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Merge pull request #9 from william-hutchison/development
Documentation and code clarity overhaul
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@@ -39,6 +39,7 @@ env: | |
run_pkgdown: 'true' | ||
has_RUnit: 'false' | ||
cache-version: 'cache-v1' | ||
run_docker: 'false' | ||
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jobs: | ||
build-check: | ||
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@@ -51,9 +52,11 @@ 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: '4.3', bioc: '3.18', cont: "bioconductor/bioconductor_docker:devel", rspm: "https://packagemanager.rstudio.com/cran/__linux__/jammy/latest" } | ||
- { os: macOS-latest, r: '4.3', bioc: '3.18'} | ||
- { os: windows-latest, r: '4.3', bioc: '3.18'} | ||
## Check https://github.com/r-lib/actions/tree/master/examples | ||
## for examples using the http-user-agent | ||
env: | ||
R_REMOTES_NO_ERRORS_FROM_WARNINGS: true | ||
RSPM: ${{ matrix.config.rspm }} | ||
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@@ -76,14 +79,15 @@ jobs: | |
## 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 | ||
uses: actions/checkout@v3 | ||
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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 | ||
with: | ||
r-version: ${{ matrix.config.r }} | ||
http-user-agent: ${{ matrix.config.http-user-agent }} | ||
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## pandoc is already included in the Bioconductor docker images | ||
- name: Setup pandoc from r-lib | ||
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@@ -96,28 +100,28 @@ jobs: | |
saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2) | ||
shell: Rscript {0} | ||
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- name: Cache R packages | ||
- name: Restore R package cache | ||
if: "!contains(github.event.head_commit.message, '/nocache') && runner.os != 'Linux'" | ||
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-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3- | ||
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||
- 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-devel-r-4.3-${{ hashFiles('.github/depends.Rds') }} | ||
restore-keys: ${{ env.cache-version }}-${{ runner.os }}-biocversion-devel-r-4.3- | ||
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||
- 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" | ||
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||
- name: Install macOS system dependencies | ||
if: matrix.config.os == 'macOS-latest' | ||
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@@ -135,10 +139,9 @@ jobs: | |
## For installing usethis's dependency gert | ||
brew install libgit2 | ||
## To fix x11/cairo error with tidyHeatmap/Complexheatmap here https://github.com/stemangiola/tidybulk/runs/1388237421?check_suite_focus=true#step:14:2134 | ||
## Suggested here https://stackoverflow.com/questions/63648591/how-to-install-x11-before-testing-with-github-actions-for-macos | ||
brew install --cask xquartz | ||
## Required for tcltk | ||
brew install xquartz --cask | ||
- name: Install Windows system dependencies | ||
if: runner.os == 'Windows' | ||
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@@ -154,7 +157,7 @@ jobs: | |
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||
- name: Set BiocVersion | ||
run: | | ||
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE) | ||
BiocManager::install(version = "${{ matrix.config.bioc }}", ask = FALSE, force = TRUE) | ||
shell: Rscript {0} | ||
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||
- name: Install dependencies pass 1 | ||
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@@ -166,22 +169,21 @@ jobs: | |
## https://github.com/r-lib/remotes/issues/296 | ||
## Ideally, all dependencies should get installed in the first pass. | ||
## For running the checks | ||
message(paste('****', Sys.time(), 'installing rcmdcheck and BiocCheck ****')) | ||
install.packages(c("rcmdcheck", "BiocCheck"), repos = BiocManager::repositories()) | ||
## 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) | ||
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = FALSE, 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") | ||
remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE, force = TRUE) | ||
shell: Rscript {0} | ||
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- name: Install BiocGenerics | ||
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@@ -192,15 +194,15 @@ jobs: | |
shell: Rscript {0} | ||
