add template file for GHA

DESCRIPTION

@@ -14,11 +14,12 @@ License: Artistic-2.0
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.0
+RoxygenNote: 7.1.1
 URL: https://github.com/lcolladotor/biocthis
 BugReports: https://support.bioconductor.org/t/biocthis
 biocViews: Software, ReportWriting
 Imports: 
+    BiocManager,
     fs,
     glue,
     rlang,

R/use_bioc_github_action.R

@@ -1,48 +1,63 @@
+.normalizeVersion <- function() {
+    if (BiocManager:::isDevel())
+        "devel"
+    else
+        paste0("RELEASE_", gsub("\\.", "_", BiocManager::version()))
+}
+
+.GHARversion <- function() {
+    rver <- with(R.version, paste(major, minor, sep = "."))
+    gsub("\\.", "-", rver)
+}
+
 #' Create a biocthis-style GitHub Actions workflow
 #'
 #' This function is very similar to `usethis::use_github_action()` except
 #' that it uses a template from `biocthis`. It creates a Bioconductor-friendly
 #' GitHub action workflow for your package. You can also use this GitHub
-#' Actions workflow by executing
-#' `usethis::use_github_action("check-bioc", "https://bit.ly/biocthis_gha", "check-bioc.yml")`
-#' without having to install `biocthis`.
+#' Actions workflow by executing `usethis::use_github_action()`.
 #'
 #' For the full history on how this GitHub Actions workflow came to be, check
 #' the "biocthis developer notes" vignette
 #' <https://lcolladotor.github.io/biocthis/articles/biocthis_dev_notes.html>.
 #'
 #' @return This function adds and/or replaces the
 #' `.github/workflows/check-bioc.yml` file in your R package.
+#'
 #' @export
+#'
 #' @import usethis
 #'
 #' @examples
 #'
 #' \dontrun{
-#' ## Run this function in your package
-#' biocthis::use_bioc_github_action()
-#'
-#' ## You can also use this GitHub Actions workflow without installing biocthis
-#' ## by running:
-#' usethis::use_github_action(
-#'     "check-bioc", "https://bit.ly/biocthis_gha",
-#'     "check-bioc.yml"
-#' )
+#'   ## Run this function in your package
+#'   biocthis::use_bioc_github_action()
 #' }
-#'
-#' ## Create an example package for illustrative purposes.
-#' ## Note: you do not need to run this for your own package!
-#' pkgdir <- biocthis_example_pkg()
-#'
-#' ## Create a GitHub Actions workflow that is Bioconductor-friendly
-#' biocthis::use_bioc_github_action()
 use_bioc_github_action <- function() {
-    usethis::use_github_action(
-        "check-bioc",
-        url = paste0(
-            "https://raw.githubusercontent.com/",
-            "lcolladotor/biocthis/",
-            "master/actions/check-bioc.yml"
-        )
+    datalist <- list(
+        version = .normalizeVersion(),
+        rversion = .GHARversion(),
+        rvernum = BiocManager:::.get_R_version()
     )
+    template <- system.file(package = "biocthis", "templates",
+        "check-bioc.yml", mustWork = TRUE)
+    contents <- readLines(template)
+    idx <- grep("[^$]\\{\\{", contents)
+    parts <- grep("[^$]\\{\\{", contents, value = TRUE)
+    pco <- vector("character", length(parts))
+    for (i in seq_along(parts)) {
+        pco[[i]] <- mapply(
+            function(x, y) {
+                parts[[i]] <<- gsub(x, y, parts[[i]], fixed = TRUE)
+            }, x = paste0("{{", names(datalist), "}}"), y = datalist
+        )[[length(datalist)]]
+    }
+    contents[idx] <- pco
+    ## code taken from usethis
+    usethis:::use_dot_github(ignore = TRUE)
+    save_as <- fs::path(".github", "workflows", "check-bioc.yml")
+    usethis:::create_directory(dirname(usethis:::proj_path(save_as)))
+    new <- usethis:::write_over(usethis:::proj_path(save_as), contents)
+    invisible(new)
 }

inst/templates/check-bioc.yml

@@ -0,0 +1,97 @@
+on:
+  push:
+  pull_request:
+
+name: R-CMD-BiocCheck
+
+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.
+
+    strategy:
+      fail-fast: false
+      matrix:
+        config:
+          - { os: ubuntu-latest, r: '{{rvernum}}', cont: bioconductor/bioconductor_docker:{{version}}, rspm: "https://packagemanager.rstudio.com/cran/__linux__/focal/latest" }
+          - { os: macOS-latest, r: '{{rvernum}}' }
+          - { os: windows-latest, r: '{{rvernum}}' }
+    env:
+      R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      RSPM: ${{ matrix.config.rspm }}
+      NOT_CRAN: true
+      TZ: UTC
+
+    steps:
+      - name: Checkout Repository
+        uses: actions/checkout@v2
+
+      - uses: r-lib/actions/setup-r@master
+        with:
+          r-version: ${{ matrix.config.r }}
+
+      - uses: r-lib/actions/setup-pandoc@master
+
+      - name: Query dependencies
+        run: |
+          install.packages('remotes')
+          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
+        shell: Rscript {0}
+
+      - name: Install Bioconductor
+        if: runner.os != 'Linux'
+        run: |
+          install.packages('BiocManager')
+          BiocManager::install(version = '{{version}}')
+        shell: Rscript {0}
+
+      - name: Cache R packages
+        if: runner.os != 'Windows'
+        uses: actions/cache@v2
+        with:
+          path: ${{ env.R_LIBS_USER }}
+          key: ${{ runner.os }}-{{rversion}}-1-${{ hashFiles('.github/depends.Rds') }}
+          restore-keys: ${{ runner.os }}-{{rversion}}-1-
+
+      - name: Install system dependencies
+        if: runner.os == 'Linux'
+        run: |
+          while read -r cmd
+          do
+            eval sudo $cmd
+          done < <(Rscript -e 'writeLines(remotes::system_requirements("ubuntu", "20.04"))')
+
+
+      - name: Install Dependencies
+        run: |
+          remotes::install_local(dependencies = TRUE, repos = BiocManager::repositories(), build_vignettes = TRUE, upgrade = TRUE)
+          BiocManager::install("rcmdcheck", update = TRUE, ask = FALSE)
+        shell: Rscript {0}
+
+      - name: Run CMD check
+        env:
+          _R_CHECK_CRAN_INCOMING_REMOTE_: false
+        run: rcmdcheck::rcmdcheck(args = c("--no-manual"), error_on = "warning", check_dir = "check")
+        shell: Rscript {0}
+
+      - name: Get Session Info
+        run: |
+          options(width = 100)
+          pkgs <- installed.packages()[, "Package"]
+          sessioninfo::session_info(pkgs, include_base = TRUE)
+        shell: Rscript {0}
+
+      - name: Run BiocCheck
+        run: |
+          BiocCheck::BiocCheck(dir('check', 'tar.gz$', full.names = TRUE), `quit-with-status` = TRUE)
+        shell: Rscript {0}
+
+      - name: Upload check results
+        if: failure()
+        uses: actions/upload-artifact@master
+        with:
+          name: ${{ runner.os }}-r-{{rversion}}-bioc-{{version}}-results
+          path: check
+