py-bluepyemodel: opensourcing with dependencies (#40592)

* py-bluepyemodel: new package with dependencies

* py-morphio: add MPI as dependency to avoid failing builds

* Formatting

* py-bluepyefe: no need to set NEURON_INIT_MPI

* py-morphio: unifurcation branch is ancient history

* py-bluepyopt: only set NEURON_INIT_MPI with +neuron

* py-efel: get rid of old version

* py-morph{-tool,io}: rename develop to master to match branch

* py-bluepyefe: unset PMI_RANK is also neuron-related

* py-bluepyopt: PMI_RANK is also neuron-related

* Implement review remarks

* py-morph-tool, py-neurom: small fixes

* py-morphio: reword dependencies

9 files changed, 266 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-bluepyefe/package.py b/var/spack/repos/builtin/packages/py-bluepyefe/package.py
new file mode 100644
index 0000000000..8a15e4edf9
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bluepyefe/package.py
@@ -0,0 +1,25 @@
+# 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 PyBluepyefe(PythonPackage):
+    """Blue Brain Python E-feature extraction"""
+
+    homepage = "https://github.com/BlueBrain/BluePyEfe"
+    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@: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"))
diff --git a/var/spack/repos/builtin/packages/py-bluepyemodel/package.py b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py
new file mode 100644
index 0000000000..f865b9791b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bluepyemodel/package.py
@@ -0,0 +1,36 @@
+# 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 PyBluepyemodel(PythonPackage):
+    """Python library to optimize and evaluate electrical models."""
+
+    homepage = "https://github.com/BlueBrain/BluePyEModel"
+    pypi = "bluepyemodel/bluepyemodel-0.0.46.tar.gz"
+
+    version("0.0.46", sha256="ad4c125e491f3337fcc341a4f389b8a616d883ce50fd77d9fb0ea6e13be5da61")
+
+    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"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-ipyparallel@6.3:", type=("build", "run"))
+    depends_on("py-tqdm", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-gitpython", type=("build", "run"))
+    depends_on("py-bluepyopt@1.12.12:", type=("build", "run"))
+    depends_on("py-bluepyefe@2.2.0:", type=("build", "run"))
+    depends_on("py-neurom@3.0:3", type=("build", "run"))
+    depends_on("py-efel@3.1:", type=("build", "run"))
+    depends_on("py-configparser", type=("build", "run"))
+    depends_on("py-morph-tool@2.8:", type=("build", "run"))
+    depends_on("py-fasteners@0.16:", type=("build", "run"))
+    depends_on("neuron+python@8.0:", type=("build", "run"))
+    depends_on("py-jinja2@3.0.3", when="@0.0.11:", type=("build", "run"))
+    depends_on("py-currentscape@0.0.11:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-bluepyopt/package.py b/var/spack/repos/builtin/packages/py-bluepyopt/package.py
new file mode 100644
index 0000000000..ccc39f9135
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bluepyopt/package.py
@@ -0,0 +1,37 @@
+# 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 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("1.14.4", 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"))
+
+    def setup_run_environment(self, env):
+        env.unset("PMI_RANK")
+        env.set("NEURON_INIT_MPI", "0")
diff --git a/var/spack/repos/builtin/packages/py-bluepyopt/pmi_rank.patch b/var/spack/repos/builtin/packages/py-bluepyopt/pmi_rank.patch
new file mode 100644
index 0000000000..21a73849b2
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-bluepyopt/pmi_rank.patch
@@ -0,0 +1,17 @@
+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/var/spack/repos/builtin/packages/py-currentscape/package.py b/var/spack/repos/builtin/packages/py-currentscape/package.py
new file mode 100644
index 0000000000..eb6d75be89
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-currentscape/package.py
@@ -0,0 +1,23 @@
+# 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 PyCurrentscape(PythonPackage):
+    """Module to easily plot the currents in electrical neuron models."""
+
+    homepage = "https://github.com/BlueBrain/Currentscape"
+    git = "https://github.com/BlueBrain/Currentscape.git"
+    pypi = "currentscape/currentscape-1.0.12.tar.gz"
+
