some cleanup and add singularity/seqtk cases #5
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name: Continuous Integration | |
on: | |
workflow_dispatch: | |
push: | |
branches: | |
- main | |
- dev | |
paths: | |
- '**.py' | |
- '.github/workflows/**' | |
pull_request: | |
branches-ignore: [] | |
jobs: | |
build-linux: | |
runs-on: ubuntu-20.04 | |
strategy: | |
max-parallel: 5 | |
matrix: | |
python: [3.8, 3.9, '3.10'] | |
fail-fast: false | |
steps: | |
- name: precleanup | |
run: | | |
sudo rm -rf /usr/share/dotnet | |
sudo rm -rf "$AGENT_TOOLSDIRECTORY" | |
- uses: actions/checkout@v2 | |
- uses: docker-practice/actions-setup-docker@master | |
- name: Test docker | |
run: | | |
set -x | |
docker version | |
docker run --rm hello-world | |
- name: install apptainer | |
run: | | |
sudo add-apt-repository -y ppa:apptainer/ppa | |
sudo apt update | |
sudo apt install -y apptainer | |
singularity version | |
- name: Set up Python 3.X | |
uses: actions/setup-python@v2 | |
with: | |
python-version: ${{ matrix.python }} | |
- name: Install Versionix using pip | |
run: | | |
pip install . | |
pip install pytest pytest-cov coverage | |
- name: Install Damona using pip | |
run: | | |
bash | |
pip install damona | |
damona | |
echo " source ~/.config/damona/damona.sh" >> ~/.bashrc | |
- name: install some tools for testing | |
run: | | |
damona create TEST | |
damona activate TEST | |
damona install bwa | |
damona install fastqc | |
echo "$DAMONA_ENV/bin" >> $GITHUB_PATH | |
export PATH=$DAMONA_ENV/bin:$PATH | |
echo $PATH | |
which bwa | |
pytest --cov-report term --cov=versionix | |
env: | |
DAMONA_EXE: /usr/share/miniconda/bin/damona | |
DAMONA_PATH: /home/runner/.config/damona | |
DAMONA_SINGULARITY_OPTIONS: "" | |
DAMONA_ENV: /home/runner/.config/damona/envs/TEST | |
- name: coveralls | |
run: | | |
coveralls --service=github | |
env: | |
GITHUB_TOKEN: ${{ github.token }} | |