn/package.py
    # to fix a typo in 0.19.0 version (https://github.com/spack/spack/pull/34284)
    # to fix a typo in 0.19.2 version (https://github.com/spack/spack/pull/34284)
    # Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
    # Spack Project Developers. See the top-level COPYRIGHT file for details.
    ......
    packages/py-scipy/package.py
    + 128
    − 91
    View file @ 1c0b3c12
    # this package was slightly adapted from the spack v0.18.1 upstream because with py-pybind11@2.10.1
    # this package was slightly adapted from the spack v0.19.2 upstream because with py-pybind11@2.10.1
    # available, the concretizer selected py-scipy@1.5:1.6.1
    # depends_on('py-pybind11@2.4.3:2.8', when='@1.8:', type=('build', 'link'))
    # depends_on("py-pybind11@2.4.3:2.8", when="@1.8:", type=("build", "link"))
    # was changed to
    # depends_on('py-pybind11@2.4.3:', when='@1.8:', type=('build', 'link'))
    # depends_on("py-pybind11@2.4.3:", when="@1.8:", type=("build", "link"))
    # Copyright 2013-2022 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.package import *
    class PyScipy(PythonPackage):
    """SciPy (pronounced "Sigh Pie") is a Scientific Library for Python.
    It provides many user-friendly and efficient numerical routines such
    ......@@ -18,107 +22,140 @@ class PyScipy(PythonPackage):
    pypi = "scipy/scipy-1.5.4.tar.gz"
    git = "https://github.com/scipy/scipy.git"
    maintainers = ['adamjstewart', 'rgommers']
    version('master', branch='master')
    version('1.8.1', sha256='9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33')
    version('1.8.0', sha256='31d4f2d6b724bc9a98e527b5849b8a7e589bf1ea630c33aa563eda912c9ff0bd')
    version('1.7.3', sha256='ab5875facfdef77e0a47d5fd39ea178b58e60e454a4c85aa1e52fcb80db7babf')
    version('1.7.2', sha256='fa2dbabaaecdb502641b0b3c00dec05fb475ae48655c66da16c9ed24eda1e711')
    version('1.7.1', sha256='6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764')
    version('1.7.0', sha256='998c5e6ea649489302de2c0bc026ed34284f531df89d2bdc8df3a0d44d165739')
    version('1.6.3', sha256='a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707')
    version('1.6.2', sha256='e9da33e21c9bc1b92c20b5328adb13e5f193b924c9b969cd700c8908f315aa59')
    version('1.6.1', sha256='c4fceb864890b6168e79b0e714c585dbe2fd4222768ee90bc1aa0f8218691b11')
    version('1.6.0', sha256='cb6dc9f82dfd95f6b9032a8d7ea70efeeb15d5b5fd6ed4e8537bb3c673580566')
    version('1.5.4', sha256='4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b')
    version('1.5.3', sha256='ddae76784574cc4c172f3d5edd7308be16078dd3b977e8746860c76c195fa707')
    version('1.5.2', sha256='066c513d90eb3fd7567a9e150828d39111ebd88d3e924cdfc9f8ce19ab6f90c9')
    version('1.5.1', sha256='039572f0ca9578a466683558c5bf1e65d442860ec6e13307d528749cfe6d07b8')
    version('1.5.0', sha256='4ff72877d19b295ee7f7727615ea8238f2d59159df0bdd98f91754be4a2767f0')
    version('1.4.1', sha256='dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59')
    version('1.4.0', sha256='31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8')
    version('1.3.3', sha256='64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a')
    version('1.3.2', sha256='a03939b431994289f39373c57bbe452974a7da724ae7f9620a1beee575434da4')
    version('1.3.1', sha256='2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5')
