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Commit d43b7ef8 authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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Merge branch 'add_snudda' into 'master' 

new version of Snudda and fixes in dependencies

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!263
parents f859a37b f92b4dce
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3 merge requests!274update branch,!267create new experimental release,!263new version of Snudda and fixes in dependencies
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packages/py-bluepyopt/package.py
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##############################################################################
# Copyright 2013-2020 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)
# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-bluepyopt/package.py)
from spack import *
......@@ -12,34 +10,39 @@ class PyBluepyopt(PythonPackage):
homepage = "https://github.com/BlueBrain/BluePyOpt"
pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
maintainers = ["hjorth", "elmath"]
# NOTE : while adding new release check pmi_rank.patch compatibility
version('1.10.38', sha256='fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc')
version('1.9.37', sha256='4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8')
version('1.9.27', sha256='4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522')
version('1.8.68', sha256='b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c')
version('1.6.56', sha256='1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9')
version('1.8.68', sha256='b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c')
version('1.9.12', sha256='7b623ab9168f460a85d952719ca5249248fc95e6f7a02658b0673b2baa0a8fc6')
version("1.12.63", sha256="ec33abe2113767420cae0317da4d61554eb934e5447cadb54d66620576b97714")
version("1.11.47", sha256="cffe1698930e3e89544c441674a5f66e310c72db27f8265b17200713d9d16614")
version("1.10.38", sha256="fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc")
version("1.9.37", sha256="4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8")
version("1.9.27", sha256="4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522")
version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
version("1.6.56", sha256="1c57c91465ca4b947fe157692e7004a3e6df02e4151e3dc77a8831382a8f1ab9")
version("1.8.68", sha256="b9d432840aab89d4863c935d3dc604816441eba02d731422b92056cee751ca9c")
version("1.9.12", sha256="7b623ab9168f460a85d952719ca5249248fc95e6f7a02658b0673b2baa0a8fc6")
# patch required to avoid hpe-mpi linked mechanism library
patch("pmi_rank.patch", when="@1.9.27:")
variant('neuron', default=True, description="Use BluePyOpt together with NEURON")
depends_on('py-setuptools', type='build')
depends_on('py-pandas', type='run')
depends_on('py-numpy', type='run')
depends_on('py-efel', type='run')
depends_on('py-deap', type='run')
depends_on('py-scoop@0.7:', type='run', when='@:1.9.37')
depends_on('py-ipyparallel', type='run')
depends_on('py-pickleshare', type='run')
depends_on('py-future', type='run')
depends_on('py-jinja2', type='run')
depends_on('py-pebble@4.3.10:', type='run')
depends_on('neuron', type='run', when='+neuron')
variant("neuron", default=True, description="Use BluePyOpt together with NEURON")
depends_on("py-setuptools", type=("build"))
depends_on("py-pandas@0.18:", type=("build","run"))
depends_on("py-numpy@1.6:", type=("build","run"))
depends_on("py-efel@2.13:", type=("build","run"))
depends_on("py-deap", type=("build","run"))
depends_on("py-deap@1.3.3:", type=("build","run"), when="@1.12.63:")
depends_on("py-scoop@0.7:", type=("build","run"), when="@:1.9.37")
depends_on("py-ipyparallel", type=("build","run"))
depends_on("py-pickleshare@0.7.3:", type=("build","run"))
depends_on("py-future", type=("build","run"))
depends_on("py-jinja2@2.8:", type=("build","run"))
depends_on("py-pebble@4.3.10:", type=("build","run"))
depends_on("neuron", type=("build","run"), when="+neuron")
def setup_run_environment(self, env):
env.unset('PMI_RANK')
env.set('NEURON_INIT_MPI', "0")
env.prepend_path('PATH', self.spec['py-ipyparallel'].prefix.bin)
env.unset("PMI_RANK")
env.set("NEURON_INIT_MPI", "0")
env.prepend_path("PATH", self.spec["py-ipyparallel"].prefix.bin)
packages/py-deap/package.py 0 → 100644
+ 24
− 0
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# (this package was adapted from the spack develop upstream as a dependency of py-bluepyopt)
# 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 *
class PyDeap(PythonPackage):
"""Distributed Evolutionary Algorithms in Python."""
