Post-release updates (#10191)

* Update link to progressr vignette in documentation

* Submit 5.3.1 to CRAN (#10164)

* Bump version

* Update NEWS.md

* Update workflow for reverse dependency checks

Add step in job to free disk space and add options to check strong / most / all dependencies

* Refactor reverse dependency check workflow

* Fix indentation in reverse_dependency_checks.yaml

* Update cran-comments.md

Author: anashen

.github/workflows/reverse_dependency_checks.yaml

@@ -2,11 +2,28 @@ name: Reverse Dependency Checks
 
 on:
   workflow_dispatch:
+    inputs:
+      which:
+        type: choice
+        description: Which dependents to check
+        options:
+          - strong
+          - most
+          - all
 
 jobs:
+  free-space:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Free some disk space # Sourced from https://github.com/r-devel/rcheckserver/blob/main/.github/workflows/build.yml#L24-L25
+        run: sudo rm -rf /usr/share/dotnet /opt/ghc "/usr/local/share/boost" "$AGENT_TOOLSDIRECTORY"
+
   # Run a reverse dependency check similar to CRAN, for more details see 
   # https://github.com/r-devel/recheck.
   check-reverse-dependencies:
+    needs: free-space
+    name: Reverse check ${{ inputs.which }} dependents
     uses: r-devel/recheck/.github/workflows/recheck.yml@v1
     with:
-      which: all
+      which: ${{ inputs.which }}

DESCRIPTION

@@ -1,5 +1,5 @@
 Package: Seurat
-Version: 5.3.0.9999
+Version: 5.3.1
 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(

NEWS.md

@@ -1,20 +1,31 @@
-# Unreleased
+# Seurat 5.3.1
 
 ## Changes
-- Added `label.size.cutoff` parameter to `DimPlot` to allow users to label only clusters above a certain size
+
+### Additions
 - Added option to use `cluster_leiden` from `igraph` when running Leiden clustering ([#9931](https://github.com/satijalab/seurat/pull/9931))
 - Added option to use `umap2` from `uwot` when running UMAP ([#9918](https://github.com/satijalab/seurat/pull/9918))
-- Updated `PseudobulkExpression` to acccount for the case that a category passed to `group.by` has only one value
-- Updated `VlnPlot` to use assay passed to the function if specified
-- Updated `FeatureScatter` to allow gene names with parentheses to be plotted
-- Updated `SingleRasterMap` to store object metadata correctly
-- Made minor edit to description of section running `DoHeatmap` in PBMC3K guided tutorial vignette
-- Updated `FindClusters` to order cluster factor levels correctly when assigning a custom cluster name
-- Updated `FindConservedMarkers` to remove NA values
-- Updated visualization functions to avoid `ggplot2::guides()` deprecation warnings
+- Added option to use `approx_pow` parameter from `uwot` when running UMAP ([#9449](https://github.com/satijalab/seurat/pull/9449))
+- Updated `LoadXenium` to add support for Xenium protein data ([#10024](https://github.com/satijalab/seurat/pull/10024))
+- Added option to specify stroke size in `FeaturePlot` ([#10053](https://github.com/satijalab/seurat/pull/10053))
+- Added `label.size.cutoff` parameter to `DimPlot` to allow users to label only clusters above a certain size ([#10092](https://github.com/satijalab/seurat/pull/10092))
+
+### Fixes
+
+- Fixed deprecated calls to Seurat functions `GetAssayData` and `PackageCheck` ([#9924](https://github.com/satijalab/seurat/pull/9924)), ([#10102](https://github.com/satijalab/seurat/pull/10102))
+- Fixed errors in `RunAzimuth` relating to `FindTransferAnchors` ([#9924](https://github.com/satijalab/seurat/pull/9924))
+- Fixed errors in `LeverageScore` relating to handling of (variable) features ([#9924](https://github.com/satijalab/seurat/pull/9924))
+- Updated `PseudobulkExpression` to acccount for the case that a category passed to `group.by` has only one value ([#10092](https://github.com/satijalab/seurat/pull/10092))
+- Updated `VlnPlot` to use assay passed to the function if specified ([#10092](https://github.com/satijalab/seurat/pull/10092))
+- Updated `FeatureScatter` to allow gene names with parentheses to be plotted ([#10092](https://github.com/satijalab/seurat/pull/10092))
+- Updated `SingleRasterMap` to store object metadata correctly ([#10092](https://github.com/satijalab/seurat/pull/10092))
+- Updated `FindClusters` to order cluster factor levels correctly when assigning a custom cluster name ([#10092](https://github.com/satijalab/seurat/pull/10092))
+- Updated `FindConservedMarkers` to remove NA values ([#9917](https://github.com/satijalab/seurat/pull/9917))
+- Updated visualization functions to avoid ggplot2 `guides`, `aes_string`, and `facet_grid` deprecation warnings ([#9409](https://github.com/satijalab/seurat/pull/9409), [#10116](https://github.com/satijalab/seurat/pull/10116))
 - Fixed `DimPlot` bug where metadata columns named 'PC_1', 'UMAP_1' etc override reduction embeddings ([#10062](https://github.com/satijalab/seurat/pull/10062))
 