    version('1.3.0', sha256='c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a')
    version('1.2.3', sha256='ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57')
    version('1.2.2', sha256='a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1')
    version('1.2.1', sha256='e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c')
    version('1.1.0', sha256='878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1')
    version('1.0.0', sha256='87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10')
    version('0.19.1', sha256='a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6')
    version('0.18.1', sha256='8ab6e9c808bf2fb3e8576cd8cf07226d9cdc18b012c06d9708429a821ac6634e')
    version('0.17.0', sha256='f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089')
    version('0.15.1', sha256='a212cbc3b79e9a563aa45fc5c517b3499198bd7eb7e7be1e047568a5f48c259a')
    version('0.15.0', sha256='0c74e31e08acc8bf9b6ceb9bced73df2ae0cc76003e0366350bc7b26292bf8b1')
    maintainers = ["adamjstewart", "rgommers"]
    version("master", branch="master")
    version("1.8.1", sha256="9e3fb1b0e896f14a85aa9a28d5f755daaeeb54c897b746df7a55ccb02b340f33")
    version("1.8.0", sha256="31d4f2d6b724bc9a98e527b5849b8a7e589bf1ea630c33aa563eda912c9ff0bd")
    version("1.7.3", sha256="ab5875facfdef77e0a47d5fd39ea178b58e60e454a4c85aa1e52fcb80db7babf")
    version("1.7.2", sha256="fa2dbabaaecdb502641b0b3c00dec05fb475ae48655c66da16c9ed24eda1e711")
    version("1.7.1", sha256="6b47d5fa7ea651054362561a28b1ccc8da9368a39514c1bbf6c0977a1c376764")
    version("1.7.0", sha256="998c5e6ea649489302de2c0bc026ed34284f531df89d2bdc8df3a0d44d165739")
    version("1.6.3", sha256="a75b014d3294fce26852a9d04ea27b5671d86736beb34acdfc05859246260707")
    version("1.6.2", sha256="e9da33e21c9bc1b92c20b5328adb13e5f193b924c9b969cd700c8908f315aa59")
    version("1.6.1", sha256="c4fceb864890b6168e79b0e714c585dbe2fd4222768ee90bc1aa0f8218691b11")
    version("1.6.0", sha256="cb6dc9f82dfd95f6b9032a8d7ea70efeeb15d5b5fd6ed4e8537bb3c673580566")
    version("1.5.4", sha256="4a453d5e5689de62e5d38edf40af3f17560bfd63c9c5bd228c18c1f99afa155b")
    version("1.5.3", sha256="ddae76784574cc4c172f3d5edd7308be16078dd3b977e8746860c76c195fa707")
    version("1.5.2", sha256="066c513d90eb3fd7567a9e150828d39111ebd88d3e924cdfc9f8ce19ab6f90c9")
    version("1.5.1", sha256="039572f0ca9578a466683558c5bf1e65d442860ec6e13307d528749cfe6d07b8")
    version("1.5.0", sha256="4ff72877d19b295ee7f7727615ea8238f2d59159df0bdd98f91754be4a2767f0")
    version("1.4.1", sha256="dee1bbf3a6c8f73b6b218cb28eed8dd13347ea2f87d572ce19b289d6fd3fbc59")
    version("1.4.0", sha256="31f7cfa93b01507c935c12b535e24812594002a02a56803d7cd063e9920d25e8")
    version("1.3.3", sha256="64bf4e8ae0db2d42b58477817f648d81e77f0b381d0ea4427385bba3f959380a")
    version("1.3.2", sha256="a03939b431994289f39373c57bbe452974a7da724ae7f9620a1beee575434da4")
    version("1.3.1", sha256="2643cfb46d97b7797d1dbdb6f3c23fe3402904e3c90e6facfe6a9b98d808c1b5")
    version("1.3.0", sha256="c3bb4bd2aca82fb498247deeac12265921fe231502a6bc6edea3ee7fe6c40a7a")
    version("1.2.3", sha256="ecbe6413ca90b8e19f8475bfa303ac001e81b04ec600d17fa7f816271f7cca57")
    version("1.2.2", sha256="a4331e0b8dab1ff75d2c67b5158a8bb9a83c799d7140094dda936d876c7cfbb1")
    version("1.2.1", sha256="e085d1babcb419bbe58e2e805ac61924dac4ca45a07c9fa081144739e500aa3c")
