Merge branch ebrains-spack-builds:master into master

packages/py-bluepyopt/package.py

+# 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"
+
+    license("LGPL-3.0-only")
+
+    # NOTE : while adding new release check pmi_rank.patch compatibility
+    version("1.14.18", sha256="23d6239294d944c8f9d4ea298091bcf243d236735844e1bcba60535a0f520ca8")
+    version("1.14.11", sha256="fe2830c36699a93d2ef9ddef316da42f9c57ca6654c92356eab973ee2298ebf7")
+    version("1.14.4", sha256="7567fd736053250ca06030f67ad93c607b100c2b98df8dc588c26b64cb3e171c")
+
+    # patch required to avoid hpe-mpi linked mechanism library
+    patch("pmi_rank.patch")
+
+    variant("scoop", default=False, description="Use BluePyOpt together with py-scoop")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.6:", type=("build", "run"))
+    depends_on("py-pandas@0.18:", type=("build", "run"))
+    depends_on("py-deap@1.3.3:", type=("build", "run"))
+    depends_on("py-efel@2.13:", type=("build", "run"))
+    depends_on("py-ipyparallel", type=("build", "run"))
+    depends_on("py-pickleshare@0.7.3:", type=("build", "run"))
+    depends_on("py-jinja2@2.8:", type=("build", "run"))
+    depends_on("py-future", type=("build", "run"))
+    depends_on("py-pebble@4.6:", type=("build", "run"))
+    depends_on("py-scoop@0.7:", type=("build", "run"), when="+scoop")
+    depends_on("neuron@7.4:", type=("build", "run"), when="@:1.14.4")
+    depends_on("neuron@7.8:", type=("build", "run"), when="@1.14.11:")
+
+    def setup_run_environment(self, env):
+        env.unset("PMI_RANK")
+        env.set("NEURON_INIT_MPI", "0")

packages/py-bluepyopt/pmi_rank.patch

+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

packages/py-snudda/package.py

@@ -24,7 +24,7 @@ class PySnudda(PythonPackage):
     depends_on("unzip",                 type=("build"))
     depends_on("py-setuptools",         type=("build"))
     depends_on("py-importlib-metadata", type=("build","run"))
-    depends_on("py-bluepyopt@1.14.11:", type=("build","run"))
+    depends_on("py-bluepyopt@1.14.18:", type=("build","run"))
     depends_on("py-h5py@3.12.1:",       type=("build","run"))
     depends_on("py-ipyparallel@8.4.1:", type=("build","run"))
     depends_on("py-matplotlib@3.8:",    type=("build","run"))

packages/py-vbi/package.py

@@ -12,6 +12,7 @@ class PyVbi(PythonPackage, CudaPackage):
     git = "https://github.com/ins-amu/vbi"
     url = "https://github.com/ins-amu/vbi/archive/refs/tags/v0.1.3.tar.gz"
 
+    version("0.1.3.2", "6de0367b15834195ad1c14c61e4286875b5fe32d86975185977065765564576d")
     version("0.1.3.1", "53f085aba83129d01a8ad6d3deadc768db38b7a8545bcbc4427e70db2b6e66c0")
     version("0.1.3", "8ccccf2bf0def2bf97f4706b8597c4cb3ac5f0cf2ac5f08566e22cd6273c1163")
     version("0.1.2", "6ccfeeec718be62a480002a8370130a3e3344955186f99ecbb15b646b68210d6")

spack.yaml

@@ -18,7 +18,7 @@ spack:
     - jaxsnn@10.0-a1
     - py-bluepyefe@2.3.6
     - py-bluepymm@0.8.7
-    - py-bluepyopt@1.14.11
+    - py-bluepyopt@1.14.18
     - py-bsb-core@5.0.2
     - py-bsb-hdf5@5.0.2
     - py-bsb-yaml@4.2.2
@@ -62,7 +62,7 @@ spack:
     - py-tvb-ext-unicore
     - py-tvb-ext-xircuits@1.1.0
     - py-viziphant@0.4.0
-    - py-vbi@0.1.3.1
+    - py-vbi@0.1.3.2
     - pynn-brainscales@10.0-a1
     - r-rgsl@0.1.1
     - r-sbtabvfgen@0.1