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Alias nodes are now created once autolayout function is calle #507

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Alias nodes are now created once autolayout function is calle

Alias nodes are now created once autolayout function is calle #507

Workflow file for this run

.github/workflows/build.yml at 423dfde
name: Build LibSBMLNetwork
on:
push:
branches:
- develop
pull_request:
branches:
- '**'
jobs:
build_on_OSs:
name: Build RoadRunner on ${{ matrix.platform.name }}-python${{ matrix.python_version }}
strategy:
fail-fast: false
matrix:
platform:
- name: macos-12-release
os_type: macos
os_name: macos-12
build_type: Release
build_python: ON
- name: macos-12-debug
os_type: macos
os_name: macos-12
build_type: Debug
build_python: ON
- name: macos-latest-release
os_type: macos
os_name: macos-latest
build_type: Release
build_python: ON
- name: macos-latest-debug
os_type: macos
os_name: macos-latest
build_type: Debug
build_python: ON
- name: ubuntu-latest-release
os_type: ubuntu
os_name: ubuntu-latest
build_type: Release
build_python: ON
- name: ubuntu-latest-debug
os_type: ubuntu
os_name: ubuntu-latest
build_type: Debug
build_python: ON
- name: windows-latest-release
os_type: windows
os_name: windows-latest
build_type: Release
build_python: ON
- name: windows-latest-debug
os_type: windows
os_name: windows-latest
build_type: Debug
build_python: OFF
- name: manylinux_2_28-release
os_type: manylinux
os_name: ubuntu-latest
container_image: quay.io/pypa/manylinux_2_28_x86_64
build_type: Release
build_python: ON
- name: manylinux_2_28-debug
os_type: manylinux
os_name: ubuntu-latest
container_image: quay.io/pypa/manylinux_2_28_x86_64
build_type: Debug
build_python: ON
libroadrunner_deps_owner: [ "sys-bio" ]
libroadrunner_deps_repo: [ "libroadrunner-deps" ]
libroadrunner_deps_name: [ "libroadrunner-deps" ]
libroadrunner_deps_release_version: [ "v2.1.2" ]
python_version: [ "3.11" ]
runs-on: ${{ matrix.platform.os_name }}
container:
image: ${{ matrix.platform.container_image || '' }}
steps:
- name: Checkout libSBMLNetwork
uses: actions/checkout@v4
- name: Set MSVC as the default compiler on Windows
if: matrix.platform.os_type == 'windows'
uses: ilammy/msvc-dev-cmd@v1.6.0
- name: Upgrade gcc on Linux
if: matrix.platform.os_type == 'manylinux'
shell: bash
run: |
if [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then
apt-get update
apt-get install -y software-properties-common
add-apt-repository -y ppa:ubuntu-toolchain-r/test
apt-get update
apt-get install -y gcc-11 g++-11
update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-11 90
update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-11 90
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
dnf install -y gcc-toolset-11
scl enable gcc-toolset-11 bash
echo "/opt/rh/gcc-toolset-11/root/usr/bin" >> "${GITHUB_PATH}"
fi
- name: Setup Ninja
uses: seanmiddleditch/gha-setup-ninja@master
- name: Get Host Architecture
shell: bash
run: |
architecture=$(uname -m)
echo "host_architecture=$architecture" >> "${GITHUB_ENV}"
if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
echo "OSX_ARCHITECTURES=$architecture" >> "${GITHUB_ENV}"
fi
- name: Install ccache
shell: bash
run: |
cd ${RUNNER_WORKSPACE}
if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
brew install ccache
elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then
sudo apt-get update
sudo apt-get install -y ccache
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
mkdir -p ccache
cd ccache
curl -L https://github.com/ccache/ccache/releases/download/v4.9.1/ccache-4.9.1.tar.gz > ccache.tar.gz
tar -zxf ccache.tar.gz
rm ccache.tar.gz
mkdir -p build-ccache
mkdir -p install-ccache
cd build-ccache
cmake -DCMAKE_INSTALL_PREFIX="$RUNNER_WORKSPACE/ccache/install-ccache" -DCMAKE_BUILD_TYPE=Release ../ccache-4.9.1
cmake --build . --target install
echo "$RUNNER_WORKSPACE/ccache/install-ccache/bin" >> "${GITHUB_PATH}"
fi
- name: Prepare ccache timestamp on non-Windows platforms
if: matrix.platform.os_type != 'windows'
id: ccache_cache_timestamp
shell: cmake -P {0}
run: |
string(TIMESTAMP current_date "%Y-%m-%d-%H;%M;%S" UTC)
message("::set-output name=timestamp::${current_date}")
