Merge branch 'devel'

Author: ErdaradunGaztea

.Rbuildignore

@@ -11,3 +11,5 @@
 ^pkgdown$
 ^cran-comments\.md$
 ^CRAN-SUBMISSION$
+^doc$
+^Meta$

.github/workflows/check-standard.yaml

@@ -20,12 +20,10 @@ jobs:
         config:
           - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          - {os: windows-latest, r: '3.6'}
           - {os: ubuntu-latest,  r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,  r: 'release'}
           - {os: ubuntu-latest,  r: 'oldrel-1'}
-          - {os: ubuntu-latest,  r: 'oldrel-2'}
-          - {os: ubuntu-latest,  r: 'oldrel-3'}
+          - {os: ubuntu-latest,  r: '4.1'}
 
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}

.github/workflows/rhub.yaml

@@ -0,0 +1,95 @@
+# R-hub's generic GitHub Actions workflow file. It's canonical location is at
+# https://github.com/r-hub/actions/blob/v1/workflows/rhub.yaml
+# You can update this file to a newer version using the rhub2 package:
+#
+# rhub::rhub_setup()
+#
+# It is unlikely that you need to modify this file manually.
+
+name: R-hub
+run-name: "${{ github.event.inputs.id }}: ${{ github.event.inputs.name || format('Manually run by {0}', github.triggering_actor) }}"
+
+on:
+  workflow_dispatch:
+    inputs:
+      config:
+        description: 'A comma separated list of R-hub platforms to use.'
+        type: string
+        default: 'linux,windows,macos'
+      name:
+        description: 'Run name. You can leave this empty now.'
+        type: string
+      id:
+        description: 'Unique ID. You can leave this empty now.'
+        type: string
+
+jobs:
+
+  setup:
+    runs-on: ubuntu-latest
+    outputs:
+      containers: ${{ steps.rhub-setup.outputs.containers }}
+      platforms: ${{ steps.rhub-setup.outputs.platforms }}
+
+    steps:
+    # NO NEED TO CHECKOUT HERE
+    - uses: r-hub/actions/setup@v1
+      with:
+        config: ${{ github.event.inputs.config }}
+      id: rhub-setup
+
+  linux-containers:
+    needs: setup
+    if: ${{ needs.setup.outputs.containers != '[]' }}
+    runs-on: ubuntu-latest
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.containers) }}
+    container:
+      image: ${{ matrix.config.container }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+
+  other-platforms:
+    needs: setup
+    if: ${{ needs.setup.outputs.platforms != '[]' }}
+    runs-on: ${{ matrix.config.os }}
+    name: ${{ matrix.config.label }}
+    strategy:
+      fail-fast: false
+      matrix:
+        config: ${{ fromJson(needs.setup.outputs.platforms) }}
+
+    steps:
+      - uses: r-hub/actions/checkout@v1
+      - uses: r-hub/actions/setup-r@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/platform-info@v1
+        with:
+          token: ${{ secrets.RHUB_TOKEN }}
+          job-config: ${{ matrix.config.job-config }}
+      - uses: r-hub/actions/setup-deps@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}
+      - uses: r-hub/actions/run-check@v1
+        with:
+          job-config: ${{ matrix.config.job-config }}
+          token: ${{ secrets.RHUB_TOKEN }}

.gitignore

@@ -41,3 +41,6 @@ vignettes/*.pdf
 *.Rproj
 .Rproj.user
 docs
+inst/doc
+/doc/
+/Meta/

