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Commit 1c83c8c1 authored by Eleni Mathioulaki's avatar Eleni Mathioulaki
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Merge branch 'update-bluebrain-packages' into 'master' 

Update bluebrain packages

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!364
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packages/py-bluepyefe/package.py 0 → 100644
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# (from https://github.com/BlueBrain/spack)
# 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)
from spack.package import *
class PyBluepyefe(PythonPackage):
"""Blue Brain Python E-feature extraction"""
homepage = "https://github.com/BlueBrain/BluePyEfe"
pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz"
git = "https://github.com/BlueBrain/BluePyEfe.git"
version("2.2.18", sha256="bfb50c6482433ec2ffb4b65b072d2778bd89ae50d92dd6830969222aabb30275")
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-neo", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
depends_on("py-efel", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
depends_on("py-h5py", type=("build", "run"))
depends_on("py-igor", type=("build", "run"))
def setup_run_environment(self, env):
env.set("NEURON_INIT_MPI", "0")
env.unset("PMI_RANK")
packages/py-bluepymm/package.py 0 → 100644
+ 36
− 0
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# (from https://github.com/BlueBrain/spack)
# 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)
from spack.package import *
class PyBluepymm(PythonPackage):
"""Blue Brain Model Management Python Library"""
homepage = "https://github.com/BlueBrain/BluePyMM"
pypi = "bluepymm/bluepymm-0.7.49.tar.gz"
version("0.7.65", sha256="024b009decd8d967b3b885421196d53670e3c0a6b75aaaa55559f148b0b0d7d4")
depends_on("py-setuptools", type="build")
depends_on("py-bluepyopt", type="run")
depends_on("py-matplotlib", type="run")
# The below dependency should disappear once
# the matplotlib package is fixed
depends_on("py-backports-functools-lru-cache", type="run", when="^python@:3.3.99")
depends_on("py-pandas", type="run")
depends_on("py-numpy", type="run")
depends_on("py-ipyparallel", type="run")
depends_on("py-lxml", type="run")
depends_on("py-sh", type="run")
depends_on("neuron", type="run")
depends_on("py-h5py", type="run")
depends_on("py-pyyaml", type="run")
def setup_run_environment(self, env):
env.unset("PMI_RANK")
env.set("NEURON_INIT_MPI", "0")
packages/py-bluepyopt/package.py
+ 20
− 19
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# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-bluepyopt/package.py)
# (from https://github.com/BlueBrain/spack)
# 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)
from spack import *
from spack.package import *
class PyBluepyopt(PythonPackage):
......@@ -10,11 +14,8 @@ 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("1.12.63", sha256="ec33abe2113767420cae0317da4d61554eb934e5447cadb54d66620576b97714")
version("1.11.47", sha256="cffe1698930e3e89544c441674a5f66e310c72db27f8265b17200713d9d16614")
version("1.13.86", sha256="37b4abcc4a53ed5af50fa0b3bc4d0003332b7f2f2b6e4d9f0b9de8638254e753")
version("1.10.38", sha256="fb1411c6a8fbfac52d36b837225bae882fd6524acfb4d0580189312ef3c1cfcc")
version("1.9.37", sha256="4399af71de48b288832e92f0de73c431bf88d6e76e2c4ea250c3b38fb38a45a8")
version("1.9.27", sha256="4cce15b92b32311c808cae5e005b664deb6e8dc5df4ca13ea7b59252ae346522")
......@@ -28,19 +29,19 @@ class PyBluepyopt(PythonPackage):
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")
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-pandas", type=("build", "run"))
depends_on("py-deap", type=("build", "run"))
depends_on("py-deap@1.3.3:", type=("build","run"), when="@1.13.86:")
depends_on("py-efel", type=("build", "run"))
depends_on("py-ipyparallel", type=("build", "run"))
depends_on("py-pickleshare", type=("build", "run"))
depends_on("py-jinja2", type=("build", "run"))
depends_on("py-future", type=("build", "run"))
depends_on("py-pebble@4.3.10:", type=("build", "run"))
depends_on("py-scoop@0.7:", type=("build", "run"), when="@:1.9.37")
depends_on("neuron", type=("build", "run"), when="+neuron")
def setup_run_environment(self, env):
env.unset("PMI_RANK")
......
packages/py-efel/package.py
+ 16
− 10
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# Copyright 2013-2021 Lawrence Livermore National Security, LLC and other
# (from https://github.com/BlueBrain/spack)
# 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)
from spack import *
from spack.package import *
class PyEfel(PythonPackage):
"""Electrophys Feature Extract Library (eFEL)
"""
"""The Electrophys Feature Extract Library (eFEL) allows
neuroscientists to automatically extract features from time series data
recorded from neurons (both in vitro and in silico).
Examples are the action potential width and amplitude in
voltage traces recorded during whole-cell patch clamp experiments.
