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Merge branch 'devel' into gene_set_enrichment_plot_complex
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@lcolladotor
lcolladotor authored Dec 13, 2024
2 parents 8de7e4c + 3fa0e52 commit 33070e1
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3 changes: 3 additions & 0 deletions .Rbuildignore
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Expand Up @@ -14,3 +14,6 @@ $run_dev.*
^pkgdown$
^codecov\.yml$
^\.github$
^spatialLIBD\.Rproj$
^doc$
^Meta$
138 changes: 83 additions & 55 deletions .github/workflows/check-bioc.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -52,9 +52,9 @@ jobs:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: '4.2', bioc: '3.16', cont: "bioconductor/bioconductor_docker:RELEASE_3_16", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
#- { os: macOS-latest, r: '4.2', bioc: '3.16'}
- { os: windows-latest, r: '4.2', bioc: '3.16'}
- { os: ubuntu-latest, r: '4.4', bioc: '3.20', cont: "bioconductor/bioconductor_docker:RELEASE_3_20", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" }
- { os: macOS-latest, r: '4.4', bioc: '3.20'}
- { os: windows-latest, r: '4.4', bioc: '3.20'}
## Check https://github.com/r-lib/actions/tree/master/examples
## for examples using the http-user-agent
env:
Expand Down Expand Up @@ -105,23 +105,23 @@ jobs:
uses: actions/cache@v3
with:
path: ${{ env.R_LIBS_USER }}
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-

- name: Cache R packages on Linux
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' "
uses: actions/cache@v3
with:
path: /home/runner/work/_temp/Library
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-${{ hashFiles('.github/depends.Rds') }}
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-

- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
echo $sysreqs
sudo -s eval "$sysreqs"
# - name: Install Linux system dependencies
# if: runner.os == 'Linux'
# run: |
# sysreqs=$(Rscript -e 'cat("apt-get update -y && apt-get install -y", paste(gsub("apt-get install -y ", "", remotes::system_requirements("ubuntu", "20.04")), collapse = " "))')
# echo $sysreqs
# sudo -s eval "$sysreqs"

- name: Install macOS system dependencies
if: matrix.config.os == 'macOS-latest'
Expand All @@ -143,6 +143,17 @@ jobs:
## Required for tcltk
brew install xquartz --cask
## Latest curl
brew install curl pkg-config
- name: Install macOS curl from source
if: matrix.config.os == 'macOS-latest'
run: |
message(paste('****', Sys.time(), 'installing curl from source ****'))
Sys.setenv(PKG_CONFIG_PATH="/opt/homebrew/opt/curl/lib/pkgconfig:/usr/local/opt/curl/lib/pkgconfig")
install.packages("curl", type = "source")
shell: Rscript {0}

- name: Install Windows system dependencies
if: runner.os == 'Windows'
run: |
Expand All @@ -169,35 +180,19 @@ jobs:
## https://github.com/r-lib/remotes/issues/296
## Ideally, all dependencies should get installed in the first pass.
## Set the repos source depending on the OS
## Alternatively use https://storage.googleapis.com/bioconductor_docker/packages/
## though based on https://bit.ly/bioc2021-package-binaries
## the Azure link will be the main one going forward.
gha_repos <- if(
.Platform$OS.type == "unix" && Sys.info()["sysname"] != "Darwin"
) c(
"AnVIL" = "https://bioconductordocker.blob.core.windows.net/packages/3.16/bioc",
BiocManager::repositories()
) else BiocManager::repositories()
## For running the checks
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****'))
install.packages(c("rcmdcheck", "BiocCheck"), repos = gha_repos)
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories())
## Pass #1 at installing dependencies
## This pass uses AnVIL-powered fast binaries
## details at https://github.com/nturaga/bioc2021-bioconductor-binaries
## The speed gains only apply to the docker builds.
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = gha_repos, build_vignettes = FALSE, upgrade = TRUE)
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, upgrade = TRUE)
continue-on-error: true
shell: Rscript {0}

- name: Install dependencies pass 2
run: |
## Pass #2 at installing dependencies
## This pass does not use AnVIL and will thus update any packages
## that have seen been updated in Bioconductor
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE)
shell: Rscript {0}
Expand All @@ -210,13 +205,13 @@ jobs:
shell: Rscript {0}

