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py-bluepyemodel: sync with upstreamed version (dependencies too) #2177

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merged 5 commits into from
Nov 7, 2023
Merged

py-bluepyemodel: sync with upstreamed version (dependencies too) #2177

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a26369f
py-bluepyemodel: sync with upstreamed version (dependencies too)
heerener Nov 1, 2023
df46a0a
py-bluepyemodel: newer version is available
heerener Nov 1, 2023
ccf9589
py-region-grower: py-morph-tool variant is called nrn now
heerener Nov 2, 2023
ffda5e7
deploy: py-morph-tool variant name has changed
heerener Nov 6, 2023
5eddc98
Merge branch 'develop' into backport-upstream
heerener Nov 6, 2023
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2 changes: 1 addition & 1 deletion bluebrain/deployment/environments/applications_nse.yaml
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Expand Up @@ -57,6 +57,6 @@ spack:
- py-minis-validation
- py-morphio
- py-neuror
- py-morph-tool+neuron
- py-morph-tool+nrn
- py-region-grower
- py-cwl-registry
2 changes: 1 addition & 1 deletion bluebrain/repo-bluebrain/packages/py-region-grower/package.py
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Expand Up @@ -24,7 +24,7 @@ class PyRegionGrower(PythonPackage):
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:3", type=("build", "run"))
depends_on("[email protected]:2 +neuron", type=("build", "run"))
depends_on("[email protected]:2 +nrn", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:3", type=("build", "run"))
depends_on("[email protected]:3", type=("build", "run"))
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9 changes: 2 additions & 7 deletions var/spack/repos/builtin/packages/py-bluepyefe/package.py
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@@ -1,4 +1,3 @@
##############################################################################
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
Expand All @@ -10,21 +9,17 @@ class PyBluepyefe(PythonPackage):
"""Blue Brain Python E-feature extraction"""

homepage = "https://github.com/BlueBrain/BluePyEfe"
pypi = "bluepyefe/bluepyefe-0.3.13.tar.gz"
pypi = "bluepyefe/bluepyefe-2.2.18.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-numpy@:1.23", 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")
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13 changes: 5 additions & 8 deletions var/spack/repos/builtin/packages/py-bluepyemodel/package.py
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Expand Up @@ -10,13 +10,15 @@ class PyBluepyemodel(PythonPackage):
"""Python library to optimize and evaluate electrical models."""

homepage = "https://github.com/BlueBrain/BluePyEModel"
pypi = "bluepyemodel/bluepyemodel-0.0.59.tar.gz"
pypi = "bluepyemodel/bluepyemodel-0.0.46.tar.gz"

version("0.0.57", sha256="0b91e39e5066ab4a996bd932577b49648169e549c5f05bb3f93e345b4b186093")
version("0.0.58", sha256="327de9d2c49e7ff83cc77850873293299d4eacf95b3cf33716e5a8501685f08c")
version("0.0.59", sha256="5e8869522d82e719f9775c2d95cfe953cedc66bc44355765a6f406289baf6791")
version("0.0.58", sha256="327de9d2c49e7ff83cc77850873293299d4eacf95b3cf33716e5a8501685f08c")
version("0.0.57", sha256="0b91e39e5066ab4a996bd932577b49648169e549c5f05bb3f93e345b4b186093")
version("0.0.46", sha256="ad4c125e491f3337fcc341a4f389b8a616d883ce50fd77d9fb0ea6e13be5da61")
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depends_on("py-setuptools", type="build")
depends_on("py-setuptools-scm", type="build")

depends_on("py-numpy", type=("build", "run"))
depends_on("py-scipy", type=("build", "run"))
Expand All @@ -35,8 +37,3 @@ class PyBluepyemodel(PythonPackage):
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]", when="@0.0.11:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))

def patch(self):
# This dependency has survived, even though the modules needing it were axed mid
# 2021
filter_file(r".*psycopg2-binary.*", "", "setup.py")
9 changes: 3 additions & 6 deletions var/spack/repos/builtin/packages/py-bluepyopt/package.py
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@@ -1,4 +1,3 @@
##############################################################################
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
Expand All @@ -18,8 +17,7 @@ class PyBluepyopt(PythonPackage):
# patch required to avoid hpe-mpi linked mechanism library
patch("pmi_rank.patch")

variant("neuron", default=True, description="Use BluePyOpt together with NEURON")
variant("scoop", default=True, description="Use BluePyOpt together with py-scoop")
variant("scoop", default=False, description="Use BluePyOpt together with py-scoop")

depends_on("py-setuptools", type="build")
depends_on("[email protected]:", type=("build", "run"))
Expand All @@ -30,11 +28,10 @@ class PyBluepyopt(PythonPackage):
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("py-future", type=("build", "run"))
depends_on("py-pebble@4.3.10:", type=("build", "run"))
depends_on("py-pebble@4.6:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"), when="+scoop")
depends_on("[email protected]:", type=("build", "run"), when="+neuron")
depends_on("[email protected]:", type=("build", "run"))

