py-multiscale-run: new Python package for BBP multiscale simulation

bluebrain/deployment/environments/applications_science.yaml

@@ -14,6 +14,7 @@ spack:
           - py-bluepyopt
           - py-bluepyparallel
           - py-connectome-manipulator
+          - py-multiscale-run
           - py-efel
           - py-synthesis-workflow
           - py-visual-cortex-analysis
@@ -47,5 +48,6 @@ spack:
     - py-bluepyparallel
     - py-connectome-manipulator+convert
     - py-efel
+    - py-multiscale-run
     - py-synthesis-workflow
     - py-visual-cortex-analysis

bluebrain/repo-bluebrain/packages/py-astrovascpy/package.py

@@ -13,12 +13,11 @@ class PyAstrovascpy(PythonPackage):
     """
 
     homepage = "https://github.com/BlueBrain/AstroVascPy"
-
-    url = "https://github.com/BlueBrain/AstroVascPy/releases/tag/0.1"
+    git = "https://github.com/BlueBrain/AstroVascPy.git"
 
     maintainers("tristan0x")
 
-    version("0.1", sha256="1e9b2036e9c1ce4cb0650612c0be2e7e7b142754e1550dfbfb0b757cee4f8bdd")
+    version("0.1.2", tag="0.1.2")
 
     variant("vtk", default=False, description="add VTK support (mainly for visualization)")
 

bluebrain/repo-bluebrain/packages/py-juliacall/package.py

@@ -0,0 +1,22 @@
+# Copyright 2013-2022 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 PyJuliacall(PythonPackage):
+    """Python and Julia in harmony."""
+
+    homepage = "https://github.com/JuliaPy/PythonCall.jl"
+    pypi = "juliacall/juliacall-0.9.15.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("0.9.15", sha256="08163ae1290dda155cdabdccc4035a4cf0c8e361522a5b3f8e6532401b4f29cc")
+
+    depends_on("py-wheel", type="build")
+
+    depends_on("py-setuptools@42:", type="build")
+    depends_on("[email protected]:,:0.2", type=["build", "run"])

bluebrain/repo-bluebrain/packages/py-juliapkg/package.py

@@ -0,0 +1,20 @@
+# Copyright 2013-2022 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 PyJuliapkg(PythonPackage):
+    """Manage your Julia dependencies from Python"""
+
+    homepage = "https://github.com/JuliaPy/pyjuliapkg"
+    pypi = "juliapkg/juliapkg-0.1.10.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("0.1.10", sha256="70507318d51ac8663e856f56048764e49f5a0c4c90d81a3712d039a316369505")
+
+    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-semantic-version", type=("build", "run"))

bluebrain/repo-bluebrain/packages/py-multiscale-run/package.py

@@ -0,0 +1,46 @@
+# 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 PyMultiscaleRun(PythonPackage):
+    """BBP multiscale simulation orchestrator"""
+
+    homepage = "https://bbpgitlab.epfl.ch/-/ide/project/molsys/multiscale_run"
+    git = "ssh://[email protected]/molsys/multiscale_run.git"
+
+    maintainers("tristan0x")
+
+    version("develop", branch="main")
+    version("0.1", tag="0.1")
+
+    depends_on("py-setuptools", type=("build", "run"))
+    depends_on("py-setuptools-scm", type=("build", "run"))
+
+    depends_on("gmsh", type=("build", "run"))
+    depends_on("julia", type=("build", "run"))
+    depends_on("neurodamus-neocortex+ngv+metabolism~~coreneuron", type=("build", "run"))
+    depends_on("py-astrovascpy", type=("build", "run"))
+    depends_on("py-bluepysnap", type=("build", "run"))
+    depends_on("[email protected]", type=("build", "run"))
+    depends_on("py-jinja2", type=("build", "run"))
+    depends_on("py-julia", type=("build", "run"))
+    depends_on("py-libsonata", type=("build", "run"))
+    depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("py-numpy", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-psutil", type=("build", "run"))
+    depends_on("py-pyyaml", type=("build", "run"))
+    depends_on("py-scipy", type=("build", "run"))
+    depends_on("py-tqdm", type=("build", "run"))
+    depends_on("steps@5:", type=("build", "run"))
+
+    depends_on("py-pytest", type="test")
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def test_install(self):
+        python("-m", "pytest", "tests/pytests")

bluebrain/repo-bluebrain/packages/py-python-gnupg/package.py

@@ -0,0 +1,21 @@
+# 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 PyPythonGnupg(PythonPackage):
+    """A Python API for GNU Privacy Guard"""
+
+    homepage = "https://github.com/vsajip/python-gnupg"
+    pypi = "python-gnupg/python-gnupg-0.5.1.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("0.5.1", sha256="5674bad4e93876c0b0d3197e314d7f942d39018bf31e2b833f6788a6813c3fb8")
+
+    depends_on("[email protected]:", type=("build"))
+
+    depends_on("py-setuptools", type="build")

bluebrain/repo-patches/packages/py-diffeqpy/package.py

@@ -0,0 +1,25 @@
+# Copyright 2013-2022 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 PyDiffeqpy(PythonPackage):
+    """Solving differential equations in Python using DifferentialEquations.jl
+    and the SciML Scientific Machine Learning organization"""
+
+    homepage = "https://github.com/SciML/diffeqpy"
+    pypi = "diffeqpy/diffeqpy-2.3.0.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("2.3.0", sha256="14d31321a5463a706733cc137d04e5bcf5cc22d44b6a44958ecd9972752041a1")
+    version("1.1.0", sha256="0ff315bf3d4345a83dc623b614e39c8365302df1cc9d36dcb8ce782d926f255b")
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("py-jill", when="@2:", type=("build", "run"))
+    depends_on("py-juliacall", when="@2:", type=("build", "run"))
+    depends_on("py-julia", when="@:2", type=("build", "run"))

bluebrain/repo-patches/packages/py-jill/package.py

@@ -0,0 +1,28 @@
+# Copyright 2013-2022 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 PyJill(PythonPackage):
+    """Julia Installer for Linux (and every other platform)"""
+
+    homepage = "https://github.com/johnnychen94/jill.py"
+    pypi = "jill/jill-0.11.1.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("0.11.1", sha256="fbfac07da3892672d09c489cf3be5d31ae38ac22b68ea49b147dbe79e339021b")
+
+    depends_on("py-setuptools", type="build")
+    depends_on("py-poetry-core", type="build")
+
+    depends_on("py-fire", type=("build", "run"))
+    depends_on("py-jsonschema", type=("build", "run"))
+    depends_on("py-python-gnupg", type=("build", "run"))
+    depends_on("py-requests", type=("build", "run"))
+    depends_on("py-requests-futures", type=("build", "run"))
+    depends_on("py-semantic-version", type=("build", "run"))
+    depends_on("py-wget", type=("build", "run"))

bluebrain/repo-patches/packages/py-julia/package.py

@@ -0,0 +1,23 @@
+# Copyright 2013-2022 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 PyJulia(PythonPackage):
+    """python interface to julia"""
+
+    homepage = "https://github.com/JuliaPy/pyjulia"
+    pypi = "julia/julia-0.6.1.tar.gz"
+
+    maintainers("tristan0x")
+
+    version("0.6.1", sha256="dbada3b47cb14b3e1893dae8339053e014cf09f8158f408b6a129ca4dfca1f61")
+
+    depends_on("[email protected]:", type=("build", "run"))
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("julia", type=("build", "run"))