152 paper submission next steps #431
Workflow file for this run
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| # Workflow triggered when we have a new release candidate | |
| # This action is adapted from https://github.com/t4d-gmbh/stubbed_versioning | |
| name: Runs on non-release pull requests | |
| on: | |
| pull_request: | |
| branches: | |
| - "*" # run for any pull request (see 1st job if condition for head name selection) | |
| jobs: | |
| should-run: | |
| if: ${{ (github.ref != 'refs/heads/main') && (!startsWith(github.head_ref, 'release-')) && (!startsWith(github.event.head_commit.message, 'noT')) }} | |
| runs-on: ubuntu-latest | |
| steps: | |
| - name: Info | |
| run: | | |
| echo "Running development tests for branch ${{ github.head_ref }}" | |
| get-target-container: | |
| needs: should-run | |
| runs-on: ubuntu-22.04 | |
| outputs: | |
| CONTAINER: ${{ steps.container.outputs.container }} | |
| steps: | |
| - name: Get container | |
| id: container | |
| env: | |
| BRANCH: ${{ github.ref_name }} | |
| run: | | |
| if [[ $BRANCH == *"__"* ]]; then | |
| echo "container=${BRANCH##*__}" >> $GITHUB_OUTPUT | |
| else | |
| echo "container=debian/clang/devel" >> $GITHUB_OUTPUT | |
| fi | |
| get_changes: | |
| needs: should-run | |
| runs-on: ubuntu-latest | |
| outputs: | |
| run_all: ${{ steps.changed_files.outputs.changed_src }} | |
| run_specific: ${{ steps.changed_files.outputs.changed_r }} | |
| env: | |
| GH_TOKEN: ${{ secrets.GITHUB_TOKEN }} | |
| OWNER: ${{ github.repository_owner }} | |
| REPO: ${{ github.event.repository.name }} | |
| EVENT: ${{ github.event.number }} # This is either the issue or pr | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Find changed files | |
| id: changed_files | |
| run: | | |
| echo "CHANGED_SRC=$(gh pr view ${{ env.EVENT }} --json 'files' --jq '.[].[] | select(.path | startswith("src/")) | .path' | xargs | sed -e 's/ /,/g')" >> $GITHUB_OUTPUT | |
| echo "CHANGED_R=$(gh pr view ${{ env.EVENT }} --json 'files' --jq '.[].[] | select(.path | startswith("R/")) | .path' | xargs | sed -e 's/ /,/g')" >> $GITHUB_OUTPUT | |
| cat $GITHUB_OUTPUT | |
| gather-tests: | |
| needs: | |
| - get_changes | |
| runs-on: ubuntu-latest | |
| outputs: | |
| testfiles: ${{ steps.get_testfiles.outputs.testfiles }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Identify tests to run | |
| id: get_testfiles | |
| run: | | |
| if [[ -z "${{ needs.get_changes.outputs.run_all }}" ]]; then | |
| if [[ -n "${{ needs.get_changes.outputs.run_specific }}" ]]; then | |
| echo "TESTFILES=$(echo ${{ needs.get_changes.outputs.run_specific }} | sed -e 's/^R\//\"tests\/testthat\/test-/g' -e 's/,R\//,\"tests\/testthat\/test-/g' | sed -e 's/.R/.R\"/g' | sed 's/.*/[\0]/')" >> $GITHUB_OUTPUT | |
| else | |
| echo "TESTFILES=[]" >> $GITHUB_OUTPUT | |
| fi | |
| else | |
| echo "TESTFILES=$(ls tests/testthat/test-*.R | jq -R -s -c 'split("\n")[:-1]')" >> $GITHUB_OUTPUT | |
| fi | |
| cat $GITHUB_OUTPUT | |
| build-install-test: | |
| if: ${{ ( needs.gather-tests.outputs.testfiles != '[]' ) }} | |
| needs: | |
| - gather-tests | |
| - get-target-container | |
| runs-on: ubuntu-22.04 | |
| # name: Testing ${{ matrix.os }} (${{ matrix.compiler}}-${{ matrix.r-version }}) | |
| name: Testing in ${{ needs.get-target-container.outputs.CONTAINER }} | |
| # runs-on: ubuntu-latest | |
| container: | |
| image: ${{ vars.CONTAINER_SOURCE }}/${{ needs.get-target-container.outputs.CONTAINER }}/abn:${{ vars.CONTAINER_VERSION || 'latest' }} | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| testfile: ${{ fromJson(needs.gather-tests.outputs.testfiles) }} | |
| env: | |
| R_KEEP_PKG_SOURCE: yes # NOTE Jo: not sure why this is here? | |
| BUILD_LOC: "./build" | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - name: Create build location | |
| run: | | |
| mkdir ${{ env.BUILD_LOC }} | |
| shell: bash | |
| - name: Disable renv | |
| run: | | |
| renv::deactivate() | |
| shell: Rscript {0} | |
| - name: Change permissions of configure | |
| run: | | |
| chmod +x configure | |
| shell: bash | |
| - name: Install package dependencies | |
| run: | | |
| devtools::install_deps(pkg = '.', dependencies = TRUE, upgrade='never') | |
| shell: Rscript {0} | |
| - name: Build the package | |
| run: | | |
| devtools::build(pkg = '.', path = '${{ env.BUILD_LOC }}/abn.tar.gz') | |
| shell: Rscript {0} | |
| - name: Install it | |
| run: | | |
| install.packages('${{ env.BUILD_LOC }}/abn.tar.gz', repos=NULL, type="source") | |
| shell: Rscript {0} | |
| - name: Running ${{ matrix.testfile }} | |
| run: | | |
| # since on a test failure devtools::test does not exit with | |
| # non-zero state we test explicitly for failed tests and exit | |
| # accordingly | |
| res=devtools::test_active_file("${{ matrix.testfile }}");df=as.data.frame(res);if(sum(df$failed) > 0 || any(df$error)) {q("no", status=1, FALSE)} | |
| shell: Rscript {0} |