Skip to content

Commit 5f1187e

Browse files
dcollins15dcollins15
authored
Merge branch 'main' into droplevels_metadata
2 parents a5d18a9 + 7f4ab4e commit 5f1187e

15 files changed

+291
-99
lines changed

‎.github/pull_request_template.md‎

Lines changed: 6 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,6 @@
1+
<!--
2+
Thanks for your interest in contributing!
3+
4+
Please refer the contributor's guide for instructions on submitting a pull request:
5+
https://github.com/satijalab/seurat-object/wiki#contributors-guide
6+
-->

‎.github/workflows/documentation.yaml‎

Lines changed: 62 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,62 @@
1+
name: Documentation
2+
3+
on:
4+
# Allow the workflow to be triggered manually.
5+
workflow_dispatch:
6+
inputs:
7+
# Allow the user to build the documentation site without deploying it.
8+
deploy:
9+
type: boolean
10+
description: "Deploy to Pages"
11+
12+
jobs:
13+
build-site:
14+
# Use the `satijalab/seurat-ci` Docker image as the runner environment.
15+
# This image is pre-configured with everything required for running
16+
# integration checks, for more details, see
17+
# https://hub.docker.com/repository/docker/satijalab/seurat-ci/general.
18+
runs-on: ubuntu-latest
19+
container:
20+
image: satijalab/seurat-ci:latest
21+
22+
steps:
23+
# Pull the latest changes from the repository down to the runner.
24+
- name: Checkout
25+
uses: actions/checkout@v4
26+
27+
# Install the package's dependencies using scripts from `littler`,
28+
# for more details see: https://eddelbuettel.github.io/littler/.
29+
- name: Install Dependencies
30+
run: installDeps.r -s
31+
32+
# Install the package and build the documentation site. By default the
33+
# site's content is written to the `docs/` directory.
34+
- name: Run pkgdown
35+
run: pkgdown::build_site_github_pages(install = TRUE)
36+
shell: Rscript {0}
37+
38+
# Archive the `docs/` directory to the `github-pages` artifact.
39+
- name: Upload Artifact
40+
uses: actions/upload-pages-artifact@v3
41+
with:
42+
path: docs/
43+
44+
deploy-pages:
45+
# Require the `build-site` job to complete successfully and for the
46+
# `deploy` input to be True.
47+
needs: build-site
48+
if: ${{ inputs.deploy }}
49+
50+
# Grant GITHUB_TOKEN the permissions required to make a Pages deployment.
51+
permissions:
52+
pages: write
53+
id-token: write
54+
55+
# Deploy to the github-pages environment.
56+
environment:
57+
name: github-pages
58+
59+
# Deploy the contents of the `github_pages` artifact.
60+
runs-on: ubuntu-latest
61+
steps:
62+
- uses: actions/deploy-pages@v4

‎.github/workflows/integration_checks.yaml‎ renamed to ‎.github/workflows/merge_checks.yaml‎

Lines changed: 24 additions & 23 deletions
Original file line numberDiff line numberDiff line change
@@ -1,23 +1,36 @@
1-
name: Integration Checks
1+
name: Pre-Merge Checks
22

3-
# Because `main` is a protected branch this workflow is triggered when a PR
4-
# is opened/updated and again when it is merged.
53
on:
6-
push:
7-
branches:
8-
- main
4+
# Trigger the workflow when a PR is opened/updated against the default or
5+
# any release branch.
96
pull_request:
10-
branches:
7+
branches:
8+
- main
9+
- 'release/*'
10+
# Trigger the workflow when commits are pushed to a release branch.
11+
# Because they are protected branches this workflow is effectively triggered
12+
# by three events:
13+
# 1. When a release branch is initially created/pushed.
14+
# 2. When a PR against the default or any release branch is opened/updated.
15+
# 3. When a PR against the default or any release branch is merged.
16+
push:
17+
branches:
1118
- main
19+
- 'release/*'
20+
# Allow the workflow to be triggered manually.
21+
workflow_dispatch:
1222

