Merge pull request #159 from mojaveazure/release/5.0.0

Release 5.0.0

.Rbuildignore

@@ -1,3 +1,5 @@
+^renv$
+^renv\.lock$
 ^.*\.Rproj$
 ^\.Rproj\.user$
 ^\.git$
@@ -20,3 +22,4 @@
 ^inst$
 ^tests$
 ^LICENSE\.md$
+^vignettes/articles$

.github/workflows/pkgdown.yaml

@@ -25,6 +25,7 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           use-public-rspm: true
+          extra-repositories: https://bnprks.r-universe.dev
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: local::.

DESCRIPTION

@@ -1,34 +1,43 @@
 Package: SeuratObject
 Type: Package
 Title: Data Structures for Single Cell Data
-Version: 4.1.4
+Version: 5.0.0
 Authors@R: c(
   person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-9448-8833')),
-  person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
   person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0002-7693-8957')),
+  person(given = "Yuhan", family = "Hao", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-1810-0822')),
+  person(given = "Austin", family = "Hartman", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0001-7278-1852')),
+  person(given = "Gesmira", family = "Molla", email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-8628-5056')),
+  person(given = 'Andrew', family = 'Butler', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0003-3608-0463')),
   person(given = 'Tim', family = 'Stuart', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),
+  person(given = "Madeline", family = "Kowalski", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0002-5655-7620")),
+  person(given = "Saket", family = "Choudhary", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-5202-7633")),
+  person(given = "Skylar", family = "Li", email = "[email protected]", role = "ctb"),
+  person(given = "Longda", family = "Jiang", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0003-4964-6497")),
   person(given = 'Jeff', family = 'Farrell', email = '[email protected]', role = 'ctb'),
   person(given = 'Shiwei', family = 'Zheng', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6682-6743')),
   person(given = 'Christoph', family = 'Hafemeister', email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0001-6365-8254')),
-  person(given = 'Patrick', family = 'Roelli', email = '[email protected]', role = 'ctb'),
-  person(given = "Yuhan", family = "Hao", email = '[email protected]', role = 'ctb', comment = c(ORCID = '0000-0002-1810-0822'))
+  person(given = 'Patrick', family = 'Roelli', email = '[email protected]', role = 'ctb')
   )
 Description: Defines S4 classes for single-cell genomic data and associated
   information, such as dimensionality reduction embeddings, nearest-neighbor
   graphs, and spatially-resolved coordinates. Provides data access methods and
   R-native hooks to ensure the Seurat object is familiar to other R users. 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>,
-  and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for
+  and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031>,
+  Hao Y, Hao S, et al (2021) <doi:10.1016/j.cell.2021.04.048> and
+  Hao Y, et al (2023) <doi:10.1101/2022.02.24.481684> for
   more details.
 URL: https://mojaveazure.github.io/seurat-object/,
     https://github.com/mojaveazure/seurat-object
-BugReports:
-      https://github.com/mojaveazure/seurat-object/issues
+BugReports: https://github.com/mojaveazure/seurat-object/issues
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 RoxygenNote: 7.2.3
+Additional_repositories:
+    https://bnprks.r-universe.dev
 Depends:
     R (>= 4.0.0),
     sp (>= 1.5.0)
@@ -44,32 +53,46 @@ Imports:
     rlang (>= 0.4.7),
     stats,
     tools,
-    utils
+    utils,
+    spam,
+    lifecycle,
+    generics
 Suggests:
+    DelayedArray,
+    fs (>= 1.5.2),
     ggplot2,
-    sf,
-    testthat
+    HDF5Array,
+    rmarkdown,
+    testthat,
+    BPCells,
+    sf (>= 1.0.0)
 Collate:
     'RcppExports.R'
     'zzz.R'
     'generics.R'
+    'keymixin.R'
     'graph.R'
+    'default.R'
     'assay.R'
+    'logmap.R'
+    'layers.R'
+    'assay5.R'
     'centroids.R'
     'command.R'
+    'compliance.R'
     'data.R'
-    'default.R'
     'jackstraw.R'
     'dimreduc.R'
     'segmentation.R'
-    'keymixin.R'
     'molecules.R'
     'spatial.R'
     'fov.R'
-    'logmap.R'
     'neighbor.R'
     'seurat.R'
+    'sparse.R'
     'utils.R'
 LinkingTo: Rcpp, RcppEigen
+Enhances:
+    Seurat
 Config/Needs/website:
     pkgdown