Update test_test.yaml #161
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name: test | |
on: | |
push: | |
branches: | |
- main | |
paths-ignore: | |
- 'README.md' | |
- 'pyproject.toml' | |
- 'docs/**' | |
- 'tutorials/**' | |
pull_request: | |
branches: | |
- main | |
paths-ignore: | |
- 'README.md' | |
- 'pyproject.toml' | |
- 'docs/**' | |
- 'tutorials/**' | |
- '.github/workflows/**' | |
workflow_dispatch: | |
workflow_call: | |
jobs: | |
build: | |
runs-on: ${{ matrix.os }} | |
strategy: | |
max-parallel: 12 | |
matrix: | |
os: [ubuntu-latest] #, macos-latest, windows-latest | |
python-version: ["3.10"] # "3.10", "3.11", "3.12" | |
steps: | |
- name: Checkout Repository | |
uses: actions/checkout@v3 | |
- name: Setup Conda for Ubuntu and Mac | |
if: matrix.os != 'windows-latest' | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
python-version: ${{ matrix.python-version }} | |
activate-environment: "test-env" | |
- name: Setup Conda for Windows | |
if: matrix.os == 'windows-latest' | |
uses: s-weigand/setup-conda@v1 | |
with: | |
python-version: ${{ matrix.python-version }} | |
activate-environment: "test-env" | |
conda-channels: anaconda, conda-forge | |
- name: Update conda and add channels | |
run: | | |
conda config --add channels bioconda | |
conda config --add channels conda-forge | |
conda update --all | |
- name: Install conda dependencies | |
run: | | |
conda install -n test-env -y "blast>=2.15.0" "bedtools>=2.30" "bowtie>=1.3.1" "bowtie2>=2.5" | |
- name: Activate Conda Environment | |
shell: bash | |
run: | | |
source $(conda info --base)/etc/profile.d/conda.sh | |
conda activate test-env | |
conda update pip | |
conda info --envs | |
- name: Install pip dependencies | |
run: | | |
python --version | |
python -m pip install --upgrade pip | |
pip install pytest | |
pip install -e . | |
- name: Test with pytest | |
run: pytest tests/test_oligo_specificity_filter.py | |