+    version("1.0.12", sha256="d83c5a58074e4d612553472a487e5d1d2854dc4d5c161817c6bafdf4a5988011")
+
+    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-setuptools-scm", type=("build",))
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-matplotlib", type=("build", "run"))
+    depends_on("py-palettable", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-efel/package.py b/var/spack/repos/builtin/packages/py-efel/package.py
new file mode 100644
index 0000000000..a33749b9af
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-efel/package.py
@@ -0,0 +1,24 @@
+# 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 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("5.2.0", sha256="ed2c5efe22a4c703a4d9e47775b939009e1456713ac896898ebabf177c60b1dc")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-numpy@1.6:", type=("build", "run"))
diff --git a/var/spack/repos/builtin/packages/py-morph-tool/package.py b/var/spack/repos/builtin/packages/py-morph-tool/package.py
new file mode 100644
index 0000000000..7927b468c0
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-morph-tool/package.py
@@ -0,0 +1,39 @@
+# 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 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("master", branch="master")
+    version("2.9.1", sha256="305e9456c8047726588b23dfa070eb95ccbe5573e9fea3e0a83dc93eacdf61dc")
+    version("2.9.0", sha256="c60d4010e17ddcc3f53c864c374fffee05713c8f8fd2ba4eed7706041ce1fa47")
+
+    variant("nrn", default=False, description="Enable additional neuron support")
+    variant("plot", default=False, description="Enable additional plotly support")
+    variant("parallel", default=False, description="Enable additional parallel support")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-setuptools-scm", type="build")
+
+    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-morphio@3", type=("build", "run"))
+    depends_on("py-neurom@3", 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@0.12.0:", type=("build", "run"))
+
+    depends_on("py-plotly@4.1.0:", type=("build", "run"), when="+plot")
+    depends_on("py-dask+bag@2.19.0:", type=("build", "run"), when="+parallel")
+    depends_on("neuron+python@7.8:", type=("build", "run"), when="+nrn")
+    depends_on("py-bluepyopt@1.9.37:", type=("build", "run"), when="+nrn")
diff --git a/var/spack/repos/builtin/packages/py-morphio/package.py b/var/spack/repos/builtin/packages/py-morphio/package.py
new file mode 100644
index 0000000000..a5a9fee7de
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-morphio/package.py
@@ -0,0 +1,30 @@
+# 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)
+
+import sys
+
+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("master", branch="master", submodules=True)
+
+    version("3.3.6", sha256="0f2e55470d92a3d89f2141ae905ee104fd16257b93dafb90682d90171de2f4e6")
+
+    depends_on("py-setuptools@24.2:", 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=("build", "run"))
+    depends_on("py-h5py@3", when="platform=windows", type=("build", "run"))
+    if sys.platform != "win32":
+        depends_on("hdf5")
diff --git a/var/spack/repos/builtin/packages/py-neurom/package.py b/var/spack/repos/builtin/packages/py-neurom/package.py
new file mode 100644
index 0000000000..19bad5fc7b
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-neurom/package.py
@@ -0,0 +1,35 @@
+# 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 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("master", branch="master")
+    version("3.2.4", sha256="a584e0979b54deee906dd716ea90de20773e20b527d83960d0fe655b0905eb4a")
+
+    variant("plotly", default=False, description="Enable plotly support")
+
+    depends_on("py-setuptools@42:", type=("build", "run"))
+    depends_on("py-setuptools-scm", type="build")
+    depends_on("python@3.8:", type=("build", "run"))
+
+    depends_on("py-click@7.0:", type=("build", "run"))
+    depends_on("py-matplotlib@3.2.1:", type=("build", "run"))
+    depends_on("py-morphio@3.3.6:", type=("build", "run"))
+    depends_on("py-numpy@1.8.0:", type=("build", "run"))
+    depends_on("py-pandas@1.0.5:", type=("build", "run"))
+    depends_on("py-pyyaml@3.10:", type=("build", "run"))
+    depends_on("py-scipy@1.2.0:", type=("build", "run"))
+    depends_on("py-tqdm@4.8.4:", 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")