snakefmt #13
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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 }}' | |
testing-R: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- "3.12" | |
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@v4 | |
# with: | |
# lfs: true | |
# fetch-depth: 2 | |
- name: Install mamba | |
run: conda install -y mamba>=1.0.0 | |
- name: Prepare environment.yml file | |
run: cp stemcnv_check/envs/general-R.yaml /tmp/environment.yml | |
- name: Update environment using mamba | |
run: mamba env update --name root --file /tmp/environment.yml | |
- name: Run tests | |
run: Rscript -e "testthat::test_local()" | |
# env: | |
# DIFF_MAIN: ${{ github.event_name == 'pull_request' }} | |
# DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }} | |
testing-py: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- "3.12" | |
steps: | |
- name: Checkout repository | |
uses: actions/checkout@v4 | |
- name: Set up Python ${{ matrix.python-version }} | |
uses: actions/setup-python@v5 | |
with: | |
python-version: ${{ matrix.python-version }} | |
cache: 'pip' | |
- name: Install dependencies | |
run: pip install .[test] | |
- run: pytest | |