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fix: chr format detection in gcnv wrappers needs to always use egrep #1595

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fix: chr format detection in gcnv wrappers needs to always use egrep

fix: chr format detection in gcnv wrappers needs to always use egrep #1595

Workflow file for this run

.github/workflows/ci.yml at 8d9d441
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