fix: remove hard coded contig names from gcnv wrappers (#489 ) (#490) #1394
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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: "3.10" | |
- name: Install dependencies | |
run: | | |
pip install -r requirements/test.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 Python code with [black](https://black.readthedocs.io): `make black` | |
- Please format your Snakemake code with [snakefmt](https://github.com/snakemake/snakefmt): `make snakefmt` | |
- Please organize your imports [isorts](https://isort.readthedocs.io): `make isort` | |
- Please ensure that your code passes [flake8](https://flake8.pycqa.org/en/latest/): `make flake8` | |
You can trigger all lints locally by running `make lint` | |
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
sphinx-docs: | |
runs-on: ubuntu-latest | |
steps: | |
- uses: actions/checkout@v1 | |
- name: Install Python | |
uses: actions/setup-python@v2 | |
with: | |
python-version: "3.10" | |
- name: Install dependencies | |
run: | | |
pip install -r requirements/test.txt | |
pip freeze | |
- name: Build documentation | |
run: | | |
cd docs | |
make html | |
testing: | |
runs-on: ubuntu-latest | |
strategy: | |
matrix: | |
python-version: | |
- "3.10" | |
# - "3.11" # no compatible pysam yet | |
# - "3.12" # no compatible pysam yet | |
needs: linting | |
steps: | |
- name: Install Python via conda | |
uses: s-weigand/setup-conda@v1 | |
with: | |
python-version: ${{ matrix.python-version }} | |
conda-channels: defaults,bioconda,conda-forge | |
- name: Checkout repository | |
uses: actions/checkout@v2 | |
with: | |
lfs: true | |
fetch-depth: 2 | |
- name: Install mamba | |
run: conda install -y mamba>=1.0.0 | |
- name: Prepare environment.yml file | |
run: > | |
cp environment.yml /tmp/environment.yml && sed -i -e | |
's/- python/- python=${{ matrix.python-version }}/' | |
/tmp/environment.yml | |
- name: Update environment using mamba | |
run: mamba env update --name root --file /tmp/environment.yml | |
- name: Fail early on htslib etc. problems | |
run: | | |
set -euo pipefail | |
bgzip -c /dev/null >/dev/null | |
samtools version | |
bcftools version | |
- name: Install some more dependencies via pip | |
# Workaround - see https://github.com/pytest-dev/pytest/issues/10420#issuecomment-1290697849 | |
run: pip install -r requirements/test.txt; pip install --ignore-installed py | |
- name: Run tests | |
run: pytest | |
env: | |
DIFF_MAIN: ${{ github.event_name == 'pull_request' }} | |
DIFF_LAST_COMMIT: ${{ github.ref == 'refs/heads/main' }} | |
- name: Create text report | |
run: coverage report | |
- name: Coveralls | |
uses: AndreMiras/coveralls-python-action@develop |