Adapt dune-geometry to overhaul of the Python-CMake interface

added missing 'include_package_data' to setup.py.in

improve on ci

add clang test

pep 42: use implicit namespace packages which make it possible to combine subpackages using editable (source) and non editable (pypi)

only use a cmake install a python module in the SKBUILD setting - for an install from build dir pip will take take of this since it is part of the setup.py file

add a stopgap solution unti ci repo up and running again

Update requirements in setup.py.in to include dune packages

[testing]

only add dune modules that have been found as requirements in setup.py.in

removed setup.py.in since the default is provided in dune-common

adapt ci yml file to python bindings on by default

disable python bindings for clang 5 (ubuntu 18) since no numpy matching numpy version can be installed from the gitlab registry

[testing]

.gitlab-ci.yml

@@ -11,22 +11,30 @@ before_script:
   - . /duneci/bin/duneci-init-job
   - duneci-install-module https://gitlab.dune-project.org/core/dune-common.git
 
-debian-11-gcc-9-17-python:
-  image: registry.dune-project.org/docker/ci/debian:11
+ubuntu-20.04-clang-10-20-nobindings:
+  image: registry.dune-project.org/docker/ci/ubuntu:20.04
   script: duneci-standard-test
+  stage: test
   variables:
-    DUNECI_TOOLCHAIN:   gcc-9-17
-    # so we need some variables to build the dune-py module during execution of the first python test:
-    # we need to find the dune mdoule
-    DUNE_CONTROL_PATH:  /duneci/modules:$CI_PROJECT_DIR
-    # the position for the dune-py module
-    DUNE_PY_DIR:        /duneci/modules/dune-py
-    DUNE_LOG_LEVEL:     DEBUG
-    # during dune-py build this variable is used - do know a way to access
-    # the CMAKE_FLAGS used to build the modules...
-    DUNE_CMAKE_FLAGS:   "-DCMAKE_CXX_COMPILER=g++-9 -DCMAKE_C_COMPILER=gcc-9 -DCMAKE_CXX_FLAGS='-std=c++17 -O2 -g -Wall -fdiagnostics-color=always' -DDUNE_ENABLE_PYTHONBINDINGS=ON -DDUNE_MAX_TEST_CORES=4 -DBUILD_SHARED_LIBS=TRUE -DDUNE_PYTHON_INSTALL_LOCATION=none -DCMAKE_POSITION_INDEPENDENT_CODE=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_LATEX=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Alberta=TRUE -DCMAKE_DISABLE_FIND_PACKAGE_Vc=TRUE -DCMAKE_DISABLE_DOCUMENTATION=TRUE"
-    # cmake flags we use for all dune moudle - important is that build shared libs is set (need some better way of doing this)
-    DUNECI_CMAKE_FLAGS: $DUNE_CMAKE_FLAGS
-    # finally set the python path to all modules
-    PYTHONPATH:         /duneci/modules/dune-common/build-cmake/python:$CI_PROJECT_DIR/build-cmake/python
+    DUNECI_TOOLCHAIN: clang-10-20
+    DUNECI_CMAKE_FLAGS: '-DDUNE_ENABLE_PYTHONBINDINGS=ON'
+  tags: [duneci]
+
+# no numpy version available for this image on the gitlab registry
+# disable python bindings for now
+ubuntu:18.04 clang-6-17:
+  image: registry.dune-project.org/docker/ci/ubuntu:18.04
+  script: duneci-standard-test
+  stage: test
+  variables:
+    DUNECI_TOOLCHAIN: clang-6-17
+    DUNECI_CMAKE_FLAGS: "-DDUNE_ENABLE_PYTHONBINDINGS=OFF"
+  tags: [duneci]
+ubuntu:18.04 clang-5-17:
+  image: registry.dune-project.org/docker/ci/ubuntu:18.04
+  script: duneci-standard-test
+  stage: test
+  variables:
+    DUNECI_TOOLCHAIN: clang-5-17
+    DUNECI_CMAKE_FLAGS: "-DDUNE_ENABLE_PYTHONBINDINGS=OFF"
   tags: [duneci]

CMakeLists.txt

@@ -27,7 +27,6 @@ add_subdirectory("lib")
 # if Python bindings are enabled, include necessary sub directories.
 if( DUNE_ENABLE_PYTHONBINDINGS )
   add_subdirectory("python")
-  dune_python_install_package(PATH python)
 endif()
 
 # finalize the dune project, e.g. generating config.h etc.

pyproject.toml

 [build-system]
-requires = ['setuptools', 'wheel', 'scikit-build', 'cmake', 'ninja', 'requests', 'dune-common>=2.8.0.dev0']
+requires = ['dune-common>=2.8.0.dev0', 'pip', 'setuptools', 'wheel', 'scikit-build', 'cmake', 'ninja', 'requests']
 build-backend = 'setuptools.build_meta'

python/CMakeLists.txt

 add_subdirectory(dune)
 
-configure_file(setup.py.in setup.py)
+dune_python_install_package(
+  PATH "."
+  CMAKE_METADATA_FILE dune/geometry/metadata.cmake
+  DEPENDS _geometry
+)

python/dune/CMakeLists.txt

 add_subdirectory(geometry)
-add_python_targets(dune
-  __init__
-)

python/dune/__init__.py

-__import__('pkg_resources').declare_namespace(__name__)

python/dune/geometry/CMakeLists.txt

@@ -5,4 +5,6 @@ add_python_targets(geometry
 )
 dune_add_pybind11_module(NAME _geometry)
 set_property(TARGET _geometry PROPERTY LINK_LIBRARIES dunecommon dunegeometry APPEND)
-install(TARGETS _geometry LIBRARY DESTINATION python/dune/geometry)
+if(SKBUILD)
+  install(TARGETS _geometry LIBRARY DESTINATION python/dune/geometry)
+endif()

python/dune/geometry/_referenceelements.py

-from ..generator.generator import SimpleGenerator
+from dune.generator.generator import SimpleGenerator
 from dune.common.hashit import hashIt
 def module(dim):
     typeName = "Dune::Geo::ReferenceElement<Dune::Geo::ReferenceElementImplementation<double," + str(dim) + "> >"

python/setup.py.in

-from setuptools import setup, find_packages
-
-pkg = [m for m in "${ProjectPythonRequires}".split(' ') if "dune" not in m]
-
-setup(name="${ProjectName}",
-    namespace_packages=['dune'],
-    description="${ProjectDescription}",
-    version="${ProjectVersionString}",
-    author="${ProjectAuthor}",
-    author_email="${ProjectMaintainerEmail}",
-    packages = find_packages(),
-    zip_safe = 0,
-    package_data = {'': ['*.so']},
-    install_requires = pkg
-  )

setup.py

+import os, sys
 try:
     from dune.packagemetadata import metaData
 except ImportError: