- remove mono-develop and R for manylinux #509

Workflow file for this run

	name: CMake (rapid build on push)

	on: [push]

	env:
	BUILD_TYPE: Release

	jobs:
	build:
	name:
	${{ matrix.platform }}, Parser option ${{ matrix.xml_parser_option }},
	with namespaces ${{ matrix.with_namespace}}, strict includes ${{
	matrix.strict }}, with examples ${{ matrix.with_examples}}, package option
	${{ matrix.package_option}}, c++ standard ${{matrix.cpp_standard}}
	strategy:
	fail-fast: false
	matrix:
	platform: [windows-latest, macos-latest, ubuntu-latest]
	xml_parser_option: ["-DWITH_EXPAT"]
	with_namespace: ["True"]
	strict: ["True"]
	with_examples: ["True"]
	package_option: ["-DWITH_ALL_PACKAGES=ON"]
	language_bindings:
	[ "-DWITH_JAVA=True -DWITH_CSHARP=True"]
	cpp_standard: [98, 20]
	runs-on: ${{ matrix.platform }}

	steps:
	- uses: actions/checkout@v4
	- uses: seanmiddleditch/gha-setup-ninja@master

	- name: Add msbuild to PATH (Windows)
	if: matrix.platform == 'windows-latest'
	uses: ilammy/msvc-dev-cmd@v1

	### configure the operating system ###
	- name: Cache Windows dependencies and SWIG
	# On Windows, the dependencies live inside the source folder, ie `.`.
	# For the CI, we put SWIG there too, for simplicity.
	if: matrix.platform == 'windows-latest'
	id: cache-win-dependencies-static
	uses: actions/cache@v4
	with:
	path: \|
	./dependencies
	key: ${{ runner.os }}-dependencies-static

	- name: Download pre-built Windows dependencies and SWIG
	# Windows dependencies have to be in a subfolder called `dependencies`, directly under the git repository root.
	# also gets SWIG, completing the set of dependencies needed for windows
	if:
	matrix.platform == 'windows-latest' &&
	steps.cache-win-dependencies-static.outputs.cache-hit != 'true'
	shell: bash
	run: \|
	curl -L https://github.com/sbmlteam/libSBML-dependencies/releases/download/latest/libSBML-dependencies-1.0.1-x64-Release-static.zip > dependencies.zip
	unzip dependencies.zip
	mv libSBML-dependencies-1.0.1-x64-Release-static dependencies

	- name: Download SWIG on Windows
	if: matrix.platform == 'windows-latest'
	shell: bash
	run: \|
	curl -L https://sourceforge.net/projects/swig/files/swigwin/swigwin-4.0.2/swigwin-4.0.2.zip/download > swig.zip
	unzip -o swig.zip -d swig
	echo $GITHUB_WORKSPACE"/swig/swigwin-4.0.2/" >> $GITHUB_PATH

	- name: setup Windows environment
	# this is separate from the SWIG download itself, because it needs to be added to the path also when SWIG is cached
	if: matrix.platform == 'windows-latest'
	shell: bash
	run: \|
	echo RUNTIME_LINKING_OPTION="-DWITH_STATIC_RUNTIME=ON" >> "${GITHUB_ENV}"
	echo PYTHON_LINKING_OPTION="-DWITH_PYTHON=ON" >> "${GITHUB_ENV}"


	- name: Install Ubuntu dependencies
	# ubuntu already has SWIG and libxml2 by default
	if: matrix.platform == 'ubuntu-latest'
	shell: bash
	run: \|
	sudo apt-get update
	sudo apt-get install -y check ccache
	echo PYTHON_LINKING_OPTION="-DWITH_PYTHON=ON -DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
	echo R_BINDINGS="-DWITH_R=True" >> "${GITHUB_ENV}"
	git clone https://github.com/libexpat/libexpat
	cmake -G Ninja -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DEXPAT_BUILD_TESTS=OFF -DEXPAT_BUILD_TOOLS=OFF -DEXPAT_BUILD_EXAMPLES=OFF -DEXPAT_SHARED_LIBS=OFF -DCMAKE_INSTALL_PREFIX=./dependencies -B libexpat -S libexpat/expat
	cmake --build libexpat
	cmake --install libexpat


	- name: Install MacOS dependencies
	# MacOS already has libxml2 by default
	if: matrix.platform == 'macos-latest'
	shell: bash
	run: \|
	brew install check swig ccache
	echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"

	### setup ccache, not on Windows ###
	- name: Prepare ccache timestamp
	if: matrix.platform != 'windows-latest'
	id: ccache_cache_timestamp
	shell: cmake -P {0}
	run: \|
	string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC)
	message("::set-output name=timestamp::${current_date}")
	- name: Set ccache cache directory
	if: matrix.platform != 'windows-latest'
	shell: bash
	run: \|
	echo "CCACHE_DIR=${{runner.workspace}}/.ccache" >> "${GITHUB_ENV}"
	echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
	- name: cache ccache files
	if: matrix.platform != 'windows-latest'
	uses: actions/cache@v4
	with:
	path: ${{runner.workspace}}/.ccache
	key:
	${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp
	}}
	restore-keys: \|
	${{ runner.os }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
	${{ runner.os }}-

