refactor: Use iRODSCommon as parent class #177
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name: CI | |
on: | |
push: | |
branches: | |
- main | |
pull_request: | |
branches_ignore: [] | |
jobs: | |
cancel-previous: | |
runs-on: ubuntu-latest | |
if: github.ref != 'refs/heads/main' | |
steps: | |
- uses: khan/[email protected] | |
with: | |
workflows: "main.yml" | |
env: | |
GITHUB_TOKEN: '${{ secrets.GITHUB_TOKEN }}' | |
linting: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.8" | |
- name: Install dependencies | |
run: | | |
pip install -r requirements/test_black.txt | |
pip freeze | |
- name: Run linting tools | |
run: | | |
make lint | |
- name: Comment PR | |
if: github.event_name == 'pull_request' && failure() | |
uses: marocchino/[email protected] | |
with: | |
message: 'Please format your code with [black](https://black.readthedocs.io): `make black`.' | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
testing: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- '3.8' | |
- '3.9' | |
- '3.10' | |
needs: linting | |
steps: | |
- name: Install Python via conda | |
uses: s-weigand/setup-conda@v1 | |
with: | |
python-version: ${{ matrix.python-version }} | |
conda-channels: defaults,bioconda,conda-forge | |
- name: Checkout repository | |
uses: actions/checkout@v2 | |
with: | |
lfs: true | |
- name: Install mamba | |
run: conda install -y mamba | |
- name: Prepare environment.yaml file | |
run: > | |
cp environment.yaml /tmp/environment.yaml && sed -i -e | |
's/- python/- python=${{ matrix.python-version }}/' | |
/tmp/environment.yaml | |
- name: Update environment using mamba | |
run: mamba env update --name root --file /tmp/environment.yaml | |
- name: Save time by installing packages via mamba. | |
run: mamba install -y pysam | |
- name: Install dependencies | |
run: | | |
pip install -r requirements/test_black.txt | |
pip freeze | |
- name: Run tests | |
run: pytest | |
- uses: codecov/codecov-action@v3 |