R-CMD-check.yaml

# For help debugging build failures open an issue on the RStudio community with the 'github-actions' tag.
# https://community.rstudio.com/new-topic?category=Package%20development&tags=github-actions
on:
  push:
    branches:
      - main
      - master
  pull_request:
    branches:
      - main
      - master

name: R-CMD-check

jobs:
  R-CMD-check:
    runs-on: ubuntu-latest
    env:
      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
      CHUNKEDGRAPH_SECRET: ${{ secrets.CHUNKEDGRAPH_SECRET }}
      CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
      FLYTABLE_TOKEN: ${{ secrets.FLYTABLE_TOKEN }}
      RETICULATE_MINICONDA_PYTHON_VERSION: 3.8
      RGL_USE_NULL: TRUE
      _R_CHECK_DONTTEST_EXAMPLES_: FALSE
      _R_CHECK_TESTS_NLINES_: 0
      _R_CHECK_CRAN_INCOMING_REMOTE_: false

    steps:
      - uses: actions/checkout@v3

      - uses: r-lib/actions/setup-r@v2
        with:
          use-public-rspm: true

      - uses: r-lib/actions/setup-pandoc@v2

      - uses: r-lib/actions/setup-r-dependencies@v2
        with:
          extra-packages: any::rcmdcheck, any::pkgdown, catmaid=natverse/rcatmaid
          needs: check

      - name: Fix Conda permissions on macOS
        if: runner.os == 'macOS'
        run: sudo chown -R $UID $CONDA

      - name: Install fafbseg + python
        run: |
          pak::local_install()
          library(fafbseg)
          simple_python()
          dr_fafbseg()
        shell: Rscript {0}

      - name: writetoken
        run: fafbseg::flywire_set_token(token=Sys.getenv("CHUNKEDGRAPH_SECRET"))
        shell: Rscript {0}

      - uses: r-lib/actions/check-r-package@v2

      - name: Upload check results
        if: failure()
        uses: actions/upload-artifact@main
        with:
          name: ${{ runner.os }}-r${{ matrix.config.r }}-results
          path: check

      - name: Upload check log results
        if: failure()
        uses: actions/upload-artifact@v2
        with:
          name: ${{ matrix.config.tag }}-results
          path: ${{ github.event.repository.name }}.Rcheck/00check.log

      - name: Test coverage
        # if: runner.os == 'macOS'
        if: ${{ runner.os == 'Linux' && matrix.config.r == 'release'}}
        run: covr::codecov(errorsAreFatal=FALSE)
        shell: Rscript {0}