Add "deprotonate" and "tautomerize" to TOML input file runtypes #284
Workflow file for this run
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| name: CI | |
| on: [push, pull_request] | |
| env: | |
| BUILD_DIR: _build | |
| PIP_PACKAGES: >- | |
| meson | |
| cmake | |
| ninja | |
| PIP_EXTRAS: >- | |
| pkgconfig | |
| numpy | |
| ase | |
| matplotlib | |
| LINUX_INTEL_COMPONENTS: >- | |
| intel-oneapi-compiler-fortran-2023.1.0 | |
| intel-oneapi-compiler-dpcpp-cpp-and-cpp-classic-2023.1.0 | |
| intel-oneapi-mkl-2023.1.0 | |
| intel-oneapi-mkl-devel-2023.1.0 | |
| jobs: | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: [ubuntu-latest] | |
| build: [cmake] | |
| build-type: [debug] | |
| compiler: [gnu] | |
| version: [11,12] | |
| include: | |
| - os: ubuntu-latest | |
| build: cmake | |
| build-type: debug | |
| compiler: intel | |
| version: 2023.1.0 | |
| - os: macos-latest | |
| build: cmake | |
| build-type: debug | |
| compiler: gnu | |
| version: 12 | |
| - os: ubuntu-latest | |
| build: cmake | |
| build-type: debugoptimized | |
| compiler: gnu | |
| version: 12 | |
| - os: ubuntu-latest | |
| build: meson | |
| build-type: debugoptimized | |
| compiler: intel | |
| version: 2023.1.0 | |
| defaults: | |
| run: | |
| shell: ${{ matrix.shell || 'bash' }} | |
| env: | |
| FC: ${{ matrix.compiler == 'intel' && 'ifort' || 'gfortran' }} | |
| CC: ${{ matrix.compiler == 'intel' && 'icx' || 'gcc' }} | |
| GCC_V: ${{ matrix.version }} | |
| PYTHON_V: 3.9 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| - uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ env.PYTHON_V }} | |
| - name: Link pre-installed GCC and FC (macOS) | |
| if: ${{ contains(matrix.os, 'macos') && matrix.compiler == 'gnu' }} | |
| run: | | |
| brew install openblas | |
| gfortran_path=$( which gfortran-${{ env.GCC_V }} ) | |
| gcc_path=$( which gcc-${{ env.GCC_V }} ) | |
| gplusplus_path=$( which g++-${{ env.GCC_V }} ) | |
| export FC=$gfortran_path | |
| export CC=$gcc_path | |
| export CXX=$gplusplus_path | |
| ln -s $gfortran_path /usr/local/bin/gfortran | |
| ln -s $gcc_path /usr/local/bin/gcc | |
| ln -s $gplusplus_path /usr/local/bin/g++ | |
| echo "PKG_CONFIG_PATH=/usr/local/opt/openblas/lib/pkgconfig" >> $GITHUB_ENV | |
| echo "LDFLAGS=-L/opt/homebrew/opt/openblas/lib" >> $GITHUB_ENV | |
| echo "CPPFLAGS=-I/opt/homebrew/opt/openblas/include" >> $GITHUB_ENV | |
| - name: Install GCC (Linux) | |
| if: ${{ contains(matrix.os, 'ubuntu') && matrix.compiler == 'gnu' }} | |
| run: | | |
| sudo add-apt-repository ppa:ubuntu-toolchain-r/test | |
| sudo apt-get update | |
| sudo apt-get install -y gcc-${{ env.GCC_V}} gfortran-${{ env.GCC_V }} | |
| sudo update-alternatives \ | |
| --install /usr/bin/gcc gcc /usr/bin/gcc-${{ env.GCC_V }} 100 \ | |
| --slave /usr/bin/gfortran gfortran /usr/bin/gfortran-${{ env.GCC_V }} \ | |
| --slave /usr/bin/gcov gcov /usr/bin/gcov-${{ env.GCC_V }} | |
| - name: Install libopenblas (Linux GNU build only) | |
| if: ${{ matrix.compiler == 'gnu' && matrix.build-type == 'debugoptimized' }} | |
| run: sudo apt-get update && sudo apt-get install -y libopenblas-dev | |
| - name: Prepare for cache restore | |
