diff --git a/packages/py-sbi/package.py b/packages/py-sbi/package.py new file mode 100644 index 0000000000000000000000000000000000000000..a560cd93431e33171296d3d6019fb1c4eade6851 --- /dev/null +++ b/packages/py-sbi/package.py @@ -0,0 +1,46 @@ +# Copyright 2013-2024 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 PySbi(PythonPackage): + """Python package for simulating biological systems.""" + + homepage = "https://sbi-dev.github.io/sbi/v0.23.3/" + url = "https://github.com/sbi-dev/sbi/archive/refs/tags/v0.23.3.tar.gz" + + version("0.23.3", "b1ef102e47c90088f2adfff5ea88b18421e84c4641ff4dd4f68c1116c296ba81") + + depends_on("python@3.9:", type=("build", "run")) + depends_on("py-setuptools", type="build") + depends_on("py-wheel", type="build") + + depends_on("py-arviz", type=("build", "run")) + depends_on("py-joblib@1.3.0:", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-notebook@:6.4.12", type=("build", "run")) + depends_on("py-numpy@:1", type=("build", "run")) + depends_on("py-pillow", type=("build", "run")) + depends_on("py-pyknos@0.16.0:", type=("build", "run")) + depends_on("py-pyro-ppl@1.3.1:", type=("build", "run")) + depends_on("py-scikit-learn", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-tensorboard", type=("build", "run")) + depends_on("py-torch@1.13.0:", type=("build", "run")) + depends_on("py-tqdm", type=("build", "run")) + depends_on("py-pymc@5.0.0:", type=("build", "run")) + depends_on("py-zuko@1.2.0:", type=("build", "run")) + + depends_on("py-pytest", type="test") + depends_on("py-torchtestcase", type="test") + + skip_modules = ["sbi.inference.snle", "sbi.inference.snpe", "sbi.inference.snre", "sbi.samplers.score", "sbi.samplers.vi"] + + @run_after("install") + @on_package_attributes(run_tests=True) + def install_test(self): + pytest = which("pytest") + pytest("-m", "not slow and not gpu") diff --git a/packages/py-vbi/package.py b/packages/py-vbi/package.py new file mode 100644 index 0000000000000000000000000000000000000000..ba2cbebbfaf174642ab2a5f6ceec614b679aba46 --- /dev/null +++ b/packages/py-vbi/package.py @@ -0,0 +1,43 @@ +# Copyright 2013-2024 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 PyVbi(PythonPackage): + + homepage = "https://vbi.readthedocs.io/latest/" + git = "https://github.com/ins-amu/vbi" + url = "https://github.com/ins-amu/vbi/archive/refs/tags/v0.1.3.tar.gz" + + version("0.1.3", "54fa2062f44c9ec8219fae3c13c52a4bd17141b5467b982987673de0662c5255") + version("0.1.2", "6ccfeeec718be62a480002a8370130a3e3344955186f99ecbb15b646b68210d6") + + depends_on("python@3.8:", type=("build","run")) + depends_on("py-setuptools", type="build") + depends_on("py-setuptools-scm", type="build") + depends_on("py-wheel", type="build") + depends_on("swig@4:", type="build") + depends_on("py-numpy", type=("build", "run")) + depends_on("py-scipy", type=("build", "run")) + depends_on("py-numba", type=("build", "run")) + depends_on("py-h5py", type=("build", "run")) + depends_on("py-pandas", type=("build", "run")) + depends_on("py-networkx", type=("build", "run")) + depends_on("py-nbconvert", type=("build", "run")) + depends_on("py-matplotlib", type=("build", "run")) + depends_on("py-tqdm", type=("build", "run")) + depends_on("py-sbi", type=("build", "run")) + depends_on("py-torch", type=("build", "run")) + depends_on("py-parameterized", type=("build", "run")) + depends_on("py-scikit-learn", type=("build", "run")) + depends_on("py-pycatch22", type=("build", "run")) + depends_on("py-pytest", type="test") + + @run_after("install") + @on_package_attributes(run_tests=True) + def install_test(self): + pytest = which("pytest") + pytest() diff --git a/spack.yaml b/spack.yaml index 055df0879fbce725996423b48ced4da122525368..b4322538a7b7260ddd215d34dcb7f2f35c813b0c 100644 --- a/spack.yaml +++ b/spack.yaml @@ -56,6 +56,7 @@ spack: - py-tvb-ext-unicore - py-tvb-ext-xircuits@1.1.0 - py-viziphant@0.4.0 + - py-vbi - pynn-brainscales@9.0-a8 - r-rgsl@0.1.1 - r-sbtabvfgen@0.1