Update and fix py-meldmd (#35783)

* Update/fix py-meldmd; update openmm

* Restrict filter_file based on openmm version

* Updates based on Adam's feedback

* [@spackbot] updating style on behalf of meyersbs

* Break up long filter_file

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

---------

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

var/spack/repos/builtin/packages/openmm/package.py

@@ -3,8 +3,6 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
-import os
-
 from spack.package import *
 
 
@@ -49,8 +47,26 @@ def patch(self):
             "wrappers/python/CMakeLists.txt",
         )
 
+    def setup_build_environment(self, env):
+        spec = self.spec
+        if "+cuda" in spec:
+            env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc)
+            env.set("CUDA_HOST_COMPILER", self.compiler.cxx)
+
     def setup_run_environment(self, env):
         spec = self.spec
         if "+cuda" in spec:
             env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc)
-            env.prepend_path("PATH", os.path.dirname(self.compiler.cc))
+            env.set("CUDA_HOST_COMPILER", self.compiler.cxx)
+
+    def setup_dependent_run_environment(self, env, dependent_spec):
+        spec = self.spec
+        if "+cuda" in spec:
+            env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc)
+            env.set("CUDA_HOST_COMPILER", self.compiler.cxx)
+
+    def setup_dependent_build_environment(self, env, dependent_spec):
+        spec = self.spec
+        if "+cuda" in spec:
+            env.set("OPENMM_CUDA_COMPILER", self.spec["cuda"].prefix.bin.nvcc)
+            env.set("CUDA_HOST_COMPILER", self.compiler.cxx)

var/spack/repos/builtin/packages/py-meldmd/package.py

@@ -3,26 +3,84 @@
 #
 # SPDX-License-Identifier: (Apache-2.0 OR MIT)
 
+import os
+
 from spack.package import *
 
 
-class PyMeldmd(PythonPackage, CudaPackage):
+class PyMeldmd(CMakePackage, PythonExtension, CudaPackage):
     """MELD is a tool for inferring the structure of
     biomolecules from sparse, ambiguous, or noisy data."""
 
     homepage = "http://meldmd.org/"
     url = "https://github.com/maccallumlab/meld/archive/refs/tags/0.4.20.tar.gz"
 
+    version("0.6.1", sha256="aae8e5bfbdacc1e6de61768a3298314c51575cda477a511e98dc11f5730fd918")
     version("0.4.20", sha256="8c8d2b713f8dc0ecc137d19945b3957e12063c8dda569696e47c8820eeac6c92")
 
+    extends("python")
+
     depends_on("python@3.6:", type=("build", "run"))
     depends_on("py-setuptools", type="build")
     depends_on("amber")
-    depends_on("openmm")
+    depends_on("openmm+cuda")
     depends_on("py-netcdf4", type=("build", "run"))
-    depends_on("py-numpy", type=("build", "run"))
+    # Meld uses np.bool, deprecated in py-numpy@1.24.0
+    # https://numpy.org/devdocs/release/1.24.0-notes.html
+    depends_on("py-numpy@:1.23", type=("build", "run"))
     depends_on("py-scipy", type=("build", "run"))
     depends_on("py-scikit-learn", type=("build", "run"))
     depends_on("py-parmed", type=("build", "run"))
     depends_on("py-tqdm", type=("build", "run"))
     depends_on("py-mpi4py", type=("build", "run"))
+    depends_on("py-pip", type="build")
+
+    # C++ / CUDA
+    depends_on("eigen", type="link")
+    depends_on("swig@4.0", type="build")
+
+    def cmake_args(self):
+        args = []
+        args.append("-DOPENMM_DIR={0}".format(self.spec["openmm"].prefix))
+        return args
+
+    root_cmakelists_dir = "plugin"
+
+    @run_after("install")
+    def install_python(self):
+        args = std_pip_args + ["--prefix=" + prefix, "."]
+        pip(*args)
+        with working_dir(join_path(self.build_directory, "python")):
+            make("MeldPluginPatch")
+            pip(*args)
+        for _, _, files in os.walk(self.spec["openmm"].prefix.lib.plugins):
+            for f in files:
+                os.symlink(
+                    join_path(self.spec["openmm"].prefix.lib.plugins, f),
+                    join_path(self.prefix.lib.plugins, f),
+                )
+
+    def patch(self):
+        filter_file(
+            "# Compile the Python module.",
+            "# Compile the Python module.\n"
+            'add_custom_target(MeldPluginPatch DEPENDS "${WRAP_FILE}")',
+            "plugin/python/CMakeLists.txt",
+            string=True,
+        )
+        # Fixed, but not versioned yet:
+        # https://github.com/maccallumlab/meld/commit/afe4b0c199e3562d112af7825f8839e76067039c
+        filter_file(
+            "MAXFLOAT", "FLT_MAX", "plugin/platforms/cuda/src/kernels/computeMeld.cu", string=True
+        )
+        # API Change: https://github.com/openmm/openmm/releases/tag/7.6.0
+        if self.spec.satisfies("^openmm@7.6.0:"):
+            filter_file("simtk.openmm", "openmm", "plugin/python/meldplugin.i", string=True)
+
+    def setup_run_environment(self, env):
+        env.set("OPENMM_PLUGIN_DIR", self.prefix.lib.plugins)
+
+    @run_after("install")
+    @on_package_attributes(run_tests=True)
+    def install_test(self):
+        python("-m", "meld.test_install")