Updating action versions #42
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| name: CI tests | |
| on: | |
| push: | |
| pull_request: | |
| # schedule: | |
| # - cron: '0 7 * * *' | |
| concurrency: | |
| group: ci-tests-${{ github.ref }}-1 | |
| cancel-in-progress: true | |
| jobs: | |
| Main: | |
| strategy: | |
| matrix: | |
| os: [ubuntu-22.04] | |
| # os: [ubuntu-18.04, ubuntu-20.04, ubuntu-22.04, macos-11, macos-12] | |
| python-version: ["3.7"] | |
| # python-version: ["3.7", "3.8", "3.9", "3.10", "3.11"] | |
| name: Python ${{ matrix.python-version }} on ${{ matrix.os }} | |
| steps: | |
| - name: Create files | |
| uses: actions/checkout@v3 | |
| - name: Set up Python | |
| uses: actions/setup-python@v4 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| architecture: 'x64' | |
| - name: Updating setuptools | |
| run: | | |
| python3 -m pip install -U pip setuptools | |
| - name: Updating pip | |
| run: | | |
| python3 -m pip install --upgrade pip | |
| - name: Installing circhemy & Python dependencies | |
| run: | | |
| python3 -m pip install ./ -v | |
| - name: Check if circhemy starts | |
| run: | | |
| circhemy --version | |
| which circhemy | |
| - name: Unzip SQLite database | |
| run: | | |
| CIRCHEMY_DB_PATH=`python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy.sqlite3.bz2 | |
| bunzip2 $CIRCHEMY_DB_PATH | |
| - name: Running circhemy convert test | |
| run: | | |
| cat `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_query.results | circhemy convert -q STDIN -i circBase -o CircAtlas2 circBase Genome > convert_output | |
| - name: Checking generated output against gold output | |
| run: | | |
| diff `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_convert.results convert_output | |
| - name: Running circhemy query test | |
| run: | | |
| circhemy query -o circBase -b *atf6 -g hg38 | cut -f1 > query_output | |
| - name: Checking generated output against gold output | |
| run: | | |
| diff `python3 -c "import site; print(site.getsitepackages()[0])"`/circhemy/data/circhemy_query.results query_output | |
| runs-on: ${{ matrix.os }} |