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^.*\.Rproj$ | ||
^\.Rproj\.user$ |
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*.html |
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## Read more about GitHub actions the features of this GitHub Actions workflow | ||
## at https://lcolladotor.github.io/biocthis/articles/biocthis.html#use_bioc_github_action | ||
## | ||
## For more details, check the biocthis developer notes vignette at | ||
## https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html | ||
## | ||
## You can add this workflow to other packages using: | ||
## > biocthis::use_bioc_github_action() | ||
## | ||
## Using GitHub Actions exposes you to many details about how R packages are | ||
## compiled and installed in several operating system.s | ||
### If you need help, please follow the steps listed at | ||
## https://github.com/r-lib/actions#where-to-find-help | ||
## | ||
## If you found an issue specific to biocthis's GHA workflow, please report it | ||
## with the information that will make it easier for others to help you. | ||
## Thank you! | ||
|
||
## Acronyms: | ||
## * GHA: GitHub Action | ||
## * OS: operating system | ||
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on: | ||
push: | ||
pull_request: | ||
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name: R-CMD-check-bioc | ||
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## These environment variables control whether to run GHA code later on that is | ||
## specific to testthat, covr, and pkgdown. | ||
## | ||
## If you need to clear the cache of packages, update the number inside | ||
## cache-version as discussed at https://github.com/r-lib/actions/issues/86. | ||
## Note that you can always run a GHA test without the cache by using the word | ||
## "/nocache" in the commit message. | ||
env: | ||
has_testthat: 'true' | ||
run_covr: 'true' | ||
run_pkgdown: 'true' | ||
has_RUnit: 'false' | ||
cache-version: 'cache-v1' | ||
run_docker: 'false' | ||
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jobs: | ||
build-check: | ||
runs-on: ${{ matrix.config.os }} | ||
name: ${{ matrix.config.os }} (${{ matrix.config.r }}) | ||
container: ${{ matrix.config.cont }} | ||
## Environment variables unique to this job. | ||
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strategy: | ||
fail-fast: false | ||
matrix: | ||
config: | ||
- { os: ubuntu-latest, r: 'devel', bioc: '3.17', cont: "bioconductor/bioconductor_docker:RELEASE_3_17", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
#- { os: macOS-latest, r: 'devel', bioc: '3.15'} | ||
#- { os: windows-latest, r: 'devel', bioc: '3.15'} | ||
# - { os: ubuntu-latest, r: '4.1', bioc: '3.14', cont: "bioconductor/bioconductor_docker:RELEASE_3_14", rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" } | ||
#- { os: macOS-latest, r: '4.1', bioc: '3.14'} | ||
#- { os: windows-latest, r: '4.1', bioc: '3.14'} | ||
env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
RSPM: ${{ matrix.config.rspm }} | ||
NOT_CRAN: true | ||
TZ: UTC | ||
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }} | ||
GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} | ||
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steps: | ||
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## Set the R library to the directory matching the | ||
## R packages cache step further below when running on Docker (Linux). | ||
- name: Set R Library home on Linux | ||
if: runner.os == 'Linux' | ||
run: | | ||
mkdir /__w/_temp/Library | ||
echo ".libPaths('/__w/_temp/Library')" > ~/.Rprofile | ||
## Most of these steps are the same as the ones in | ||
## https://github.com/r-lib/actions/blob/master/examples/check-standard.yaml | ||
## If they update their steps, we will also need to update ours. | ||
- name: Checkout Repository | ||
uses: actions/checkout@v2 | ||
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## R is already included in the Bioconductor docker images | ||
- name: Setup R from r-lib | ||
if: runner.os != 'Linux' | ||
uses: r-lib/actions/setup-r@v2-branch | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
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## pandoc is already included in the Bioconductor docker images | ||
- name: Setup pandoc from r-lib | ||
if: runner.os != 'Linux' | ||
uses: r-lib/actions/setup-pandoc@v2-branch | ||
|
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- name: Query dependencies | ||
run: | | ||
install.packages('remotes') | ||
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
shell: Rscript {0} | ||
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- name: Cache R packages | ||
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
uses: actions/cache@v2 | ||
with: | ||
path: ${{ env.R_LIBS_USER }} | ||
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | ||