    version("1.1.0", sha256="878352408424dffaa695ffedf2f9f92844e116686923ed9aa8626fc30d32cfd1")
    version("1.0.0", sha256="87ea1f11a0e9ec08c264dc64551d501fa307289460705f6fccd84cbfc7926d10")
    version("0.19.1", sha256="a19a2ca7a7336495ec180adeaa0dfdcf41e96dbbee90d51c3ed828ba570884e6")
    version("0.18.1", sha256="8ab6e9c808bf2fb3e8576cd8cf07226d9cdc18b012c06d9708429a821ac6634e")
    version("0.17.0", sha256="f600b755fb69437d0f70361f9e560ab4d304b1b66987ed5a28bdd9dd7793e089")
    version("0.15.1", sha256="a212cbc3b79e9a563aa45fc5c517b3499198bd7eb7e7be1e047568a5f48c259a")
    version("0.15.0", sha256="0c74e31e08acc8bf9b6ceb9bced73df2ae0cc76003e0366350bc7b26292bf8b1")
    # pyproject.toml
    depends_on('py-wheel@:0.37', type='build')
    depends_on('py-setuptools', type='build')
    depends_on('py-setuptools@:51.0.0', when='@1.6', type='build')
    depends_on('py-setuptools@:57', when='@1.7', type='build')
    depends_on('py-setuptools@:59', when='@1.8:', type='build')
    depends_on('py-cython@0.29.18:2', when='@1.7:', type='build')
    depends_on('py-pybind11@2.2.4:', when='@1.4.0', type=('build', 'link'))
    depends_on('py-pybind11@2.4.0:', when='@1.4.1:1.4', type=('build', 'link'))
    depends_on('py-pybind11@2.4.3:', when='@1.5:1.6.1', type=('build', 'link'))
    depends_on('py-pybind11@2.4.3:2.6', when='@1.6.2:1.7.1', type=('build', 'link'))
    depends_on('py-pybind11@2.4.3:2.7', when='@1.7.2:1.7', type=('build', 'link'))
    depends_on('py-pybind11@2.4.3:', when='@1.8:', type=('build', 'link'))
    depends_on('py-pythran@0.9.11', when='@1.7.0:1.7.1', type=('build', 'link'))
    depends_on('py-pythran@0.9.12:0.9', when='@1.7.2:1.7', type=('build', 'link'))
    depends_on('py-pythran@0.10:', when='@1.8:', type=('build', 'link'))
    depends_on("py-wheel@:0.37", type="build")
    depends_on("py-setuptools", type="build")
    depends_on("py-setuptools@:51.0.0", when="@1.6", type="build")
    depends_on("py-setuptools@:57", when="@1.7", type="build")
    depends_on("py-setuptools@:59", when="@1.8:", type="build")
    depends_on("py-cython@0.29.18:2", when="@1.7:", type="build")
    depends_on("py-pybind11@2.2.4:", when="@1.4.0", type=("build", "link"))
    depends_on("py-pybind11@2.4.0:", when="@1.4.1:1.4", type=("build", "link"))
    depends_on("py-pybind11@2.4.3:", when="@1.5:1.6.1", type=("build", "link"))
    depends_on("py-pybind11@2.4.3:2.6", when="@1.6.2:1.7.1", type=("build", "link"))
    depends_on("py-pybind11@2.4.3:2.7", when="@1.7.2:1.7", type=("build", "link"))
    depends_on("py-pybind11@2.4.3:", when="@1.8:", type=("build", "link"))
    depends_on("py-pythran@0.9.11", when="@1.7.0:1.7.1", type=("build", "link"))
    depends_on("py-pythran@0.9.12:0.9", when="@1.7.2:1.7", type=("build", "link"))
    depends_on("py-pythran@0.10:", when="@1.8:", type=("build", "link"))
    # setup.py
    depends_on('py-numpy@1.5.1:+blas+lapack', when='@:0.15', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.6.2:+blas+lapack', when='@0.16:0.17', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.7.1:+blas+lapack', when='@0.18.0:0.18', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.8.2:+blas+lapack', when='@0.19:1.2', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.13.3:+blas+lapack', when='@1.3:1.4', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.14.5:+blas+lapack', when='@1.5.0:1.5', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.16.5:+blas+lapack', when='@1.6:1.6.1', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.16.5:1.22+blas+lapack', when='@1.6.2:1.7', type=('build', 'link', 'run'))
