diff --git a/packages/py-bluepyefe/package.py b/packages/py-bluepyefe/package.py
deleted file mode 100644
index df41cbc82b834f1dff745497c9870c3f64a8850a..0000000000000000000000000000000000000000
--- a/packages/py-bluepyefe/package.py
+++ /dev/null
@@ -1,32 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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")
diff --git a/packages/py-bluepymm/package.py b/packages/py-bluepymm/package.py
index 5fa0d410efb5f17afb9c0b097d9103a06329fc71..7b1a4c2c57c21cc53b04efab833fa99f8f4a89f6 100644
--- a/packages/py-bluepymm/package.py
+++ b/packages/py-bluepymm/package.py
@@ -14,15 +14,12 @@ class PyBluepymm(PythonPackage):
homepage = "https://github.com/BlueBrain/BluePyMM"
pypi = "bluepymm/bluepymm-0.7.49.tar.gz"
+ version("0.8.7", sha256="f0e5d4e113b19f71398d0796d5182f322c48c2ab07793ce8d0e4771a251914ab")
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
- # not needed with EBRAINS python version:
- # 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")
diff --git a/packages/py-bluepyopt/package.py b/packages/py-bluepyopt/package.py
deleted file mode 100644
index 16a10d59fbbbaaf96b1ab3a48c39535655efddb1..0000000000000000000000000000000000000000
--- a/packages/py-bluepyopt/package.py
+++ /dev/null
@@ -1,49 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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 PyBluepyopt(PythonPackage):
- """Bluebrain Python Optimisation Library"""
-
- homepage = "https://github.com/BlueBrain/BluePyOpt"
- pypi = "bluepyopt/bluepyopt-1.9.27.tar.gz"
-
- # NOTE : while adding new release check pmi_rank.patch compatibility
- version("1.13.86", sha256="37b4abcc4a53ed5af50fa0b3bc4d0003332b7f2f2b6e4d9f0b9de8638254e753")
- 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-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")
- env.set("NEURON_INIT_MPI", "0")
- env.prepend_path("PATH", self.spec["py-ipyparallel"].prefix.bin)
diff --git a/packages/py-bluepyopt/pmi_rank.patch b/packages/py-bluepyopt/pmi_rank.patch
deleted file mode 100644
index 21a73849b2868389f5e05d9670adc0fb18fadab5..0000000000000000000000000000000000000000
--- a/packages/py-bluepyopt/pmi_rank.patch
+++ /dev/null
@@ -1,17 +0,0 @@
-diff --git a/bluepyopt/ephys/simulators.py b/bluepyopt/ephys/simulators.py
-index e71ad8b..3c93237 100644
---- a/bluepyopt/ephys/simulators.py
-+++ b/bluepyopt/ephys/simulators.py
-@@ -89,6 +89,12 @@ class NrnSimulator(object):
- NrnSimulator._nrn_disable_banner()
- self.banner_disabled = True
-
-+ # certain mpi libraries (hpe-mpt) use PMI_RANK env variable to initialize
-+ # MPI before calling MPI_Init (which is undesirable). Unset this variable
-+ # if exist to avoid issue with loading neuron and mechanism library.
-+ if 'PMI_RANK' in os.environ:
-+ os.environ.pop("PMI_RANK")
-+
- import neuron # NOQA
-
- return neuron
diff --git a/packages/py-efel/package.py b/packages/py-efel/package.py
deleted file mode 100644
index c7b5d571240653f1b86b62a9d5277a7e07eee98f..0000000000000000000000000000000000000000
--- a/packages/py-efel/package.py
+++ /dev/null
@@ -1,28 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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 PyEfel(PythonPackage):
- """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-3.0.80.tar.gz"
-
- version("4.0.4", sha256="258c506776df609edc799338fd773e78f0f0315fd6f3e2f969478bda401a8894")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-numpy", type="run")
- depends_on("py-six", type="run")
diff --git a/packages/py-libsonata/package.py b/packages/py-libsonata/package.py
index b8b9695afd610e318efe161acbd6baab951a0283..80fe984b8068d6c64763c3bb7c32d73d74a075f3 100644
--- a/packages/py-libsonata/package.py
+++ b/packages/py-libsonata/package.py
@@ -39,3 +39,4 @@ class PyLibsonata(PythonPackage):
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:")
+
diff --git a/packages/py-morph-tool/package.py b/packages/py-morph-tool/package.py
deleted file mode 100644
index 3c483b74f26e3609cba86f8a68aeff0ddd4aa318..0000000000000000000000000000000000000000
--- a/packages/py-morph-tool/package.py
+++ /dev/null
@@ -1,40 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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 PyMorphTool(PythonPackage):
- """Python morphology manipulation toolkit"""
-
- homepage = "https://github.com/BlueBrain/morph-tool"
- git = "https://github.com/BlueBrain/morph-tool.git"
- pypi = "morph-tool/morph-tool-2.9.1.tar.gz"
-
- version("develop", branch="master")
- version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
- version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")
-
- variant("neuron", default=False, description="Enable additional neuron support")
-
