Fixes #293 and integrates pyrodigal v3 and pyrodigal-gv releases, add… #105
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name: CI | |
on: [push,pull_request] | |
jobs: | |
tests: | |
name: "Python ${{ matrix.python-version }}" | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -el {0} | |
strategy: | |
matrix: | |
os: [macos-latest, ubuntu-latest] | |
python-version: ["3.9"] | |
steps: | |
- uses: "actions/checkout@v3" | |
with: | |
fetch-depth: 0 | |
# Setup env | |
- uses: "conda-incubator/setup-miniconda@v2" | |
with: | |
activate-environment: pharokka_env | |
environment-file: environment.yml | |
python-version: ${{ matrix.python-version }} | |
auto-activate-base: false | |
miniforge-variant: Mambaforge | |
channels: conda-forge,bioconda,defaults | |
channel-priority: strict | |
auto-update-conda: true | |
- name: Install pharokka | |
shell: bash -l {0} | |
run: | | |
mamba install python=${{ matrix.python-version }} | |
python -m pip install --upgrade pip | |
pip install -e . | |
- name: Run tests and collect coverage | |
run: pytest --cov=./ --cov-report=xml | |
- name: Upload coverage reports to Codecov | |
uses: codecov/codecov-action@v3 | |
env: | |
CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} |