- name: Install covr
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("covr")
shell: Rscript {0}

- name: Install pkgdown
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
remotes::install_cran("pkgdown")
shell: Rscript {0}
Expand All @@ -237,7 +232,7 @@ jobs:
rcmdcheck::rcmdcheck(
args = c("--no-manual", "--no-vignettes", "--timings"),
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"),
error_on = "error",
error_on = "warning",
check_dir = "check"
)
shell: Rscript {0}
Expand Down Expand Up @@ -267,17 +262,17 @@ jobs:
shell: Rscript {0}

- name: Test coverage
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux'
run: |
covr::codecov()
covr::codecov(coverage = covr::package_coverage(type = "all"))
shell: Rscript {0}

- name: Install package
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: R CMD INSTALL .

- name: Build pkgdown site
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
shell: Rscript {0}
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE)
Expand All @@ -286,12 +281,12 @@ jobs:
## makes the git history recognizable by pkgdown.

- name: Install deploy dependencies
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
run: |
apt-get update && apt-get -y install rsync
- name: Deploy pkgdown site to GitHub pages 🚀
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux'
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux'
uses: JamesIves/github-pages-deploy-action@releases/v4
with:
clean: false
Expand All @@ -302,21 +297,54 @@ jobs:
if: failure()
uses: actions/upload-artifact@master
with:
name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results
name: ${{ runner.os }}-biocversion-RELEASE_3_20-r-4.4-results
path: check

## Note that DOCKER_PASSWORD is really a token for your dockerhub
## account, not your actual dockerhub account password.
## This comes from
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html#6-add-secrets-to-github-repo
## Check https://github.com/docker/build-push-action/tree/releases/v1
## for more details.
- uses: docker/build-push-action@v1
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' "

## Code adapted from
## https://github.com/waldronlab/cBioPortalData/blob/e0440a4445f0cc731e426363a76faa22ee5e0f9d/.github/workflows/devel_check_dock.yml#L65-L92
docker-build-and-push:
runs-on: ubuntu-latest
needs: build-check
steps:
- name: Checkout Repository
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: actions/checkout@v3

- name: Register repo name
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
id: reg_repo_name
run: |
echo CONT_IMG_NAME=$(echo ${{ github.event.repository.name }} | tr '[:upper:]' '[:lower:]') >> $GITHUB_ENV
- name: Set up QEMU
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-qemu-action@v2

- name: Set up Docker Buildx
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/setup-buildx-action@v2

- name: Login to Docker Hub
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel'"
uses: docker/login-action@v2
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
## Note that DOCKERHUB_TOKEN is really a token for your dockerhub
## account, not your actual dockerhub account password. You can get it
## from https://hub.docker.com/settings/security.
## Check https://github.com/docker/build-push-action/tree/v4.0.0
## for more details.
## Alternatively, try checking
## https://seandavi.github.io/BuildABiocWorkshop/articles/HOWTO_BUILD_WORKSHOP.html.

