Merge branch 'add-snudda' into 'master'

(fix) Add snudda dependencies from BlueBrainProject repo and activate

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!116

packages/py-bluepyopt/package.py

+##############################################################################
+# 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 *
+
+
+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('1.10.38', 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-pandas', type='run')
+    depends_on('py-numpy', type='run')
+    depends_on('py-efel', type='run')
+    depends_on('py-deap', type='run')
+    depends_on('py-scoop@0.7:', type='run', when='@:1.9.37')
+    depends_on('py-ipyparallel', type='run')
+    depends_on('py-pickleshare', type='run')
+    depends_on('py-future', type='run')
+    depends_on('py-jinja2', type='run')
+    depends_on('py-pebble@4.3.10:', type='run')
+    depends_on('neuron', type='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)

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-libsonata/package.py

+# 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 *
+
+
+class PyLibsonata(PythonPackage):
+    """SONATA files reader"""
+
+    homepage = "https://github.com/BlueBrain/libsonata"
+    git = "https://github.com/BlueBrain/libsonata.git"
+
+    version('develop', branch='master', submodules=True, get_full_repo=True)
+    version('0.1.12', tag='v0.1.12', submodules=True, get_full_repo=True)
+    version('0.1.11', tag='v0.1.11', submodules=True, get_full_repo=True)
+    version('0.1.10', tag='v0.1.10', submodules=True, get_full_repo=True)
+    # Important: v0.1.9 is not Spack-compatible (use v0.1.10: instead)
+    # version('0.1.9', tag='v0.1.9', submodules=True, get_full_repo=True)
+    version('0.1.8', tag='v0.1.8', submodules=True, get_full_repo=True)
+    version('0.1.6', tag='v0.1.6', submodules=True, get_full_repo=True)
+    version('0.1.5', tag='v0.1.5', submodules=True, get_full_repo=True)
+    version('0.1.4', tag='v0.1.4', submodules=True, get_full_repo=True)
+    version('0.1.3', tag='v0.1.3', submodules=True, get_full_repo=True)
+    version('0.1.0', tag='v0.1.0', submodules=True, get_full_repo=True)
+    version('0.0.3', tag='v0.0.3', submodules=True)
+
+    depends_on('cmake@3.3:', type='build')
+    depends_on('hdf5')
+    depends_on('py-pybind11')
+
+    depends_on('py-numpy@1.12:', type=('build', 'run'))
+    depends_on('py-setuptools', type='build', when='@0.1:')
+    depends_on('py-setuptools-scm', type='build', when='@0.1:')

packages/py-pebble/package.py

+# 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 *
+
+
+class PyPebble(PythonPackage):
+    """Python API to manage threads and processes within an application."""
+
+    homepage = "https://github.com/noxdafox/pebble"
+    pypi = "pebble/Pebble-4.5.0.tar.gz"
+    git = "https://github.com/noxdafox/pebble.git"
+
+    version('4.5.0', sha256='2de3cd11aa068e0c4a4abbaf8d4ecfdac409d8bfb78a4c211a01f6a4fb17a35f')
+    version('4.4.1', sha256='7c4d68a3479140cba74d7454d8190e2cb1a93213b44b5befe3c53c201beb8317')
+    version('4.3.10', sha256='c39a7bf99af6525fcf0783a8859fb10a4f20f4f988ddb66fd6fa7588f9c91731')
+
+    depends_on('py-setuptools', type=('build', 'run'))
+    depends_on('py-futures', type='run', when='^python@:2.9.9')

packages/py-pyswarms/package.py

+from spack import *
+
+
+class PyPyswarms(PythonPackage):
+
+    homepage = "https://github.com/ljvmiranda921/pyswarms"
+    pypi = "pyswarms/pyswarms-1.3.0.tar.gz"
+
+    version('1.3.0', sha256='1204aa9c332c662113e3c37d1b109906f4a0859b29ded80c1582dc66387ce34b') 
+
+    depends_on('py-scipy',	type=('build', 'run'))
+    depends_on('py-numpy',	type=('build', 'run'))
+    depends_on('py-matplotlib@1.3.1:',	type=('build', 'run'))
+    depends_on('py-attrs',	type=('build', 'run'))
+    depends_on('py-tqdm',	type=('build', 'run'))
+    depends_on('py-future',	type=('build', 'run'))
+    depends_on('py-pyyaml',	type=('build', 'run'))

packages/snudda/package.py → packages/py-snudda/package.py

 from spack import *
 
-class Snudda(Package):
+class PySnudda(Package):
     homepage = 'https://pypi.org/project/snudda/'
     url      = 'https://pypi.org/packages/source/s/snudda/snudda-1.2.9-py3-none-any.whl'
     list_url = 'https://pypi.org/simple/snudda/'
@@ -12,19 +12,19 @@ class Snudda(Package):
     depends_on('python@3.8:', type=('build','run'))
     depends_on('py-pip', type='build')
     depends_on('unzip', type='build')
-    #depends_on('py-bluepyopt', type=('build','run')) must get this from BlueBrainProject https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-bluepyopt
+    depends_on('py-bluepyopt', type=('build','run')) # got this from BlueBrainProject https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-bluepyopt
     depends_on('py-h5py', type=('build','run'))
     depends_on('py-ipyparallel', type=('build','run'))
     depends_on('py-matplotlib', type=('build','run'))
     depends_on('py-mpi4py', type=('build','run'))
     depends_on('py-numpy', type=('build','run'))
     depends_on('py-scipy', type=('build','run'))
-    #depends_on('py-libsonata', type=('build','run')) - get it from https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-libsonata
+    depends_on('py-libsonata', type=('build','run')) # got it from https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-libsonata
     depends_on('py-pyzmq', type=('build','run'))
     depends_on('py-numexpr', type=('build','run'))
     depends_on('py-argparse', type=('build','run'))
     depends_on('neuron', type=('build','run'))
-    #depends_on('pyswarms', type=('build','run')) - must package this
+    depends_on('py-pyswarms', type=('build','run'))
     depends_on('py-setuptools', type=('build','run'))
     depends_on('py-psutil', type=('build','run'))
     depends_on('py-cython', type=('build','run'))

spack.yaml

@@ -52,6 +52,7 @@ spack:
     - py-lfpy@2.2.6
     - py-elephant
     - py-frites
+    - py-snudda
     #- biobb-common
     #- biobb-md
     #- apbs