Merge pull request #3 from jwokaty/devel

Update after 3.23 release

Author: jwokaty

.github/workflows/pkgdown.yml .github/workflows/quarto.yml.github/workflows/pkgdown.yml renamed to .github/workflows/quarto.yml

@@ -7,26 +7,23 @@ on:
     - cron: "30 16 * * *" # 2:30pm ET 
   workflow_dispatch:
 
-name: pkgdown
+name: quarto
 
 jobs:
-  pkgdown:
+  quarto:
     runs-on: ubuntu-latest
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
     steps:
       - uses: actions/checkout@v4
 
-      - uses: r-lib/actions/setup-r@v2
-        with:
-          use-public-rspm: true
+      - uses: quarto-dev/quarto-actions/setup@v2 
 
-      - uses: quarto-dev/quarto-actions/setup@v2
+      - uses: r-lib/actions/setup-r@v2
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: |
-            any::pkgdown
             any::remotes
             local::.
           needs: website
@@ -35,9 +32,8 @@ jobs:
         run: BiocManager::install("Bioconductor/biocUniTools")
         shell: Rscript {0}
 
-      - name: Build site
-        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE, quiet = FALSE)
-        shell: Rscript {0}
+      - name: Render
+        run: quarto render
 
       - name: Deploy to GitHub pages
         uses: JamesIves/github-pages-deploy-action@v4

.gitignore

@@ -2,3 +2,5 @@ vignettes/*_files/*
 vignettes/*.html
 docs
 .Rhistory
+
+/.quarto/

DESCRIPTION

@@ -29,6 +29,6 @@ Suggests:
     testthat (>= 3.0.0)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.3.3
 VignetteBuilder: quarto
 Config/testthat/edition: 3
+Config/roxygen2/version: 8.0.0

NAMESPACE

@@ -1,5 +1,6 @@
 # Generated by roxygen2: do not edit by hand
 
+export(.expand_jobs)
 export(filter_by_arch)
 export(get_binary_os)
 export(get_candidates)

R/utils.R

@@ -196,6 +196,9 @@ get_raw_uni_df <- function(uni) {
 #'
 #' @noRd
 match_binaries <- function(binaries, r_xy, os, arch) {
+    if (nrow(binaries) == 0)
+        return(binaries)
+    
     if (!"arch" %in% names(binaries))
         binaries$arch <- NA_character_
     binaries_os_ <- get_binary_os(binaries$os)
@@ -210,24 +213,23 @@ match_binaries <- function(binaries, r_xy, os, arch) {
                  arch_match, ]
 }
 
