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pythonapp.yml
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# This workflow will install Python dependencies, run tests and lint with a single version of Python
# For more information see: https://help.github.com/actions/language-and-framework-guides/using-python-with-github-actions
name: Python application
on:
push:
branches: [ spectrumAI ]
pull_request:
branches: [ spectrumAI ]
jobs:
build:
runs-on: ubuntu-latest
strategy:
matrix:
python-version: [3.7, 3.8]
steps:
- uses: actions/checkout@v2
- name: Set up Python ${{ matrix.python-version }}
uses: actions/setup-python@v1
with:
python-version: ${{ matrix.python-version }}
- name: Setup Miniconda
uses: conda-incubator/[email protected]
with:
use-mamba: true
auto-activate-base: true
- name: Install dependencies
shell: bash -l {0}
run: |
conda install --channel conda-forge --channel bioconda bedtools htslib
python -m pip install --upgrade pip
pip install flake8 pytest
if [ -f requirements.txt ]; then pip install -r requirements.txt; fi
- name: Lint with flake8
shell: bash -l {0}
run: |
# stop the build if there are Python syntax errors or undefined names
flake8 . --count --select=E9,F63,F7,F82 --show-source --statistics
# exit-zero treats all errors as warnings. The GitHub editor is 127 chars wide
flake8 . --count --exit-zero --max-complexity=10 --max-line-length=127 --statistics
- name: Test with pytest
shell: bash -l {0}
run: |
python setup.py install
cd pypgatk
python tests/pypgatk_tests.py
- name: Update changelog
uses: heinrichreimer/[email protected]
with:
token: ${{ secrets.GITHUB_TOKEN }}
- name: Update repo with new version info
uses: EndBug/add-and-commit@v7
with:
add: CHANGELOG.md
author_name: Release Auto-Commit
author_email: [email protected]
branch: dev
message: Updates version info for ${{github.event.release.name}}
- name: Generate coverage report
shell: bash -l {0}
run: |
pip install pytest
pip install pytest-cov
python setup.py install
cd pypgatk
pytest --cov=./ --cov-report=xml tests/*