1323
jobs:
1424
check-package:
15-
runs-on: ubuntu-latest
16-
25+
# Override the default job name to differentiate it from similar jobs in
26+
# other workflows.
27+
name: "check-package (r2u)"
28+
1729
# Use the `satijalab/seurat-ci` Docker image as the runner environment.
1830
# This image is pre-configured with everything required for running
1931
# integration checks, for more details, see
2032
# https://hub.docker.com/repository/docker/satijalab/seurat-ci/general.
33+
runs-on: ubuntu-latest
2134
container:
2235
image: satijalab/seurat-ci:latest
2336

@@ -28,22 +41,10 @@ jobs:
2841

2942
# Install the package and all its dependencies using scripts from
3043
# `littler`, see https://eddelbuettel.github.io/littler/ for details.
31-
# `Seurat` is listed under "Enhances" so it also needs to be installed.
3244
- name: Install Dependencies
33-
run: installDeps.r -s && install.r Seurat
34-
45+
run: installDeps.r -s
46+
3547
# Run CRAN checks, if any ERRORs or WARNINGs are raised the check fails.
3648
- name: Run Checks
3749
run: rcmdcheck::rcmdcheck(args = "--as-cran", error_on="warning")
3850
shell: Rscript {0}
39-
40-
# Build the `pkgdown` site, if any errors are raised the check fails.
41-
- name: Build Website
42-
# Run this step even if the previous one failed.
43-
if: always()
44-
run: |
45-
pkgdown::build_site_github_pages(
46-
new_process = FALSE,
47-
install = FALSE
48-
)
49-
shell: Rscript {0}

‎.github/workflows/pkgdown.yaml‎

Lines changed: 0 additions & 42 deletions
This file was deleted.

‎.github/workflows/release_checks.yaml‎

Lines changed: 80 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,80 @@
1+
name: Pre-Release Checks
2+
3+
on:
4+
# Trigger the workflow when a PR opened/updated against a release branch.
5+
pull_request:
6+
branches:
7+
- 'release/*'
8+
# Trigger the workflow when commits are pushed to a release branch.
9+
# Because they are protected branches this workflow is effectively triggered
10+
# by three events:
11+
# 1. When a release branch is initially created/pushed.
12+
# 2. When a PR against a release branch is opened/updated.
13+
# 3. When a PR against a release branch is merged.
14+
push:
15+
branches:
16+
- 'release/*'
17+
# Allow the workflow to be triggered manually.
18+
workflow_dispatch:
19+
20+
jobs:
21+
# Run CRAN checks, for more details see https://github.com/r-lib/actions.
22+
check-package:
23+
# System dependencies for cannot be automatically resolved by
24+
# `r-lib/actions/setup-r@v2` for macos or windows - to avoid having to
25+
# maintain separate logic to infer and install system of those operating
26+
# systems we'll only run integration checks with the ubuntu
27+
runs-on: ubuntu-latest
28+
29+
# Run checks with R-release, R-devel, and R-oldrelease.
30+
strategy:
31+
# Make sure each job runs independently. When `fail-fast` is true
32+
# (by default) all jobs in the matrix are cancelled as soon as one fails.
33+
fail-fast: false
34+
matrix:
35+
r-version: ['release', 'devel', 'oldrel']
36+
37+
# Override the default job name to display the current R version name in
38+
# parentheses (e.g. "check-package (R-release)").
39+
name: "check-package (R-${{ matrix.r-version }})"
40+
41+
steps:
42+
# Pull the latest changes from the repository down to the runner.
43+
- name: Checkout
44+
uses: actions/checkout@v4
45+
46+
# Install R and any system dependencies.
47+
- name: Setup R
48+
uses: r-lib/actions/setup-r@v2
49+
with:
50+
# Install the R version specified by the current strategy.
51+
r-version: ${{ matrix.r-version }}
52+
# Use pre-built binaries from Posit's public package manager to
53+
# speed up R dependency installation.
54+
use-public-rspm: true
55+
# Specify additional repositories to pull dependencies not
56+
# available on CRAN (i.e. `BPCells`).
57+
extra-repositories: 'https://bnprks.r-universe.dev'
58+
59+
# Install R dependencies.
60+
- name: Install Dependencies
61+
uses: r-lib/actions/setup-r-dependencies@v2
62+
with:
63+
extra-packages:
64+
any::rcmdcheck
65+
any::pkgdown
66+
# Installed packages are cached by default - force an upgrade to the
67+
# latest version of all dependencies.
68+
upgrade: 'TRUE'
69+
70+
# Run CRAN checks - fails if any ERRORs or WARNINGs are raised in which
71+
# case the `rcmdcheck` output will be uploaded as an artifact.
72+
- name: Run Checks
73+
uses: r-lib/actions/check-r-package@v2
74+
env:
75+
# Suppress NOTEs that are accepted by CRAN, see:
76+
# https://www.rdocumentation.org/packages/rcmdcheck/versions/1.4.0/topics/rcmdcheck
77+
_R_CHECK_PKG_SIZES_: false
78+
_R_CHECK_RD_XREFS_: false
79+
_R_CHECK_CRAN_INCOMING_NOTE_GNU_MAKE_: false
80+
_R_CHECK_PACKAGE_DATASETS_SUPPRESS_NOTES_: true

