Fix potentially rare db migration bug #71
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| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: cli-pytest | |
| on: | |
| push: | |
| branches: [ master, dev ] | |
| pull_request: | |
| branches: [ master, dev ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: [3.6, 3.7, 3.8, 3.9] | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Create directories | |
| run: mkdir -p ./cli/src/rnpfind/ro-data/hg38-human-genome/ | |
| # - name: Install tools | |
| # run: sudo apt install wget && sudo apt install gzip | |
| - name: Download chromosome 4 | |
| working-directory: ./cli/src/rnpfind/ro-data/hg38-human-genome/ | |
| run: wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr4.fa.gz && gzip -d chr4.fa.gz | |
| - name: Download chromosome 11 | |
| working-directory: ./cli/src/rnpfind/ro-data/hg38-human-genome/ | |
| run: wget https://hgdownload.soe.ucsc.edu/goldenPath/hg38/chromosomes/chr11.fa.gz && gzip -d chr11.fa.gz | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - name: Install dependencies | |
| working-directory: ./cli | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| - name: Lint with flake8 | |
| run: | | |
| # stop the build if there are Python syntax errors or undefined names | |
| flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics | |
| # exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| working-directory: ./cli | |
| run: | | |
| pytest |