Test PR for CI #40
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Test Atlas perl modules | |
| on: [pull_request] | |
| jobs: | |
| setup: | |
| name: ${{ matrix.os }}) | |
| runs-on: ${{ matrix.os }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| os: ["ubuntu-latest", "macos-latest"] | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| steps: | |
| - uses: actions/checkout@v2 | |
| - name: Checkout config repo | |
| uses: actions/checkout@v2 | |
| with: | |
| repository: ebi-gene-expression-group/metadata-validation-config | |
| path: config | |
| - name: Add workspace to path | |
| run: | | |
| echo "${GITHUB_WORKSPACE}" >> $GITHUB_PATH | |
| echo "${GITHUB_WORKSPACE}/tests" >> $GITHUB_PATH | |
| - name: Cache conda | |
| uses: actions/cache@v1 | |
| env: | |
| # Increase this value to reset cache if etc/example-environment.yml has not changed | |
| CACHE_NUMBER: 0 | |
| with: | |
| path: ~/conda_pkgs_dir | |
| key: | |
| ${{ matrix.os }}-conda-${{ env.CACHE_NUMBER }}-${{hashFiles('test-environment.yml') }} | |
| # We use conda to install magetab-curation-scripts, which will also | |
| # install perl-atlas-modules and grab all the dependencies for us. Then | |
| # we just copy the perl modules and supporting files to overwrite the | |
| # installed ones for testing of the current codebase. | |
| - uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: test | |
| environment-file: test-environment.yml | |
| python-version: 3.6 | |
| channels: conda-forge,bioconda,defaults,ebi-gene-expression-group | |
| allow-softlinks: true | |
| channel-priority: flexible | |
| show-channel-urls: true | |
| use-only-tar-bz2: true | |
| - shell: bash -l {0} | |
| run: | | |
| rm -rf ${CONDA_PREFIX}/atlasprod/perl_modules | |
| cp -r perl_modules ${CONDA_PREFIX}/atlasprod | |
| rm -rf ${CONDA_PREFIX}/atlasprod/supporting_files | |
| cp -r supporting_files ${CONDA_PREFIX}/atlasprod | |
| - name: Run tests | |
| env: | |
| FASTQ_FILE_REPORT: 'http://ftp.ebi.ac.uk/pub/databases/ena/report/fastqFileReport.gz' | |
| run: | | |
| run-tests.sh |