v.0.2.2.2

Merge pull request #33 from mokymai/devel
mokymai · Aug 8, 2023 · dca2be0 · dca2be0
2 parents 6acd975 + fec24ec
commit dca2be0
Show file tree

Hide file tree

Showing 25 changed files with 710 additions and 859 deletions.
diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
@@ -5,24 +5,36 @@ on:
     branches: [main, master, devel]
   pull_request:
     branches: [main, master, devel]
+  schedule:
+    # (see https://crontab.guru)
+    - cron: "30 3 * */2 TUE"
+  workflow_dispatch:
 
 name: R-CMD-check
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.event.pull_request.number || github.ref }}
+  cancel-in-progress: true
+
 jobs:
   R-CMD-check:
     runs-on: ${{ matrix.config.os }}
 
+    concurrency:
+      group: >
+        ${{ github.workflow }}-${{ matrix.config.os }}-${{ matrix.config.r }})-
+        ${{ github.event_name != 'pull_request' || github.run_id }}
+      cancel-in-progress: true
+
     name: ${{ matrix.config.os }} (R-${{ matrix.config.r }})
 
     strategy:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
+          - {os: macos-latest,   r: 'release'}
           - {os: windows-latest, r: 'release'}
-          # - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
-          - {os: ubuntu-latest,   r: 'release'}
-          # - {os: ubuntu-latest,   r: 'oldrel-1'}
+          - {os: ubuntu-latest,  r: 'release'}
 
     env:
       R_KEEP_PKG_SOURCE: yes
@@ -36,11 +48,9 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
-          http-user-agent: ${{ matrix.config.http-user-agent }}
           use-public-rspm: true
           extra-repositories: "https://mokymai.github.io/download/"
 
-
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
           extra-packages: any::rcmdcheck

diff --git a/.github/workflows/drat--publish-package.yaml b/.github/workflows/drat--publish-package.yaml
@@ -1,9 +1,9 @@
 on:
   push:
-    branches:
-      - master
+    branches: [master, main]
+  workflow_dispatch:
 
-name: Publish package
+name: Publish package (drat)
 
 jobs:
   drat:
@@ -24,13 +24,13 @@ jobs:
 
     env:
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
+      GITHUB_PAT:  ${{ secrets.GITHUB_TOKEN }}
       SOURCE_REPO: ${{ github.repository }}
       DEST_REPO:   mokymai/download
       TMP_DIR:     tmp_dir
-      CACHE_VERSION: 1
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v3
 
       - name: Info
         run: |
@@ -39,33 +39,20 @@ jobs:
       - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
+          use-public-rspm: true
+          extra-repositories: "https://mokymai.github.io/download/"
 
-      - name: Query dependencies
-        run: |
-          install.packages('remotes')
-          saveRDS(remotes::dev_package_deps(dependencies = TRUE), ".github/depends.Rds", version = 2)
-          writeLines(sprintf("R-%i.%i", getRversion()$major, getRversion()$minor), ".github/R-version")
-        shell: Rscript {0}
-
-      - name: Restore R package cache
-        # if: runner.os != 'Windows'
-        uses: actions/cache@v2
+      - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          path: ${{ env.R_LIBS_USER }}
-          key: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${CACHE_VERSION}-${{ hashFiles('.github/depends.Rds') }}
-          restore-keys: ${{ runner.os }}-${{ hashFiles('.github/R-version') }}-${CACHE_VERSION}-
-
-      - name: Install dependencies
-        shell: Rscript {0}
-        run: |
-          remotes::install_cran(c("roxygen2", "devtools", "drat"))
-          remotes::install_deps(dependencies = TRUE)
+          cache-version: 1
+          extra-packages: |
+            roxygen2
+            devtools
+            drat
 
       - name: Roxygenize
         shell: Rscript {0}
-        run: |
-          roxygen2::roxygenize()
-
+        run:   roxygen2::roxygenize()
 
       - name: Build source package
         if: runner.os == 'Windows' && matrix.config.r == 'release'
@@ -91,7 +78,7 @@ jobs:
           TOKEN: ${{ secrets.DEPLOY_DRAT_TOKEN }}
 