    depends_on('py-numpy@1.17.3:1.24+blas+lapack', when='@1.8:', type=('build', 'link', 'run'))
    depends_on('python@2.6:2.8,3.2:', when='@:0.17', type=('build', 'link', 'run'))
    depends_on('python@2.7:2.8,3.4:', when='@0.18:1.2', type=('build', 'link', 'run'))
    depends_on('python@3.5:', when='@1.3:1.4', type=('build', 'link', 'run'))
    depends_on('python@3.6:', when='@1.5.0:1.5', type=('build', 'link', 'run'))
    depends_on('python@3.7:', when='@1.6:1.6.1', type=('build', 'link', 'run'))
    depends_on('python@3.7:3.9', when='@1.6.2:1.7.1', type=('build', 'link', 'run'))
    depends_on('python@3.7:3.10', when='@1.7.2:1.7', type=('build', 'link', 'run'))
    depends_on('python@3.8:3.10', when='@1.8:', type=('build', 'link', 'run'))
    depends_on('py-pytest', type='test')
    # NOTE: scipy picks up Blas/Lapack from numpy, see
    # http://www.scipy.org/scipylib/building/linux.html#step-4-build-numpy-1-5-0
    depends_on('blas')
    depends_on('lapack')
    depends_on("py-numpy@1.5.1:+blas+lapack", when="@:0.15", type=("build", "link", "run"))
    depends_on("py-numpy@1.6.2:+blas+lapack", when="@0.16:0.17", type=("build", "link", "run"))
    depends_on("py-numpy@1.7.1:+blas+lapack", when="@0.18.0:0.18", type=("build", "link", "run"))
    depends_on("py-numpy@1.8.2:+blas+lapack", when="@0.19:1.2", type=("build", "link", "run"))
    depends_on("py-numpy@1.13.3:+blas+lapack", when="@1.3:1.4", type=("build", "link", "run"))
    depends_on("py-numpy@1.14.5:+blas+lapack", when="@1.5.0:1.5", type=("build", "link", "run"))
    depends_on("py-numpy@1.16.5:+blas+lapack", when="@1.6:1.6.1", type=("build", "link", "run"))
    depends_on(
    "py-numpy@1.16.5:1.22+blas+lapack", when="@1.6.2:1.7", type=("build", "link", "run")
    )
    depends_on("py-numpy@1.17.3:1.24+blas+lapack", when="@1.8:", type=("build", "link", "run"))
    depends_on("python@2.6:2.8,3.2:", when="@:0.17", type=("build", "link", "run"))
    depends_on("python@2.7:2.8,3.4:", when="@0.18:1.2", type=("build", "link", "run"))
    depends_on("python@3.5:", when="@1.3:1.4", type=("build", "link", "run"))
    depends_on("python@3.6:", when="@1.5.0:1.5", type=("build", "link", "run"))
    depends_on("python@3.7:", when="@1.6:1.6.1", type=("build", "link", "run"))
    depends_on("python@3.7:3.9", when="@1.6.2:1.7.1", type=("build", "link", "run"))
    depends_on("python@3.7:3.10", when="@1.7.2:1.7", type=("build", "link", "run"))
    depends_on("python@3.8:3.10", when="@1.8:", type=("build", "link", "run"))
    depends_on("py-pytest", type="test")
    # NOTE: scipy should use the same Blas/Lapack as numpy
    # This is achieved by calling the set_blas_lapack() and setup_build_environment()
    # from numpy in the scipy spec
    depends_on("blas")
    depends_on("lapack")
    # https://github.com/scipy/scipy/wiki/Dropping-support-for-Accelerate
    depends_on('lapack@3.4.1:', when='@1.2:')
    depends_on("lapack@3.4.1:", when="@1.2:")
    # https://github.com/scipy/scipy/pull/11324
    conflicts("@1.4.0:1.4.1", when="target=ppc64le:")
    # https://github.com/scipy/scipy/issues/12860
    patch('https://git.sagemath.org/sage.git/plain/build/pkgs/scipy/patches/extern_decls.patch?id=711fe05025795e44b84233e065d240859ccae5bd',
