first attempt to change from csv to parquet #221
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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://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.9 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.9 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| 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 | |
| run: | | |
| python setup.py install | |
| python tests/test_proteomicslfq.py | |
| - name: Test LFQ dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/lfq/lfq.zip | |
| unzip -d ./lfq lfq.zip | |
| python setup.py install | |
| multiqc -f ./lfq --config ./lfq/multiqc_config.yml -o ./results_lfq | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_lfq | |
| path: ./results_lfq | |
| - name: Test TMT dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/tmt-replicates/tmt-replicates.zip | |
| unzip -d ./tmt tmt-replicates.zip | |
| python setup.py install | |
| multiqc -f ./tmt --config ./tmt/multiqc_config.yml -o ./results_tmt | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_tmt | |
| path: ./results_tmt | |
| - name: Test DIA dataset | |
| run: | | |
| wget -nv https://ftp.pride.ebi.ac.uk/pub/databases/pride/resources/proteomes/pmultiqc/dia/dia.zip | |
| unzip -d ./dia dia.zip | |
| python setup.py install | |
| multiqc -f ./dia --config ./dia/multiqc_config.yml -o ./results_dia | |
| - uses: actions/upload-artifact@v1 | |
| if: always() | |
| name: Upload results | |
| with: | |
| name: results_dia | |
| path: ./results_dia | |