Merge pull request #9538 from satijalab/ci_revamp

Revamp CI checks

.Rbuildignore

@@ -4,11 +4,8 @@
 ^\.Rproj\.user$
 ^.*\.old$
 .git
-.travis.yml
 appveyor.yml
-azure-pipelines.yml
 cran-comments.md
-travis_setup.sh
 CODE_OF_CONDUCT.md
 ^_pkgdown\.yaml$
 ^docs$

.github/workflows/integration_checks.yaml

@@ -1,5 +1,7 @@
 name: Integration Checks
 
+# Because `develop` is a protected branch this workflow is triggered when a PR 
+# is opened/updated and again when it is merged.
 on:
   push:
     branches: 
@@ -11,5 +13,38 @@ on:
 jobs:
   check-package:
     runs-on: ubuntu-latest
+
+    # 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:
-      - run: echo "This is a placeholder workflow."
+      # Pull the latest changes from the repository down to the runner.
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      # Install the package and all its dependencies using scripts from 
+      # `littler`, see https://eddelbuettel.github.io/littler/ for details. 
+      - name: Install Dependencies
+        run: installDeps.r -s
+
+      # Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails.
+      # Certain tests are skipped when running as CRAN—skip all tests so they
+      # can be run together in a subsequent step.
+      - name: Run CRAN Checks (no tests)
+        run: |
+          rcmdcheck::rcmdcheck(
+            args = c("--as-cran", "--no-tests"), 
+            error_on="warning"
+          )
+        shell: Rscript {0}
+
+      # Because tests weren't included in CRAN checks, run them here.
+      - name: Run Tests
+        # Run this step even if the previous one failed.
+        if: always()
+        run: testthat::test_local()
+        shell: Rscript {0}

DESCRIPTION

@@ -1,6 +1,5 @@
 Package: Seurat
-Version: 5.1.0.9006
-Date: 2024-09-29
+Version: 5.1.0.9007
 Title: Tools for Single Cell Genomics
 Description: A toolkit for quality control, analysis, and exploration of single cell RNA sequencing data. 'Seurat' aims to enable users to identify and interpret sources of heterogeneity from single cell transcriptomic measurements, and to integrate diverse types of single cell data. See Satija R, Farrell J, Gennert D, et al (2015) <doi:10.1038/nbt.3192>, Macosko E, Basu A, Satija R, et al (2015) <doi:10.1016/j.cell.2015.05.002>, Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>, and Hao, Hao, et al (2020) <doi:10.1101/2020.10.12.335331> for more details.
 Authors@R: c(
@@ -29,6 +28,7 @@ Authors@R: c(
   person(given = "Shiwei", family = "Zheng", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
   person("Satija Lab and Collaborators", role = "fnd")
   )
+License: MIT + file LICENSE
 URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
 Additional_repositories: https://satijalab.r-universe.dev, https://bnprks.r-universe.dev
@@ -90,9 +90,44 @@ Imports:
     tools,
     utils,
     uwot (>= 0.1.10)
+Suggests:
+    ape,
+    arrow,
+    Biobase,
+    BiocGenerics,
+    BPCells,
+    data.table,
+    DESeq2,
+    DelayedArray,
+    enrichR,
+    GenomicRanges,
+    GenomeInfoDb,
+    glmGamPoi,
+    ggrastr,
+    harmony,
+    hdf5r,
+    IRanges,
+    limma,
+    MAST,
+    metap,
+    mixtools,
+    monocle,
+    presto,
+    rsvd,
+    R.utils,
+    Rfast2,
+    rtracklayer,
+    S4Vectors,
+    sf (>= 1.0.0),
+    SingleCellExperiment,
+    SummarizedExperiment,
+    testthat,
+    VGAM
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
-License: MIT + file LICENSE
+BuildManual: true
+Encoding: UTF-8
 LazyData: true
+RoxygenNote: 7.3.2
 Collate:
     'RcppExports.R'
     'reexports.R'
@@ -114,36 +149,3 @@ Collate:
     'sketching.R'
     'tree.R'
     'utilities.R'
-RoxygenNote: 7.3.2
-Encoding: UTF-8
-Suggests:
-    ape,
-    arrow,
-    BPCells,
-    rsvd,
-    testthat,
-    hdf5r,
-    S4Vectors,
-    SummarizedExperiment,
-    SingleCellExperiment,
-    MAST,
-    DESeq2,
-    BiocGenerics,
-    GenomicRanges,
-    GenomeInfoDb,
-    IRanges,
-    rtracklayer,
-    Rfast2,
-    monocle,
-    Biobase,
-    VGAM,
-    limma,
-    metap,
-    enrichR,
-    mixtools,
-    ggrastr,
-    data.table,
-    R.utils,
-    presto,
-    DelayedArray,
-    harmony

appveyor.yml

@@ -22,6 +22,8 @@ environment:
     PYTHON: "C:\\Python36-x64"
     RETICULATE_PYTHON: "C:\\Python36-x64"
     CRAN: "https://cloud.r-project.org"
+    R_LIBCURL_SSL_REVOKE_BEST_EFFORT: "TRUE"
+    CURL_SSL_BACKEND: "openssl"
 
 build_script:
   - travis-tool.sh install_deps