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Merge branch 'develop'
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saketkc committed Nov 5, 2023
2 parents 57564e2 + 53cf1f8 commit ca4c48b
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2 changes: 2 additions & 0 deletions .Rbuildignore
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@@ -1,3 +1,5 @@
^renv$
^renv\.lock$
^.*\.Rproj$
^\.Rproj\.user$
^.*\.old$
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24 changes: 16 additions & 8 deletions .github/workflows/R_CMD_check.yaml
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Expand Up @@ -5,6 +5,9 @@ on:
- develop
pull_request:

env:
GITHUB_PAT: ${{ secrets.PAT }}

jobs:
r-cmd-check:

Expand All @@ -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
38 changes: 28 additions & 10 deletions DESCRIPTION
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@@ -1,22 +1,26 @@
Package: Seurat
Version: 4.4.0
Date: 2023-09-26
Version: 5.0.0
Date: 2023-10-23
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 = "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")),
Expand All @@ -26,15 +30,19 @@ 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 (>= 5.0.0)
Imports:
cluster,
cowplot,
fastDummies,
fitdistrplus,
future,
future.apply,
generics (>= 0.1.3),
ggplot2 (>= 3.3.0),
ggrepel,
ggridges,
Expand All @@ -48,6 +56,7 @@ Imports:
jsonlite,
KernSmooth,
leiden (>= 0.3.1),
lifecycle,
lmtest,
MASS,
Matrix (>= 1.5-0),
Expand All @@ -63,22 +72,23 @@ Imports:
RColorBrewer,
Rcpp (>= 1.0.7),
RcppAnnoy (>= 0.0.18),
RcppHNSW,
reticulate,
rlang,
ROCR,
RSpectra,
Rtsne,
scales,
scattermore (>= 1.2),
sctransform (>= 0.4.0),
SeuratObject (>= 4.1.4),
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
Expand All @@ -93,16 +103,21 @@ 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: 7.2.3
Encoding: UTF-8
Suggests:
ape,
BPCells,
rsvd,
testthat,
hdf5r,
Expand All @@ -126,4 +141,7 @@ Suggests:
mixtools,
ggrastr,
data.table,
R.utils
R.utils,
presto,
DelayedArray,
harmony
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