       - name: Git clone DEST_REPO
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
         with:
           repository: ${{ env.DEST_REPO }} # 'mokymai/download'
           ref:   'master'

diff --git a/.github/workflows/pkgdown.yaml b/.github/workflows/pkgdown.yaml
@@ -1,11 +1,13 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
 on:
   push:
-    branches: [main, master, devel]
+    branches: [main, master]
   release:
     types: [published]
   workflow_dispatch:
 
-name: Update website
+name: Update website (pkgdown)
 
 jobs:
   pkgdown:
@@ -15,16 +17,17 @@ jobs:
       group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
     env:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
-
+    permissions:
+      contents: write
     steps:
       - uses: actions/checkout@v3
 
       - uses: r-lib/actions/setup-pandoc@v2
 
       - uses: r-lib/actions/setup-r@v2
         with:
+          r-version: "release"
           use-public-rspm: true
-          r-version: 'release'
           extra-repositories: "https://mokymai.github.io/download/"
 
       - uses: r-lib/actions/setup-r-dependencies@v2
@@ -62,7 +65,7 @@ jobs:
 
       - name: Deploy to GitHub pages 🚀
         if: github.event_name != 'pull_request'
-        uses: JamesIves/github-pages-deploy-action@4.1.4
+        uses: JamesIves/github-pages-deploy-action@v4
         with:
           clean: false
           branch: gh-pages

diff --git a/DESCRIPTION b/DESCRIPTION
@@ -1,8 +1,8 @@
 Package: bio
 Type: Package
 Title: Resources Manager for BS-2023
-Version: 0.2.2.1
-Date: 2023-04-23
+Version: 0.2.2.2
+Date: 2023-08-08
 Authors@R: 
     person("Vilmantas", "Gegzna", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0002-9500-5167"),
@@ -22,7 +22,7 @@ RoxygenNote: 7.2.3
 Additional_repositories:
   https://mokymai.github.io/download/
 Imports:
-  backup.tools (>= 0.0.1),
+  backup.tools,
   checkmate,
   clipr,
   crayon,
@@ -37,12 +37,10 @@ Imports:
   purrr,
   quarto,
   readr (>= 2.0.0),
-  rematch2,
   remotes,
   rlang,
   rstudioapi (>= 0.13),
-  snippets (>= 0.0.9),
-  stringi,
+  snippets,
   stringr,
   styler,
   tibble (>= 3.1.4),

diff --git a/NAMESPACE b/NAMESPACE
@@ -8,8 +8,6 @@ export(check_updates_pkg_bio)
 export(check_updates_rcmdr_biostat)
 export(check_user_info)
 export(compare_version)
-export(emokymai_browse_assingment)
-export(emokymai_submit_assingment)
 export(get_last_pkgs_installation_status)
 export(get_os_type)
 export(get_path_desktop)
@@ -46,23 +44,18 @@ export(open_rstudio_snippets_dir)
 export(open_rstudio_system_dictionaries_dir)
 export(open_rstudio_user_dictionaries_dir)
 export(open_user_proj_list)
+export(pkg_list_archived_versions)
 export(read_projects)
 export(restart_r)
 export(restart_rstudio)
 export(rstudio_compare_user_settings)
 export(rstudio_delete_spellcheck_dictionaries)
 export(rstudio_download_spellcheck_dictionaries)
 export(rstudio_install_spellcheck_dictionaries)
-export(rstudio_install_spellcheck_dictionary_lt)
 export(rstudio_reload_ui)
 export(rstudio_reset_keybindings)
 export(rstudio_reset_user_settings)
 export(rstudio_restart_r)
-export(to_ascii_lower)
-export(u_check_filename)
-export(u_create_filename)
-export(u_parse_filename)
-export(u_prepare_assignment_dc)
 export(update_pkg_bio)
 export(update_pkg_rcmdr_biostat)
 export(update_pkg_snippets)
@@ -82,6 +75,7 @@ importFrom(magrittr,"%>%")
 importFrom(rlang,.data)
 importFrom(snippets,get_path_rstudio_snippets_dir)
 importFrom(snippets,open_rstudio_snippets_dir)
+importFrom(stats,na.omit)
 importFrom(stats,setNames)
 importFrom(usethis,ui_code)
 importFrom(usethis,ui_done)

