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refactor: Omit logger from coverage reports #114

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refactor: Omit logger from coverage reports

refactor: Omit logger from coverage reports #114

Workflow file for this run

.github/workflows/main.yml at 690a19c
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: ${{ matrix.python-version }}
conda-channels: defaults,bioconda,conda-forge
- name: Checkout repository
uses: actions/checkout@v2
with:
lfs: true
- name: Install mamba
run: conda install -y mamba==0.27.0
- name: Prepare environment.yaml file
run: >
cp environment.yaml /tmp/environment.yaml && sed -i -e
's/- python/- python=${{ 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