CRAN-SUBMISSION

@@ -1,8 +1,8 @@
 Package: woodendesc
 Type: Package
 Title: Find Packages and Their Dependencies in Any 'R' Repository
-Version: 0.1.0
-Date: 2023-04-17
+Version: 0.2.0
+Date: 2025-01-26
 Authors@R: c(person("Laura", "Bakala",
              email = "erdaradun.gaztea@gmail.com",
              role = c("cre", "aut", "cph"),
@@ -15,21 +15,24 @@ Description: Simplifies getting the available packages, their version codes and
 License: GPL (>= 3)
 Encoding: UTF-8
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.1.0)
 Imports: 
-    digest,
-    httr,
+    httr2 (>= 1.0.0),
+    rlang (>= 1.0.0),
+    utils,
     versionsort (>= 1.1.0)
 Suggests: 
     covr,
-    httptest,
+    httptest2,
+    knitr,
+    rmarkdown,
     testthat (>= 3.0.0),
     usethis,
-    vcr,
     withr,
     xml2
 Config/testthat/edition: 3
 URL: https://github.com/turtletopia/woodendesc,
     https://turtletopia.github.io/woodendesc/
+VignetteBuilder: knitr

DESCRIPTION

@@ -32,6 +32,11 @@ export(wood_github_latest)
 export(wood_github_packages)
 export(wood_github_tags)
 export(wood_github_versions)
+export(wood_gitlab_dependencies)
+export(wood_gitlab_latest)
+export(wood_gitlab_packages)
+export(wood_gitlab_tags)
+export(wood_gitlab_versions)
 export(wood_local_dependencies)
 export(wood_local_packages)
 export(wood_local_versions)
@@ -43,15 +48,3 @@ export(wood_url_dependencies)
 export(wood_url_packages)
 export(wood_url_version)
 export(wood_versions)
-importFrom(digest,digest)
-importFrom(httr,GET)
-importFrom(httr,content)
-importFrom(httr,status_code)
-importFrom(httr,stop_for_status)
-importFrom(stats,setNames)
-importFrom(utils,URLencode)
-importFrom(utils,install.packages)
-importFrom(utils,installed.packages)
-importFrom(utils,menu)
-importFrom(versionsort,ver_latest)
-importFrom(versionsort,ver_sort)

NAMESPACE

@@ -1,3 +1,11 @@
+# woodendesc 0.2.0
+
+* Reimplemented the code, replacing {httr} with {httr2}.
+* Updated code to reflect API changes in Bioconductor and R-universe.
+* Added support for GitLab.
+* Bioconductor data for releases 1.5-1.7 is no longer available.
+* Dropped support for older R versions (< 4.1.0) because they increased maintenance complexity significantly.
+
 # woodendesc 0.1.0
 
 * Added a `NEWS.md` file to track changes to the package.

NEWS.md

@@ -51,7 +51,7 @@ assert_param_url_repo <- function(value) {
   assert_no_NA(value, "repository")
 }
 
-assert_param_gh_user <- function(value) {
+assert_param_git_user <- function(value) {
   assert_string(value, "user")
   assert_length_1(value, "user")
   assert_no_NA(value, "user")

R/assert-parameters.R

@@ -11,33 +11,26 @@
 #' * `version` (minimum version requirement or `NA` if none),
 #' * `type` (dependency type, e.g. `"Imports"`).
 #'
-#' @examples
-#' \donttest{
+#' @examplesIf !woodendesc:::is_cran_check()
 #' wood_bioc_dependencies("Biostrings")
 #'
 #' # Will dependencies change?
 #' wood_bioc_dependencies("Biostrings", "devel")
 #' # And what about dependencies in the past?
 #' wood_bioc_dependencies("Biostrings", "2.10")
-#' wood_bioc_dependencies("Biostrings", "1.5")
-#' }
+#' wood_bioc_dependencies("Biostrings", "1.8")
 #'
 #' @family bioc
 #' @family dependencies
 #' @export
 wood_bioc_dependencies <- function(package, release = "release") {
   assert_param_package(package)
   assert_param_bioc_release(release)
+  validate_bioc_release(release)
 
   desc <- bioc_PACKAGES_cache(release)[[package]]
 
-  # TODO: extract as validate_bioc_package()
-  if (is.null(desc)) {
-    stopf(
-      "Can't find package `%1$s` in Bioconductor release `%2$s`.",
-      package, release
-    )
-  }
+  validate_bioc_package(desc, package, release)
 
   extract_dependencies(desc)
 }