Add a `py-gmxapi` package. (#35738)

* Add a `py-gmxapi` package.

This package provides the Python package for the GROMACS
public API. The Python package is not strongly coupled to
a specific GROMACS _version_, but its compiled extension module
is strongly coupled to a specific GROMACS _installation_.

* Update conflict info.

In order to allow `^gromacs@2022.1` while rejecting `^gromacs@2022`,
we need to compare to `gromacs@2022.0`.

* Apply suggestions from code review

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

* Apply suggestions from code review.

* Simplify build system structure.
* Update dependencies for completeness.

* Update var/spack/repos/builtin/packages/py-gmxapi/package.py

Per code review, pretend gmxapi <0.4 doesn't exist, for simplicity.

* Update var/spack/repos/builtin/packages/py-gmxapi/package.py

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

* Update var/spack/repos/builtin/packages/py-gmxapi/package.py

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

---------

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

1 files changed, 48 insertions, 0 deletions

diff --git a/var/spack/repos/builtin/packages/py-gmxapi/package.py b/var/spack/repos/builtin/packages/py-gmxapi/package.py
new file mode 100644
index 0000000000..673693b518
--- /dev/null
+++ b/var/spack/repos/builtin/packages/py-gmxapi/package.py
@@ -0,0 +1,48 @@
+# 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)
+import os
+
+from spack.package import *
+
+
+class PyGmxapi(PythonPackage):
+    """Python bindings and ensemble workflow management for GROMACS.
+
+    The GROMACS C++ API is affected by its package variants. You can
+    specify a particular GROMACS API by making the dependency variant explicit.
+    E.g. ``spack install gmxapi ^gromacs+mpi~double``
+    """
+
+    homepage = "https://manual.gromacs.org/current/gmxapi/index.html"
+    maintainers("eirrgang", "peterkasson")
+
+    pypi = "gmxapi/gmxapi-0.4.0.tar.gz"
+    version("0.4.0", sha256="7fd58e6a4b1391043379e8ba55555ebeba255c5b394f5df9d676e6a5571d7eba")
+
+    depends_on("gromacs@2022.1:~mdrun_only+shared")
+    depends_on("mpi")
+    depends_on("py-cmake@3.16:", type="build")
+    depends_on("py-importlib-metadata", type="test", when="^python@:3.7")
+    depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("py-networkx@2.0:", type=("build", "run"))
+    depends_on("py-numpy@1.8:", type=("build", "run"))
+    depends_on("py-setuptools@42:", type="build")
+    depends_on("py-packaging", type=("build", "run"))
+    depends_on("py-pybind11@2.6:", type=("build", "run"))
+    depends_on("py-pytest@4.6:", type="test")
+    depends_on("py-wheel", type="build")
+
+    def setup_build_environment(self, env):
+        env.set("GROMACS_DIR", self.spec["gromacs"].prefix)
+        env.set("gmxapi_ROOT", self.spec["gromacs"].prefix)
+        env.set("Python3_ROOT", self.spec["python"].home)
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        with working_dir("spack-test", create=True):
+            # test include helper points to right location
+            python = self.spec["python"].command
+            python("-m", "pytest", "-x", os.path.join(self.build_directory, "test"))