-# Seurat 5.3.0
+
+# Seurat 5.3.0 (2025-04-23)
 
 ## Changes
 - Fixed `PseudobulkExpression` to forward relevant arguments to `NormalizeData` ([#9840](https://github.com/satijalab/seurat/pull/9840))

cran-comments.md

@@ -0,0 +1,55 @@
+# Seurat v5.3.1
+
+## Test environments
+* ubuntu 20.04 (local) (R 4.3.2)
+* macOS 15.6.1 (local) (R 4.5.1)
+* ubuntu 24.04 (GitHub Actions Runner): R-oldrelease, R-release, R-devel
+* [win-builder](https://win-builder.r-project.org/): R-oldrelease, R-release, R-devel
+* [macOS builder](https://mac.r-project.org/macbuilder/submit.html): R-release, R-devel
+
+## R CMD check results
+**Status: OK**
+
+There were no ERRORs or WARNINGs.
+
+There were four NOTEs given by win-builder (oldrel):
+
+```
+* checking CRAN incoming feasibility ... [42s] NOTE
+Maintainer: 'Rahul Satija <seurat@nygenome.org>'
+
+Suggests or Enhances not in mainstream repositories:
+  BPCells, presto
+Availability using Additional_repositories specification:
+  BPCells   yes   https://bnprks.r-universe.dev   
+  presto    yes   https://satijalab.r-universe.dev
+```
+
+The maintainer remains Rahul Satija and the email is correct. BPCells and presto are hosted on R-universe and used conditionally in Seurat.
+
+```
+* checking package dependencies ... NOTE
+Packages suggested but not available for checking: 'BPCells', 'presto'
+```
+
+BPCells and presto are hosted on R-universe and used conditionally in Seurat.
+
+```
+* checking DESCRIPTION meta-information ... NOTE
+Author field differs from that derived from Authors@R
+```
+
+There seems to be a slight difference in ORCID formatting between Author and Authors@R; the information in both is the same.
+
+```
+* checking Rd cross-references ... NOTE
+Package unavailable to check Rd xrefs: 'BPCells'
+```
+
+BPCells is listed under "Suggests"; it is hosted on R-universe and used conditionally in Seurat.
+
+## Reverse dependency check results
+We checked 145 reverse dependencies (69 from CRAN + 76 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package.
+
+ * We saw 0 new problems
+ * We failed to check 15 packages (conos, CytoSimplex, DIscBIO, DR.SC, harmony, Platypus, PopComm, PoweREST, PRECAST, ProFAST, RepeatedHighDim, RESET, rPanglaoDB, sccore, SpaCCI)

man/PrepSCTFindMarkers.Rd

@@ -5,4 +5,4 @@
 #' the function call in \code{\link[progressr]{with_progress}} or run
 #' \code{\link[progressr:handlers]{handlers(global = TRUE)}} before running
 #' this function. For more details about \pkg{progressr}, please read
-#' \href{https://progressr.futureverse.org/articles/progressr-intro.html}{\code{vignette("progressr-intro")}}
+#' \href{https://progressr.futureverse.org/articles/progressr-01-intro.html}{\code{vignette("progressr-intro")}}