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)
5 changes: 1 addition & 4 deletions var/spack/repos/builtin/packages/py-currentscape/package.py
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Expand Up @@ -13,10 +13,7 @@ class PyCurrentscape(PythonPackage):
git = "https://github.com/BlueBrain/Currentscape.git"
pypi = "currentscape/currentscape-1.0.12.tar.gz"

version(
"1.0.12",
sha256="d83c5a58074e4d612553472a487e5d1d2854dc4d5c161817c6bafdf4a5988011",
)
version("1.0.12", sha256="d83c5a58074e4d612553472a487e5d1d2854dc4d5c161817c6bafdf4a5988011")

depends_on("py-setuptools", type=("build", "run"))
depends_on("py-setuptools-scm", type=("build",))
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1 change: 0 additions & 1 deletion var/spack/repos/builtin/packages/py-efel/package.py
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@@ -1,4 +1,3 @@
##############################################################################
# Copyright 2013-2023 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
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20 changes: 10 additions & 10 deletions var/spack/repos/builtin/packages/py-morph-tool/package.py
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Expand Up @@ -13,27 +13,27 @@ class PyMorphTool(PythonPackage):
git = "https://github.com/BlueBrain/morph-tool.git"
pypi = "morph-tool/morph-tool-2.9.1.tar.gz"

version("develop", branch="master")
version("master", branch="master")
version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")

variant("neuron", default=False, description="Enable additional neuron support")
variant("plotly", default=False, description="Enable additional plotly support")
variant("nrn", default=False, description="Enable additional neuron support")
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variant("plot", default=False, description="Enable additional plotly support")
variant("parallel", default=False, description="Enable additional parallel support")

depends_on("py-setuptools", type=("build", "run"))
depends_on("py-setuptools-scm", type=("build", "run"))
depends_on("py-setuptools", type="build")
depends_on("py-setuptools-scm", type="build")

depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("py-morphio@3,develop", type=("build", "run"))
depends_on("py-neurom@3,develop", type=("build", "run"))
depends_on("py-morphio@3", type=("build", "run"))
depends_on("py-neurom@3", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))

depends_on("[email protected]:", type=("build", "run"), when="+plotly")
depends_on("[email protected]:", type=("build", "run"), when="+plot")
depends_on("[email protected]:", type=("build", "run"), when="+parallel")
depends_on("[email protected]:", type=("build", "run"), when="+neuron")
depends_on("[email protected]:", type=("build", "run"), when="+neuron")
depends_on("[email protected]:", type=("build", "run"), when="+nrn")
depends_on("[email protected]:", type=("build", "run"), when="+nrn")
7 changes: 3 additions & 4 deletions var/spack/repos/builtin/packages/py-morphio/package.py
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Expand Up @@ -19,13 +19,12 @@ class PyMorphio(PythonPackage):

version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6")

depends_on("py-setuptools", type="build")
depends_on("py-setuptools@24.2:", type="build")
depends_on("py-setuptools-scm", type="build")

depends_on("ninja", type="build")
depends_on("[email protected]:", type="build")
depends_on("[email protected]:", type=("build", "run"))
if sys.platform == "win32":
depends_on("py-h5py@3", type=("build", "run"))
else:
depends_on("py-h5py@3", when="platform=windows", type=("build", "run"))
if sys.platform != "win32":
depends_on("hdf5")
6 changes: 3 additions & 3 deletions var/spack/repos/builtin/packages/py-neurom/package.py
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Expand Up @@ -13,14 +13,14 @@ class PyNeurom(PythonPackage):
git = "https://github.com/BlueBrain/NeuroM.git"
pypi = "neurom/neurom-2.2.1.tar.gz"

version("develop", branch="master")
version("master", branch="master")
version("3.2.4", sha256="a584e0979b54deee906dd716ea90de20773e20b527d83960d0fe655b0905eb4a")

variant("plotly", default=False, description="Enable plotly support")

depends_on("py-setuptools@0.42:", type=("build", "run"))
depends_on("py-setuptools@42:", type=("build", "run"))
depends_on("py-setuptools-scm", type="build")
depends_on("py-wheel", type="build")
depends_on("[email protected]:", type=("build", "run"))

depends_on("[email protected]:", type=("build", "run"))
depends_on("[email protected]:", type=("build", "run"))
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