The user of the library provides a set of traces and selects the
features to be calculated. The library will then extract the requested
features and return the values to the user."""
homepage = "https://github.com/BlueBrain/eFEL"
pypi = "efel/efel-4.0.4.tar.gz"
git = "https://github.com/BlueBrain/eFEL.git"
pypi = "efel/efel-3.0.80.tar.gz"
version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
depends_on("python@3.6.9:")
depends_on("py-setuptools", type=("build"))
depends_on("py-numpy@1.6:", type=("build", "run"))
depends_on("py-six", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type="run")
depends_on("py-six", type="run")
packages/py-igor/package.py 0 → 100644
+ 21
− 0
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# (backported from Spack v0.20.0)
# 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.package import *
class PyIgor(PythonPackage):
"""igor: interface for reading binary IGOR files."""
homepage = "http://blog.tremily.us/posts/igor/"
pypi = "igor/igor-0.3.tar.gz"
version("0.3", sha256="b04ac38c68fb81cf3167a9981dc5a20379112d40268bb72c5a8514dc8051abba")
depends_on("py-setuptools", type="build")
depends_on("py-numpy", type=("build", "run"))
depends_on("py-matplotlib", type=("build", "run"))
\ No newline at end of file
packages/py-libsonata/package.py
+ 17
− 9
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# (this package was adapted from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-libsonata/package.py)
# (from https://github.com/BlueBrain/spack)
# 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)
from spack import *
from spack.package import *
class PyLibsonata(PythonPackage):
......@@ -10,12 +14,15 @@ 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("develop", branch="master", get_full_repo=True)
version("0.1.22", sha256="4adbb32ed2fac5d3c74bde03a5e2adb319724d324318a2a7dc2ef3c30f817b2c")
version("0.1.21", sha256="5b280d82cb21a745d9cdb736c00446e0209494c21d2d17a2c878fabf23a08b68")
version("0.1.20", sha256="f2e63a26dcf045bb7424e236e12f9b9ef8c46c356e953d26555f313f5763651e")
version("0.1.18", sha256="1b13728cbffbcb74cc864c7bc186e568945e25c260f732ffa872437c081fd9b4")
version("0.1.17", sha256="d122dd9fce82c8ce1621746ed9029e7db0d319fb94f6a737fb14f572f632f7b4")
version("0.1.16", sha256="49ced56992ba8be8aa6638525e8078b7e3ce0d5c05c34ee90746cab02bb5185a")
version("0.1.15", sha256="8c7c509db692b482cba5b0453579747db5a981ce5b3c13da96b14ae0332a6e81")
version("0.1.14", sha256="a5c75df1c3ef6fac10d92fb6781643e0834e5c35debe77693686dab8bfcf221f")
......@@ -24,9 +31,10 @@ class PyLibsonata(PythonPackage):
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("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"))
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:")
packages/py-morph-tool/package.py
+ 9
− 2
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# (from https://github.com/BlueBrain/spack)
# 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)
from spack.package import *
......@@ -25,5 +32,5 @@ class PyMorphTool(PythonPackage):
depends_on("neuron+python@7.8:", type=("build", "run"))
depends_on("py-bluepyopt@1.9.37:", type=("build", "run"))
depends_on("py-neurom@3.0:3.999", type=("build", "run"))
depends_on("py-morphio@3.0:3.999", type=("build", "run"))
depends_on("py-neurom@3.0:3.999,develop", type=("build", "run"))
depends_on("py-morphio@3.0:3.999,develop", type=("build", "run"))
packages/py-morphio/package.py
+ 4
− 3
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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# (from https://github.com/BlueBrain/spack)
# 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)
#
# from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-morphio/package.py
from spack.package import *
......@@ -18,6 +18,7 @@ class PyMorphio(PythonPackage):
version("develop", branch="master", submodules=True)
version("unifurcation", branch="unifurcation", submodules=True)
version("3.3.5", sha256="9e6cfebaea32080131b2b08a4a32dfbe92b18427a3e557861e27c4131f7542ac")
version("3.3.4", sha256="b70c6884e9b835560501f798c75c9cc7eaf3162cba1d930b5a9b854bb9ea60dc")
version("3.3.3", sha256="f6d91970cfd734b2e5fb8f9239a0bfa00519fe082dd8e403e4cc204dbdf0a9fa")
version("3.3.2", sha256="fc961defbfbfb3f11360954fb3ec51373eaff25b154fa31d6b31decca6937780")
......
packages/py-neurom/package.py
+ 3
− 3
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# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# (from https://github.com/BlueBrain/spack)
# 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)
#
# from https://github.com/BlueBrain/spack/blob/develop/bluebrain/repo-bluebrain/packages/py-neurom/package.py
from spack.package import *
......
packages/py-neuror/package.py
+ 7
− 0
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# (from https://github.com/BlueBrain/spack)
# Copyright 2013-2021 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 *
......
spack.yaml
+ 5
− 1
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......@@ -25,6 +25,9 @@ spack:
- nest@3.5_rc1 +sonata
- neuron@8.2.2 +mpi
- nglview@3.0.4
- py-bluepyefe@2.2.18
- py-bluepymm@0.7.65
- py-bluepyopt@1.13.86
- py-brian2@2.5.0.2
- py-cerebrus@1.3.4
- py-ebrains-drive@0.5.1
......@@ -41,12 +44,13 @@ spack:
- py-lazyarray@0.5.2
- py-lfpy@2.3
- py-lfpykit@0.5
- py-libsonata@0.1.22
- py-nameparser@1.1.1
- py-neo@0.12.0
- py-nestml@5.2.0
- py-netpyne@1.0.4.1
- py-neuror@1.4.2
- py-neurom@3.2.2
- py-neuror@1.4.2
- py-nixio@1.5.3
- py-pdb2pqr@3.5.2
- py-pynn@0.11.0 +mpi
......
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