Merge pull request #12 from KWB-R/dev

Prepare next release

.github/workflows/R-CMD-check.yaml

@@ -32,15 +32,16 @@ jobs:
       GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
       R_REMOTES_NO_ERRORS_FROM_WARNINGS: true
       RSPM: ${{ matrix.config.rspm }}
+      SERVERNAME: 'kwb-servername'
 
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
         with:
           r-version: ${{ matrix.config.r }}
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |
@@ -76,7 +77,7 @@ jobs:
 
       - name: Upload check results
         if: failure()
-        uses: actions/upload-artifact@master
+        uses: actions/upload-artifact@v3
         with:
           name: ${{ runner.os }}-r${{ matrix.config.r }}-results
           path: check

.github/workflows/pkgdown.yaml

@@ -15,9 +15,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

.github/workflows/test-coverage.yaml

@@ -18,9 +18,9 @@ jobs:
     steps:
       - uses: actions/checkout@v2
 
-      - uses: r-lib/actions/setup-r@master
+      - uses: r-lib/actions/setup-r@v2
 
-      - uses: r-lib/actions/setup-pandoc@master
+      - uses: r-lib/actions/setup-pandoc@v2
 
       - name: Query dependencies
         run: |

.gitignore

@@ -2,4 +2,6 @@
 .Rhistory
 .RData
 .Ruserdata
-R/\.*
+R/\.*
+inst/doc
+tests/testthat/Rplots.pdf

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: kwb.package
 Title: Install / Unstall KWB Packages and Show Package Dependencies
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: c(
     person("Hauke", "Sonnenberg", , "[email protected]", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9134-2871")),
@@ -19,19 +19,23 @@ License: MIT + file LICENSE
 URL: https://github.com/kwb-r/kwb.package
 BugReports: https://github.com/kwb-r/kwb.package/issues
 Imports: 
-    devtools,
     gh,
-    jsonlite,
     kwb.utils (>= 0.5.0),
+    magrittr,
     mvbutils,
     networkD3,
     remotes,
     withr
 Suggests: 
     covr,
-    pkgmeta
+    knitr,
+    pkgmeta,
+    rmarkdown,
+    testthat (>= 3.0.0)
 Remotes: 
     github::kwb-r/kwb.utils,
     github::kwb-r/pkgmeta
 Encoding: UTF-8
-RoxygenNote: 7.1.2
+RoxygenNote: 7.3.1
+VignetteBuilder: knitr
+Config/testthat/edition: 3

NAMESPACE

@@ -1,35 +1,45 @@
 # Generated by roxygen2: do not edit by hand
 
+export("%>%")
 export(addNodeLabels)
 export(anglesToPoints)
 export(archivedCranVersions)
 export(compareInstalledVersions)
 export(copyBasePackages)
+export(cranVersions)
 export(detachAllNonSystemPackages)
 export(detachRecursively)
 export(downloadGitHubPackage)
 export(downloadPackagesFromSnapshot)
 export(drawDependencies)
-export(drawLink)
 export(equidistantAngles)
 export(exampleLinksAndNodes)
+export(getAuthors)
+export(getCranPackageDatabase)
+export(getDependencyData)
 export(getPackageFilesToInstall)
+export(getPackageLicences)
 export(getRVersionMajorMinor)
 export(githubVersions)
 export(gradToRad)
+export(hasGplLicence)
 export(initLocalCRAN)
 export(installGithubPackages)
 export(installRemotes)
 export(installedDependencies)
 export(installedKwbPackages)
 export(packageDependencies)
+export(packageDependenciesByType)
 export(packageString)
 export(plotAllDependencies)
 export(plotDependencies)
 export(plotNodes)
+export(plotPackageVersions)
 export(plotSankeyNetwork)
 export(provideInLocalCRAN)
 export(setOptionsForPackrat)
+export(sortedDependencies)
+export(stopIfNotInstalled)
 export(systemPackages)
 export(toLinksAndNodes)
 export(toNodes)
@@ -38,23 +48,33 @@ importFrom(gh,gh)
 importFrom(grDevices,rainbow)
 importFrom(graphics,arrows)
 importFrom(graphics,plot)
-importFrom(kwb.utils,assignPackageObjects)
 importFrom(kwb.utils,catAndRun)
+importFrom(kwb.utils,catIf)
 importFrom(kwb.utils,createDirectory)
 importFrom(kwb.utils,defaultIfNA)
+importFrom(kwb.utils,defaultIfNULL)
+importFrom(kwb.utils,excludeNULL)
 importFrom(kwb.utils,extractSubstring)
+importFrom(kwb.utils,fullySorted)
 importFrom(kwb.utils,getAttribute)
-importFrom(kwb.utils,hsRenameColumns)
-importFrom(kwb.utils,moveColumnsToFront)
+importFrom(kwb.utils,get_homedir)
+importFrom(kwb.utils,hsRestoreAttributes)
+importFrom(kwb.utils,lastElement)
 importFrom(kwb.utils,noFactorDataFrame)
+importFrom(kwb.utils,noSuchElements)
 importFrom(kwb.utils,orderBy)
 importFrom(kwb.utils,rbindAll)
 importFrom(kwb.utils,removeColumns)
+importFrom(kwb.utils,renameColumns)
 importFrom(kwb.utils,resetRowNames)
+importFrom(kwb.utils,resolve)
+importFrom(kwb.utils,runInDirectory)
 importFrom(kwb.utils,safePath)
 importFrom(kwb.utils,safeRowBind)
 importFrom(kwb.utils,selectColumns)
 importFrom(kwb.utils,selectElements)
+importFrom(kwb.utils,stopFormatted)
+importFrom(magrittr,"%>%")
 importFrom(mvbutils,foodweb)
 importFrom(networkD3,sankeyNetwork)
 importFrom(remotes,github_remote)

