Bump actions/download-artifact from 1 to 4.1.7 in /.github/workflows #42
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| name: CI | |
| on: | |
| push: | |
| paths-ignore: | |
| - 'README.md' | |
| - 'LICENSE' | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| download_taxonomy: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: Install | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| python -m pip install . | |
| - name: Download taxonomy | |
| run: contigtax download taxonomy | |
| - name: Upload taxonomy | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: taxonomy | |
| path: taxonomy | |
| build: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| matrix: | |
| python-version: [3.6, 3.7, 3.8, 3.9] | |
| os: [ubuntu-latest, macos-latest] | |
| needs: download_taxonomy | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - uses: s-weigand/setup-conda@v1 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install flake8 pytest | |
| pip install -r requirements.txt | |
| - 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: Install base env | |
| run: conda install -n base -c bioconda diamond | |
| - name: Install package | |
| run: python -m pip install . | |
| - name: Test with pytest | |
| run: python -m pytest | |
| - name: Format fasta | |
| run: | | |
| gzip -c tests/data/uniref100.fasta > uniref100.fasta.gz | |
| contigtax format -m uniref100.map.gz uniref100.fasta.gz uniref100.reformat.fasta.gz | |
| - name: Download taxonomy | |
| uses: actions/[email protected] | |
| with: | |
| name: taxonomy | |
| - name: Build | |
| run: contigtax build -d uniref100.dmnd uniref100.reformat.fasta.gz uniref100.map.gz taxonomy/nodes.dmp | |
| - name: Search | |
| run: contigtax search --taxonmap uniref100.map.gz -p 4 tests/data/shreds.fasta uniref100.dmnd shreds.tsv.gz | |
| - name: Assign | |
| run: contigtax assign --taxidout taxids.tsv -p 4 shreds.tsv.gz taxonomy.tsv | |
| - name: Evaluate | |
| run: | | |
| mkdir -p ${{ github.workspace }}/${{ matrix.python-version }}/evaluate | |
| evaluate_contigtax.py taxids.tsv tests/data/shreds.taxids.tsv >${{ github.workspace }}/${{ matrix.python-version }}/evaluate/eval.tsv 2>${{ github.workspace }}/${{ matrix.python-version }}/evaluate/eval.log | |
| - name: Archive evaluation results | |
| uses: actions/upload-artifact@v1 | |
| with: | |
| name: ${{ runner.os }}-python-${{ matrix.python-version }}-eval | |
| path: ${{ github.workspace }}/${{ matrix.python-version }}/evaluate |