added comments to show sectioning of xmsannotator workflow #111
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| # This is a basic workflow to help you get started with Actions | |
| name: R Conda | |
| # Controls when the workflow will run | |
| on: | |
| # Triggers the workflow on push or pull request events but only for the main branch | |
| push: | |
| branches: [ main ] | |
| pull_request: | |
| branches: [ main ] | |
| # Allows you to run this workflow manually from the Actions tab | |
| workflow_dispatch: | |
| # A workflow run is made up of one or more jobs that can run sequentially or in parallel | |
| jobs: | |
| # This workflow contains a single job called "build" | |
| build: | |
| # The type of runner that the job will run on | |
| runs-on: ubuntu-latest | |
| env: | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| defaults: | |
| run: | |
| shell: bash -l {0} | |
| # Steps represent a sequence of tasks that will be executed as part of the job | |
| steps: | |
| # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it | |
| - uses: actions/checkout@v3 | |
| - name: Create conda environment | |
| uses: conda-incubator/setup-miniconda@v2 | |
| with: | |
| activate-environment: recetox-xmsannotator-dev | |
| auto-update-conda: true | |
| environment-file: conda/environment-dev.yaml | |
| auto-activate-base: false | |
| - run: | | |
| conda init bash | |
| conda env list | |
| - name: Fetch batch1_neg test data | |
| run: wget -P tests/testthat/test-data/batch1_neg -i tests/remote-files/fetch_batch1_neg.txt | |
| - name: Fetch qc_solvent test data | |
| run: wget -P tests/testthat/test-data/qc_solvent -i tests/remote-files/fetch_qc_solvent.txt | |
| - name: Fetch sourceforge test data | |
| run: wget -P tests/testthat/test-data/sourceforge -i tests/remote-files/fetch_sourceforge.txt | |
| - name: Fetch qc_matrix test data | |
| run: wget -P tests/testthat/test-data/qc_matrix -i tests/remote-files/fetch_qc_matrix.txt | |
| - name: Test coverage | |
| run: | | |
| conda activate recetox-xmsannotator-dev | |
| Rscript -e "options(covr.gcov=''); covr::codecov(quiet = FALSE)" |