Adapt Snakefile #7
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| # GitHub Actions workflow for testing and continuous integration. | |
| # | |
| # This file performs testing using tox and tox.ini to define and configure the test environments. | |
| name: CI tests | |
| on: | |
| push: | |
| branches: | |
| - main # GitHub now defaults to 'main' as the name of the primary branch. Change this as needed. | |
| # tags: # run CI if specific tags are pushed | |
| pull_request: | |
| # branches: # only build on PRs against 'main' if you need to further limit when CI is run. | |
| # - main | |
| jobs: | |
| # Github Actions supports ubuntu, windows, and macos virtual environments: | |
| # https://help.github.com/en/actions/reference/virtual-environments-for-github-hosted-runners | |
| ci_tests: | |
| name: CI tests | |
| runs-on: ubuntu-latest | |
| env: | |
| CACHE_NUMBER: 0 | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v3 | |
| with: | |
| fetch-depth: 0 | |
| - name: Setup mambaforge | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| miniforge-variant: Mambaforge | |
| miniforge-version: latest | |
| activate-environment: snakemake-workflow-fermi-lat | |
| use-mamba: true | |
| - name: Cache conda environment | |
| uses: actions/cache@v2 | |
| with: | |
| path: ${{ env.CONDA }}/envs | |
| key: | |
| conda-${{ runner.os }}--${{ runner.arch }}--${{hashFiles('environment.yaml') }}-${{ env.CACHE_NUMBER }} | |
| id: cache | |
| - name: Update environment | |
| run: | |
| mamba env update -f environment.yaml | |
| if: steps.cache.outputs.cache-hit != 'true' | |
| - name: Download test files | |
| run: | | |
| cd data | |
| wget https://github.com/adonath/snakemake-workflow-fermi-lat-test-data/raw/main/L231017092559388FF7BE86_PH00.fits | |
| wget https://github.com/adonath/snakemake-workflow-fermi-lat-test-data/raw/main/L231017092559388FF7BE86_SC00.fits | |
| - name: Run tests | |
| shell: bash -l {0} | |
| run: | | |
| snakemake -c2 |