-#' Flatten raw universe data.frame by matching R, OS, and arch information from
-#'  `_jobs` with `_binaries`
+#'  get_uni_df helper to expand `_jobs`
 #' 
 #' @description
-#' Adds additional columns to `_jobs_r_xy`, `_binaries_r_xy`,
-#' `_jobs_type`, `_jobs_arch`, `_jobs_os_`, `_binaries_os_`
+#' Adds additional columns to `_jobs_r_xy`, `_jobs_type`, `_jobs_arch`,
+#' `_jobs_os_`
 #' 
-#' @param raw_df raw data.frame from R Universe API
+#' @param df data.frame unprocessed data from R Universe API
 #' 
 #' @returns data.frame
 #' 
 #' @examples
 #' raw_df <- get_raw_uni_df("bioc")
-#' get_uni_df(raw_df)
+#' df <- .expand_jobs(raw_df)
 #'
 #' @export
-get_uni_df <- function(raw_df) {
-    uni_df <- raw_df |>
+.expand_jobs <- function(df) {
+    df |>
         tidyr::unnest(`_jobs`, names_sep = "_", names_repair = "unique") |>
         dplyr::mutate(
             `_jobs_r_xy` = r_xy_ver(`_jobs_r`),
@@ -242,23 +244,63 @@ get_uni_df <- function(raw_df) {
                 .default = NA),
             `_jobs_os_` = dplyr::if_else(`_jobs_type` == "binary",
                                          get_binary_os(stringr::str_split_i(`_jobs_config`, "-", 1)),
-                                         "linux")) |>
-        (\(df) dplyr::bind_rows(
-            df |>
-                dplyr::filter(`_jobs_type` == "binary") |>
-                dplyr::mutate(`_binaries` = purrr::pmap(
-                    list(`_binaries`, `_jobs_r_xy`, `_jobs_os_`, `_jobs_arch`),
-                    match_binaries)) |>
-                tidyr::unnest(`_binaries`, names_sep = "_", names_repair = "unique",
-                              keep_empty = TRUE) |>
-                dplyr::mutate(`_binaries_os_` = get_binary_os(`_binaries_os`),
-                              `_binaries_r_xy` = dplyr::if_else(is.na(`_binaries_r`),
-                                                                NA_character_,
-                                                                r_xy_ver(`_binaries_r`))),
-            df |>
-                dplyr::filter(`_jobs_type` %in% c("bioc-checks", "source")) |>
-                dplyr::select(-`_binaries`) |>
-                dplyr::mutate(`_binaries_r_xy` = NA_character_)))() |>
+                                         "linux"))
+}
+
+#' get_uni_df helper to expand `_binaries` and match with `_job`-related columns
+#' 
+#' @description
+#' Adds additional columns to `_binaries_r_xy` and `_binaries_os_`
+#' 
+#' @param df data.frame data processed from R Universe API
+#' 
+#' @returns data.frame
+#' 
+#' @examples
+#' raw_df <- get_raw_uni_df("bioc")
+#' df <- .expand_jobs(df)
+#' df <- .expand_binaries(df)
+#'
+#' @noRd
+.expand_binaries <- function(df) {
+    dplyr::bind_rows(
+        df |>
+            dplyr::filter(`_jobs_type` == "binary") |>
+            dplyr::mutate(`_binaries` = purrr::pmap(
+                list(`_binaries`, `_jobs_r_xy`, `_jobs_os_`, `_jobs_arch`),
+                match_binaries)) |>
+            tidyr::unnest(`_binaries`, names_sep = "_", names_repair = "unique",
+                          keep_empty = TRUE) |>
+            dplyr::mutate(`_binaries_os_` = get_binary_os(`_binaries_os`),
+                          `_binaries_r_xy` = dplyr::if_else(is.na(`_binaries_r`),
+                                                            NA_character_,
+                                                            r_xy_ver(`_binaries_r`))),
+        df |>
+            dplyr::filter(`_jobs_type` %in% c("bioc-checks", "source")) |>
+            dplyr::select(-`_binaries`) |>
+            dplyr::mutate(`_binaries_r_xy` = NA_character_))
+}
+
+#' Flatten raw universe data.frame by matching R, OS, and arch information from
+#'  `_jobs` with `_binaries`
+#' 
+#' @description
+#' Adds additional columns to `_jobs_r_xy`, `_binaries_r_xy`,
+#' `_jobs_type`, `_jobs_arch`, `_jobs_os_`, `_binaries_os_`
+#' 
+#' @param raw_df raw data.frame from R Universe API
+#' 
+#' @returns data.frame
+#' 
+#' @examples
+#' raw_df <- get_raw_uni_df("bioc")
+#' get_uni_df(raw_df)
+#'
+#' @export
+get_uni_df <- function(raw_df) {
+    uni_df <- raw_df |>
+        .expand_jobs() |>
+        .expand_binaries() |>
         dplyr::filter(
             (`_jobs_type` == "binary" & (`_jobs_r_xy` == `_binaries_r_xy` | is.na(`_binaries_r_xy`))) |
                 (`_jobs_type` %in% c("bioc-checks", "source")))
@@ -278,7 +320,8 @@ get_uni_df <- function(raw_df) {
 #' @returns data.frame packages in a universe
 #'
 #' @examples
-#' get_jobs("bioc", "devel", "4.6.0", "3.23")
+#' bu <- get_uni_for_bioc_version("devel")
+#' get_jobs(bu$ru_uni, bu$bioc_branch, bu$r_version, bu$bioc_version)
 #'
 #' @export
 get_jobs <- function(uni, uni_os_branch, r_version, bioc_version) {
@@ -330,7 +373,8 @@ get_jobs <- function(uni, uni_os_branch, r_version, bioc_version) {
 #' @returns data.frame
 #' 
 #' @examples
-#' df <- get_jobs("bioc", "devel", "4.6.0", "3.23", "macosx", "arm64")
+#' bu <- get_uni_for_bioc_version("devel")
+#' df <- get_jobs(bu$ru_uni, bu$bioc_branch, bu$r_version, bu$bioc_version)
 #' filter_by_arch(df, "macosx", "arm64")
 #' 
 #' @export
@@ -371,7 +415,9 @@ filter_by_arch <- function(df, os, arch = NA) {
 #' @returns data.frame of filtered candidate packages
 #'
 #' @examples
-#' candidates <- get_candidates("bioc", "devel", "4.6.0", "3.23", "windows",
+#' bu <- get_uni_for_bioc_version("devel")
+#' candidates <- get_candidates(bu$ru_uni, bu$bioc_branch, bu$r_version,
+#'                              bu$bioc_version, "windows",
 #'                              commit = TRUE)
 #'
 #' @export
@@ -423,22 +469,29 @@ get_candidates <- function(uni, uni_os_branch, r_version, bioc_version, os,
 
