Merge pull request #34 from bigbio/dev #209
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| # This workflow will install Python dependencies, run tests and lint with a single version of Python | |
| # For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ "main" ] | |
| pull_request: | |
| branches: [ "main" ] | |
| permissions: | |
| contents: read | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Set up Python 3.11 | |
| uses: actions/setup-python@v5 | |
| with: | |
| python-version: "3.11" | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest | |
| if [ -f requirements.txt ]; then pip install -r requirements.txt; fi | |
| pip install poetry | |
| poetry build | |
| pip install dist/*.whl | |
| - 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 | |
| env: | |
| CUDA_VISIBLE_DEVICES: "-1" | |
| run: | | |
| poetry run pytest -vv | |
| - name: Download test files | |
| env: | |
| CUDA_VISIBLE_DEVICES: "-1" | |
| run: | | |
| wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML | |
| wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML | |
| wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/191126_AMLM_THY01-DN4_Thymus_Tue39L243_10_DDA_2_400-1000mz_msms40_standard.mzML | |
| wget https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/quantms-ci-github/quantms-utils/191126_AMLM_THY01-DN4_Thymus_Tue39L243_10_DDA_2_400-1000mz_msms40_standard_comet.idXML | |
| - name: Test ms2pip ms2rescore | |
| env: | |
| CUDA_VISIBLE_DEVICES: "-1" | |
| run: | | |
| rescoring msrescore2feature --idxml TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01_comet.idXML --mzml TMT_Erwinia_1uLSike_Top10HCD_isol2_45stepped_60min_01.mzML --processes 2 --feature_generators 'ms2pip,deeplc' | |
| - name: Test alphapeptdeep ms2rescore | |
| env: | |
| CUDA_VISIBLE_DEVICES: "-1" | |
| run: | | |
| rescoring msrescore2feature --idxml 191126_AMLM_THY01-DN4_Thymus_Tue39L243_10_DDA_2_400-1000mz_msms40_standard_comet.idXML --mzml 191126_AMLM_THY01-DN4_Thymus_Tue39L243_10_DDA_2_400-1000mz_msms40_standard.mzML --processes 8 -o test3.idXML --feature_generators 'alphapeptdeep' | |
| - name: Upload coverage reports to Codecov | |
| uses: codecov/codecov-action@v5 | |
| with: | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| slug: bigbio/quantms-rescoring |