Conversion bruker data #165
Workflow file for this run
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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: Continuous integration Unit tests | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| PythonBlack: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Check code lints with Black | |
| uses: psf/black@stable | |
| # If the above check failed, post a comment on the PR explaining the failure | |
| - name: Post PR comment | |
| if: failure() | |
| uses: mshick/add-pr-comment@v1 | |
| with: | |
| message: | | |
| ## Python linting (`black`) is failing | |
| To keep the code consistent with lots of contributors, we run automated code consistency checks. | |
| To fix this CI test, please run: | |
| * Install [`black`](https://black.readthedocs.io/en/stable/): `pip install black` | |
| * Fix formatting errors in your pipeline: `black .` | |
| Once you push these changes the test should pass, and you can hide this comment :+1: | |
| We highly recommend setting up Black in your code editor so that this formatting is done automatically on save. Ask about it on Slack for help! | |
| Thanks again for your contribution! | |
| repo-token: ${{ secrets.GITHUB_TOKEN }} | |
| allow-repeats: false | |
| isort: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Check out source-code repository | |
| uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v2 | |
| with: | |
| python-version: 3.8 | |
| - name: python-isort | |
| uses: isort/[email protected] | |
| with: | |
| isortVersion: "latest" | |
| requirementsFiles: "requirements.txt requirements-dev.txt" | |
| build: | |
| runs-on: ubuntu-latest | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Set up Python 3.8 | |
| uses: actions/setup-python@v1 | |
| with: | |
| python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| pip install -r requirements.txt | |
| - name: Install package | |
| run: python setup.py install | |
| - name: Test OpenMS converter | |
| run: | | |
| cd sdrf_pipelines | |
| for sdrf in testdata/*/*.sdrf.tsv | |
| do | |
| pushd $(dirname $sdrf) | |
| python ../../parse_sdrf.py convert-openms -s $(pwd)/../../$sdrf -t2 | |
| diff -c experimental_design.tsv expected_experimental_design.tsv >> ../../failures.txt | |
| diff -c expected_openms.tsv openms.tsv >> ../../failures.txt | |
| popd | |
| done | |
| if [ -s failures.txt ] | |
| then | |
| exit 1 | |
| fi |