Merge branch 'master' into 'master'

Add py-tvb-multiscale

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!371

packages/py-annarchy/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 PyAnnarchy(PythonPackage):
+    """
+    ANNarchy (Artificial Neural Networks architect) is a neural simulator designed
+    for distributed rate-coded or spiking neural networks.
+    """
+
+    homepage = "https://annarchy.readthedocs.io/en/latest/"
+    pypi = 'ANNarchy/ANNarchy-4.7.2.5.tar.gz'
+
+    maintainers = ['dionperd', 'paulapopa', "ldomide"]
+
+    version('4.7.2.5', 'b7ef91cc4415e078e386eb30e595922c9f0ef90ad1340a12dc5ca46e728a7bb2')
+
+    # python_requires
+    depends_on('python@3.8:3.10', type=('build', 'run'))
+
+    # setup_requires
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type='build')  # >= 40.0
+
+    # install_requires
+    # TODO: Find package for g++ >= 6.1 ( >= 7.4 recommended )
+    depends_on("cmake", type=('build', 'run'))  # TODO: Find out if this will install make >= 3.0
+    depends_on('py-numpy', type=('build', 'run'))  # >= 1.13
+    depends_on('py-scipy', type=('build', 'run'))  # >= 0.19
+    depends_on('py-sympy', type=('build', 'run'))  # >= 1.6
+    depends_on('py-matplotlib', type=('build', 'run'))  # >= 2.0
+    depends_on('py-cython', type=('build', 'run'))  # >= 0.20
+
+    # Highly recommended:
+    # pyqtgraph >= 0.9.8 (to visualize some of the provided examples. The OpenGL backend can also be needed)
+    depends_on('py-lxml', type=('build', 'run'))  # lxml >= 3.0 (to save the networks in .xml format)
+    # pandoc >= 2.0 (for reporting):
+    # https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/pango/package.py
+    depends_on('pandoc', type=('build', 'run'))
+    # tensorboardX (for the logging extension):
+    # https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-tensorboardx/package.py
+    depends_on('py-tensorboardx', type=('build', 'run'))
+
+    # Test dependency
+    depends_on('py-pytest@:7.1', type='test')
+
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        pytest = which('pytest')
+        pytest()

packages/py-pyspike/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 PyPyspike(PythonPackage):
+    """
+    PySpike is a Python library for the numerical analysis of spike train similarity.
+    """
+
+    homepage = "https://github.com/mariomulansky/PySpike"
+    pypi = 'pyspike/pyspike-0.7.0.tar.gz'
+
+    maintainers = ['dionperd', 'paulapopa', "ldomide"]
+
+    version('0.7.0', 'a5d1c1472d3e7c3ac85c8a4ce069d750cca02acf18f185677b29c0a757e78efe')
+
+    # python_requires
+    depends_on('python@3.8:3.10', type=('build', 'run'))
+
+    # setup_requires
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type=('build'))
+
+    # install_requires
+    depends_on('py-numpy', type=('build', 'run'))
+    depends_on('py-scipy', type=('build', 'run'))
+    depends_on('py-matplotlib', type=('build', 'run'))
+    depends_on('py-pytest', type=('build', 'run'))
+    depends_on('py-cython', type=('build', 'run'))
+
+    # Test dependency
+    depends_on('py-pytest@:7.1', type='test')
+    
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        pytest = which('pytest')
+        pytest()

packages/py-tvb-contrib/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 PyTvbContrib(PythonPackage):
+    """
+    Various auxiliary scripts used with TVB.
+    """
+
+    homepage = "https://www.thevirtualbrain.org/"
+    pypi = 'tvb-contrib/tvb-contrib-2.8.1.tar.gz'
+
+    maintainers = ['dionperd', 'paulapopa', "ldomide"]
+
+    version('2.8.1', '0b9bc5f837913f1cba007d25ae94c9df51bf43bf19c9fb2af14a90cb6a1e1a66')
+
+    # python_requires
+    depends_on('python@3.8:3.10', type=('build', 'run'))
+
+    # setup_requires
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type='build')
+
+    # install_requires
+    depends_on('py-tvb-library', type=('build', 'run'))
+    depends_on('py-xarray', type=('build', 'run'))
+    depends_on('py-scikit-learn', type=('build', 'run'))
+
+    # py-dill:
+    # https://github.com/spack/spack/blob/develop/var/spack/repos/builtin/packages/py-dill/package.py
+    depends_on('py-dill', type=('build', 'run'))
+
+    # Test dependency
+    depends_on('py-pytest@:7.1', type='test')
+    
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+       pytest = which('pytest')
+       pytest()
+    

packages/py-tvb-multiscale/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 PyTvbMultiscale(PythonPackage):
+    """
+    Toolbox for Co-Simulation of TVB with NEST, NetPyNE and ANNarchy.
+    """
+
+    homepage = "https://github.com/the-virtual-brain/tvb-multiscale"
+    # url = "https://github.com/the-virtual-brain/tvb-multiscale/archive/refs/tags/2.0.2.tar.gz"
+    url = "https://github.com/the-virtual-brain/tvb-multiscale/archive/refs/tags/2.0.3.dev.tar.gz"
+
+    maintainers = ['dionperd', 'paulapopa', "ldomide"]
+
+    # version('2.0.2', sha256='647079e649225c7e9029bea9485872836a6dfe027a29718413e1e9e00255f4e6')
+    version('2.0.3.dev', sha256='3763c709ccb554a4bb1a38350a8137e2287e4859ef5cd13ca744db3351ab0def')
+
+    # python_requires
+    depends_on('python@3.8:3.10', type=('build', 'run'))
+
+    # setup_requires
+    depends_on('py-pip', type='build')
+    depends_on('py-setuptools', type='build')
+
+    # install_requires
+    depends_on('py-tvb-framework', type=('build', 'run'))
+    depends_on('py-tvb-contrib', type=('build', 'run'))
+    depends_on('nest', type=('build', 'run'))
+    depends_on('py-netpyne', type=('build', 'run'))
+    depends_on('py-annarchy', type=('build', 'run'))  # TODO!
+    depends_on('py-nestml', type=('build', 'run'))
+    depends_on('py-elephant', type=('build', 'run'))
+    depends_on('py-pyspike', type=('build', 'run'))
+
+    # Test dependency
+    depends_on('py-pytest@:7.1', type='test')
+    
+    @run_after('install')
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        pytest = which('pytest')
+        pytest('tvb_multiscale/tests')

spack.yaml

@@ -45,10 +45,12 @@ spack:
     - py-siibra@0.4a57
     - py-snudda@1.4.71
     - py-spynnaker@7.0.0
+    - py-tvb-contrib@2.8.1
     - py-tvb-data@2.7
     - py-tvb-framework@2.8.1.1
     - py-tvb-gdist@2.2
     - py-tvb-library@2.8.1
+    - py-tvb-multiscale@2.0.3.dev
     - py-tvb-storage@2.8.1
     - py-viziphant@0.3.0
     - pynn-brainscales@6.0-rc2