‎.github/workflows/reverse_dependency_checks.yaml‎

Lines changed: 12 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,12 @@
1+
name: Reverse Dependency Checks
2+
3+
on:
4+
workflow_dispatch:
5+
6+
jobs:
7+
# Run a reverse dependency check similar to CRAN, for more details see
8+
# https://github.com/r-devel/recheck.
9+
check-reverse-dependencies:
10+
uses: r-devel/recheck/.github/workflows/recheck.yml@v1
11+
with:
12+
which: all

‎DESCRIPTION‎

Lines changed: 1 addition & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,6 @@
11
Package: SeuratObject
22
Title: Data Structures for Single Cell Data
3-
Version: 5.0.99.9008
3+
Version: 5.0.99.9011
44
Authors@R: c(
55
person(given = 'Paul', family = 'Hoffman', email = '[email protected]', role = 'aut', comment = c(ORCID = '0000-0002-7693-8957')),
66
person(given = 'Rahul', family = 'Satija', email = '[email protected]', role = c('aut', 'cre'), comment = c(ORCID = '0000-0001-9448-8833')),
@@ -67,7 +67,6 @@ Suggests:
6767
sf (>= 1.0.0),
6868
testthat
6969
LinkingTo: Rcpp, RcppEigen
70-
Enhances: Seurat
7170
Config/Needs/website: pkgdown
7271
BuildManual: true
7372
Encoding: UTF-8

‎NAMESPACE‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -255,15 +255,19 @@ S3method(ReorderIdent,Seurat)
255255
S3method(S4ToList,default)
256256
S3method(S4ToList,list)
257257
S3method(SVFInfo,Assay)
258+
S3method(SVFInfo,Assay5)
258259
S3method(SVFInfo,Seurat)
260+
S3method(SVFInfo,StdAssay)
259261
S3method(SetAssayData,Assay)
260262
S3method(SetAssayData,Seurat)
261263
S3method(SetAssayData,StdAssay)
262264
S3method(SetIdent,Seurat)
263265
S3method(Simplify,Molecules)
264266
S3method(Simplify,Spatial)
265267
S3method(SpatiallyVariableFeatures,Assay)
268+
S3method(SpatiallyVariableFeatures,Assay5)
266269
S3method(SpatiallyVariableFeatures,Seurat)
270+
S3method(SpatiallyVariableFeatures,StdAssay)
267271
S3method(StashIdent,Seurat)
268272
S3method(Stdev,DimReduc)
269273
S3method(Stdev,Seurat)

‎NEWS.md‎

Lines changed: 4 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1,6 +1,10 @@
11
# Unreleased
22

33
## Changes:
4+
- Drop `Seurat` from `Enhances`; update `.IsFutureSeurat` to avoid calling `requireNamespace('Seurat', ...)` (#250)
5+
- Update the `VariableFeatures.StdAssay` setter to apply a speedup (#240)
6+
- Add `SVFInfo.Assay5` & `SpatiallyVariableFeatures.Assay5` (#242)
7+
- Fix bug in `SpatiallyVariableFeatures.Assay` (#242)
48
- Fix bug in `merge.Seurat` (#246)
59
- Fix bug in `VariableFeatures.StdAssay` (#245)
610
- Fix bug in `HVFInfo.StdAssay` (#244)

0 commit comments

Comments
 (0)