diff --git a/R/dictionaries.R b/R/dictionaries.R
@@ -77,8 +77,6 @@ open_rstudio_internal_dictionaries_dir <- function() {
 #' @description
 #' - `rstudio_download_spellcheck_dictionaries()`
 #'  downloads and updates RStudio (system) spellchecking dictionaries.
-#' - `rstudio_download_spellcheck_dictionaries_lt()`
-#'  installs improved Lithuanian spellchecking dictionary.
 #' - `rstudio_delete_spellcheck_dictionaries()`
 #'  deletes RStudio (system) spellchecking dictionaries.
 #'
@@ -92,7 +90,6 @@ open_rstudio_internal_dictionaries_dir <- function() {
 #' \dontrun{\donttest{
 #' rstudio_delete_spellcheck_dictionaries()
 #' rstudio_download_spellcheck_dictionaries()
-#' rstudio_install_spellcheck_dictionary_lt()
 #' }}
 
 rstudio_install_spellcheck_dictionaries <- function(secure = TRUE) {
@@ -109,10 +106,7 @@ rstudio_install_spellcheck_dictionaries <- function(secure = TRUE) {
 rstudio_download_spellcheck_dictionaries <- rstudio_install_spellcheck_dictionaries
 
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
-#' @name spelling
-#' @export
-#' @concept r and rstudio settings
-#' @concept dictionaries
+
 rstudio_install_spellcheck_dictionary_lt <- function() {
 
   tryCatch({

diff --git a/R/helpers.R b/R/helpers.R
@@ -28,8 +28,8 @@ get_upgrade_str <- function(upgrade) {
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 ui_msg_restart_rstudio <- function() {
   usethis::ui_todo(paste0(
-    "To take effect, {underline('RStudio')} should be ",
-    "{underline('closed and reopened')}."
+    "To apply all changes, {underline('close and reopen')} ",
+    "{underline('RStudio')}."
   ))
 }
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

diff --git a/R/packages--check.R b/R/packages--check.R
@@ -339,6 +339,48 @@ get_pkgs_cran_details <- function(repos = NULL) {
   cran_all
 }
 
+#' Get previous package versions available on CRAN
+#'
+#' Function to scrape the CRAN website and retrieve archived (old) package versions
+#'
+#' @param package (character)
+#'        Package name.
+#'
+#' @return Vector with version numbers (the current version is not present).
+#' @export
+#'
+#' @importFrom stats na.omit
+#'
+#' @examples
+#' pkg_list_archived_versions("ggplot2")
+#'
+#' pkg_list_archived_versions("none")
+pkg_list_archived_versions <- function(package) {
+
+  # Base URL of archived packages on CRAN
+  url <- "https://cran.r-project.org/src/contrib/Archive/"
+
+  # Create the complete URL for the package
+  package_url <- paste0(url, package)
+
+  # Extract the webpage table rows containing the package versions
+  rows <- try(
+    suppressWarnings(readLines(package_url, warn = FALSE)),
+    silent = TRUE
+  )
+
+  if (inherits(rows, "try-error")) {
+    return(as.numeric_version(NULL))
+  }
+
+  # Extract the archived versions
+  rows |>
+    stringr::str_extract(stringr::str_glue("{package}_(.*?)[.]tar[.]gz"), 1) |>
+    na.omit() |>
+    as.numeric_version() |>
+    sort(decreasing = TRUE)
+}
+
 # ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 #' Get Details About Non-CRAN Package Installation
 #'

diff --git a/R/settings.R b/R/settings.R
@@ -45,7 +45,7 @@ restriction_status <- function(ignore_ip = getOption("bio.ignore_ip", FALSE),
 #' 1) Resets RStudio state and user preferences (incl. color scheme)
 #' 2) Clears function history, plot history, console, recent project list, etc.
 #' 3) Closes unnecessary windows
-#' 4) Resets custom keybindings to "bio-default"
+#' 4) Resets custom key bindings to "bio-default"
 #' 5) Resets R Markdown and R snippets to defaults in package "snippets"
 #' 6) Creates folder "~/R/darbinis" and starts using it as working directory
 #'    when no project is used.