Merge branch 'develop' into stephen/cellranger-9.0

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^.*\.old$

.github/workflows/R_CMD_check.yaml

@@ -5,6 +5,9 @@ on:
             - develop
     pull_request:
 
+env:
+  GITHUB_PAT: ${{ secrets.PAT }}
+
 jobs:
     r-cmd-check:
 
@@ -13,21 +16,26 @@ jobs:
         name: R CMD check
         container:
             image: satijalab/seurat:develop
-        runs-on: self-hosted 
+        runs-on: [ self-hosted ]
 
         steps:
-            - uses: actions/checkout@v2
+            - uses: actions/checkout@v3
             - name: Remove vignettes dir
               run: rm -rf 'vignettes/'
               shell: bash
 
+            - name: Install additional dependencies
+              run: |
+                  Rscript -e "remotes::install_github('mojaveazure/seurat-object', ref = 'feat/CalN_generic')"
+                  Rscript -e "remotes::install_github('bnprks/BPCells')"
+
             - name: Check
               run:  devtools::check(args = "--no-manual", error_on = "warning", check_dir = "check", force_suggests = FALSE)
               shell: Rscript {0}
 
-            - name: Upload check results
-              if: failure()
-              uses: actions/upload-artifact@master
-              with:
-                  name: results
-                  path: check
+#            - name: Upload check results
+#              if: failure()
+#              uses: actions/upload-artifact@master
+#              with:
+#                  name: results
+#                  path: check

.github/workflows/integration_checks.yaml

@@ -0,0 +1,15 @@
+name: Integration Checks
+
+on:
+  push:
+    branches: 
+    - develop
+  pull_request:
+    branches: 
+    - develop
+
+jobs:
+  check-package:
+    runs-on: ubuntu-latest
+    steps:
+      - run: echo "This is a placeholder workflow."

DESCRIPTION

@@ -1,22 +1,27 @@
 Package: Seurat
-Version: 4.3.0.9002
-Date: 2023-02-01
+Version: 5.1.0.9006
+Date: 2024-09-29
 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(
   person(given = "Andrew", family = "Butler", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
   person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = 'David', family = 'Collins', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
   person(given = "Charlotte", family = "Darby", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
   person(given = "Jeff", family = "Farrell", email = "[email protected]", role = "ctb"),
+  person(given = "Isabella", family = "Grabski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
   person(given = "Christoph", family = "Hafemeister", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
   person(given = "Yuhan", family = "Hao", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
   person(given = "Austin", family = "Hartman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
-  person(given = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
+  person(given = "Paul", family = "Hoffman", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-7693-8957")),
   person(given = "Jaison", family = "Jain", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
+  person(given = "Longda", family = "Jiang", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
   person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
+  person(given = "Skylar", family = "Li", email = "[email protected]", role = "ctb"),
+  person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')),
   person(given = "Efthymia", family = "Papalexi", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
   person(given = "Patrick", family = "Roelli", email = "[email protected]", role = "ctb"),
-  person(given = "Rahul", family = "Satija", email = "rsatija@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9448-8833")),
+  person(given = "Rahul", family = "Satija", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0001-9448-8833")),
   person(given = "Karthik", family = "Shekhar", email = "[email protected]", role = "ctb"),
   person(given = "Avi", family = "Srivastava", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
   person(given = "Tim", family = "Stuart", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-3044-0897")),
@@ -26,15 +31,19 @@ Authors@R: c(
   )
 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
 Depends:
     R (>= 4.0.0),
-    methods
+    methods,
+    SeuratObject (>= 5.0.2)
 Imports:
     cluster,
     cowplot,
+    fastDummies,
     fitdistrplus,
     future,
     future.apply,
+    generics (>= 0.1.3),
     ggplot2 (>= 3.3.0),
     ggrepel,
     ggridges,
@@ -48,6 +57,7 @@ Imports:
     jsonlite,
     KernSmooth,
     leiden (>= 0.3.1),
+    lifecycle,
     lmtest,
     MASS,
     Matrix (>= 1.5-0),
@@ -58,26 +68,28 @@ Imports:
     plotly (>= 4.9.0),
     png,
     progressr,
+    purrr,
     RANN,
     RColorBrewer,
     Rcpp (>= 1.0.7),
     RcppAnnoy (>= 0.0.18),
+    RcppHNSW,
     reticulate,
     rlang,
     ROCR,
+    RSpectra,
     Rtsne,
     scales,
-    scattermore (>= 0.7),
-    sctransform (>= 0.3.5),
-    SeuratObject (>= 4.1.3),
+    scattermore (>= 1.2),
+    sctransform (>= 0.4.1),
     shiny,
     spatstat.explore,
     spatstat.geom,
     stats,
     tibble,
     tools,
     utils,
-    uwot (>= 0.1.14)
+    uwot (>= 0.1.10)
 LinkingTo: Rcpp (>= 0.11.0), RcppEigen, RcppProgress
 License: MIT + file LICENSE
 LazyData: true
@@ -92,16 +104,22 @@ Collate:
     'differential_expression.R'
     'dimensional_reduction.R'
     'integration.R'
+    'zzz.R'
+    'integration5.R'
     'mixscape.R'
     'objects.R'
     'preprocessing.R'
+    'preprocessing5.R'
+    'roxygen.R'
+    'sketching.R'
     'tree.R'
     'utilities.R'
-    'zzz.R'
-RoxygenNote: 7.2.2
+RoxygenNote: 7.3.2
 Encoding: UTF-8
 Suggests:
     ape,
+    arrow,
+    BPCells,
     rsvd,
     testthat,
     hdf5r,
@@ -125,4 +143,7 @@ Suggests:
     mixtools,
     ggrastr,
     data.table,
-    R.utils
+    R.utils,
+    presto,
+    DelayedArray,
+    harmony