- name: Build and Push Docker
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && github.ref == 'refs/heads/devel' && success()"
uses: docker/build-push-action@v4
with:
username: ${{ secrets.DOCKER_USERNAME }}
password: ${{ secrets.DOCKER_PASSWORD }}
repository: lieberinstitute/spatiallibd
tag_with_ref: true
tag_with_sha: true
tags: latest
context: .
push: true
tags: >
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:latest,
${{ secrets.DOCKERHUB_USERNAME }}/${{ env.CONT_IMG_NAME }}:devel
2 changes: 2 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -7,3 +7,5 @@ data-raw/spatialLIBD_files
docs/
rsconnect
*.Rproj
/doc/
/Meta/
18 changes: 12 additions & 6 deletions DESCRIPTION
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Original file line number Diff line number Diff line change
@@ -1,8 +1,8 @@
Package: spatialLIBD
Title: spatialLIBD: an R/Bioconductor package to visualize spatially-resolved
transcriptomics data
Version: 1.11.8
Date: 2023-02-22
Version: 1.19.3
Date: 2024-12-12
Authors@R:
c(
person("Leonardo", "Collado-Torres", role = c("aut", "cre"),
Expand Down Expand Up @@ -55,7 +55,6 @@ Imports:
scater,
DT,
ExperimentHub,
RColorBrewer,
SummarizedExperiment,
stats,
graphics,
Expand All @@ -76,8 +75,13 @@ Imports:
scuttle,
edgeR,
limma,
statmod
RoxygenNote: 7.2.3
statmod,
MatrixGenerics,
rlang,
dplyr,
ComplexHeatmap,
circlize
RoxygenNote: 7.3.2
Roxygen: list(markdown = TRUE)
URL: https://github.com/LieberInstitute/spatialLIBD
BugReports: https://support.bioconductor.org/tag/spatialLIBD
Expand All @@ -90,7 +94,9 @@ Suggests:
covr,
here,
BiocManager,
lobstr
lobstr,
DropletUtils,
RColorBrewer
VignetteBuilder: knitr
biocViews: Homo_sapiens_Data, ExperimentHub, SequencingData, SingleCellData,
ExpressionData, Tissue, PackageTypeData, SpatialData
Expand Down
18 changes: 16 additions & 2 deletions NAMESPACE
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
export(add10xVisiumAnalysis)
export(add_images)
export(add_key)
export(add_qc_metrics)
export(annotate_registered_clusters)
export(check_modeling_results)
export(check_sce)
Expand Down Expand Up @@ -46,6 +47,7 @@ export(vis_gene_p)
export(vis_grid_clus)
export(vis_grid_gene)
import(ExperimentHub)
import(MatrixGenerics)
import(SingleCellExperiment)
import(ggplot2)
import(grid)
Expand All @@ -54,12 +56,15 @@ import(plotly, except = last_plot)
import(shiny)
importFrom(AnnotationHub,query)
importFrom(BiocGenerics,which)
importFrom(ComplexHeatmap,Heatmap)
importFrom(ComplexHeatmap,anno_barplot)
importFrom(ComplexHeatmap,columnAnnotation)
importFrom(ComplexHeatmap,rowAnnotation)
importFrom(DT,DTOutput)
importFrom(DT,renderDT)
importFrom(GenomicRanges,seqnames)
importFrom(IRanges,CharacterList)
importFrom(IRanges,IntegerList)
importFrom(RColorBrewer,brewer.pal)
importFrom(S4Vectors,"mcols<-")
importFrom(S4Vectors,DataFrame)
importFrom(S4Vectors,mcols)
Expand All @@ -82,14 +87,20 @@ importFrom(SummarizedExperiment,"rowRanges<-")
importFrom(SummarizedExperiment,assay)
importFrom(SummarizedExperiment,assayNames)
importFrom(SummarizedExperiment,assays)
importFrom(SummarizedExperiment,colData)
importFrom(benchmarkme,get_ram)
importFrom(circlize,colorRamp2)
importFrom(cowplot,plot_grid)
importFrom(dplyr,group_by)
importFrom(dplyr,left_join)
importFrom(dplyr,mutate)
importFrom(dplyr,select)
importFrom(dplyr,summarize)
importFrom(edgeR,calcNormFactors)
importFrom(edgeR,filterByExpr)
importFrom(fields,image.plot)
importFrom(golem,with_golem_options)
importFrom(grDevices,as.raster)
importFrom(grDevices,colorRampPalette)
importFrom(grDevices,dev.off)
importFrom(grDevices,pdf)
importFrom(graphics,abline)
Expand Down Expand Up @@ -121,9 +132,11 @@ importFrom(magick,image_transparent)
importFrom(methods,is)
importFrom(methods,new)
importFrom(png,readPNG)
importFrom(rlang,arg_match)
importFrom(rtracklayer,import)
importFrom(scater,plotReducedDim)
importFrom(scuttle,aggregateAcrossCells)
importFrom(scuttle,isOutlier)
importFrom(sessioninfo,session_info)
importFrom(shiny,shinyApp)
importFrom(shinyWidgets,pickerInput)
Expand All @@ -137,6 +150,7 @@ importFrom(stats,hclust)
importFrom(stats,median)
importFrom(stats,model.matrix)
importFrom(stats,p.adjust)
importFrom(stats,prcomp)
importFrom(stats,reshape)
importFrom(stats,setNames)
importFrom(tibble,tibble)
Expand Down
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