Merge pull request satijalab#514 from satijalab/release/4.0.0

Prep for CRAN release of 4.0.0

.Rbuildignore

@@ -8,3 +8,8 @@ azure-pipelines.yml
 cran-comments.md
 travis_setup.sh
 CODE_OF_CONDUCT.md
+^_pkgdown\.yaml$
+^docs$
+^pkgdown$
+^index\.md$
+^vignettes$

.github/workflows/R_CMD_check.yaml

@@ -17,9 +17,12 @@ jobs:
 
         steps:
             - uses: actions/checkout@v2
+            - name: Remove vignettes dir
+              run: rm -rf 'vignettes/'
+              shell: bash
 
             - name: Check
-              run: rcmdcheck::rcmdcheck(args = "--no-manual", error_on = "warning", check_dir = "check")
+              run:  devtools::check(args = "--no-manual", error_on = "warning", check_dir = "check")
               shell: Rscript {0}
 
             - name: Upload check results

.gitignore

@@ -7,3 +7,4 @@ src/*.so
 src/*.dll
 .DS_Store
 *.pdf
+docs/

DESCRIPTION

@@ -1,25 +1,32 @@
 Package: Seurat
-Version: 3.2.3
-Date: 2020-12-14
+Version: 4.0.0
+Date: 2021-01-27
 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>, and Stuart T, Butler A, et al (2019) <doi:10.1016/j.cell.2019.05.031> for more details.
+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 = '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 = 'Tim', family = 'Stuart', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-3044-0897')),
-  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 = "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 = "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 = "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 = "Paul", family = "Hoffman", email = "[email protected]", role = c("aut", "cre"), 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 = "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 = "[email protected]", role = "ctb", 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")),
+  person(given = "Kristof", family = "Torkenczy", email = "", role = "ctb", comment = c(ORCID = "0000-0002-4869-7957")),
+  person(given = "Shiwei", family = "Zheng", email = "[email protected]", role = "ctb", comment = c(ORCID = "0000-0001-6682-6743")),
+  person("Satija Lab and Collaborators", role = "fnd")
   )
 URL: https://satijalab.org/seurat, https://github.com/satijalab/seurat
 BugReports: https://github.com/satijalab/seurat/issues
-Additional_repositories: https://mojaveazure.github.io/loomR
 Depends:
-    R (>= 3.6.0),
-    methods,
+    R (>= 4.0.0),
+    methods
 Imports:
     cluster,
     cowplot,
@@ -51,15 +58,15 @@ Imports:
     RANN,
     RColorBrewer,
     Rcpp,
-    RcppAnnoy,
+    RcppAnnoy (>= 0.0.18),
     reticulate,
     rlang,
     ROCR,
-    rsvd,
     Rtsne,
     scales,
     scattermore (>= 0.7),
-    sctransform (>= 0.3.1),
+    sctransform (>= 0.3.2),
+    SeuratObject,
     shiny,
     spatstat,
     stats,
@@ -72,6 +79,7 @@ License: GPL-3 | file LICENSE
 LazyData: true
 Collate:
     'RcppExports.R'
+    'reexports.R'
     'generics.R'
     'clustering.R'
     'visualization.R'
@@ -80,6 +88,7 @@ Collate:
     'differential_expression.R'
     'dimensional_reduction.R'
     'integration.R'
+    'mixscape.R'
     'objects.R'
     'preprocessing.R'
     'tree.R'
@@ -88,8 +97,8 @@ Collate:
 RoxygenNote: 7.1.1
 Encoding: UTF-8
 Suggests:
-    loomR,
     ape,
+    rsvd,
     testthat,
     hdf5r,
     S4Vectors,
@@ -107,4 +116,6 @@ Suggests:
     Biobase,
     VGAM,
     limma,
-    metap
+    metap,
+    enrichR,
+    mixtools