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Update GitHub actions based on those used by {rhdf5} (#378)
* Add R-CMD-check-bioc GHA * Remove rhdf5 reinstall from pkgdown GHA * Add test-coverage GHA * Use latest OS versions in R-CMD-check-bioc GHA * Only run BiocCheck on Ubuntu devel * Run usethis::use_coverage() * Remove R-CMD-check GHA * Use checkout@v5 in R-CMD-check-bioc * Show testthat output and update results * Adjust directory to show testthat output * Try finding check directory * Try manually setting paths * Show working directory * Add Linux dependencies for rhdf5 * Show more paths... * Fix working-dir variable * Normalise working dir * Use R to normalise paths for Windows compatibility * Move paths after R is installed * Adjust path logic * Use R to set paths * Fix path name * Only normalise output paths * More path fixes * Adjust check path for non-Windows * Fix typo * Fix .Platform instead of platform * Fix pkg_dir instead of pkg_name * Tidy R-CMD-check-bioc workflow * Add Linux dependencies to test-coverage GHA * Restore README whitespace * Fix README whitespace * Run R-CMD-check-bioc on all PRs Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Use checkout@v5 in test-coverage Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> * Remove README.md whitespace Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com> --------- Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
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‎.Rbuildignore‎

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^Meta$
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^man/figures/*\.svg$
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^data$
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^codecov\.yml$

‎.github/workflows/R-CMD-check-bioc.yaml‎

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# Based on workflows from https://github.com/Huber-group-EMBL/rhdf5
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# Uses steps from https://github.com/grimbough/bioc-actions
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on:
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push:
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branches:
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- devel
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pull_request:
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name: R-CMD-check-bioc
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concurrency:
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group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
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cancel-in-progress: true
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
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jobs:
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R-CMD-check-bioc:
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runs-on: ${{ matrix.config.os }}
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name: ${{ matrix.config.os }} (${{ matrix.config.bioc-version }})
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strategy:
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fail-fast: false
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matrix:
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config:
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- { os: windows-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', Ncpus: 2}
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- { os: macOS-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', Ncpus: 3}
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- { os: macOS-15-intel, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', Ncpus: 3}
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- { os: ubuntu-latest, bioc-version: 'devel', bioc-mirror: 'https://bioconductor.posit.co/', Ncpus: 4}
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- { os: ubuntu-latest, bioc-version: 'release', bioc-mirror: 'https://packagemanager.posit.co/bioconductor', Ncpus: 4}
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steps:
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## R CMD check complains about Windows line endings without this
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- name: Configure git
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run: |
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git config --global core.autocrlf false
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- name: Checkout repository
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uses: actions/checkout@v5
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get -y install hdf5-tools libsz2 libaec-dev
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- name: Setup R and Bioconductor
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uses: grimbough/bioc-actions/setup-bioc@v1
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with:
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bioc-version: ${{ matrix.config.bioc-version }}
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bioc-mirror: ${{ matrix.config.bioc-mirror }}
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- name: Set paths
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id: set-paths
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run: |
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current_dir <- getwd()
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cat("Current dir:", normalizePath(current_dir), "\n")
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sep <- ifelse(.Platform$OS.type == "windows", "\\\\", "/")
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pkg_name <- basename(current_dir)
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cat("Package name:", pkg_name, "\n")
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cat("pkg-name=", pkg_name, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
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working_dir <- ".."
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working_dir_norm <- normalizePath(working_dir)
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cat("Working dir:", working_dir_norm, "\n")
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cat("working-dir=", working_dir_norm, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
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pkg_dir <- file.path(working_dir, pkg_name)
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pkg_dir_norm <- normalizePath(pkg_dir)
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cat("Package dir:", pkg_dir_norm, "\n")
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cat("pkg-dir=", pkg_dir_norm, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
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# Handle different behavior of normalizePath on Windows
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check_dir <- if (.Platform$OS.type == "windows") {
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paste0(pkg_dir, ".Rcheck")
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} else {
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paste0(normalizePath(pkg_dir), ".Rcheck")
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}
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check_dir_norm <- normalizePath(check_dir)
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cat("Check dir:", check_dir_norm, "\n")
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cat("check-dir=", check_dir_norm, "\n", file = Sys.getenv("GITHUB_OUTPUT"), sep = "", append = TRUE)
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shell: Rscript {0}
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- name: Install pandoc
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uses: r-lib/actions/setup-pandoc@v2
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::rcmdcheck
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needs: check
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- name: Bioc - Build, Install, Check
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uses: grimbough/bioc-actions/build-install-check@v1
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- name: Show testthat output
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run: |
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find . -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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working-directory: ${{ steps.set-paths.outputs.working-dir }}
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- name: Upload check results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: ${{ format('{0}-{1}-bioc-{2}-results', runner.os, runner.arch, env.R_BIOC_VERSION ) }}
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path: ${{ steps.set-paths.outputs.check-dir }}
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- name: Run BiocCheck
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if: matrix.config.os == 'ubuntu-latest' && matrix.config.bioc-version == 'devel'
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uses: grimbough/bioc-actions/run-BiocCheck@v1
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with:
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error-on: 'never'
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arguments: '--no-check-bioc-help'

