Merge pull request #548 from gagneurlab/dev #902
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name: Build | |
on: [push,pull_request] | |
jobs: | |
build-linux: | |
runs-on: ubuntu-latest | |
# container: | |
# image: mambaorg/micromamba:latest | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Setup environment with micromamba | |
uses: mamba-org/provision-with-micromamba@v10 | |
- name: Check micromamba install | |
shell: bash -l {0} | |
run: | | |
micromamba --version | |
micromamba env list | |
# - name: Install dependencies | |
# run: mamba env update -f environment.yml | |
- name: Lint with flake8 | |
shell: bash -l {0} | |
run: | | |
# stop the build if there are Python syntax errors or undefined names | |
flake8 . --count --builtins="snakemake" --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: Install DROP | |
shell: bash -l {0} | |
run: pip install -e . | |
- name: Test with pytest | |
shell: bash -l {0} | |
env: | |
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
run: | | |
micromamba install pytest | |
pip install -r tests/requirements.txt | |
pytest |