[FEATURE] CWL/CTD support #853
Workflow file for this run
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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 | tee | grep 2880b1ab21aa50f45ed896cfd470559717094f15 | |
cwltool raptor.cwl workflow/cwl/tests/raptor-build-16_bins_window_19.yml | tee | grep 3b802449bf5c611c2f68a8ed86ee3d62e4638af9 |