Merge pull request #220 from natverse/fix/flywire_xyz2id-usevoxdims #479
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| # 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: ${{ matrix.config.os }} | |
| name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | |
| strategy: | |
| fail-fast: false | |
| matrix: | |
| config: | |
| # - {os: windows-latest, r: 'release'} | |
| - {os: macOS-latest, r: 'release'} | |
| - {os: ubuntu-latest, r: 'release'} | |
| # - {os: ubuntu-20.04, r: 'devel'} | |
| 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: "3.10.14" | |
| 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 | |
| r-version: ${{ matrix.config.r }} | |
| - 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, any::hdf5r, any::arrow | |
| needs: check | |
| - name: Fix Conda permissions on macOS | |
| if: runner.os == 'macOS-setaside' | |
| run: sudo chown -R $UID $CONDA | |
| - name: Install fafbseg + python | |
| run: | | |
| pak::local_install() | |
| library(fafbseg) | |
| simple_python() | |
| # arrow::install_pyarrow() | |
| # just install miniconda to start with | |
| # fafbseg:::simple_python_base("basic", miniconda=TRUE) | |
| # now install defined package versions | |
| # reticulate::py_install('botocore==1.35.17', pip = T, pip_options='--upgrade --prefer-binary') | |
| # reticulate::py_install('boto3==1.35.17', pip = T, pip_options='--upgrade --prefer-binary') | |
| # reticulate::py_install('google_auth==2.34.0', pip = T, pip_options='--upgrade --prefer-binary') | |
| # reticulate::py_install('cloud-volume==10.4.0', pip = T, pip_options='--upgrade --prefer-binary') | |
| # reticulate::py_install('caveclient==5.29.1', pip = T, pip_options='--upgrade --prefer-binary') | |
| # now install the rest | |
| simple_python(pkgs = 'fafbseg') | |
| dr_fafbseg() | |
| 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@v4 | |
| 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} |