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|
name: CMake (Extensive build on PR to develepment)
on:
pull_request:
types: [opened, synchronize, ready_for_review, reopened] # defaults + ready_to_review
branches:
- development
env:
BUILD_TYPE: Release
jobs:
build:
if: github.event.pull_request.draft == false # avoid triggering on draft
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}}
strategy:
fail-fast: false
matrix:
xml_parser_option: ["-DWITH_LIBXML"]
platform: [windows-latest, macos-latest, ubuntu-latest]
with_namespace: ["True", "False"]
strict: ["True"]
with_examples: ["True"]
package_option:
["", "-DWITH_STABLE_PACKAGES=ON", "-DWITH_ALL_PACKAGES=ON"]
language_bindings:
["-DWITH_JAVA=True -DWITH_CSHARP=True -DWITH_PYTHON=True -DWITH_R=OFF"]
include:
# to test the other two XML parsers while avoiding a combinatorial explosion in the number of jobs,
# we additionally include just two runs / OS : one for Expat, and one for Xerces
# extra Windows runs
- xml_parser_option: "-DWITH_EXPAT"
platform: windows-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
- xml_parser_option: "-DWITH_XERCES"
platform: windows-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
# extra MacOS runs
- xml_parser_option: "-DWITH_EXPAT"
platform: macos-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
- xml_parser_option: "-DWITH_XERCES"
platform: macos-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
# extra Ubuntu runs
- xml_parser_option: "-DWITH_EXPAT"
platform: ubuntu-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
- xml_parser_option: "-DWITH_XERCES"
platform: ubuntu-latest
with_namespace: "True"
strict: "True"
with_examples: "True"
package_option: "-DWITH_ALL_PACKAGES=ON"
language_bindings: ""
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
./swig
key: ${{ runner.os }}-dependencies-static-2
- 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.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
curl -L https://prdownloads.sourceforge.net/swig/swigwin-3.0.12.zip > swig.zip
unzip -o swig.zip -d swig
- 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 $GITHUB_WORKSPACE"/swig/swigwin-3.0.12/" >> $GITHUB_PATH
echo RUNTIME_LINKING_OPTION="-DWITH_STATIC_RUNTIME=ON" >> "${GITHUB_ENV}"
./dev/utilities/expdef/expdef64.exe -dRlib.def -l R.dll
echo R_PLATFORM_SPECIFIC_OPTIONS="-DR_LIB=${GITHUB_WORKSPACE}\Rlib.lib" >> "${GITHUB_ENV}"
- name: Find Windows R include path
# robust to R version changing
if: matrix.platform == 'windows-latest'
shell: bash
run: |
cd /c/Program\ Files/R/
R_INCLUDE_DIR_VERSION=$(ls -d *)
echo R_INCLUDE_PATH="/c/Program Files/R/"$R_INCLUDE_DIR_VERSION"/include" >> "${GITHUB_ENV}"
- name: Install Ubuntu dependencies
# ubuntu already has SWIG and libxml2 by default
if: matrix.platform == 'ubuntu-latest'
shell: bash
run: |
# add mono using instructions from: https://www.mono-project.com/download/stable/#download-lin
sudo apt install ca-certificates gnupg
sudo gpg --homedir /tmp --no-default-keyring --keyring /usr/share/keyrings/mono-official-archive-keyring.gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 3FA7E0328081BFF6A14DA29AA6A19B38D3D831EF
echo "deb [signed-by=/usr/share/keyrings/mono-official-archive-keyring.gpg] https://download.mono-project.com/repo/ubuntu stable-focal main" | sudo tee /etc/apt/sources.list.d/mono-official-stable.list
sudo apt update
sudo apt install -y mono-devel
sudo apt-get install -y check libxerces-c-dev expat ccache
echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${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 xerces-c expat ccache
echo PYTHON_LINKING_OPTION="-DPYTHON_USE_DYNAMIC_LOOKUP=ON" >> "${GITHUB_ENV}"
- name: Unix R options
if: matrix.platform != 'windows-latest'
shell: bash
run:
echo R_PLATFORM_SPECIFIC_OPTIONS="-DWITH_CREATE_R_SOURCE=ON
-DWITH_SKIP_R_BINARY=ON" >> "${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:
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{
matrix.with_namespace }}-${{ matrix.strict }}-${{
steps.ccache_cache_timestamp.outputs.timestamp }}
restore-keys: |
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}-${{ steps.ccache_cache_timestamp.outputs.timestamp }}
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}-
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}-
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-${{ matrix.strict }}-
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-${{ matrix.with_namespace }}-
${{ runner.os }}-test-${{ matrix.xml_parser_option }}-
${{ runner.os }}-test-
${{ runner.os }}-
### build the project ###
- name: Create Build Environment
run: cmake -E make_directory ${{runner.workspace}}/build
- name: Configure CMake for default XML_parser (LIBXML2)
if: matrix.xml_parser_option == '-DWITH_LIBXML' # default option, no need to specify -DWITH_LIBXML=...
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=11 \
-DWITH_CHECK=True \
-DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
-DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
-DWITH_EXAMPLES=${{matrix.with_examples}} \
${{matrix.package_option}} \
${{matrix.language_bindings}} \
${R_PLATFORM_SPECIFIC_OPTIONS} \
-DR_INCLUDE_DIRS="$R_INCLUDE_PATH" \
${RUNTIME_LINKING_OPTION} \
${PYTHON_LINKING_OPTION}
- name: Configure CMake for non-default XML_parser
if: matrix.xml_parser_option != '-DWITH_LIBXML'
shell: bash
working-directory: ${{runner.workspace}}/build
run: |
cmake $GITHUB_WORKSPACE \
-DCMAKE_BUILD_TYPE=$BUILD_TYPE \
-DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
-DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
-DCMAKE_CXX_STANDARD=11 \
-DWITH_CHECK=True \
-DWITH_CPP_NAMESPACE=${{matrix.with_namespace}} \
-DLIBSBML_USE_STRICT_INCLUDES=${{matrix.strict}} \
-DWITH_EXAMPLES=${{matrix.with_examples}} \
-DWITH_LIBXML=False \
${{matrix.xml_parser_option}}=True\
${{matrix.package_option}} \
${{matrix.language_bindings}} \
${RUNTIME_LINKING_OPTION} \
${PYTHON_LINKING_OPTION}
- name: Build
working-directory: ${{runner.workspace}}/build
shell: bash
run: cmake --build . --config $BUILD_TYPE
# - name: Build Unix R binaries from source package
# if: matrix.platform != 'windows-latest' && matrix.xml_parser_option == '-DWITH_LIBXML'
# shell: bash
# working-directory: ${{runner.workspace}}/build
# run: |
# mkdir r-binaries
# R CMD INSTALL -l r-binaries --build ./src/bindings/r/out/libSBML_5.19.3.tar.gz
### 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
|
