circtools CI #953
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| name: circtools CI | |
| on: | |
| push: | |
| pull_request: | |
| schedule: | |
| - cron: '0 11 * * *' | |
| concurrency: | |
| group: ci-tests-${{ github.ref }}-1 | |
| cancel-in-progress: false | |
| jobs: | |
| Main: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04] | |
| # os: [ubuntu-20.04, ubuntu-22.04, ubuntu-24.04, macos-12, macos-13] | |
| # R: ['4.2.0', '4.3.0', '4.4.0' ] | |
| R: ['4.4.0' ] | |
| python-version: ["3.8", "3.9", "3.10", "3.11"] | |
| #os: [ubuntu-22.04] | |
| #os: [ macos-11] | |
| #R: ['4.2.0' ] | |
| # python-version: ["3.11"] | |
| name: R ${{ matrix.R }} | Python ${{ matrix.python-version }} | ${{ matrix.os }} | |
| steps: | |
| - name: Create files | |
| uses: actions/checkout@v4 | |
| with: | |
| ref: master | |
| - name: Set up Python | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Updating setuptools | |
| run: | | |
| python3 -m pip install -U pip setuptools | |
| - name: Installing circtools & Python dependencies | |
| run: | | |
| python3 -m pip install numpy wheel Cython | |
| if [ "$RUNNER_OS" == "ubuntu-22.04"]; then | |
| apt-get install libblas-dev libatlas-base-dev liblapack-dev -y | |
| fi | |
| if [ "$RUNNER_OS" == "macOS"]; then | |
| export SYSTEM_VERSION_COMPAT=1 | |
| sudo rm -rf /Library/Developer/CommandLineTools | |
| sudo xcode-select --install | |
| python3 -m pip install ./ | |
| else | |
| python3 -m pip install ./ | |
| fi | |
| - name: Set up R | |
| uses: r-lib/actions/setup-r@v2 | |
| with: | |
| r-version: ${{ matrix.R }} | |
| - name: Set up R dependencies | |
| uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| cache-version: 1 | |
| extra-packages: | | |
| local::circtools/contrib/circtest | |
| local::circtools/contrib/primex | |
| - name: Checking library loading | |
| run: Rscript -e 'library(primex)' | |
| - name: Check if circtools starts | |
| run: | | |
| circtools --version | |
| which circtools | |
| - name: Downloading circtools detect test data | |
| run: | | |
| wget https://links.jakobilab.org/circtools_github_test_data -O circtools_detect_ci_input_data.tar.bz2 | |
| tar xvf circtools_detect_ci_input_data.tar.bz2 | |
| - name: Running circtools detect with minimal data set | |
| run: | | |
| cd circtools_detect_ci_input_data | |
| circtools detect @samplesheet -ss -T 2 -D -an chr1.gtf -A chr1.fa -B @bam_files.txt -M -Nr 2 2 -fg -G -F -L 20 -O circtools_ci -k | |
| - name: Checking generated output against master output | |
| run: | | |
| cd circtools_detect_ci_input_data | |
| cd circtools_ci | |
| ls -la | |
| wc -l * | |
| diff ../circtools_master/LinearCount LinearCount | |
| if [ "$RUNNER_OS" == "Linux" ]; then | |
| sha1sum -c ../circtools_master/sha1sums.txt | |
| elif [ "$RUNNER_OS" == "macOS" ]; then | |
| shasum -c ../circtools_master/sha1sums.txt | |
| fi | |
| runs-on: ${{ matrix.os }} |