fix duplicate listing when finding flytable base #45
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| # Workflow derived from https://github.com/r-lib/actions/tree/v2/examples | |
| # Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help | |
| on: | |
| push: | |
| branches: [main, master] | |
| pull_request: | |
| branches: [main, master] | |
| name: test-coverage.yaml | |
| permissions: read-all | |
| jobs: | |
| test-coverage: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| CHUNKEDGRAPH_SECRET: ${{ secrets.CHUNKEDGRAPH_SECRET }} | |
| CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }} | |
| FLYTABLE_TOKEN: ${{ secrets.FLYTABLE_TOKEN }} | |
| RGL_USE_NULL: TRUE | |
| _R_CHECK_DONTTEST_EXAMPLES_: FALSE | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| _R_CHECK_CRAN_INCOMING_REMOTE_: false | |
| FLYWIRE_PRINCIPLES: IAGREETOTHEFLYWIREPRINCIPLES | |
| steps: | |
| - uses: actions/checkout@v4 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::covr, any::xml2, catmaid=natverse/rcatmaid, any::hdf5r, any::arrow | |
| needs: coverage | |
| - name: Install fafbseg + python | |
| run: | | |
| pak::local_install() | |
| library(fafbseg) | |
| simple_python() | |
| simple_python(pkgs = 'fafbseg') | |
| dr_fafbseg() | |
| shell: Rscript {0} | |
| - name: Test coverage | |
| run: | | |
| cov <- covr::package_coverage( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package") | |
| ) | |
| covr::to_cobertura(cov) | |
| shell: Rscript {0} | |
| - uses: codecov/codecov-action@v4 | |
| with: | |
| # fail_ci_if_error: ${{ github.event_name != 'pull_request' && true || false }} | |
| fail_ci_if_error: false | |
| file: ./cobertura.xml | |
| plugin: noop | |
| disable_search: true | |
| token: ${{ secrets.CODECOV_TOKEN }} | |
| - name: Show testthat output | |
| if: always() | |
| run: | | |
| ## -------------------------------------------------------------------- | |
| find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true | |
| shell: bash | |
| - name: Upload test results | |
| if: failure() | |
| uses: actions/upload-artifact@v4 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |