[FEATURE] CWL/CTD support #865
Workflow file for this run
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Linux | |
| on: | |
| push: | |
| branches: | |
| - 'main' | |
| pull_request: | |
| types: | |
| - unlabeled | |
| workflow_dispatch: | |
| concurrency: | |
| group: linux-${{ github.event.pull_request.number || github.ref }} | |
| cancel-in-progress: ${{ github.event_name != 'push' }} | |
| env: | |
| CMAKE_VERSION: 3.18.4 | |
| SHARG_NO_VERSION_CHECK: 1 | |
| TZ: Europe/Berlin | |
| defaults: | |
| run: | |
| shell: bash -Eeuxo pipefail {0} | |
| jobs: | |
| build: | |
| name: ${{ matrix.name }} | |
| runs-on: ubuntu-22.04 | |
| timeout-minutes: 120 | |
| if: github.repository_owner == 'seqan' || github.event_name == 'workflow_dispatch' || github.event.label.name == 'lint' | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| include: | |
| - name: "gcc12" | |
| cxx: "g++-12" | |
| cc: "gcc-12" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++23" | |
| - name: "gcc11" | |
| cxx: "g++-11" | |
| cc: "gcc-11" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++23" | |
| - name: "gcc10" | |
| cxx: "g++-10" | |
| cc: "gcc-10" | |
| build: unit | |
| build_type: Release | |
| cxx_flags: "-std=c++20" | |
| steps: | |
| - name: Checkout | |
| uses: actions/checkout@v3 | |
| with: | |
| path: raptor | |
| fetch-depth: 2 | |
| submodules: true | |
| - name: Add package source | |
| run: bash ./raptor/lib/seqan3/.github/workflows/scripts/configure_apt.sh | |
| - name: Install CMake | |
| run: bash ./raptor/lib/seqan3/.github/workflows/scripts/install_cmake.sh | |
| - name: Install ccache | |
| run: sudo apt-get install --yes ccache | |
| - name: Install compiler ${{ matrix.cxx }} | |
| run: sudo apt-get install --yes ${{ matrix.cxx }} | |
| - name: Load ccache | |
| uses: actions/cache@v3 | |
| with: | |
| path: .ccache | |
| key: ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }}-${{ github.run_number }} | |
| # Restoring: From current branch, otherwise from base branch, otherwise from any branch. | |
| restore-keys: | | |
| ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.ref }} | |
| ${{ runner.os }}-${{ matrix.name }}-ccache-${{ github.base_ref }} | |
| ${{ runner.os }}-${{ matrix.name }}-ccache- | |
| - name: Tool versions | |
| run: | | |
| env cmake --version | |
| env ${{ matrix.cxx }} --version | |
| - name: Configure tests | |
| env: | |
| CXX: ${{ matrix.cxx }} | |
| CC: ${{ matrix.cc }} | |
| run: | | |
| mkdir build | |
| cd build | |
| cmake ../raptor/test/${{ matrix.build }} -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \ | |
| -DCMAKE_CXX_FLAGS="${{ matrix.cxx_flags }} -Wno-interference-size" \ | |
| -DRAPTOR_NATIVE_BUILD=OFF | |
| make -j2 gtest_build | |
| - name: Build tests | |
| env: | |
| CCACHE_BASEDIR: ${{ github.workspace }} | |
| CCACHE_DIR: ${{ github.workspace }}/.ccache | |
| CCACHE_COMPRESS: true | |
| CCACHE_COMPRESSLEVEL: 12 | |
| CCACHE_MAXSIZE: 150M | |
| CCACHE_IGNOREOPTIONS: "-fprofile-abs-path" | |
| run: | | |
| ccache -z | |
| cd build | |
| make -k -j2 | |
| ccache -sv | |
| - name: Run tests | |
| run: | | |
| cd build | |
| ctest . -j2 --output-on-failure | |
| - name: Install pipx & cwltool | |
| run: | | |
| sudo apt-get install --yes pipx | |
| pipx install cwltool | |
| - name: extract CWL descriptions | |
| run: | | |
| build/bin/raptor build --export-help cwl > raptor/raptor.cwl | |
| cd raptor | |
| export PATH=$PATH:$PWD/../build/bin | |
| cwltool --validate raptor.cwl | |
| cwltool raptor.cwl workflow/cwl/tests/raptor-build-0_bins_window_19.yml | grep 098169f476fb949b0d08f2d1e05881049819b811 | |
| cwltool raptor.cwl workflow/cwl/tests/raptor-build-16_bins_window_19.yml | grep 64a4328eb3dab99bf6ecd38f84f4ae45fd01a4dd |