Merge pull request #74 from bigbio/dev #201
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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://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-python | |
| name: Python package | |
| on: | |
| push: | |
| branches: [ "master" ] | |
| pull_request: | |
| branches: [ "master" ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| python-version: ["3.8"] | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - name: Set up Python ${{ matrix.python-version }} | |
| uses: actions/setup-python@v3 | |
| with: | |
| python-version: ${{ matrix.python-version }} | |
| - 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 | |
| - 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 unittest | |
| run: | | |
| python setup.py install | |
| python -m unittest | |
| - name: Test commandline tool help | |
| run: | | |
| ibaqpy --help | |
| - name: Test commandline normalization features | |
| run: | | |
| rm -rfv tests/example/PXD017834-ibaq-norm.csv | |
| rm -rfv tests/example/PXD017834-peptides-norm.csv | |
| ibaqpy features2peptides --parquet tests/example/feature.parquet --sdrf tests/example/PXD017834-TMT.sdrf.tsv --min_aa 7 --min_unique 2 --remove_ids data/contaminants_ids.tsv --remove_decoy_contaminants --remove_low_frequency_peptides --output tests/example/PXD017834-peptides-norm.csv --skip_normalization --nmethod median --pnmethod max_min --log2 --save_parquet |