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- name: Cache R packages on Linux | ||
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os == 'Linux' " | ||
uses: actions/cache@v2 | ||
with: | ||
path: /home/runner/work/_temp/Library | ||
key: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-${{ hashFiles('.github/depends.Rds') }} | ||
|
||
- name: Install Linux system dependencies | ||
if: runner.os == 'Linux' | ||
run: | | ||
sysreqs=$(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' | ||
run: | | ||
## Enable installing XML from source if needed | ||
brew install libxml2 | ||
echo "XML_CONFIG=/usr/local/opt/libxml2/bin/xml2-config" >> $GITHUB_ENV | ||
## Required to install magick as noted at | ||
## https://github.com/r-lib/usethis/commit/f1f1e0d10c1ebc75fd4c18fa7e2de4551fd9978f#diff-9bfee71065492f63457918efcd912cf2 | ||
brew install imagemagick@6 | ||
## For textshaping, required by ragg, and required by pkgdown | ||
brew install harfbuzz fribidi | ||
## For installing usethis's dependency gert | ||
brew install libgit2 | ||
- name: Install Windows system dependencies | ||
if: runner.os == 'Windows' | ||
run: | | ||
## Edit below if you have any Windows system dependencies | ||
shell: Rscript {0} | ||
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- name: Install BiocManager | ||
run: | | ||
message(paste('****', Sys.time(), 'installing BiocManager ****')) | ||
remotes::install_cran("BiocManager") | ||
shell: Rscript {0} | ||
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- name: Set BiocVersion | ||
run: | | ||
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | ||
shell: Rscript {0} | ||
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- name: Install dependencies pass 1 | ||
run: | | ||
## Try installing the package dependencies in steps. First the local | ||
## dependencies, then any remaining dependencies to avoid the | ||
## issues described at | ||
## https://stat.ethz.ch/pipermail/bioc-devel/2020-April/016675.html | ||
## https://github.com/r-lib/remotes/issues/296 | ||
## Ideally, all dependencies should get installed in the first pass. | ||
## Pass #1 at installing dependencies | ||
message(paste('****', Sys.time(), 'pass number 1 at installing dependencies: local dependencies ****')) | ||
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE) | ||
continue-on-error: true | ||
shell: Rscript {0} | ||
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- name: Install dependencies pass 2 | ||
run: | | ||
## Pass #2 at installing dependencies | ||
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) | ||
## For running the checks | ||
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
remotes::install_cran("rcmdcheck") | ||
BiocManager::install("BiocCheck") | ||
shell: Rscript {0} | ||
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- name: Install BiocGenerics | ||
if: env.has_RUnit == 'true' | ||
run: | | ||
## Install BiocGenerics | ||
BiocManager::install("BiocGenerics") | ||
shell: Rscript {0} | ||
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- name: Install covr | ||
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' | ||
run: | | ||
remotes::install_cran("covr") | ||
shell: Rscript {0} | ||
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- name: Install pkgdown and deps | ||
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' | ||
run: | | ||
remotes::install_cran("pkgdown") | ||
shell: Rscript {0} | ||
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- name: Session info | ||
run: | | ||
options(width = 100) | ||
pkgs <- installed.packages()[, "Package"] | ||
sessioninfo::session_info(pkgs, include_base = TRUE) | ||
shell: Rscript {0} | ||
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- name: Run CMD check | ||
env: | ||
_R_CHECK_CRAN_INCOMING_: false | ||
run: | | ||
rcmdcheck::rcmdcheck( | ||
args = c("--no-build-vignettes", "--no-manual", "--timings"), | ||
build_args = c("--no-manual", "--no-resave-data"), | ||
error_on = "warning", | ||
check_dir = "check" | ||
) | ||
shell: Rscript {0} | ||
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## Might need an to add this to the if: && runner.os == 'Linux' | ||
- name: Reveal testthat details | ||
if: env.has_testthat == 'true' | ||
run: find . -name testthat.Rout -exec cat '{}' ';' | ||
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- name: Run RUnit tests | ||
if: env.has_RUnit == 'true' | ||
run: | | ||
BiocGenerics:::testPackage() | ||
shell: Rscript {0} | ||
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- name: Run BiocCheck | ||
env: | ||
DISPLAY: 99.0 | ||
run: | | ||
BiocCheck::BiocCheck( | ||
dir('check', 'tar.gz$', full.names = TRUE), | ||
`quit-with-status` = TRUE, | ||
`no-check-R-ver` = TRUE, | ||
`no-check-bioc-help` = TRUE | ||
) | ||
shell: Rscript {0} | ||
|
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- name: Test coverage | ||