NEWS.md

@@ -1,3 +1,57 @@
+# Current Development
+
+# [kwb.package 0.4.0](https://github.com/KWB-R/kwb.package/releases/tag/v0.4.0) <small>2024-05-05</small>
+
+The following public functions were added:
+
+- getAuthors()
+- getCranPackageDatabase()
+- getDependencyData()
+- getPackageLicences()
+- hasGplLicence()
+- packageDependenciesByType()
+- plotPackageVersions()
+- sortedDependencies(): Was private before. The argument "pattern" is no longer
+  supported.
+- stopIfNotInstalled()
+
+The following public functions were modified:
+
+- packageDependencies: add arguments "db", "which", "verbose"
+
+The following public functions were deleted:
+
+- drawLink(): It was a one-liner and only used once within the package
+
+The following private functions were added:
+
+- allDeps()
+- draw_circles()
+- map_to_range()
+- pathDescription()
+- polar_to_xy()
+- readDescription()
+- remotes_github_pat() -> remotes:::github_pat()
+- remotes_parse_deps() -> remotes:::parse_deps()
+- remotes_read_dcf() -> remotes:::read_dcf()
+- remotes_untar_description() -> remotes:::untar_description()
+- seq_rad_len()
+- untarDescriptionFromUrl()
+
+The following private functions were modified:
+
+- cranVersions(): add argument "dbg"
+- loadDescriptionFromArchiveUrl(): add argument "path"
+- loadDescriptionFromWeb(): add arguments "path", "cache"
+- readGithubPackageDescription: add argument "destdir"
+- stop_(): rename to cleanStop()
+
+Further changes:
+
+- Add Tests
+- Add vignette "Tutorial"
+- Update GitHub action files (e.g. master -> v2)
+
 # [kwb.package 0.3.0](https://github.com/KWB-R/kwb.package/releases/tag/v0.3.0) <small>2022-06-11</small>
 
 * Harmonise with R package [kwb.pkgbuild](https://kwb-r.github.io/kwb.pkgbuild)

R/allDeps.R

@@ -0,0 +1,41 @@
+# allDeps ----------------------------------------------------------------------
+allDeps <- function(
+  name, 
+  version = NA, 
+  depth = 1L, 
+  max_depth = 9L,
+  cache = list()
+)
+{
+  pkg <- loadDescriptionFromWeb(name, version)
+
+  stopifnot(is.na(version) || identical(version, pkg$version))
+
+  deps <- parsePackageDeps(pkg)
+
+  if (inherits(deps, "try-error") || nrow(deps) == 0L) {
+    return(NULL)
+  }
+
+  message("depth: ", depth)
+
+  deps$depth <- depth
+  deps$namever <- paste(name, version, sep = ":")
+
+  if (depth == max_depth) {
+    message("maximum depth (", max_depth, ") reached.")
+    return(deps)
+  }
+
+  child_deps <- lapply(seq_len(nrow(deps)), function(i) {
+    allDeps(deps$name[i], deps$version[i], depth + 1L, max_depth)
+  })
+
+  child_deps <- excludeNull(child_deps, dbg = FALSE)
+
+  if (length(child_deps) > 0L) {
+    deps <- rbind(deps, do.call(rbind, child_deps))
+  }
+
+  deps
+}

