diff --git a/packages/py-bluepyopt/package.py b/packages/py-bluepyopt/package.py
deleted file mode 100644
index 7c2b821b9c0da8a7a897eeb435a7e8a02b88a38a..0000000000000000000000000000000000000000
--- a/packages/py-bluepyopt/package.py
+++ /dev/null
@@ -1,45 +0,0 @@
-##############################################################################
-# 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)
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-libsonata/package.py b/packages/py-libsonata/package.py
deleted file mode 100644
index 6ac7d2105103dd1609b191e7de35477cbbd70470..0000000000000000000000000000000000000000
--- a/packages/py-libsonata/package.py
+++ /dev/null
@@ -1,35 +0,0 @@
-# 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:')
diff --git a/packages/py-pebble/package.py b/packages/py-pebble/package.py
deleted file mode 100644
index ab9ef132377410fe695ee9f603df530860e67054..0000000000000000000000000000000000000000
--- a/packages/py-pebble/package.py
+++ /dev/null
@@ -1,21 +0,0 @@
-# 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')
diff --git a/packages/py-pyswarms/package.py b/packages/py-pyswarms/package.py
deleted file mode 100644
index eb83ce579fc31b6af20764bcafaa74ee90e6ba10..0000000000000000000000000000000000000000
--- a/packages/py-pyswarms/package.py
+++ /dev/null
@@ -1,17 +0,0 @@
-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'))
diff --git a/packages/py-snudda/package.py b/packages/snudda/package.py
similarity index 74%
rename from packages/py-snudda/package.py
rename to packages/snudda/package.py
index fd31f40ea321998513e1e21c5f38963450829452..3ba55c98e191002241ea03f18b8a9792ed93c0b2 100644
--- a/packages/py-snudda/package.py
+++ b/packages/snudda/package.py
@@ -1,6 +1,6 @@
from spack import *
-class PySnudda(Package):
+class Snudda(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 PySnudda(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')) # got this from BlueBrainProject https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-bluepyopt
+ #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-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')) # got it from https://github.com/BlueBrain/spack/tree/develop/var/spack/repos/builtin/packages/py-libsonata
+ #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-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'))
+ #depends_on('pyswarms', type=('build','run')) - must package this
depends_on('py-setuptools', type=('build','run'))
depends_on('py-psutil', type=('build','run'))
depends_on('py-cython', type=('build','run'))
diff --git a/spack.yaml b/spack.yaml
index 123090250adbdbd5a5c3309045a8dc2c7a8ea572..4fd7d59500b01b29c8eca17fc2429dd6db1f70b7 100644
--- a/spack.yaml
+++ b/spack.yaml
@@ -52,7 +52,6 @@ spack:
- py-lfpy@2.2.6
- py-elephant
- py-frites
- - py-snudda
#- biobb-common
#- biobb-md
#- apbs