Integration Tests #362
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name: Integration Tests | |
on: | |
pull_request: # Run on all pull requests | |
push: | |
branches: # Run on any push to master and development | |
- master | |
- development | |
schedule: # Run weekly on master and development | |
- cron: 0 2 * * 0 | |
branches: master | |
- cron: 0 2 * * 0 | |
branches: development | |
jobs: | |
build: | |
runs-on: ubuntu-latest | |
env: | |
DATABASE_COMMITS: '--resfinder-commit fa32d9a3cf0c12ec70ca4e90c45c0d590ee810bd --pointfinder-commit 8c694b9f336153e6d618b897b3b4930961521eb8 --plasmidfinder-commit c18e08c17a5988d4f075fc1171636e47546a323d' | |
strategy: | |
fail-fast: False | |
matrix: | |
include: | |
- python-version: "3.9" | |
other-packages: "mlst numpy pandas" | |
steps: | |
- uses: actions/checkout@v2 | |
- name: Setup Conda with Python ${{ matrix.python-version }} | |
uses: conda-incubator/setup-miniconda@v2 | |
with: | |
miniconda-version: "latest" | |
activate-environment: staramr-env | |
python-version: ${{ matrix.python-version }} | |
- name: Install conda packages | |
shell: bash -l {0} | |
run: | | |
conda info | |
conda list | |
conda config --add channels defaults | |
conda config --add channels conda-forge | |
conda config --add channels bioconda | |
conda install -n base conda-libmamba-solver | |
conda config --set solver libmamba | |
conda install Cython blast git perl-list-moreutils ${{ matrix.other-packages }} -y | |
- name: Setup python packages | |
shell: bash -l {0} | |
run: | | |
python --version | |
python setup.py -q install | |
- name: Build database | |
shell: bash -l {0} | |
run: staramr db build --dir staramr/databases/data ${{ env.DATABASE_COMMITS }} | |
- name: Run Tests | |
shell: bash -l {0} | |
run: python setup.py test |