- name: Set ccache cache directory on non-Windows
if: matrix.platform.os_type != 'windows'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}
echo "CCACHE_DIR=${RUNNER_WORKSPACE}/.ccache" >> "${GITHUB_ENV}"
echo "COMPILER_LAUNCHER=ccache" >> "${GITHUB_ENV}"
- name: Cache ccache files on non-Windows
if: matrix.platform.os_type != 'windows'
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 }}-
- name: Setup Python for non-Manylinux platforms
if: matrix.platform.build_python == 'ON' && matrix.platform.os_type != 'manylinux'
uses: actions/setup-python@v4
with:
python-version: ${{ matrix.python_version }}
- name: Setup Python for Manylinux platforms
if: matrix.platform.build_python == 'ON' && matrix.platform.os_type == 'manylinux'
shell: bash
run: |
dnf install -y wget
wget https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh
bash Miniconda3-latest-Linux-x86_64.sh -b -p /Miniconda3
/Miniconda3/bin/conda create -y --name python${{ matrix.python_version }} python=${{ matrix.python_version }}
/Miniconda3/bin/conda init && bash ~/.bashrc && . ~/.bashrc cd ${RUNNER_WORKSPACE}
echo "export PATH=/Miniconda3/envs/python${{ matrix.python_version }}/bin:$PATH" >> "${GITHUB_ENV}"
- name: Download Dependencies binaries
shell: bash
run: |
cd ${RUNNER_WORKSPACE}
mkdir -p ${{ matrix.libroadrunner_deps_name }}-binaries
cd ${{ matrix.libroadrunner_deps_name }}-binaries
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio")
binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-msvc${compiler_version}-${host_architecture}-${{ matrix.platform.build_type }}
elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
os_version=$(sw_vers -productVersion | cut -d '.' -f 1)
binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then
os_version=$(lsb_release -rs | cut -d '.' -f 1)
binary_file_name=${{ matrix.libroadrunner_deps_name }}-${{ matrix.platform.os_type }}-${os_version}-${host_architecture}-${{ matrix.platform.build_type }}
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
os_name="${{ matrix.platform.name }}"
os_name_without_build_type="${os_name%%-*}"
binary_file_name=${{ matrix.libroadrunner_deps_name }}-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }}
fi
curl -LO "https://github.com/${{ matrix.libroadrunner_deps_owner }}/${{ matrix.libroadrunner_deps_repo }}/releases/download/${{ matrix.libroadrunner_deps_release_version }}/$binary_file_name.zip"
unzip -q $binary_file_name.zip
rm $binary_file_name.zip
echo DEPENDENCIES_INSTALL_PREFIX="${RUNNER_WORKSPACE}/${{ matrix.libroadrunner_deps_name }}-binaries" >> "${GITHUB_ENV}"
- name: Create build directory
shell: bash
run: mkdir -p ${RUNNER_WORKSPACE}/build-libsbmlnetwork
- name: Configure CMake for libBMLNetwork
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/build-libsbmlnetwork
cmake $GITHUB_WORKSPACE \
-G "Ninja" \
-DCMAKE_C_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
-DCMAKE_CXX_COMPILER_LAUNCHER=${COMPILER_LAUNCHER} \
-DCMAKE_BUILD_TYPE=${{ matrix.platform.build_type }} \
-DCMAKE_OSX_ARCHITECTURES=${OSX_ARCHITECTURES} \
-DCMAKE_INSTALL_PREFIX="${RUNNER_WORKSPACE}/install-libsbmlnetwork" \
-DDEPENDENCIES_INSTALL_PREFIX=${DEPENDENCIES_INSTALL_PREFIX} \
-DWITH_PYTHON=${{ matrix.platform.build_python }} \
-DPYTHON_INSTALL_WITH_SETUP="ON"
- name: Build and install libSBMLNetwork
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/build-libsbmlnetwork
cmake --build . --target install --config ${{ matrix.platform.build_type }}
- name: Install python packages
if: matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
python -m pip install pytest ipython setuptools wheel
python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
python -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
python${{ matrix.python_version }} -m pip install --trusted-host pypi.org --trusted-host pypi.python.org --trusted-host files.pythonhosted.org pytest ipython setuptools wheel
python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
else
python${{ matrix.python_version }} -m pip install pytest ipython setuptools wheel
python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
python${{ matrix.python_version }} -m pip install ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
