Merge pull request #94 from bio-ontology-research-group/dependabot/pi… #17
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| # This workflow will install Python dependencies, run tests and lint with a variety of Python versions | |
| # For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions | |
| name: Python Unit Tests | |
| on: | |
| push: | |
| branches: [ "main", develop ] | |
| pull_request: | |
| branches: [ "main", develop ] | |
| jobs: | |
| python-3-9: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.9"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: anaconda-client-env | |
| environment-file: envs/environment_3_9.yml | |
| auto-activate-base: false | |
| channels: conda-forge | |
| use-mamba: true | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 nose pinocchio nose-exclude coverage | |
| 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics | |
| - name: Test with nose | |
| run: | | |
| nosetests tests | |
| python-3-10: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.10"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: anaconda-client-env | |
| environment-file: envs/environment_3_10.yml | |
| auto-activate-base: false | |
| channels: conda-forge | |
| use-mamba: true | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest coverage pytest-faulthandler | |
| 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest -m "not slow" -p no:faulthandler | |
| python-3-11: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.11"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: anaconda-client-env | |
| environment-file: envs/environment_3_11.yml | |
| auto-activate-base: false | |
| channels: conda-forge | |
| use-mamba: true | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest coverage pytest-faulthandler | |
| 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest -m "not slow" -p no:faulthandler | |
| python-3-12: | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest"] | |
| python-version: ["3.12"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| auto-update-conda: true | |
| python-version: ${{ matrix.python-version }} | |
| activate-environment: anaconda-client-env | |
| environment-file: envs/environment_3_12.yml | |
| auto-activate-base: false | |
| channels: conda-forge | |
| use-mamba: true | |
| - name: Install dependencies | |
| run: | | |
| python -m pip install --upgrade pip | |
| python -m pip install flake8 pytest coverage pytest-faulthandler | |
| 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 mowl --count --exit-zero --max-complexity=20 --max-line-length=127 --statistics | |
| - name: Test with pytest | |
| run: | | |
| pytest -m "not slow" -p no:faulthandler |