- depends_on("py-setuptools", type=("build", "run"))
-
- depends_on("py-click@6.7:", type=("build", "run"))
- depends_on("py-deprecation@2.1.0:", type=("build", "run"))
- depends_on("py-more-itertools@8.6.0:", type=("build", "run"))
- depends_on("py-numpy@1.14:", type=("build", "run"))
- depends_on("py-pandas@1.0.3:", type=("build", "run"))
- depends_on("py-xmltodict@0.12:", type=("build", "run"))
-
- depends_on("py-plotly@4.1:", type=("build", "run"))
- depends_on("py-dask@2.19:", type=("build", "run"))
- depends_on("neuron+python@7.8:", type=("build", "run"))
- depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+neuron")
-
- depends_on("py-neurom@3.0:3.999,develop", type=("build", "run"))
- depends_on("py-morphio@3.3.6:3,develop", type=("build", "run"), when="@2.9.1:")
- depends_on("py-morphio@3.0:3,develop", type=("build", "run"), when="@2.9.0")
diff --git a/packages/py-morphio/package.py b/packages/py-morphio/package.py
deleted file mode 100644
index a2957888bc407e5fb41895837c43e10b55bf2b74..0000000000000000000000000000000000000000
--- a/packages/py-morphio/package.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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 PyMorphio(PythonPackage):
- """Python library for reading / writing morphology files"""
-
- homepage = "https://github.com/BlueBrain/MorphIO"
- git = "https://github.com/BlueBrain/MorphIO.git"
- pypi = "morphio/MorphIO-3.3.2.tar.gz"
-
- version("develop", branch="master", submodules=True)
- version("unifurcation", branch="unifurcation", submodules=True)
-
- version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6")
- version("3.3.5", sha256="9e6cfebaea32080131b2b08a4a32dfbe92b18427a3e557861e27c4131f7542ac")
- version("3.3.4", sha256="b70c6884e9b835560501f798c75c9cc7eaf3162cba1d930b5a9b854bb9ea60dc")
- version("3.3.3", sha256="f6d91970cfd734b2e5fb8f9239a0bfa00519fe082dd8e403e4cc204dbdf0a9fa")
- version("3.3.2", sha256="fc961defbfbfb3f11360954fb3ec51373eaff25b154fa31d6b31decca6937780")
- version("3.1.1", sha256="ad9f0e363f09f03c6eda54f5f3b006d204236677d2f2c9675421e0441033a503")
- version("2.7.1", sha256="3f3e2229da85e874527775fce080f712b6dc287edc44b90b6de35d17b34badff")
-
- depends_on("py-setuptools", type="build")
- depends_on("py-setuptools-scm", type="build")
-
- depends_on("ninja", type="build")
- depends_on("cmake@3.2:", type="build")
- depends_on("py-numpy@1.14.1:", type="run")
- depends_on("hdf5")
diff --git a/packages/py-neurom/package.py b/packages/py-neurom/package.py
deleted file mode 100644
index b902984e57d086b767acbbe0e9af3fa2c7182830..0000000000000000000000000000000000000000
--- a/packages/py-neurom/package.py
+++ /dev/null
@@ -1,37 +0,0 @@
-# (from https://github.com/BlueBrain/spack)
-
-# Copyright 2013-2024 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 PyNeurom(PythonPackage):
- """Python library neuron morphology analysis"""
-
- homepage = "https://github.com/BlueBrain/NeuroM"
- git = "https://github.com/BlueBrain/NeuroM.git"
- pypi = "neurom/neurom-2.2.1.tar.gz"
-
- version("develop", branch="master")
- version("3.2.2", sha256="bc442cf5193289b893a66d5e541868f84bb120b03395b03ce2423c19729b92de")
-
- variant("plotly", default=False, description="Enable plotly support")
-
- depends_on("py-setuptools@0.42:", type=("build", "run"))
- depends_on("py-setuptools-scm", type="build")
- depends_on("py-wheel", type="build")
-
- depends_on("py-click@7.0:", type=("build", "run"))
- depends_on("py-numpy@1.8.0:", type=("build", "run"))
- depends_on("py-pyyaml@3.10:", type=("build", "run"))
- depends_on("py-tqdm@4.8.4:", type=("build", "run"))
- depends_on("py-matplotlib@3.2.1:", type=("build", "run"))
- depends_on("py-scipy@1.2.0:", type=("build", "run"))
- depends_on("py-plotly@3.6.0:", type=("build", "run"), when="+plotly")
- depends_on("py-psutil@5.5.1:", type=("build", "run"), when="+plotly")
-
- depends_on("py-morphio@3.1.1:", type=("build", "run"))
- depends_on("py-pandas@1.0.5:", type=("build", "run"))
diff --git a/spack.yaml b/spack.yaml
index e465a5a424f084d492719d720b1648e68ec02f5b..99226cda88406ea35e90564cf8b964eca17bad63 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -16,14 +16,14 @@ spack:
- nest@3.8 +sonata
- neuron@8.2.3 +mpi
- jaxsnn@9.0-a8
- - py-bluepyefe@2.2.18
- - py-bluepymm@0.7.65
- - py-bluepyopt@1.13.86
+ - py-bluepyefe@2.3.6
+ - py-bluepymm@0.8.7
+ - py-bluepyopt@1.14.11
- py-bsb@4.0.0a57
- py-ebrains-drive@0.6.0
- py-ebrains-kg-core@0.9.15
- py-ebrains-validation-client@0.9.1
- - py-efel@4.0.4
+ - py-efel@5.2.0
- py-elephant@1.1.0
- py-fairgraph@0.12.1
- py-frites@0.4.4
@@ -38,7 +38,7 @@ spack:
- py-neo@0.13.3
- py-nestml@8.0.0
- py-netpyne@1.0.6
- - py-neurom@3.2.2
+ - py-neurom@3.2.4
- py-neuror@1.6.4
- py-pynn@0.12.3 +mpi
- py-pyunicore@1.1.1