fi
- name: Run libSBMLNetwork tests
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork/tests
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
python -m pytest -p no:cacheprovider
else
python${{ matrix.python_version }} -m pytest -p no:cacheprovider
fi
- name: Set artifacts path and name
shell: bash
run: |
cd ${RUNNER_WORKSPACE}
artifacts_name=""
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
compiler_version=$(ls "C:\Program Files\Microsoft Visual Studio")
echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-msvc$compiler_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}"
elif [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
os_version=$(sw_vers -productVersion | cut -d '.' -f 1)
echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-$os_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}"
elif [ "${{ matrix.platform.os_type }}" == 'ubuntu' ]; then
os_version=$(lsb_release -rs | cut -d '.' -f 1)
echo "artifacts_name=libsbmlnetwork-${{ matrix.platform.os_type }}-$os_version-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}"
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
os_name="${{ matrix.platform.name }}"
os_name_without_build_type="${os_name%%-*}"
echo "artifacts_name=libsbmlnetwork-${os_name_without_build_type}-${host_architecture}-${{ matrix.platform.build_type }}" >> "${GITHUB_ENV}"
fi
echo "artifacts_path=../install-libsbmlnetwork" >> "${GITHUB_ENV}"
- name: Upload libSBMLNetwork binaries
uses: actions/upload-artifact@v1
with:
name: ${{env.artifacts_name}}
path: ${{env.artifacts_path}}
- name: Create libSBMLNetwork Python wheel artifacts
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
python setup.py bdist_wheel
else
python${{ matrix.python_version }} setup.py bdist_wheel
fi
- name: Rename libSBMLNetwork Python wheel artifacts
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork
if [ "${{ matrix.platform.os_type }}" == 'macos' ]; then
mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/universal2/${host_architecture}/g")
elif [ "${{ matrix.platform.os_type }}" == 'manylinux' ]; then
mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/linux/manylinux_2_28/g")
fi
python_version_number=$(echo "${{ matrix.python_version }}" | tr -d '.')
mv dist/libsbmlnetwork*.whl $(echo dist/libsbmlnetwork*.whl | sed "s/cp${python_version_number}-cp${python_version_number}/py3-none/g")
- name: Create SBMLNetwork Python wheel artifacts
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork
if [ "${{ matrix.platform.os_type }}" == 'windows' ]; then
python setup.py bdist_wheel
else
python${{ matrix.python_version }} setup.py bdist_wheel
fi
- name: Set Python wheel artifacts path and name
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
shell: bash
run: |
cd ${RUNNER_WORKSPACE}/install-libsbmlnetwork/lib/python/site-packages
libsbmlnetwork_python_wheel_file_name=$(ls libsbmlnetwork/dist | grep '^libsbmlnetwork')
echo "libsbmlnetwork_python_wheel_artifacts_name=${libsbmlnetwork_python_wheel_file_name}" >> "${GITHUB_ENV}"
sbmlnetwork_python_wheel_file_name=$(ls sbmlnetwork/dist | grep '^sbmlnetwork')
echo "sbmlnetwork_python_wheel_artifacts_name=${sbmlnetwork_python_wheel_file_name}" >> "${GITHUB_ENV}"
# we need to use relative path as actions/upload-artifact@v1 cannot find it on containerized runners
echo "libsbmlnetwork_python_wheel_artifacts_file=../install-libsbmlnetwork/lib/python/site-packages/libsbmlnetwork/dist/$libsbmlnetwork_python_wheel_file_name" >> "${GITHUB_ENV}"
echo "sbmlnetwork_python_wheel_artifacts_file=../install-libsbmlnetwork/lib/python/site-packages/sbmlnetwork/dist/$sbmlnetwork_python_wheel_file_name" >> "${GITHUB_ENV}"
- name: Upload libSBMLNetwork Python wheel artifacts
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
uses: actions/upload-artifact@v1
with:
name: ${{env.libsbmlnetwork_python_wheel_artifacts_name}}
path: ${{env.libsbmlnetwork_python_wheel_artifacts_file}}
- name: Upload SBMLNetwork Python wheel artifacts
if: matrix.platform.build_type == 'Release' && matrix.platform.build_python == 'ON'
uses: actions/upload-artifact@v1
with:
name: ${{env.sbmlnetwork_python_wheel_artifacts_name}}
path: ${{env.sbmlnetwork_python_wheel_artifacts_file}}