R/archivedCranVersions.R

@@ -1,76 +1,10 @@
-# isOnCran ---------------------------------------------------------------------
-isOnCran <- function(name)
-{
-  nrow(currentCranVersion(name)) > 0L
-}
-
-# cranVersions -----------------------------------------------------------------
-#' @noMd
-#' @noRd
-#' @keywords internal
-#' @importFrom kwb.utils removeColumns safeRowBind
-cranVersions <- function(name)
-{
-  current <- currentCranVersion(name)
-
-  if (nrow(current) == 0L) {
-    message(sprintf("Package '%s' does not seem to be on CRAN.", name))
-    return(NULL)
-  }
-
-  archived <- archivedCranVersions(name)
-
-  current$package_source_url <- getUrl(
-    "cran_package_file", package = name, version = current$version
-  )
-
-  archived$package_source_url <- sprintf(
-    getUrl("cran_archive_file", package = name, package_filename = "%s"), 
-    archived$archive_file
-  )
-
-  result <- kwb.utils::safeRowBind(archived, current)
-
-  kwb.utils::removeColumns(result, "archive_file")
-}
-
-# currentCranVersion -----------------------------------------------------------
-#' @noMd
-#' @noRd
-#' @keywords internal
-#' @importFrom kwb.utils noFactorDataFrame
-currentCranVersion <- function(name)
-{
-  src <- readLinesFromUrl(getUrl("cran_package", package = name))
-
-  if (is.null(src)) {
-    return(kwb.utils::noFactorDataFrame(
-      package = character(0L),
-      version = character(0L),
-      date = as.Date(character(0L)),
-      date_type = character(0L)
-    ))
-  }
-
-  extract <- function(x) {
-    gsub("<td>|</td>", "", src[grep(sprintf("<td>%s:</td>", x), src) + 1L])
-  }
-
-  kwb.utils::noFactorDataFrame(
-    package = name,
-    version = extract("Version"),
-    date = as.Date(extract("Published")),
-    date_type = "published"
-  )
-}
+# archivedCranVersions ---------------------------------------------------------
 
-#' archivedCranVersions --------------------------------------------------------
 #' Archived CRAN versions
 #' 
 #' @param package package name
 #' @param ref_date  default: NULL
 #' @export
-#' @importFrom kwb.utils extractSubstring noFactorDataFrame
 #' @examples 
 #' packages <- c("ggplot2", "swmmr", "kwb.hantush")
 #' archivedCranVersions(packages)
@@ -86,7 +20,7 @@ archivedCranVersions <- function(package, ref_date = NULL)
   src <- readLinesFromUrl(getUrl("cran_archive", package = package))
 
   if (is.null(src)) {
-    return(kwb.utils::noFactorDataFrame(
+    return(noFactorDataFrame(
       package = character(0L),
       version = character(0L),
       date = as.Date(character(0L)),
@@ -99,7 +33,7 @@ archivedCranVersions <- function(package, ref_date = NULL)
     "href=\"(%s_(.*)\\.tar\\.gz)\".*(\\d{4}-\\d{2}-\\d{2}) ", package
   )
 
-  versions <- cbind(package = package, kwb.utils::extractSubstring(
+  versions <- cbind(package = package, extractSubstring(
     pattern = pattern,
     x = grep(pattern, src, value = TRUE), 
     index = c(
@@ -124,12 +58,11 @@ archivedCranVersions <- function(package, ref_date = NULL)
 #' @noRd
 #' @keywords internal
 #' @importFrom utils tail
-#' @importFrom kwb.utils resetRowNames
 getLastVersionBefore <- function(version_dates, ref_date)
 {
   X = unname(split(version_dates, version_dates$package))
 
   last_before <- function(x) utils::tail(x[x$date <= ref_date, ], 1L)
 
-  kwb.utils::resetRowNames(do.call(rbind, lapply(X, last_before)))
+  resetRowNames(do.call(rbind, lapply(X, last_before)))
 }