py-amici, py-python-libsbml: new packages (#35532)

* py-amici, py-python-libsbml: new packages

* Apply suggestions from code review

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

* Swig and cmake are build-only dependencies

* cmake as a run dependency after all

* py-amici: default boost and hdf5 variants to True

---------

Co-authored-by: Adam J. Stewart <ajstewart426@gmail.com>

2 files changed, 68 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-amici/package.py b/var/spack/repos/builtin/packages/py-amici/package.py
new file mode 100644
index 0000000000..ffa03c928f
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-amici/package.py
@@ -0,0 +1,45 @@
+# 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 PyAmici(PythonPackage):
+    """Advanced Multilanguage Interface for CVODES and IDAS"""
+
+    homepage = "https://github.com/AMICI-dev/AMICI"
+    pypi = "amici/amici-0.11.28.tar.gz"
+
+    version("0.16.0", sha256="1a2d6633ec34241d8d8b496d18d4318482cffe125e9ddf3ca6cac5d36d235f38")
+    version("0.11.28", sha256="a8ddda70d8ebdc40600b4ad2ea02eb26e765ca0e594b957f61866b8c84255d5b")
+
+    variant("boost", default=True, description="Enable boost support")
+    variant("hdf5", default=True, description="Enable HDF5 support")
+
+    depends_on("py-setuptools@48:", type=("build", "run"))
+
+    depends_on("blas", type=("build", "run"))
+    depends_on("boost", when="+boost", type=("build", "run"))
+    depends_on("hdf5", when="+hdf5", type=("build", "run"))
+    depends_on("swig@3.0:", type=("build", "run"))
+
+    depends_on("python@3.8:", type=("build", "run"))
+    depends_on("py-sympy@1.9:", type=("build", "run"))
+    depends_on("py-numpy@1.17.5:", when="^python@3.8", type=("build", "run"))
+    depends_on("py-numpy@1.19.3:", when="^python@3.9", type=("build", "run"))
+    depends_on("py-numpy@1.21.4:", when="^python@3.10:", type=("build", "run"))
+    depends_on("py-python-libsbml", type=("build", "run"))
+    depends_on("py-h5py", type=("build", "run"))
+    depends_on("py-pandas", type=("build", "run"))
+    depends_on("py-pkgconfig", type=("build", "run"))
+    depends_on("py-wurlitzer", type=("build", "run"))
+    depends_on("py-toposort", type=("build", "run"))
+    depends_on("py-mpmath", when="@0.16.0:", type=("build", "run"))
+
+    def setup_run_environment(self, env):
+        env.set("BLAS_LIBS", " ".join(self.spec["blas"].libs))
+
+    def setup_build_environment(self, env):
+        env.set("BLAS_LIBS", " ".join(self.spec["blas"].libs))
diff --git a/var/spack/repos/builtin/packages/py-python-libsbml/package.py b/var/spack/repos/builtin/packages/py-python-libsbml/package.py
new file mode 100644
index 0000000000..ac47367362
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-python-libsbml/package.py
@@ -0,0 +1,23 @@
+# 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 PyPythonLibsbml(PythonPackage):
+    """LibSBML is a library for reading, writing and manipulating the Systems Biology
+    Markup Language (SBML)."""
+
+    homepage = "https://sbml.org/"
+    git = "https://github.com/sbmlteam/python-libsbml.git"
+    pypi = "python-libsbml/python-libsbml-5.19.7.tar.gz"
+
+    version("5.19.7", sha256="447b1fde7aceccd11a93dc9f589ffd9319ba854d7b7583f911259a8b0127ab7b")
+    version("5.19.5", tag="v5.19.5", submodules=True)
+
+    depends_on("py-setuptools", type="build")
+
+    depends_on("swig", type="build")
+    depends_on("cmake", type=("build", "run"))