    sha256='5433f60831cb554101520a8f8871ac5a32c95f7a971ccd68b69049535b106780', when='@1.2:1.5.3')
    patch(
    "https://git.sagemath.org/sage.git/plain/build/pkgs/scipy/patches/extern_decls.patch?id=711fe05025795e44b84233e065d240859ccae5bd",
    sha256="5433f60831cb554101520a8f8871ac5a32c95f7a971ccd68b69049535b106780",
    when="@1.2:1.5.3",
    )
    patch("scipy-clang.patch", when="@1.5.0:1.6.3 %clang")
    @run_before("install")
    def set_blas_lapack(self):
    # Pick up Blas/Lapack from numpy
    self.spec["py-numpy"].package.set_blas_lapack()
    patch('scipy-clang.patch', when='@1.5.0:1.6.3 %clang')
    @run_before("install")
    def set_fortran_compiler(self):
    if self.spec.satisfies("%fj"):
    with open("setup.cfg", "w") as f:
    f.write("[config_fc]\n")
    f.write("fcompiler = fujitsu\n")
    elif self.spec.satisfies("%intel") or self.spec.satisfies("%oneapi"):
    if self.spec.satisfies("target=x86:"):
    with open("setup.cfg", "w") as f:
    f.write("[config_fc]\n")
    f.write("fcompiler = intel\n")
    elif self.spec.satisfies("target=x86_64:"):
    with open("setup.cfg", "w") as f:
    f.write("[config_fc]\n")
    f.write("fcompiler = intelem\n")
    def setup_build_environment(self, env):
    # https://github.com/scipy/scipy/issues/9080
    env.set('F90', spack_fc)
    env.set("F90", spack_fc)
    # https://github.com/scipy/scipy/issues/11611
    if self.spec.satisfies('@:1.4 %gcc@10:'):
    env.set('FFLAGS', '-fallow-argument-mismatch')
    if self.spec.satisfies("@:1.4 %gcc@10:"):
    env.set("FFLAGS", "-fallow-argument-mismatch")
    if self.spec.satisfies("^py-numpy@1.16:1.17"):
    env.set("NPY_DISTUTILS_APPEND_FLAGS", "1")
    def install_options(self, spec, prefix):
    args = []
    if spec.satisfies('%fj'):
    args.extend(['config_fc', '--fcompiler=fujitsu'])
    return args
    # https://github.com/scipy/scipy/issues/14935
    if self.spec.satisfies("%intel ^py-pythran") or self.spec.satisfies("%oneapi ^py-pythran"):
    if self.spec["py-pythran"].version < Version("0.12"):
    env.set("SCIPY_USE_PYTHRAN", "0")
    @run_after('install')
    # Pick up Blas/Lapack from numpy
    self.spec["py-numpy"].package.setup_build_environment(env)
    @run_after("install")
    @on_package_attributes(run_tests=True)
    def install_test(self):
    with working_dir('spack-test', create=True):
    python('-c', 'import scipy; scipy.test("full", verbose=2)')
    with working_dir("spack-test", create=True):
    python("-c", 'import scipy; scipy.test("full", verbose=2)')
    packages/py-torch/package.py
    + 412
    − 314
    View file @ 1c0b3c12
    This diff is collapsed.
    packages/r-irkernel/package.py
    + 26
    − 22
    View file @ 1c0b3c12
    # this package was adapted from Spack upstream v0.18.1, to change the dependency on py-jupyter to py-jupyter-client
    # this package was adapted from Spack upstream v0.19.2, to change the dependency on py-jupyter to py-jupyter-client
    # Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
    # Spack Project Developers. See the top-level COPYRIGHT file for details.
    ......@@ -6,34 +6,38 @@
    # SPDX-License-Identifier: (Apache-2.0 OR MIT)
    from spack import *
    from spack.package import *
    class RIrkernel(RPackage):
    """Native R Kernel for the 'Jupyter Notebook'.