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- 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} | ||
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- 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") | ||
remotes::install_github("r-lib/pkgdown") | ||
shell: Rscript {0} | ||
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- name: Session info | ||
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@@ -213,10 +215,12 @@ jobs: | |
- name: Run CMD check | ||
env: | ||
_R_CHECK_CRAN_INCOMING_: false | ||
DISPLAY: 99.0 | ||
run: | | ||
options(crayon.enabled = TRUE) | ||
rcmdcheck::rcmdcheck( | ||
args = c("--no-build-vignettes", "--no-manual", "--timings"), | ||
build_args = c("--no-manual", "--no-resave-data"), | ||
args = c("--no-manual", "--no-vignettes", "--timings"), | ||
build_args = c("--no-manual", "--keep-empty-dirs", "--no-resave-data"), | ||
error_on = "warning", | ||
check_dir = "check" | ||
) | ||
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@@ -234,45 +238,52 @@ jobs: | |
shell: Rscript {0} | ||
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- name: Run BiocCheck | ||
env: | ||
DISPLAY: 99.0 | ||
run: | | ||
BiocCheck::BiocCheck( | ||
dir('check', 'tar.gz$', full.names = TRUE), | ||
`quit-with-status` = TRUE, | ||
`no-check-R-ver` = TRUE, | ||
`no-check-bioc-help` = TRUE, | ||
`no-check-library-calls` = TRUE, | ||
`no-check-coding-practices` = TRUE | ||
`no-check-bioc-help` = TRUE | ||
) | ||
shell: Rscript {0} | ||
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- name: Test coverage | ||
if: github.ref == 'refs/heads/master' && env.run_covr == 'true' && runner.os == 'Linux' | ||
if: github.ref == 'refs/heads/devel' && env.run_covr == 'true' && runner.os == 'Linux' | ||
run: | | ||
covr::codecov() | ||
shell: Rscript {0} | ||
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||
- name: Install package | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
if: github.ref == 'refs/heads/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
run: R CMD INSTALL . | ||
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||
- name: Deploy package | ||
if: github.ref == 'refs/heads/master' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
run: | | ||
## Temporary workaround for https://github.com/actions/checkout/issues/766 | ||
git config --global --add safe.directory "$GITHUB_WORKSPACE" | ||
git config --local user.email "[email protected]" | ||
git config --local user.name "GitHub Actions" | ||
Rscript -e "pkgdown::deploy_to_branch(new_process = FALSE)" | ||
shell: bash {0} | ||
- name: Build pkgdown site | ||
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) | ||
## 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: Install deploy dependencies | ||
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/devel' && env.run_pkgdown == 'true' && runner.os == 'Linux' | ||
uses: JamesIves/github-pages-deploy-action@releases/v4 | ||
with: | ||
clean: false | ||
branch: gh-pages | ||
folder: docs | ||
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- name: Upload check results | ||
if: failure() | ||
uses: actions/upload-artifact@v3 | ||
uses: actions/upload-artifact@master | ||
with: | ||
name: ${{ runner.os }}-biocversion-RELEASE_3_16-r-4.2-results | ||
path: check | ||
name: ${{ runner.os }}-biocversion-devel-r-4.3-results | ||
path: check |
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@@ -1,20 +1,22 @@ | ||
Type: Package | ||
Package: tidySpatialExperiment | ||
Title: Brings SpatialExperiment to the Tidyverse | ||
Version: 0.0.4 | ||
Title: Brings SpatialExperiment to the tidyverse | ||
Version: 0.99.0 | ||
Authors@R: c( | ||
person("William", "Hutchison", email = "[email protected]", role = c("aut", "cre")), | ||
person("Stefano", "Mangiola", email = "[email protected]", role = "aut") | ||
) | ||
Description: tidySpatialExperiment is an adapter that abstracts the 'SpatialExperiment' container | ||
in the form of a tibble and allows data manipulation, plotting and nesting using 'tidyverse'. | ||
Description: tidySpatialExperiment is an adapter that abstracts the SpatialExperiment container | ||
in the form of a tibble and allows data manipulation, plotting and nesting using functions from | ||
the tidyverse ecosystem. | ||
License: GPL-3 | ||
Depends: | ||
R (>= 4.1.0), | ||
ttservice, | ||
R (>= 4.3.0), | ||
SingleCellExperiment, | ||
SpatialExperiment | ||
SpatialExperiment, | ||
tidySingleCellExperiment, | ||
Imports: | ||
ttservice, | ||
SummarizedExperiment, | ||
BiocGenerics, | ||
dplyr, | ||
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