update vignettes (part 2) #274
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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 "[email protected]" | |
| 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 | |