Merge pull request #9567 from satijalab/release/5.2.0

Release/5.2.0

.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

@@ -0,0 +1,52 @@
+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: 
+    - develop
+    - master
+  pull_request:
+    branches: 
+    - develop
+    - master
+
+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:
+      # 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
-Date: 2024-05-08
+Version: 5.2.0
 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 = "szheng@nygenome.org", 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
@@ -56,7 +56,7 @@ Imports:
     irlba,
     jsonlite,
     KernSmooth,
-    leiden (>= 0.3.1),
+    leidenbase,
     lifecycle,
     lmtest,
     MASS,
@@ -68,7 +68,6 @@ Imports:
     plotly (>= 4.9.0),
     png,
     progressr,
-    purrr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
@@ -90,9 +89,44 @@ 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 +148,3 @@ Collate:
     'sketching.R'
     'tree.R'
     'utilities.R'
-RoxygenNote: 7.3.1
-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

NAMESPACE

@@ -49,6 +49,7 @@ S3method(GetAssay,Seurat)
 S3method(GetImage,STARmap)
 S3method(GetImage,SlideSeq)
 S3method(GetImage,VisiumV1)
+S3method(GetImage,VisiumV2)
 S3method(GetTissueCoordinates,STARmap)
 S3method(GetTissueCoordinates,SlideSeq)
 S3method(GetTissueCoordinates,VisiumV1)
@@ -107,6 +108,7 @@ S3method(RunPCA,StdAssay)
 S3method(RunPCA,default)
 S3method(RunSLSI,Assay)
 S3method(RunSLSI,Seurat)
+S3method(RunSLSI,StdAssay)
 S3method(RunSLSI,default)
 S3method(RunSPCA,Assay)
 S3method(RunSPCA,Assay5)
@@ -384,6 +386,7 @@ export(RunCCA)
 export(RunGraphLaplacian)
 export(RunICA)
 export(RunLDA)
+export(RunLeiden)
 export(RunMarkVario)
 export(RunMixscape)
 export(RunMoransI)
@@ -546,6 +549,7 @@ importFrom(SeuratObject,CreateAssayObject)
 importFrom(SeuratObject,CreateCentroids)
 importFrom(SeuratObject,CreateDimReducObject)
 importFrom(SeuratObject,CreateFOV)
+importFrom(SeuratObject,CreateMolecules)
 importFrom(SeuratObject,CreateSegmentation)
 importFrom(SeuratObject,CreateSeuratObject)
 importFrom(SeuratObject,DefaultAssay)
@@ -752,7 +756,6 @@ importFrom(igraph,plot.igraph)
 importFrom(irlba,irlba)
 importFrom(jsonlite,fromJSON)
 importFrom(jsonlite,read_json)
-importFrom(leiden,leiden)
 importFrom(lifecycle,deprecate_soft)
 importFrom(lifecycle,deprecate_stop)
 importFrom(lifecycle,deprecate_warn)
@@ -794,7 +797,6 @@ importFrom(plotly,plot_ly)
 importFrom(plotly,raster2uri)
 importFrom(png,readPNG)
 importFrom(progressr,progressor)
-importFrom(purrr,imap)
 importFrom(reticulate,import)
 importFrom(reticulate,py_module_available)
 importFrom(reticulate,py_set_seed)

NEWS.md

@@ -1,3 +1,22 @@
+# Seurat 5.2.0 (2024-12-20)
+
+## Changes
+- Added `group.by` parameter to `FindAllMarkers`, allowing users to regroup their data using a non-default identity class prior to performing differential expression ([#9550](https://github.com/satijalab/seurat/pull/9550))
+- Added `image.type` parameter to `Read10X_Image` enabling `VisiumV1` instances to be populated instead of instances of the default `VisiumV2` class ([#9556](https://github.com/satijalab/seurat/pull/9556))
+- Fixed `IntegrateLayers` to respect the `dims.to.integrate` parameter
+- Added `stroke.size` parameter to `DimPlot` ([#8180](https://github.com/satijalab/seurat/pull/8180))
+- Updated `RunLeiden` to use the `leidenbase` package instead of `leiden`; deprecated the `method` parameter for `RunLeiden` and `FindClusters`; updated `RunLeiden` to reset `random.seed` to 1 if the value is 0 or less ([#6792](https://github.com/satijalab/seurat/pull/6792))
+- Updated `RunPCA` to use the `BPCells`-provided SVD solver on `BPCells` matrices; updated `JackStraw` to support `BPCells` matrices ([#8271](https://github.com/satijalab/seurat/pull/8271))
+- Fixed `RunPCA` to avoid converting `BPCells` matrices into dense matrices - significantly reduces the function's memory usage when running on `BPCells` matrices ([#8966](https://github.com/satijalab/seurat/pull/8966))
+- Updated `RunSLSI` to support `BPCells` matrices
+- Updated `RunUMAP` to support `umap-learn` version >= 0.5.0 ([#9559](https://github.com/satijalab/seurat/pull/9559))
+- Updated `LoadXenium` and `ReadXenium` to accommodate the output from `XOA` v3.0; updated `LoadXenium` to provide more fine-grained control over the datatypes parsed in, including nucleus segmentation masks, segmentation methods, and other experimental metadata; updated `ReadXenium` to load cell_feature_matrix.h5 when present in favor of the MEX format files; updated `ReadXenium` to load .parquet files using `arrow` instead of .csv.gz files to support XOA 3.0 ([#8604](https://github.com/satijalab/seurat/pull/8605))
+- Fixed `LoadXenium` to accommodate datasets without "Blank Codeword" or "Unassigned Codeword" matrices([#9135](https://github.com/satijalab/seurat/pull/9135))
+- Fixed `ReadXenium` to properly parse multiple molecular outputs at once ([#8265](https://github.com/satijalab/seurat/issues/8265))
+- Added `features` parameter to `LeverageScore` and `SketchData`
+- Updated `SketchData`'s `ncells` parameter to accept integer vector
+
+
 # Seurat 5.1.0 (2024-05-08)
 
 ## Changes
@@ -222,6 +241,7 @@
 - Add `rlsi` option for `FindIntegrationAnchors()`
 
 ## Changes
+- 
 - Preserve feature metadata when converting from `SingleCellExperiment` to `SeuratObject` class
 ([#4205](https://github.com/satijalab/seurat/issues/4205))
 - Preserve multiple assays when converting from `SingleCellExperiment` to `SeuratObject` class