MUSIC wheel

* retrieve include dirs + MPI include dirs
* neuronmusic package
* handle rpath

Drop setup.py.in leftover

packaging/python/build_wheels.bash

@@ -60,7 +60,7 @@ pip_numpy_install() {
 
     # older version for apple m1 as building from source fails
     if [[ `uname -m` == 'arm64' ]]; then
-      numpy_ver="numpy==1.21.3"
+      numpy_ver="numpy==1.23.5"
     fi
 
     echo " - pip install $numpy_ver"
@@ -168,6 +168,9 @@ build_wheel_osx() {
         echo " - Python installation is universal2 and we are on arm64, setting _PYTHON_HOST_PLATFORM to: ${_PYTHON_HOST_PLATFORM}"
         export ARCHFLAGS="-arch arm64"
         echo " - Setting ARCHFLAGS to: ${ARCHFLAGS}"
+        # This is a shortcut to have a successful delocate-wheel. See:
+        # https://github.com/matthew-brett/delocate/issues/153
+        python -c "import os,delocate; print(os.path.join(os.path.dirname(delocate.__file__), 'tools.py'));quit()"  | xargs -I{} sed -i."" "s/first, /input.pop('i386',None); first, /g" {}
       else
         export _PYTHON_HOST_PLATFORM="${py_platform/universal2/x86_64}"
         echo " - Python installation is universal2 and we are on x84_64, setting _PYTHON_HOST_PLATFORM to: ${_PYTHON_HOST_PLATFORM}"

setup.py

@@ -174,7 +174,22 @@ def run(self, *args, **kw):
         the CMake building, sets the extension build environment and collects files.
         """
         for ext in self.extensions:
-
+            if ext.name == "neuronmusic" and not just_extensions:
+                # Since MUSIC is not a CMakeAugmentedExtension, we need to add the include_dirs manually
+                # Of interest are the include_dirs for the MPI library and the CMAKE_PREFIX_PATH
+                if self.cmake_prefix:
+                    ext.include_dirs += [
+                        os.path.join(inc_dir, "include")
+                        for inc_dir in self.cmake_prefix.split(";")
+                    ]
+                # Look for NRN_MPI_DYNAMIC in cmake_defs, split it and add to include_dirs
+                if self.cmake_defs:
+                    for cmake_def in self.cmake_defs.split(","):
+                        if cmake_def.startswith("NRN_MPI_DYNAMIC"):
+                            ext.include_dirs += cmake_def.split("=")[1].split(";")
+                            break
+
+                continue
             if isinstance(ext, CMakeAugmentedExtension):
                 if ext.cmake_done:
                     continue
@@ -382,7 +397,9 @@ def setup_package():
         "neuron.rxd",
         "neuron.crxd",
         "neuron.gui2",
-    ] + (["neuron.rxd.geometry3d"] if Components.RX3D else [])
+    ]
+    py_packages += ["neuron.rxd.geometry3d"] if Components.RX3D else []
+    #py_packages += ["neuronmusic"] if Components.MUSIC else []
 
     REL_RPATH = "@loader_path" if sys.platform[:6] == "darwin" else "$ORIGIN"
 
@@ -407,6 +424,8 @@ def setup_package():
     # Get extra_compile_args and  extra_link_args from environment variable
     extra_link_args = os.environ.get("LDFLAGS", "").split()
     extra_compile_args = os.environ.get("CFLAGS", "").split()
+    logging.info("CFLAGS %s" % str(extra_compile_args))
+    logging.info("LDFLAGS %s" % str(extra_link_args))
 
     extensions = [
         CMakeAugmentedExtension(
@@ -456,12 +475,21 @@ def setup_package():
     ]
 
     if Components.MUSIC:
+        music_libraries = ["nrniv"]
+        if not just_extensions:
+            music_libraries.append("nrnmusic")
         extensions += [
             CyExtension(
                 "neuronmusic",
                 ["src/neuronmusic/neuronmusic.pyx"],
+                libraries=music_libraries,
+                library_dirs=[os.path.join(cmake_build_dir, "lib")],
                 include_dirs=["src/nrnpython", "src/nrnmusic"],
-                **extension_common_params,
+                language="c++",
+                extra_link_args=extra_link_args
+                + ["-Wl,-rpath,{}{}".format(REL_RPATH, "/neuron/.data/lib/")]
+                if not just_extensions
+                else [],
             )
         ]
 

src/nrniv/CMakeLists.txt

@@ -458,9 +458,6 @@ if(NRN_ENABLE_MPI)
     if(NRN_ENABLE_MUSIC)
       # libnrnmusic does not depend explicitly on MPI so don't need mpi version specific versions.
       set(libnrnmusic "nrnmusic")
-      set(NRNMUSIC_DYNAM_LIB
-          "'${libnrnmusic}'"
-          PARENT_SCOPE)
       add_library(${libnrnmusic}_lib SHARED ${NRN_MUSIC_SRC_FILES})
       target_include_directories(${libnrnmusic}_lib BEFORE PUBLIC ${include})
       add_dependencies(${libnrnmusic}_lib nrniv_lib ${libname}_lib)

test/music_tests/runtests.py

@@ -25,6 +25,7 @@ def run(cmd):
     result = subprocess.run(cmd, shell=True, env=my_env, capture_output=True, text=True)
     if result.returncode != 0:
         print(result.stderr)
+        print(result.stdout)
     result.check_returncode()
     return result