    The R kernel for the 'Jupyter' environment executes R code which the
    front-end ('Jupyter Notebook' or other front-ends) submits to the kernel
    via the network."""
    cran = "IRkernel"
    version('1.3', sha256='5a7fcbfd978dfb3cca6702a68a21c147551995fc400084ae8382ffcbbdae1903')
    version('1.2', sha256='5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91')
    version('0.7',
    git="https://github.com/IRkernel/IRkernel.git",
    commit='9cdd284e03eb42d03fab18544b81f486852d5fe0',
    deprecated=True)
    depends_on('r@3.2.0:', type=('build', 'run'))
    depends_on('r-repr@0.4.99:', type=('build', 'run'))
    depends_on('r-evaluate@0.10:', type=('build', 'run'))
    depends_on('r-irdisplay@0.3.0.9999:', type=('build', 'run'))
    depends_on('r-pbdzmq@0.2-1:', type=('build', 'run'))
    depends_on('r-crayon', type=('build', 'run'))
    depends_on('r-jsonlite@0.9.6:', type=('build', 'run'))
    depends_on('r-uuid', type=('build', 'run'))
    depends_on('r-digest', type=('build', 'run'))
    depends_on('py-jupyter-client', type='run')
    depends_on('r-evaluate@0.5.4:', type=('build', 'run'), when='@0.7')
    depends_on('r-devtools', type=('build', 'run'), when='@0.7')
    version("1.3.1", sha256="3186e3a177c7246d45218af55f8b10836540e68a2d106858a0385f7d741b640c")
    version("1.3", sha256="5a7fcbfd978dfb3cca6702a68a21c147551995fc400084ae8382ffcbbdae1903")
    version("1.2", sha256="5fb4dbdb741d05043120a8be0eb73f054b607d9854f314bd79cfec08d219ff91")
    version(
    "0.7",
    git="https://github.com/IRkernel/IRkernel.git",
    commit="9cdd284e03eb42d03fab18544b81f486852d5fe0",
    deprecated=True,
    )
    depends_on("r@3.2.0:", type=("build", "run"))
    depends_on("r-repr@0.4.99:", type=("build", "run"))
    depends_on("r-evaluate@0.10:", type=("build", "run"))
    depends_on("r-irdisplay@0.3.0.9999:", type=("build", "run"))
    depends_on("r-pbdzmq@0.2-1:", type=("build", "run"))
    depends_on("r-crayon", type=("build", "run"))
    depends_on("r-jsonlite@0.9.6:", type=("build", "run"))
    depends_on("r-uuid", type=("build", "run"))
    depends_on("r-digest", type=("build", "run"))
    depends_on("py-jupyter-client", type="run")
    depends_on("r-evaluate@0.5.4:", type=("build", "run"), when="@0.7")
    depends_on("r-devtools", type=("build", "run"), when="@0.7")
    packages/sbml/package.py
    + 85
    − 82
    View file @ 1c0b3c12
    # this package was adapted from Spack upstream v0.19.2, to fix some issues with finding existing libs/headers
    # Copyright 2013-2022 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 *
    from spack.package import *
    class Sbml(CMakePackage):
    """Library for the Systems Biology Markup Language"""
    homepage = "https://sbml.org"
    maintainers = ['rblake-llnl']
    version('5.19.0', sha256='a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547')
    version('5.18.0', sha256='6c01be2306ec0c9656b59cb082eb7b90176c39506dd0f912b02e08298a553360')
    version('5.17.0', sha256='189216e1472777e4464b791c506b79267d07a5454cb23ac991452711f8e0ed3a')
    version('5.16.0', sha256='c6855481434dd2a667fef73e1ff2feade509aa2f3a76d4d06e29022975ce1496')
    version('5.15.0', sha256='c779c2a8a97c5480fe044028099d928a327261fb68cf08657ec8d4f3b3fc0a21')
    version('5.13.0', sha256='e58430edb1b454d7414bcf1be0549bf6860a6d19d73232eb58211559485c2c05')
    version('5.12.0', sha256='c637494b19269947fc90ebe479b624d36f80d1cb5569e45cd76ddde81dd28ae4')