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' | ||
run: | | ||
covr::codecov(type="all", commentDontrun=FALSE) | ||
shell: Rscript {0} | ||
|
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- name: Install package | ||
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' | ||
run: R CMD INSTALL . | ||
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- name: Deploy package | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' && matrix.config.r == 'devel' | ||
run: | | ||
git config --local user.name "$GITHUB_ACTOR" | ||
git config --local user.email "[email protected]" | ||
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
shell: bash {0} | ||
## Note that you need to run pkgdown::deploy_to_branch(new_process = FALSE) | ||
## at least one locally before this will work. This creates the gh-pages | ||
## branch (erasing anything you haven't version controlled!) and | ||
## makes the git history recognizable by pkgdown. | ||
|
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- name: Upload check results | ||
if: failure() | ||
uses: actions/upload-artifact@master | ||
with: | ||
name: ${{ runner.os }}-biocversion-${{ matrix.config.bioc }}-r-${{ matrix.config.r }}-results | ||
path: check | ||
|
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- uses: docker/build-push-action@v1 | ||
if: "!contains(github.event.head_commit.message, '/nodocker') && env.run_docker == 'true' && runner.os == 'Linux' " | ||
with: | ||
username: ${{ secrets.DOCKER_USERNAME }} | ||
password: ${{ secrets.DOCKER_PASSWORD }} | ||
repository: davislaboratory/standR | ||
tag_with_ref: true | ||
tag_with_sha: true | ||
tags: latest |
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# History files | ||
.Rhistory | ||
.Rapp.history | ||
.Rproj.user | ||
*.Rproj | ||
|
||
# Session Data files | ||
.RData | ||
|
||
# User-specific files | ||
.Ruserdata | ||
|
||
# Example code in package build process | ||
*-Ex.R | ||
|
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# Output files from R CMD build | ||
/*.tar.gz | ||
|
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# Output files from R CMD check | ||
/*.Rcheck/ | ||
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# RStudio files | ||
.Rproj.user/ | ||
|
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# produced vignettes | ||
vignettes/*.html | ||
vignettes/*.pdf | ||
|
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# OAuth2 token, see https://github.com/hadley/httr/releases/tag/v0.3 | ||
.httr-oauth | ||
|
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# knitr and R markdown default cache directories | ||
*_cache/ | ||
/cache/ | ||
|
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# Temporary files created by R markdown | ||
*.utf8.md | ||
*.knit.md | ||
|
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# R Environment Variables | ||
.Renviron | ||
inst/doc | ||
doc | ||
|
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# Rproj | ||
hoodscanR.Rproj |
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Package: hoodscanR | ||
Title: Spatial cellular neighbourhood scanning in R | ||
Version: 0.99.0 | ||
Authors@R: | ||
c(person(given = "Ning", | ||
family = "Liu", | ||
role = c("aut", "cre"), | ||
email = "[email protected]", | ||
comment = c(ORCID = "0000-0002-9487-9305")), | ||
person(given = "Jarryd", | ||
family = "Martin", | ||
role = c("aut"), | ||
email = "", | ||
comment = c(ORCID = ""))) | ||
Description: hoodscanR is an user-friendly R package providing functions to assist | ||
cellular neighborhood analysis of any spatial transcriptomics data with single-cell resolution. | ||
All functions in the package are built based on the SpatialExperiment object, | ||
allowing integration into various spatial transcriptomics-related packages from Bioconductor. | ||
The package can result in cell-level neighborhood annotation output, along with funtions to | ||
perform neighborhood colocalization analysis and neighborhood-based cell clustering. | ||
biocViews: Spatial, Transcriptomics, SingleCell, Clustering | ||
License: GPL-3 + file LICENSE | ||
URL: https://github.com/DavisLaboratory/hoodscanR | ||
BugReports: https://github.com/DavisLaboratory/hoodscanR/issues | ||
Encoding: UTF-8 | ||
LazyData: false | ||
Roxygen: list(markdown = TRUE) | ||
RoxygenNote: 7.2.3 | ||
Imports: | ||
knitr, | ||
rmarkdown, | ||
SpatialExperiment, | ||
SummarizedExperiment, | ||
circlize, | ||
ComplexHeatmap, | ||
scico, | ||
rlang, | ||
S4Vectors, | ||
dplyr, | ||
tibble, | ||
utils, | ||
ggplot2, | ||
tidyr, | ||
grid, | ||
methods, | ||
stats, | ||
RANN, | ||
Rcpp (>= 1.0.9) | ||
LinkingTo: | ||
Rcpp | ||
Suggests: | ||
testthat (>= 3.0.0) | ||
Config/testthat/edition: 3 | ||
Depends: | ||
R (>= 4.3) | ||
VignetteBuilder: knitr |
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