 #' Get information about R Universe building a Bioconductor version
 #'
-#' @param version character Bioconductor version
+#' @param version character Bioconductor version, "devel", or "release"
 #'
+#' @examples
+#' bu <- get_uni_for_bioc_version("devel")
+#' 
 #' @export
 get_uni_for_bioc_version <- function(version) {
     bioc_yaml <- yaml::read_yaml("https://bioconductor.org/config.yaml")
-    
-    stopifnot(version %in% bioc_yaml$versions)
-    bioc_branch <- ifelse(bioc_yaml$devel_version == version, "devel",
-                          "release")
-    ru_uni <- ifelse(bioc_branch == "devel", "bioc", "bioc-release")
-    if (bioc_branch == "devel")
+    stopifnot(version %in% c(bioc_yaml$versions, "release", "devel"))
+
+    if (version %in% c("devel", bioc_yaml$devel_version)) {
+        bioc_version <- bioc_yaml$devel_version
+        bioc_branch <- "devel"
+        ru_uni <- "bioc"
         r_version <- bioc_yaml$r_version_associated_with_devel
-    else
+    } else {
+        bioc_version <- bioc_yaml$release_version
+        bioc_branch <- "release"
+        ru_uni <- "bioc-release"
         r_version <- bioc_yaml$r_version_associated_with_release
-
-    list(bioc_version = version,
+    }
+    
+    list(bioc_version = bioc_version,
          bioc_branch = bioc_branch,
          ru_uni = ru_uni,
          r_version = r_version)
@@ -458,7 +511,9 @@ get_uni_for_bioc_version <- function(version) {
 #' @returns vector of the full path of binaries removed
 #'
 #' @examples
-#' remove_old_binaries("/home/biocpush/PACKAGES/3.22/bioc", "4.6.0", "windows")
+#' bu <- get_uni_for_bioc_version("devel")
+#' repo_root <- paste0("/home/biocpush/PACKAGES/", bu$bioc_version, "/bioc")
+#' remove_old_binaries(repo_root, bu$bioc_version, "windows")
 #'
 #' @export
 remove_old_binaries <- function(repo_root, r_version, os, macosx_name = NA,

_quarto.yml

@@ -0,0 +1,15 @@
+project:
+  type: website
+  output-dir: docs
+
+website:
+  title: "biocUniTools"
+  navbar:
+    left:
+      - text: "Bioconductor in R Universe: Linux with Criteria on Commits and Vignettes"
+        href: vignettes/index.html
+
+format:
+  html:
+    theme: cosmo
+    toc: true