    version('5.11.4', sha256='6429188b689b331b0b8f2c8b55b3f2339196ccd4c93191648fa767e1d02152a3')
    version('5.11.0', sha256='b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b')
    version('5.10.2', sha256='83f32a143cf657672b1050f5f79d3591c418fc59570d180fb1f39b103f4e5286')
    version('5.10.0', sha256='2cd8b37018ce8b1df869c8c182803addbce6d451512ae25a7f527b49981f0966')
    maintainers = ["rblake-llnl"]
    version("5.19.0", sha256="a7f0e18be78ff0e064e4cdb1cd86634d08bc33be5250db4a1878bd81eeb8b547")
    version("5.18.0", sha256="6c01be2306ec0c9656b59cb082eb7b90176c39506dd0f912b02e08298a553360")
    version("5.17.0", sha256="189216e1472777e4464b791c506b79267d07a5454cb23ac991452711f8e0ed3a")
    version("5.16.0", sha256="c6855481434dd2a667fef73e1ff2feade509aa2f3a76d4d06e29022975ce1496")
    version("5.15.0", sha256="c779c2a8a97c5480fe044028099d928a327261fb68cf08657ec8d4f3b3fc0a21")
    version("5.13.0", sha256="e58430edb1b454d7414bcf1be0549bf6860a6d19d73232eb58211559485c2c05")
    version("5.12.0", sha256="c637494b19269947fc90ebe479b624d36f80d1cb5569e45cd76ddde81dd28ae4")
    version("5.11.4", sha256="6429188b689b331b0b8f2c8b55b3f2339196ccd4c93191648fa767e1d02152a3")
    version("5.11.0", sha256="b21931ca7461494915c617b30d4a9f2cafe831d6ce74989b3e5874e6e3c3f72b")
    version("5.10.2", sha256="83f32a143cf657672b1050f5f79d3591c418fc59570d180fb1f39b103f4e5286")
    version("5.10.0", sha256="2cd8b37018ce8b1df869c8c182803addbce6d451512ae25a7f527b49981f0966")
    def url_for_version(self, version):
    url = "https://downloads.sourceforge.net/project/sbml/libsbml/{0}/stable/libSBML-{1}-core-plus-packages-src.tar.gz".format(version, version)
    url = "https://downloads.sourceforge.net/project/sbml/libsbml/{0}/stable/libSBML-{1}-core-plus-packages-src.tar.gz".format(
    version, version
    )
    return url
    variant('python', default=False,
    description='Build with python support')
    depends_on('python', when="+python")
    variant("python", default=False, description="Build with python support")
    depends_on("python", when="+python")
    variant('perl', default=False,
    description='Build with perl support')
    depends_on('perl', when="+perl")
    variant("perl", default=False, description="Build with perl support")
    depends_on("perl", when="+perl")
    variant('ruby', default=False,
    description='Build with ruby support')
    depends_on('ruby', when="+ruby")
    variant("ruby", default=False, description="Build with ruby support")
    depends_on("ruby", when="+ruby")
    variant('r', default=False,
    description='Build with R support')
    depends_on('r', when="+r")
    variant("r", default=False, description="Build with R support")
    depends_on("r", when="+r")
    variant('octave', default=False,
    description='Build with octave support')
    depends_on('octave', when="+octave")
    variant("octave", default=False, description="Build with octave support")
    depends_on("octave", when="+octave")
    variant('matlab', default=False,
    description='Build with matlab support')
    depends_on('matlab', when="+matlab")
    variant("matlab", default=False, description="Build with matlab support")
    depends_on("matlab", when="+matlab")
    variant('java', default=False,
    description='Build with java support')
    depends_on('java', when="+java")
    variant("java", default=False, description="Build with java support")
    depends_on("java", when="+java")
    variant('mono', default=False,
    description='Build with mono support')
    depends_on('mono', when="+mono")
