Test #19
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name: Test | |
on: | |
push: | |
branches: [master] | |
pull_request: | |
branches: [master] | |
schedule: | |
- cron: "0 5 1,15 * *" | |
concurrency: | |
group: ${{ github.workflow }}-${{ github.ref }} | |
cancel-in-progress: true | |
jobs: | |
test: | |
runs-on: ${{ matrix.os }} | |
defaults: | |
run: | |
shell: bash -l {0} # -e to fail on error | |
strategy: | |
fail-fast: false | |
matrix: | |
os: [ubuntu-latest, macos-13] | |
python: ["3.7", "3.8", "3.9", "3.10", "3.11"] | |
name: ${{ matrix.name }} Python ${{ matrix.python }} | |
env: | |
OS: ${{ matrix.os }} | |
PYTHON: ${{ matrix.python }} | |
steps: | |
- uses: actions/checkout@v3 | |
# - name: Set up Python ${{ matrix.python }} | |
# uses: actions/setup-python@v4 | |
# with: | |
# python-version: ${{ matrix.python }} | |
# cache: "pip" | |
# cache-dependency-path: "**/pyproject.toml" | |
- uses: conda-incubator/setup-miniconda@v3 | |
with: | |
mamba-version: "*" | |
auto-update-conda: true | |
auto-activate-base: false | |
python-version: ${{ matrix.python }} | |
channels: conda-forge, bioconda, defaults | |
activate-environment: test_dbcan | |
environment-file: envs/test.yml | |
- name: export test_dbcan environment | |
run: mamba env export | |
# - name: Install test dependencies | |
# run: | | |
# python -m pip install --upgrade pip wheel | |
# - name: create run_dbcan environment | |
# run: conda create -n run_dbcan python=${{ matrix.python }} | |
# - name: activate run_dbcan environment | |
# run: conda activate run_dbcan | |
- name: Install dependencies | |
run: | | |
pip install ${{ matrix.pip-flags }} ".[dev,test]" | |
# - name: Add conda to PATH | |
# run: | | |
# echo ::add-path::$CONDA/bin | |
- name: Build dbCAN Database | |
run: | | |
dbcan_build --cpus 1 --db-dir db --clean | |
# conda install -y -c bioconda -c conda-forge hmmer diamond blast prodigal | |
- name: Test | |
env: | |
MPLBACKEND: agg | |
PLATFORM: ${{ matrix.os }} | |
DISPLAY: :42 | |
run: | | |
coverage run -m pytest -v --color=yes |