pin numpy in environment.yml #95
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| # This workflow will install Python dependencies, run lint and nose tests. | |
| # https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: continuous integration | |
| on: | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| jobs: | |
| canceller: | |
| runs-on: ubuntu-18.04 | |
| steps: | |
| - name: cancel previous runs | |
| uses: styfle/[email protected] | |
| with: | |
| access_token: ${{ github.token }} | |
| tests: | |
| runs-on: ${{ matrix.os }} | |
| defaults: | |
| run: | |
| # Use a login shell, so that ~/.bash_profile is executed and | |
| # the conda environment gets initialised. | |
| shell: bash -l {0} | |
| strategy: | |
| matrix: | |
| os: [ubuntu-18.04, macos-10.15] | |
| #python-version: [3.6, 3.8] | |
| env: | |
| CONDA_ENV_NAME: genomatnn | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: find conda | |
| id: find-conda | |
| run: | | |
| echo "::set-output name=CONDA::$CONDA" | |
| - name: fix conda permissions | |
| if: runner.os == 'macOS' | |
| run: | | |
| # Fix incorrect conda permissions on mac that prevent cache restore. | |
| sudo chown -R $USER:staff $CONDA | |
| - name: cache conda | |
| id: cache | |
| uses: actions/cache@v2 | |
| env: | |
| # Increase this to reset the cache if the key hasn't changed. | |
| CACHE_NUM: 0 | |
| with: | |
| path: | | |
| ${{ steps.find-conda.outputs.CONDA }}/envs/${{ env.CONDA_ENV_NAME }} | |
| ~/.bash_profile | |
| key: ${{ runner.os }}-${{ matrix.python }}-conda-${{ hashFiles('environment.yml', 'requirements.txt') }}-${{ env.CACHE_NUM }} | |
| - name: install conda | |
| uses: conda-incubator/setup-miniconda@v2 | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| with: | |
| activate-environment: ${{ env.CONDA_ENV_NAME }} | |
| environment-file: environment.yml | |
| #python-version: ${{ matrix.python }} | |
| channels: conda-forge | |
| channel-priority: strict | |
| auto-update-conda: true | |
| use-only-tar-bz2: true | |
| - name: move profile | |
| if: steps.cache.outputs.cache-hit != 'true' && runner.os != 'Windows' | |
| run: | | |
| # The setup-miniconda action leaves different shell init files for | |
| # different OSes. Bash gives priority to ~/.bash_profile, so here we | |
| # ensure that's used for all platforms. | |
| mv ~/.profile ~/.bash_profile | |
| - name: Build | |
| run: | | |
| python setup.py build_ext -i | |
| - name: Lint with flake8 | |
| run: | | |
| pip install flake8 | |
| # 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. | |
| flake8 . --count --exit-zero --max-complexity=10 --max-line-length=89 --statistics | |
| - name: Test with nose | |
| run: | | |
| nosetests -v tests | |