‎.github/workflows/R-CMD-check.yaml‎

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‎.github/workflows/pkgdown.yaml‎

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extra-packages: local::.
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needs: website
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# Avoid a caching issue where {rhdf5} was not restored properly
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- name: Reinstall {rhdf5} and check availability
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run: |
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BiocManager::install(c("rhdf5", "Rhdf5lib"), force = TRUE)
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if (requireNamespace("rhdf5")) {
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cat(as.character(packageVersion("rhdf5")))
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} else {
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stop("rhdf5 not found")
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}
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shell: Rscript {0}
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- name: Build site
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run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
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shell: Rscript {0}

‎.github/workflows/test-coverage.yaml‎

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# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
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# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
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on:
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workflow_dispatch:
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push:
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branches: devel
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pull_request:
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name: test-coverage.yaml
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permissions: read-all
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jobs:
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test-coverage:
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runs-on: ubuntu-latest
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env:
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GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v5
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- name: Install Linux dependencies
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if: runner.os == 'Linux'
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run: |
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sudo apt-get update
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sudo apt-get -y install hdf5-tools libsz2 libaec-dev
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- name: Setup R
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uses: r-lib/actions/setup-r@v2
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with:
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use-public-rspm: true
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- name: Install R dependencies
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uses: r-lib/actions/setup-r-dependencies@v2
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with:
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extra-packages: any::covr, any::xml2
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needs: coverage
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- name: Test coverage
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run: |
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cov <- covr::package_coverage(
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quiet = FALSE,
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clean = FALSE,
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install_path = file.path(normalizePath(Sys.getenv("RUNNER_TEMP"), winslash = "/"), "package")
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)
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print(cov)
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covr::to_cobertura(cov)
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shell: Rscript {0}
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- name: Upload coverage to Codecov
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uses: codecov/codecov-action@v5
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with:
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# Fail if error if not on PR, or if on PR and token is given
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fail_ci_if_error: ${{ github.event_name != 'pull_request' || secrets.CODECOV_TOKEN }}
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files: ./cobertura.xml
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plugins: noop
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disable_search: true
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token: ${{ secrets.CODECOV_TOKEN }}
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- name: Show testthat output
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if: always()
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run: |
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## --------------------------------------------------------------------
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find '${{ runner.temp }}/package' -name 'testthat.Rout*' -exec cat '{}' \; || true
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shell: bash
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- name: Upload test results
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if: failure()
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uses: actions/upload-artifact@v4
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with:
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name: coverage-test-failures
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path: ${{ runner.temp }}/package

‎README.md‎

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<!-- badges: start -->
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[![Lifecycle: stable](https://img.shields.io/badge/lifecycle-stable-brightgreen.svg)](https://lifecycle.r-lib.org/articles/stages.html#stable)
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[![R-CMD-check](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check.yaml/badge.svg)](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check.yaml)
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[![R-CMD-check-bioc](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check-bioc.yaml/badge.svg)](https://github.com/scverse/anndataR/actions/workflows/R-CMD-check-bioc.yaml)
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[![Codecov test coverage](https://codecov.io/gh/scverse/anndataR/graph/badge.svg)](https://app.codecov.io/gh/scverse/anndataR)
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[![Bioc release status](http://www.bioconductor.org/shields/build/release/bioc/anndataR.svg)](https://bioconductor.org/checkResults/release/bioc-LATEST/anndataR)
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[![Bioc devel status](http://www.bioconductor.org/shields/build/devel/bioc/anndataR.svg)](https://bioconductor.org/checkResults/devel/bioc-LATEST/anndataR)
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[![Bioc downloads rank](https://bioconductor.org/shields/downloads/release/anndataR.svg)](http://bioconductor.org/packages/stats/bioc/anndataR/)
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`vignette("anndataR", package = "anndataR")`
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- [**Read/write `Seurat` objects**](https://anndatar.data-intuitive.com/articles/usage_seurat.html): How to convert between `AnnData` and `Seurat` objects.
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`vignette("usage_seurat", package = "anndataR")`
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- [**Read/write `SingleCellExperiment` objects**](https://anndatar.data-intuitive.com/articles/usage_singlecellexperiment.html): How to convert between `AnnData` and `SingleCellExperiment` objects
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- [**Read/write `SingleCellExperiment` objects**](https://anndatar.data-intuitive.com/articles/usage_singlecellexperiment.html): How to convert between `AnnData` and `SingleCellExperiment` objects
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`vignette("usage_singlecellexperiment", package = "anndataR")`
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- [**Software Design**](https://anndatar.data-intuitive.com/articles/software_design.html): An overview of the design of the package
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- [**Development Status**](https://anndatar.data-intuitive.com/articles/development_status.html): An overview of the development status of the package
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## Citing **{anndataR}**
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If you use **{anndataR}** in your work, please cite [_"anndataR improves interoperability between R and Python in single-cell transcriptomics"_](https://doi.org/10.1101/2025.08.18.669052):

‎codecov.yml‎

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comment: false
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coverage:
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status:
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project:
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default:
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target: auto
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threshold: 1%
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informational: true
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patch:
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default:
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target: auto
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threshold: 1%
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informational: true

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