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check-bioc.yml
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on:
push:
branches:
- master
- devel
name: check-bioc
jobs:
build-check:
runs-on: ${{ matrix.config.os }}
name: ${{ matrix.config.os }} (${{ matrix.config.r }})
container: ${{ matrix.config.cont }}
strategy:
fail-fast: false
matrix:
config:
- { os: ubuntu-latest, r: 'release', rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
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 }}
steps:
- name: Checkout Repository
uses: actions/checkout@v3
- name: Setup R from r-lib
uses: r-lib/actions/setup-r@v2
with:
r-version: ${{ matrix.config.r }}
- name: Setup pandoc from r-lib
uses: r-lib/actions/setup-pandoc@v2
- name: Query dependencies
uses: r-lib/actions/setup-r-dependencies@v2
with:
extra-packages: any::rcmdcheck
needs: check
- name: Install Linux system dependencies
if: runner.os == 'Linux'
run: |
Rscript -e 'install.packages("remotes")'
sysreqs=$(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"
# SpatialExperiment (magick) dependency
sudo apt-get install -y libmagick++-dev
- name: Install BiocManager
run: |
message(paste('****', Sys.time(), 'installing BiocManager ****'))
remotes::install_cran("BiocManager")
shell: Rscript {0}
- name: Set BiocVersion
run: |
BiocManager::install(ask = FALSE)
shell: Rscript {0}
- name: Install remaining 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_deps(dependencies = TRUE, repos = BiocManager::repositories(), upgrade = "always")
continue-on-error: true
shell: Rscript {0}
- name: Install remaining dependencies pass 2
run: |
## Pass #2 at installing dependencies
message(paste('****', Sys.time(), 'pass number 2 at installing dependencies: any remaining dependencies ****'))
remotes::install_deps(dependencies = TRUE, repos = BiocManager::repositories(), upgrade = "always")
## For producing vignette pdf output
remotes::install_cran(c("tinytex", "igraph", "magick"))
tinytex::install_tinytex()
tinytex::tlmgr_update()
tinytex::tlmgr_install("pdfcrop")
## For running the checks
message(paste('****', Sys.time(), 'installing BiocCheck ****'))
BiocManager::install("BiocCheck")
shell: Rscript {0}
- name: Session info
run: |
options(width = 100)
pkgs <- installed.packages()[, "Package"]
sessioninfo::session_info(pkgs, include_base = TRUE)
shell: Rscript {0}
- name: Run BiocCheck
run: |
BiocCheck::BiocCheck(
`quit-with-status` = TRUE,
`no-check-R-ver` = TRUE,
`no-check-bioc-help` = TRUE
)
shell: Rscript {0}
# - name: Test coverage
# if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
# run: |
# covr::codecov()
# shell: Rscript {0}
- name: Install package
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: R CMD INSTALL .
- name: Set up package deployment
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: |
git config --local user.email "actions@github.com"
git config --local user.name "GitHub Actions"
shell: bash {0}
## Changing package deployment to make the necessary changes to the vignette files
- name: Deploy package
if: github.ref == 'refs/heads/master' && runner.os == 'Linux'
run: |
BiocManager::install(c("decoupleR", "SpatialExperiment"), ask = FALSE)
install.packages(c("pkgdown", "sctransform"))
install.packages(c("stringi", "ridge"), type="source", repos="https://cloud.r-project.org/")
BiocManager::install("OmnipathR", ask=FALSE)
install.packages(c("janitor", "reticulate", "Seurat", "SeuratObject"))
## modified from pkgdown::deploy_to_branch
deploy_to_branch_mod <- function(pkg = ".", commit_message = pkgdown:::construct_commit_message(pkg),
clean = TRUE, branch = "gh-pages", remote = "origin", github_pages = (branch ==
"gh-pages"), ...)
{
dest_dir <- fs::dir_create(fs::file_temp())
on.exit(fs::dir_delete(dest_dir))
if (!pkgdown:::git_has_remote_branch(remote, branch)) {
old_branch <- pkgdown:::git_current_branch()
pkgdown:::git("checkout", "--orphan", branch)
pkgdown:::git("rm", "-rf", "--quiet", ".")
pkgdown:::git("commit", "--allow-empty", "-m", sprintf("init %s branch",
branch))
pkgdown:::git("push", remote, paste0("HEAD:", branch))
pkgdown:::git("checkout", old_branch)
}
pkgdown:::git("remote", "set-branches", remote, branch)
pkgdown:::git("fetch", remote, branch)
pkgdown:::github_worktree_add(dest_dir, remote, branch)
on.exit(pkgdown:::github_worktree_remove(dest_dir), add = TRUE)
pkg <- pkgdown::as_pkgdown(pkg, override = list(destination = dest_dir))
if (clean) {
cli::rule("Cleaning files from old site", line = 1)
pkgdown::clean_site(pkg)
}
pkgdown::build_site(pkg, devel = FALSE, preview = FALSE, install = FALSE,
...)
unlink(paste0(dest_dir, c("/reference/.misty.temp", "/reference/results")), recursive = TRUE)
if (github_pages) {
pkgdown:::build_github_pages(pkg)
}
pkgdown:::github_push(dest_dir, commit_message, remote, branch)
invisible()
}
pkg <- pkgdown::as_pkgdown(pkg = ".")
vignettes <- pkg$vignettes$file_in
original <- purrr::map(vignettes, function(vignette){
content <- rmarkdown:::partition_yaml_front_matter(xfun::read_utf8(vignette))
rmd.front <- content$front_matter
from.to <- (grep("(output:|vignette:)", rmd.front))
rmd.front <- rmd.front[-seq(from.to[1]+1, from.to[2]-1)]
rmd.front[from.to[1]] <- "output:\n BiocStyle::html_document:\n toc_float: true\n df_print: kable"
rmd.front <- sub("- Jožef", " <br/>Jožef", rmd.front)
rmd.body <- content$body
xfun::write_utf8(c(rmd.front, rmd.body), vignette)
content
})
deploy_to_branch_mod(new_process = FALSE)
purrr::walk2(original, vignettes, ~xfun::write_utf8(c(.x$front_matter, .x$body), .y))
shell: Rscript {0}
##Dockerize
-
name: Login to DockerHub
if: "!contains(github.event.head_commit.message, '/nodocker') && runner.os == 'Linux'"
uses: docker/login-action@v1
with:
username: ${{ secrets.DOCKERHUB_USERNAME }}
password: ${{ secrets.DOCKERHUB_TOKEN }}
-
name: Build and push master
if: "!contains(github.event.head_commit.message, '/nodocker') && runner.os == 'Linux' && github.ref == 'refs/heads/master'"
uses: docker/build-push-action@v2
with:
push: true
tags: tanevski/mistyr:master,tanevski/mistyr:latest
-
name: Build and push other
if: "!contains(github.event.head_commit.message, '/nodocker') && runner.os == 'Linux' && github.ref == 'refs/heads/devel'"
uses: docker/build-push-action@v2
with:
push: true
tags: tanevski/mistyr:devel