updated workflow #131
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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 | |
| # trigger workflow | |
| name: Python application | |
| on: | |
| push: | |
| branches: [ master ] | |
| pull_request: | |
| branches: [ master ] | |
| jobs: | |
| build: | |
| runs-on: ubuntu-latest | |
| container: thyscbio/bio:v3.0.5 | |
| steps: | |
| - uses: actions/checkout@v2 | |
| #- name: Set up Python 3.8 | |
| # uses: actions/setup-python@v2 | |
| # with: | |
| # python-version: 3.8 | |
| - name: Install dependencies | |
| run: | | |
| git clone https://thys_potgieter@bitbucket.org/thys_potgieter/cbio-proteogenomics-tests.git | |
| pip3 install --upgrade pip | |
| pip3 install flake8 pytest | |
| #if [ -f requirements.txt ]; then pip3 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: | | |
| pwd | |
| export PATH=$PATH::/__w/proteomics-pipelines/proteomics-pipelines/bin/python:/__w/proteomics-pipelines/proteomics-pipelines/bin/bash:/__w/proteomics-pipelines/proteomics-pipelines/bin/R:/__w/proteomics-pipelines/proteomics-pipelines/bin/perl | |
| export PYTHONPATH=$PYTHONPATH::/__w/proteomics-pipelines/proteomics-pipelines/lib | |
| echo $PATH | |
| cd cbio-proteogenomics-tests/lib && pytest -v |