	### build the project ###
	- name: Create Build Environment
	run: cmake -E make_directory ${{runner.workspace}}/build

	- name: Configure CMake for the selected XML_parser
	shell: bash
	working-directory: ${{runner.workspace}}/build
	run: \|
	cmake $GITHUB_WORKSPACE \
	-G "Ninja" \
	-DCMAKE_BUILD_TYPE=$BUILD_TYPE \
	-DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
	-DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
	-DCMAKE_CXX_STANDARD=${{matrix.cpp_standard}} \
	-DWITH_CHECK=True \
	-DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
	-DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
	-DWITH_EXAMPLES=${{matrix.with_examples}} \
	-DWITH_LIBXML=OFF \
	${{matrix.xml_parser_option}}=True \
	${{matrix.package_option}} \
	${{matrix.language_bindings}} \
	${R_BINDINGS} \
	${RUNTIME_LINKING_OPTION} \
	${PYTHON_LINKING_OPTION}

	- name: Build
	working-directory: ${{runner.workspace}}/build
	shell: bash
	run: cmake --build . --config $BUILD_TYPE

	### run tests ###
	- name: Test
	if: matrix.platform == 'macos-latest'
	working-directory: ${{runner.workspace}}/build
	shell: bash
	run: ctest -V -C $BUILD_TYPE -E test_cs

	- name: Test
	if: matrix.platform != 'macos-latest'
	working-directory: ${{runner.workspace}}/build
	shell: bash
	run: ctest -V -C $BUILD_TYPE

	manylinuxbuild:
	name:
	${{ matrix.container }}, Parser option ${{ matrix.xml_parser_option }},
	with namespaces ${{ matrix.with_namespace}}, strict includes ${{
	matrix.strict }}, with examples ${{ matrix.with_examples}}, package option
	${{ matrix.package_option}}
	strategy:
	fail-fast: false
	matrix:
	platform: [ubuntu-latest]
	xml_parser_option: ["-DWITH_LIBXML"]
	with_namespace: ["True"]
	strict: ["True"]
	with_examples: ["True"]
	package_option: ["-DWITH_STABLE_PACKAGES=ON"]
	cpp_standard: [98, 20]
	language_bindings:
	["-DWITH_JAVA=True -DWITH_PYTHON=True"]
	container: ["quay.io/pypa/manylinux_2_28_x86_64"]
	runs-on: ${{ matrix.platform }}
	container: ${{ matrix.container}}

	steps:
	- uses: actions/checkout@v4
	- name: install Swig 4 from source
	run: \|
	yum install -y pcre-devel
	echo "SWIG_DIR=/usr/local/swig/" >> "${GITHUB_ENV}"
	curl -L https://sourceforge.net/projects/swig/files/swig/swig-4.0.2/swig-4.0.2.tar.gz/download > swig.tar.gz
	tar -zxvf swig.tar.gz
	cd swig-4.0.2/
	./configure --disable-dependency-tracking --prefix=$SWIG_DIR
	make clean
	make -j 2
	make install
	swig -version
	- name: install CMake using pip
	run: \|
	/opt/python/cp38-cp38/bin/pip install cmake
	ln -s /opt/python/cp38-cp38/bin/cmake /usr/bin/cmake
	ln -s /opt/python/cp38-cp38/bin/ctest /usr/bin/ctest
	cmake --version
	ctest --version
	- name: Install dependencies, configure, build
	run: \|
	yum install -y libxml2-devel check-devel java-devel
	cd ..
	mkdir build
	cd build
	cmake ../libsbml \
	-DCMAKE_BUILD_TYPE=$BUILD_TYPE \
	-DCMAKE_CXX_STANDARD=${{matrix.cpp_standard}} \
	-DWITH_CHECK=True \
	-DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
	-DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
	-DWITH_EXAMPLES=${{matrix.with_examples}} \
	-DWITH_LIBXML=OFF \
	${{matrix.xml_parser_option}}=True \
	${{matrix.package_option}} \
	${{matrix.language_bindings}} \
	-DPYTHON_EXECUTABLE=/opt/python/cp38-cp38/bin/python \
	-DPYTHON_INCLUDE_DIR=/opt/python/cp38-cp38/include/python3.8/ \
	-DWITH_STATIC_RUNTIME=ON \
	-DPYTHON_USE_DYNAMIC_LOOKUP=ON
	cmake --build . --config $BUILD_TYPE

	- name: Test
	run: \|
	cd ../build
	ctest -V -C $BUILD_TYPE

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- remove mono-develop and R for manylinux #509

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- remove mono-develop and R for manylinux #509

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