document use of hclust object as input #88
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| # Workflow derived from https://github.com/r-lib/actions/tree/master/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: R-CMD-check | |
| jobs: | |
| R-CMD-check: | |
| runs-on: ubuntu-latest | |
| env: | |
| GITHUB_PAT: ${{ secrets.GJPAT2 }} | |
| # GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | |
| R_KEEP_PKG_SOURCE: yes | |
| R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | |
| RGL_USE_NULL: TRUE | |
| _R_CHECK_DONTTEST_EXAMPLES_: FALSE | |
| _R_CHECK_TESTS_NLINES_: 0 | |
| NEUPRINT_TOKEN: ${{ secrets.NEUPRINT_TOKEN }} | |
| CLIO_TOKEN: ${{ secrets.CLIO_TOKEN }} | |
| FLYWIRE_PRINCIPLES: IAGREETOTHEFLYWIREPRINCIPLES | |
| steps: | |
| - uses: actions/checkout@v3 | |
| - uses: r-lib/actions/setup-r@v2 | |
| with: | |
| use-public-rspm: true | |
| - uses: r-lib/actions/setup-r-dependencies@v2 | |
| with: | |
| extra-packages: any::rcmdcheck, any::devtools, any::covr, any::pkgdown, catmaid=natverse/rcatmaid, flyconnectome/malecns | |
| needs: check, coverage | |
| - name: Add some R options for later steps | |
| run: | | |
| cat("\noptions(fafbseg.use_static_celltypes=TRUE)\n", file = "~/.Rprofile", append = TRUE) | |
| shell: Rscript {0} | |
| # nb we'll need both data dumps in the vignettes | |
| - name: Download flywire data | |
| run: | | |
| fafbseg::download_flywire_release_data(version=630) | |
| fafbseg::download_flywire_release_data(version=783) | |
| shell: Rscript {0} | |
| - uses: r-lib/actions/check-r-package@v2 | |
| - name: Deploy package | |
| run: | | |
| git config --local user.name "$GITHUB_ACTOR" | |
| git config --local user.email "$GITHUB_ACTOR@users.noreply.github.com" | |
| Rscript -e 'devtools::install(); pkgdown::deploy_to_branch(new_process = FALSE)' | |
| - name: Test coverage | |
| run: | | |
| covr::codecov( | |
| quiet = FALSE, | |
| clean = FALSE, | |
| install_path = file.path(Sys.getenv("RUNNER_TEMP"), "package") | |
| ) | |
| shell: Rscript {0} | |
| - 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@v3 | |
| with: | |
| name: coverage-test-failures | |
| path: ${{ runner.temp }}/package |