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"))
packages/py-efel/package.py
+ 4
− 4
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......@@ -14,8 +14,8 @@ class PyEfel(PythonPackage):
pypi = "efel/efel-4.0.4.tar.gz"
git = "https://github.com/BlueBrain/eFEL.git"
version('4.0.4', sha256='258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894')
version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
depends_on('python@3.6.9:')
depends_on('py-numpy@1.6:', type=('build', 'run'))
depends_on('py-six', type=('build', 'run'))
\ No newline at end of file
depends_on("python@3.6.9:")
depends_on("py-numpy@1.6:", type=("build", "run"))
depends_on("py-six", type=("build", "run"))
packages/py-libsonata/package.py
+ 19
− 20
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# Copyright 2013-2018 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)
# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-libsonata/package.py)
from spack import *
......@@ -12,22 +10,23 @@ class PyLibsonata(PythonPackage):
homepage = "https://github.com/BlueBrain/libsonata"
git = "https://github.com/BlueBrain/libsonata.git"
pypi = "libsonata/libsonata-0.1.14.tar.gz"
maintainers = ["hjorth", "elmath"]
submodules = True
version('develop', branch='master')
version('0.1.16', sha256='49ced56992ba8be8aa6638525e8078b7e3ce0d5c05c34ee90746cab02bb5185a')
version('0.1.15', sha256='8c7c509db692b482cba5b0453579747db5a981ce5b3c13da96b14ae0332a6e81')
version('0.1.14', sha256='a5c75df1c3ef6fac10d92fb6781643e0834e5c35debe77693686dab8bfcf221f')
version('0.1.13', sha256='8263938e49b501c477f626b4c25e0c74e91152268830c69aabc96eeb263c6eea')
version('0.1.12', sha256='f0fa0f3b129d28e41b337ce2c39c3604990752de8e485327ec9df3bf0360e9c1')
version('0.1.11', sha256='95f302818971fec3f19ef18febd5c31c580490692138c8e4fe3534104d88b5e0')
version('0.1.10', sha256='7ef9f911f7ea31da5ff5306d8372ec194d223850aede0878ac2a921ce049bbb2')
depends_on('cmake@3.3:', type='build')
depends_on('hdf5')
depends_on('py-pybind11')
depends_on('py-numpy@1.17:', type=('build', 'run'))
depends_on('py-setuptools', type='build', when='@0.1:')
depends_on('py-setuptools-scm', type='build', when='@0.1:')
version("develop", branch="master")
version("0.1.16", sha256="49ced56992ba8be8aa6638525e8078b7e3ce0d5c05c34ee90746cab02bb5185a")
version("0.1.15", sha256="8c7c509db692b482cba5b0453579747db5a981ce5b3c13da96b14ae0332a6e81")
version("0.1.14", sha256="a5c75df1c3ef6fac10d92fb6781643e0834e5c35debe77693686dab8bfcf221f")
version("0.1.13", sha256="8263938e49b501c477f626b4c25e0c74e91152268830c69aabc96eeb263c6eea")
version("0.1.12", sha256="f0fa0f3b129d28e41b337ce2c39c3604990752de8e485327ec9df3bf0360e9c1")
version("0.1.11", sha256="95f302818971fec3f19ef18febd5c31c580490692138c8e4fe3534104d88b5e0")
version("0.1.10", sha256="7ef9f911f7ea31da5ff5306d8372ec194d223850aede0878ac2a921ce049bbb2")
depends_on("hdf5")
depends_on("py-pybind11")
depends_on("cmake@3.3:", type=("build"))
depends_on("py-setuptools", type=("build"), when="@0.1:")
depends_on("py-setuptools-scm", type=("build"), when="@0.1:")
depends_on("py-numpy@1.17:", type=("build", "run"))
packages/py-pebble/package.py
+ 11
− 9
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# Copyright 2013-2020 Lawrence Livermore National Security, LLC and other
# (this package was adapted from the spack develop upstream as a dependency of py-bluepyopt)
# 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 *
class PyPebble(PythonPackage):
"""Python API to manage threads and processes within an application."""
"""Threading and multiprocessing eye-candy."""
homepage = "https://github.com/noxdafox/pebble"
pypi = "pebble/Pebble-4.5.0.tar.gz"
git = "https://github.com/noxdafox/pebble.git"
pypi = "Pebble/Pebble-5.0.3.tar.gz"
version('4.5.0', sha256='2de3cd11aa068e0c4a4abbaf8d4ecfdac409d8bfb78a4c211a01f6a4fb17a35f')
version('4.4.1', sha256='7c4d68a3479140cba74d7454d8190e2cb1a93213b44b5befe3c53c201beb8317')
version('4.3.10', sha256='c39a7bf99af6525fcf0783a8859fb10a4f20f4f988ddb66fd6fa7588f9c91731')
maintainers = ["hjorth", "elmath"]
version("5.0.3", sha256="bdcfd9ea7e0aedb895b204177c19e6d6543d9962f4e3402ebab2175004863da8")
depends_on('py-setuptools', type=('build', 'run'))
depends_on('py-futures', type='run', when='^python@:2.9.9')
depends_on("python@3.6:", type=("build", "run"))
depends_on("py-setuptools", type=("build"))
packages/py-pyswarms/package.py
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− 8
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......@@ -6,12 +6,14 @@ class PyPyswarms(PythonPackage):
homepage = "https://github.com/ljvmiranda921/pyswarms"
pypi = "pyswarms/pyswarms-1.3.0.tar.gz"
version('1.3.0', sha256='1204aa9c332c662113e3c37d1b109906f4a0859b29ded80c1582dc66387ce34b')
maintainers = ["hjorth", "elmath"]
depends_on('py-scipy', type=('build', 'run'))
depends_on('py-numpy', type=('build', 'run'))
depends_on('py-matplotlib@1.3.1:', type=('build', 'run'))
depends_on('py-attrs', type=('build', 'run'))
depends_on('py-tqdm', type=('build', 'run'))
depends_on('py-future', type=('build', 'run'))
depends_on('py-pyyaml', type=('build', 'run'))
version("1.3.0", sha256="1204aa9c332c662113e3c37d1b109906f4a0859b29ded80c1582dc66387ce34b")
depends_on("py-scipy", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-matplotlib@1.3.1:", type=("build", "run"))
depends_on("py-attrs", type=("build", "run"))
depends_on("py-tqdm", type=("build", "run"))
depends_on("py-future", type=("build", "run"))
depends_on("py-pyyaml", type=("build", "run"))
packages/py-snudda/package.py
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from spack import *
class PySnudda(Package):
homepage = 'https://pypi.org/project/snudda/'
url = 'https://files.pythonhosted.org/packages/py3/s/snudda/snudda-1.2.9-py3-none-any.whl'
list_url = 'https://pypi.org/simple/snudda/'
maintainers = ['hjorth','akarmas']
version('1.3.2', '2306ec50acead5fd4f988ec373f19718', expand=False)
class PySnudda(PythonPackage):
"""Snudda creates the connectivity for realistic networks of simulated neurons in silico in a bottom up fashion that can then be simulated using the NEURON software."""
homepage = "https://pypi.org/project/snudda/"
pypi = "snudda/snudda-1.4.0.tar.gz"
maintainers = ["hjorth", "elmath"]
depends_on('python@3.8:', type=('build','run'))
depends_on('py-pip', type='build')
depends_on('unzip', type='build')
depends_on('py-bluepyopt', type=('build','run')) # got this from BlueBrainProject https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-bluepyopt/package.py
depends_on('py-h5py', type=('build','run'))
depends_on('py-ipyparallel', type=('build','run'))
depends_on('py-matplotlib', type=('build','run'))
depends_on('py-mpi4py', type=('build','run'))
depends_on('py-numpy', type=('build','run'))
depends_on('py-scipy', type=('build','run'))
depends_on('py-libsonata', type=('build','run')) # got it from from BlueBrainProject https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-libsonata/package.py
depends_on('py-pyzmq', type=('build','run'))
depends_on('py-numexpr', type=('build','run'))
depends_on('neuron', type=('build','run'))
depends_on('py-pyswarms', type=('build','run'))
depends_on('py-setuptools', type=('build'))
depends_on('py-psutil', type=('build','run'))
depends_on('py-cython', type=('build','run'))
depends_on('py-numba', type=('build','run'))
version("1.4.0", "55f9b398b01b34bf3cec28c8a3aebc78")
version("1.3.2", "2306ec50acead5fd4f988ec373f19718", url="https://files.pythonhosted.org/packages/py3/s/snudda/snudda-1.2.9-py3-none-any.whl", expand=False)
def install(self, spec, prefix):
pip = which('pip')
pip('install', self.stage.archive_file, '--prefix={0}'.format(prefix))
depends_on("unzip", type=("build"))
depends_on("py-setuptools", type=("build"))
depends_on("py-bluepyopt@1.11.7:", type=("build","run"))
depends_on("py-h5py@3.2.1:", type=("build","run"))
depends_on("py-ipyparallel@6.3.0:", type=("build","run"))
depends_on("py-matplotlib@3.3.4:", type=("build","run"))
depends_on("py-mpi4py@3.0.3:", type=("build","run"))
depends_on("py-numpy@1.20.2:", type=("build","run"))
depends_on("py-scipy@1.6.3:", type=("build","run"))
depends_on("py-libsonata@0.0.2:", type=("build","run"))
depends_on("py-pyzmq@22.0.3:", type=("build","run"))
depends_on("py-numexpr@2.7.3:", type=("build","run"))
depends_on("neuron@7.8.2:", type=("build","run"))
depends_on("py-pyswarms@1.3.0:", type=("build","run"))
depends_on("py-psutil", type=("build","run"))
depends_on("py-cython", type=("build","run"))
depends_on("py-numba@0.53.1:", type=("build","run"))
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