| if: ${{ matrix.compiler == 'intel' }} | |
| run: | | |
| sudo mkdir -p /opt/intel | |
| sudo chown $USER /opt/intel | |
| - name: Cache Intel install | |
| if: ${{ matrix.compiler == 'intel' }} | |
| id: cache-install | |
| uses: actions/cache@v4 | |
| with: | |
| path: /opt/intel/oneapi | |
| key: install-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.os }} | |
| - name: Install Intel (Linux) | |
| if: ${{ contains(matrix.os, 'ubuntu') && contains(matrix.compiler, 'intel') && steps.cache-install.outputs.cache-hit != 'true' }} | |
| run: | | |
| wget https://apt.repos.intel.com/intel-gpg-keys/${{ env.KEY }} | |
| sudo apt-key add ${{ env.KEY }} | |
| rm ${{ env.KEY }} | |
| echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list | |
| sudo apt-get update | |
| sudo apt-get install ${{ env.PKG }} | |
| env: | |
| KEY: GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB | |
| PKG: ${{ env.LINUX_INTEL_COMPONENTS }} | |
| - name: Setup Intel oneAPI environment | |
| if: ${{ matrix.compiler == 'intel' }} | |
| run: | | |
| source /opt/intel/oneapi/setvars.sh | |
| printenv >> $GITHUB_ENV | |
| - name: Git Sumbodules checkout | |
| run: | | |
| git submodule update --init | |
| - name: Install build and test dependencies | |
| if: ${{ ! contains(matrix.os, 'windows') }} | |
| run: pip3 install ${{ env.PIP_PACKAGES }} ${{ env.PIP_EXTRAS }} | |
| - name: Configure build (meson) | |
| if: ${{ matrix.build == 'meson' }} | |
| run: >- | |
| meson setup ${{ env.BUILD_DIR }} | |
| --buildtype=debugoptimized | |
| --prefix=$PWD/_dist | |
| --libdir=lib | |
| --warnlevel=0 | |
| # ${{ env.MESON_ARGS }} | |
| # env: | |
| # COVERAGE: ${{ matrix.build-type == 'coverage' }} | |
| # MESON_ARGS: >- | |
| # ${{ matrix.compiler == 'intel' && '-Dfortran_link_args=-qopenmp -Dapi=false' || '' }} | |
| # ${{ contains(matrix.os, 'macos') && '-Dlapack=openblas' || '' }} | |
| - name: Configure build (CMake, debug) | |
| if: ${{ matrix.build == 'cmake' && matrix.build-type == 'debug' }} | |
| run: >- | |
| cmake -B${{ env.BUILD_DIR }} | |
| -GNinja | |
| -DCMAKE_BUILD_TYPE=Debug | |
| -DCMAKE_INSTALL_PREFIX=$PWD/_dist | |
| -DCMAKE_INSTALL_LIBDIR=lib | |
| - name: Configure build (CMake, static) | |
| if: ${{ matrix.build == 'cmake' && matrix.build-type == 'debugoptimized' }} | |
| run: >- | |
| cmake -B${{ env.BUILD_DIR }} | |
| -GNinja | |
| -DCMAKE_BUILD_TYPE=RelWithDebInfo | |
| -DCMAKE_INSTALL_PREFIX=$PWD/_dist | |
| -DCMAKE_INSTALL_LIBDIR=lib | |
| -DSTATICBUILD=ON | |
| - name: Build project | |
| run: ninja -C ${{ env.BUILD_DIR }} | |
| - name: Run unit tests (ctest) | |
| if: ${{ matrix.build == 'cmake' && matrix.compiler == 'gnu' }} | |
| run: | | |
| ctest --output-on-failure --parallel 2 -R '^crest/' | |
| working-directory: ${{ env.BUILD_DIR }} | |
| env: | |
| OMP_NUM_THREADS: 1,2,1 | |
| - name: Install project | |
| run: | | |
| ninja -C ${{ env.BUILD_DIR }} install | |
| echo "CREST_PREFIX=$PWD/_dist" >> $GITHUB_ENV | |
| - name: Create package | |
| if: ${{ matrix.build-type == 'debugoptimized' }} | |
| run: | | |
| mkdir crest | |
| cp COPYING crest/LICENSE | |
