From cae687bb0e575d47c3734ac42eb08bb210c517fe Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 20 Nov 2024 16:53:13 -0500 Subject: [PATCH 1/6] Fixup tests/testthat.R --- tests/testthat.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/tests/testthat.R b/tests/testthat.R index 72a15ce4..6d1340cf 100644 --- a/tests/testthat.R +++ b/tests/testthat.R @@ -1,4 +1,4 @@ library(testthat) -library(Seurat) +library(SeuratObject) -test_check("Seurat") +test_check("SeuratObject") From 32f76f6c66649b0539be8944d561238e259c1281 Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 20 Nov 2024 16:53:24 -0500 Subject: [PATCH 2/6] Drop tests from .Rbuildignore --- .Rbuildignore | 1 - 1 file changed, 1 deletion(-) diff --git a/.Rbuildignore b/.Rbuildignore index 36d6f51a..a0f69929 100644 --- a/.Rbuildignore +++ b/.Rbuildignore @@ -20,6 +20,5 @@ ^.*\.Rds$ ^data-raw$ ^inst$ -^tests$ ^LICENSE\.md$ ^vignettes/articles$ From b486bd5c5b0b3aa714d653a39da91ef3e4062d27 Mon Sep 17 00:00:00 2001 From: David Collins Date: Wed, 20 Nov 2024 21:42:41 -0500 Subject: [PATCH 3/6] Add rspm install/config to R setup --- .github/workflows/integration_checks.yaml | 3 +++ 1 file changed, 3 insertions(+) diff --git a/.github/workflows/integration_checks.yaml b/.github/workflows/integration_checks.yaml index d28c9d9f..9bad1749 100644 --- a/.github/workflows/integration_checks.yaml +++ b/.github/workflows/integration_checks.yaml @@ -36,6 +36,9 @@ jobs: with: # install the R version specified by the current strategy r-version: ${{ matrix.r-version }} + # rspm provides pre-compiles binary packages, providing faster + # more reliable installs + use-public-rspm: true # specify additional repositories to pull dependencies not # available on CRAN (i.e. `BPCells`) extra-repositories: ${{ 'https://bnprks.r-universe.dev' }} From 7cdcea5a78ae7e058ddd1662536252d723c6dce8 Mon Sep 17 00:00:00 2001 From: David Collins Date: Tue, 19 Nov 2024 00:49:52 -0500 Subject: [PATCH 4/6] Update integration checks to use seurat-ci image Stop using r-lib/actions/ --- .github/workflows/integration_checks.yaml | 65 +++++++---------------- 1 file changed, 18 insertions(+), 47 deletions(-) diff --git a/.github/workflows/integration_checks.yaml b/.github/workflows/integration_checks.yaml index 9bad1749..26acfc71 100644 --- a/.github/workflows/integration_checks.yaml +++ b/.github/workflows/integration_checks.yaml @@ -1,9 +1,7 @@ -# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples -# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help name: Integration Checks -# because `main` is a protected branch this workflow is triggered when a PR -# is opened/updated and again when it is merged +# Because `main` is a protected branch this workflow is triggered when a PR +# is opened/updated and again when it is merged. on: push: branches: @@ -14,60 +12,33 @@ on: jobs: check-package: - # system dependencies for cannot be automatically resolved by - # `r-lib/actions/setup-r@v2` for macos or windows - to avoid having to - # maintain separate logic to infer and install system of those operating - # systems we'll only run integration checks with the ubuntu runs-on: ubuntu-latest - - # run integration checks with R-release, R-devel, and R-oldrelease - strategy: - matrix: - r-version: ['release', 'devel', 'oldrel'] + + # Use the `satijalab/seurat-ci` Docker image as the runner environment. + # This image is pre-configured with everything required for running + # integration checks, for more details, see + # https://hub.docker.com/repository/docker/satijalab/seurat-ci/general. + container: + image: satijalab/seurat-ci:latest steps: - # pull the latest changes from the repository down to the runner + # Pull the latest changes from the repository down to the runner. - name: Checkout uses: actions/checkout@v4 - - # install R and any system dependencies - - name: Setup R - uses: r-lib/actions/setup-r@v2 - with: - # install the R version specified by the current strategy - r-version: ${{ matrix.r-version }} - # rspm provides pre-compiles binary packages, providing faster - # more reliable installs - use-public-rspm: true - # specify additional repositories to pull dependencies not - # available on CRAN (i.e. `BPCells`) - extra-repositories: ${{ 'https://bnprks.r-universe.dev' }} - # install R dependencies + # Install the package and all its dependencies using scripts from + # `littler`, see https://eddelbuettel.github.io/littler/ for details. + # `Seurat` is listed under "Enhances" so it also needs to be installed. - name: Install Dependencies - uses: r-lib/actions/setup-r-dependencies@v2 - with: - extra-packages: - any::rcmdcheck - any::pkgdown - # installed packages are cached by default - force an upgrade to the - # latest version of all dependencies - upgrade: 'TRUE' + run: installDeps.r -s && install.r Seurat - # run CRAN checks - fails if any ERRORs or WARNINGs are raised in which - # case the `rcmdcheck` output will be uploaded as an artifact + # Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails. - name: Run Checks - uses: r-lib/actions/check-r-package@v2 - env: - # suppress NOTEs that are accepted by CRAN - # see: https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck - _R_CHECK_PKG_SIZES_: false - _R_CHECK_RD_XREFS_: false - _R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: false - _R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true + run: rcmdcheck::rcmdcheck(args = "--as-cran", error_on="warning") + shell: Rscript {0} continue-on-error: true - # build pkgdown site + # Build the pkgdown site. - name: Build Website run: | pkgdown::build_site_github_pages( From 55f7055640512cccde5c7ecc75d3d05045c473da Mon Sep 17 00:00:00 2001 From: David Collins Date: Thu, 5 Dec 2024 05:44:50 -0500 Subject: [PATCH 5/6] Make small comment tweak --- .github/workflows/integration_checks.yaml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/.github/workflows/integration_checks.yaml b/.github/workflows/integration_checks.yaml index 26acfc71..297acdb9 100644 --- a/.github/workflows/integration_checks.yaml +++ b/.github/workflows/integration_checks.yaml @@ -38,7 +38,7 @@ jobs: shell: Rscript {0} continue-on-error: true - # Build the pkgdown site. + # Build the `pkgdown` site, if any errors are raised the check fails. - name: Build Website run: | pkgdown::build_site_github_pages( From bd85e0c9c1c151788f7bc6562f6e6f111ad4a982 Mon Sep 17 00:00:00 2001 From: David Collins Date: Thu, 5 Dec 2024 08:35:55 -0500 Subject: [PATCH 6/6] Bump version --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 7e8f2525..48cc1e08 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: SeuratObject Type: Package Title: Data Structures for Single Cell Data -Version: 5.0.99.9001 +Version: 5.0.99.9002 Authors@R: c( person(given = 'Paul', family = 'Hoffman', email = 'hoff0792@alumni.umn.edu', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')), person(given = 'Rahul', family = 'Satija', email = 'seurat@nygenome.org', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),