Merge branch 'develop' into stephen/cellranger-9.0

Author: stephenwilliams22

.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 = "abutler@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-3608-0463")),
   person(given = "Saket", family = "Choudhary", email = "schoudhary@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = 'David', family = 'Collins', email = 'dcollins@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0001-9243-7821')),
   person(given = "Charlotte", family = "Darby", email = "cdarby@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-2195-5300")),
   person(given = "Jeff", family = "Farrell", email = "jfarrell@g.harvard.edu", role = "ctb"),
+  person(given = "Isabella", family = "Grabski", email = "igrabski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-0616-5469")),
   person(given = "Christoph", family = "Hafemeister", email = "chafemeister@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-6365-8254")),
   person(given = "Yuhan", family = "Hao", email = "yhao@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-1810-0822")),
   person(given = "Austin", family = "Hartman", email = "ahartman@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-7278-1852")),
-  person(given = "Paul", family = "Hoffman", email = "seurat@nygenome.org", role = c("aut", "cre"), comment = c(ORCID = "0000-0002-7693-8957")),
+  person(given = "Paul", family = "Hoffman", email = "hoff0792@umn.edu", role = "ctb", comment = c(ORCID = "0000-0002-7693-8957")),
   person(given = "Jaison", family = "Jain", email = "jjain@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-9478-5018")),
+  person(given = "Longda", family = "Jiang", email = "ljiang@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
   person(given = "Madeline", family = "Kowalski", email = "mkowalski@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
+  person(given = "Skylar", family = "Li", email = "sli@nygenome.org", role = "ctb"),
+  person(given = "Gesmira", family = "Molla", email = 'gmolla@nygenome.org', role = 'ctb', comment = c(ORCID = '0000-0002-8628-5056')),
   person(given = "Efthymia", family = "Papalexi", email = "epapalexi@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-5898-694X")),
   person(given = "Patrick", family = "Roelli", email = "proelli@nygenome.org", 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 = "kshekhar@berkeley.edu", role = "ctb"),
   person(given = "Avi", family = "Srivastava", email = "asrivastava@nygenome.org", role = "ctb", comment = c(ORCID = "0000-0001-9798-2079")),
   person(given = "Tim", family = "Stuart", email = "tstuart@nygenome.org", 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