| cp COPYING.LESSER crest/LICENSE.LESSER | |
| cp _dist/bin/crest crest/ | |
| tar cvf ${{ env.OUTPUT }} crest | |
| xz -T0 ${{ env.OUTPUT }} | |
| echo "CREST_OUTPUT=${{ env.OUTPUT }}.xz" >> $GITHUB_ENV | |
| env: | |
| OUTPUT: crest-${{ matrix.compiler }}-${{ matrix.version }}-${{ matrix.os }}.tar | |
| - name: Upload package | |
| if: ${{ matrix.build-type == 'debugoptimized' }} | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: ${{ env.CREST_OUTPUT }} | |
| path: ${{ env.CREST_OUTPUT }} | |
| continuous-delivery: | |
| if: github.event_name == 'push' | |
| runs-on: ubuntu-latest | |
| needs: | |
| - build | |
| env: | |
| GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| RELEASE_TAG: latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Install github-release | |
| run: | | |
| go install github.com/github-release/github-release@latest | |
| echo "GOPATH=$(go env GOPATH)" >> $GITHUB_ENV | |
| echo "$(go env GOPATH)/bin" >> $GITHUB_PATH | |
| - name: Set environment variables | |
| run: | | |
| echo "GITHUB_USER=$( echo ${{ github.repository }} | cut -d/ -f1 )" >> $GITHUB_ENV | |
| echo "GITHUB_REPO=$( echo ${{ github.repository }} | cut -d/ -f2 )" >> $GITHUB_ENV | |
| - name: Move/Create continuous tag | |
| run: | | |
| git tag --force ${{ env.RELEASE_TAG }} ${{ github.sha }} | |
| git push --tags --force | |
| - name: Get Time | |
| run: echo "TIME=$(date -u '+%Y/%m/%d, %H:%M')" >> $GITHUB_ENV | |
| - name: Check continuous release status | |
| run: | | |
| if ! github-release info -t ${{ env.RELEASE_TAG }} > /dev/null 2>&1; then | |
| echo "RELEASE_COMMAND=release" >> $GITHUB_ENV | |
| else | |
| echo "RELEASE_COMMAND=edit" >> $GITHUB_ENV | |
| fi | |
| - name: Setup continuous release | |
| run: >- | |
| github-release ${{ env.RELEASE_COMMAND }} | |
| --tag ${{ env.RELEASE_TAG }} | |
| --name "Continuous release version" | |
| --description "$DESCRIPTION" | |
| --pre-release | |
| env: | |
| DESCRIPTION: | | |
| Created on ${{ env.TIME }} UTC by @${{ github.actor }} with commit ${{ github.sha }}. | |
| This is an automated distribution of the latest CREST version. | |
| This version is only minimally tested and may be unstable or even crash. | |
| Use with caution! | |
| https://github.com/${{ github.repository }}/actions/runs/${{ github.run_id }} | |
| - name: Download Artifacts | |
| uses: actions/download-artifact@v4 | |
| with: | |
| path: ${{ github.workspace }} # This will download all files | |
| - name: Create SHA256 checksums | |
| run: | | |
| for dir in crest-*.tar.xz; do | |
| if [ -d "$dir" ]; then | |
| sha256sum "$dir/$dir" > "$dir.sha256.txt" | |
| fi | |
| done | |
| - name: Upload CREST tarballs to release | |
| run: | | |
| for dir in crest-*.tar.xz; do | |
| if [ -d "$dir" ]; then | |
| github-release upload \ | |
| --tag ${{ env.RELEASE_TAG }} \ | |
| --replace \ | |
| --name "${dir}" \ | |
| --file "$dir/$dir" | |
| fi | |
| done | |
| - name: Upload SHA256 checksums to release | |
| run: | | |
| for file in crest-*.tar.xz.sha256.txt; do | |
| github-release upload \ | |
| --tag ${{ env.RELEASE_TAG }} \ | |
| --replace \ | |
| --name "$file" \ | |
| --file "$file" | |
| done | |