binned points structure for sequencing-based technologies #100
Workflow file for this run
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| name: Feature Branch Checks | |
| on: | |
| pull_request: | |
| branches: [ "dev" ] | |
| jobs: | |
| unit-tests: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| permissions: | |
| contents: write | |
| packages: read | |
| actions: read | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: giotto-deps | |
| run: remotes::install_github('drieslab/GiottoUtils', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| shell: Rscript {0} | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Build and install | |
| run: | | |
| R CMD build . --no-build-vignettes | |
| R CMD INSTALL *.tar.gz | |
| - name: Run tests | |
| run: | | |
| remotes::install_github('drieslab/GiottoData', upgrade = 'never', auth_token = Sys.getenv("GITHUB_PAT")) | |
| library(testthat) | |
| library(GiottoClass) | |
| test_dir("tests/testthat") | |
| shell: Rscript {0} | |
| lintr: | |
| runs-on: ubuntu-latest | |
| timeout-minutes: 60 | |
| permissions: | |
| contents: write | |
| packages: read | |
| actions: read | |
| security-events: write | |
| container: | |
| image: ghcr.io/drieslab/ci-giottosuite/ci-env | |
| credentials: | |
| username: ${{ github.actor }} | |
| password: ${{ secrets.GITHUB_TOKEN }} | |
| steps: | |
| - name: Checkout code | |
| uses: actions/checkout@v4 | |
| with: | |
| fetch-depth: 0 # Fetch all history and tags | |
| - name: Set up GitHub token for R | |
| run: echo "GITHUB_PAT=${{ secrets.GITHUB_TOKEN }}" >> $GITHUB_ENV | |
| - name: catch R deps not in container | |
| run: devtools::install_deps() | |
| shell: Rscript {0} | |
| - name: Run lintr | |
| run: | | |
| results <- lintr::lint_package( | |
| ".", | |
| exclusions = list("tests", "vignettes", "pkgdown"), | |
| linters = lintr::linters_with_defaults( | |
| indentation_linter = lintr::indentation_linter(indent = 4L), | |
| object_name_linter = lintr::object_name_linter(styles = c("camelCase", "symbols", "snake_case", "UPPERCASE")) | |
| ) | |
| ) | |
| # Fix any invalid column numbers | |
| for (i in seq_along(results)) { | |
| if (!is.null(results[[i]]$column_number) && results[[i]]$column_number < 1) { | |
| results[[i]]$column_number <- 1 | |
| } | |
| } | |
| lintr::sarif_output(results, "lintr-results.sarif") | |
| shell: Rscript {0} | |
| continue-on-error: true | |
| - name: Upload analysis results to GitHub | |
| uses: github/codeql-action/upload-sarif@v3 | |
| with: | |
| sarif_file: lintr-results.sarif | |
| wait-for-processing: true |