    variant("mono", default=False, description="Build with mono support")
    depends_on("mono", when="+mono")
    variant('cpp', default=False,
    description="All c++ includes should be under a namespace")
    variant("cpp", default=False, description="All c++ includes should be under a namespace")
    depends_on('swig@2:', type='build')
    depends_on('cmake', type='build')
    depends_on('zlib')
    depends_on('bzip2')
    depends_on('libxml2')
    depends_on("swig@2:", type="build")
    depends_on("cmake", type="build")
    depends_on("zlib")
    depends_on("bzip2")
    depends_on("libxml2")
    def cmake_args(self):
    spec = self.spec
    ......@@ -89,48 +84,56 @@ class Sbml(CMakePackage):
    "-DWITH_XERCES:BOOL=OFF",
    "-DWITH_ZLIB:BOOL=ON",
    ]
    args.append(self.define_from_variant('WITH_CPP_NAMESPACE', 'cpp'))
    if '+python' in spec:
    args.extend([
    "-DWITH_PYTHON:BOOL=ON",
    "-DWITH_PYTHON_INCLUDE:PATH=%s" % spec['python'].prefix,
    ])
    args.append(self.define_from_variant("WITH_CPP_NAMESPACE", "cpp"))
    if "+python" in spec:
    args.extend(
    [
    "-DWITH_PYTHON:BOOL=ON",
    "-DWITH_PYTHON_INCLUDE:PATH=%s" % spec["python"].prefix,
    ]
    )
    else:
    args.append('-DWITH_PYTHON:BOOL=OFF')
    args.append(self.define_from_variant('WITH_CSHARP', 'mono'))
    if '+java' in spec:
    args.extend([
    "-DWITH_JAVA:BOOL=ON",
    "-DJDK_PATH:STRING=%s" % spec['java'].prefix,
    "-DJAVA_INCLUDE_PATH:STRING=%s" % spec['java'].prefix,
    ])
    args.append("-DWITH_PYTHON:BOOL=OFF")
    args.append(self.define_from_variant("WITH_CSHARP", "mono"))
    if "+java" in spec:
    args.extend(
    [
    "-DWITH_JAVA:BOOL=ON",
    "-DJDK_PATH:STRING=%s" % spec["java"].prefix,
    "-DJAVA_INCLUDE_PATH:STRING=%s" % spec["java"].prefix,
    ]
    )
    else:
    args.append('-DWITH_JAVA:BOOL=OFF')
    if '+matlab' in spec:
    args.extend([
    "-DWITH_MATLAB:BOOL=ON",
    "-DMATLAB_ROOT_PATH:PATH=%s" % spec['matlab'].prefix,
    "-DWITH_MATLAB_MEX:BOOL=ON",
    ])
    args.append("-DWITH_JAVA:BOOL=OFF")
    if "+matlab" in spec:
    args.extend(
    [
    "-DWITH_MATLAB:BOOL=ON",
    "-DMATLAB_ROOT_PATH:PATH=%s" % spec["matlab"].prefix,
    "-DWITH_MATLAB_MEX:BOOL=ON",
    ]
    )
    else:
    args.append('-DWITH_MATLAB:BOOL=OFF')
    args.append("-DWITH_MATLAB:BOOL=OFF")
    # fix issue with finding existing R libs/headers
    if '+r' in spec:
    args.extend([
    "-DR_LIB=%s" % spec['r'].prefix,
    "-DR_INCLUDE_DIRS=%s" % spec['r'].prefix.rlib.R.include
    ])
    args.append(self.define_from_variant('WITH_OCTAVE', 'octave'))
    args.append(self.define_from_variant('WITH_PERL', 'perl'))
    args.append(self.define_from_variant('WITH_R', 'r'))
    args.append(self.define_from_variant('WITH_RUBY', 'ruby'))
    if "+r" in spec:
    args.extend(
    [
    "-DR_LIB=%s" % spec["r"].prefix,
    "-DR_INCLUDE_DIRS=%s" % spec["r"].prefix.rlib.R.include
    ]
    )
    args.append(self.define_from_variant("WITH_OCTAVE", "octave"))
    args.append(self.define_from_variant("WITH_PERL", "perl"))
    args.append(self.define_from_variant("WITH_R", "r"))
    args.append(self.define_from_variant("WITH_RUBY", "ruby"))
    # fix issue with finding existing libxml2
    args.append('-DLIBXML_INCLUDE_DIR=%s' % spec['libxml2'].prefix.include.libxml2)
    args.append("-DLIBXML_INCLUDE_DIR=%s" % spec["libxml2"].prefix.include.libxml2)
    return args
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