Skip to content

Integration Tests

Integration Tests #362

Workflow file for this run

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