update pkgdown building

pepkit · Nov 17, 2023 · e64d909 · e64d909
1 parent 43a0fd2
commit e64d909
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Showing 36 changed files with 64 additions and 11 deletions.
diff --git a/R/config.R b/R/config.R
@@ -57,6 +57,7 @@ setMethod(
 #' x = list(a=list(b=list(c="~/test.txt")))
 #' .expandList(x)
 #' @export
+#' @keywords internal
 .expandList <- function(x) {
   if (is.list(x))
     return(lapply(x, .expandList))
@@ -79,6 +80,7 @@ setMethod(
 #' l = list(a="a", b="b")
 #' .getSubscript(l, 1) == .getSubscript(l, "a")
 #' @export
+#' @keywords internal
 .getSubscript <- function(lst, i) {
   if (is.character(i))
     return(grep(paste0("^", i, "$"), names(lst)))
@@ -183,6 +185,7 @@ setMethod(
 #' @param object an object of \code{"\linkS4class{Config}"}
 #'
 #' @return an object of \code{"\linkS4class{Config}"}
+#' @keywords internal
 setGeneric(".reformat", function(object)
   standardGeneric(".reformat"))
 
@@ -264,6 +267,7 @@ setMethod(
 #' @param filename file path to config file
 #'
 #' @seealso \url{https://pep.databio.org/}
+#' @keywords internal
 .loadConfig = function(filename = NULL,
                        amendments = NULL) {
   if (!file.exists(filename)) {
@@ -320,6 +324,7 @@ setMethod(
 #' @return possibly updated config
 #'
 #' @return config
+#' @keywords internal
 .applyAmendments = function(cfg, amendments = NULL) {
   if (!is.null(amendments)) {
     for (amendment in amendments) {
@@ -344,6 +349,7 @@ setMethod(
 #'
 #' @return config data enriched in imported sections, if imports existed in the
 #'  input
+#' @keywords internal
 .applyImports = function(cfg_data, filename) {
   if (!CFG_P_MODIFIERS_KEY %in% names(cfg_data) ||
       !CFG_IMPORT_KEY %in% names(cfg_data[[CFG_P_MODIFIERS_KEY]]))
@@ -365,6 +371,7 @@ setMethod(
 #' @param filename path to the config file
 #'
 #' @return string project name
+#' @keywords internal
 .inferProjectName = function(cfg, filename) {
   if (!is.null(cfg$name))
     return(cfg$name)

diff --git a/R/project.R b/R/project.R
@@ -145,6 +145,7 @@ setMethod(
 #' @param object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return modified Project object
+#' @keywords internal
 setGeneric(".modifySamples", function(object)
     standardGeneric(".modifySamples"))
 
@@ -375,6 +376,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .removeAttrs <- function(.Object) {
     if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
         return(.Object)
@@ -399,6 +401,7 @@ setMethod(
 #' @param .Object an object of \code{\link{Project-class}}
 #'
 #' @return an object of \code{\link{Project-class}}
+#' @keywords internal
 .appendAttrs <- function(.Object) {
     if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
         return(.Object)
@@ -432,6 +435,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .duplicateAttrs <- function(.Object) {
     if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
         return(.Object)
@@ -450,6 +454,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .implyAttrs = function(.Object) {
     if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
         return(.Object)
@@ -499,6 +504,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .deriveAttrs = function(.Object) {
     if (!CFG_S_MODIFIERS_KEY %in% names(config(.Object)))
         return(.Object)
@@ -539,6 +545,7 @@ setMethod(
 #' @param sampleTablePath a character string indicating a path to the sample table
 #'
 #' @return an data.frame with samples; one sample per row
+#' @keywords internal
 .loadSampleAnnotation = function(sampleTablePath) {
     if (.safeFileExists(sampleTablePath)) {
         samples = data.table::fread(sampleTablePath)
@@ -555,6 +562,7 @@ setMethod(
 #' @param path string, a path to the subsample table to read and incorporate
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .loadSubsampleAnnotation = function(.Object, path) {
     if (.safeFileExists(path)) {
         subsamplesTable = data.table::fread(path)
@@ -608,6 +616,7 @@ setMethod(
 #' @param subsampleAannotationPaths a vector of strings specifying the paths to sample
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .mergeAttrs = function(.Object, subsampleAannotationPaths) {
     if (is.null(subsampleAannotationPaths))
         return(.Object)
@@ -625,6 +634,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #'
 #' @return an object of \code{"\linkS4class{Project}"}
+#' @keywords internal
 .autoMergeDuplicatedNames = function(.Object) {
     s = sampleTable(.Object)
     sampleNames = s[[.Object@sampleNameAttr]]
@@ -675,6 +685,7 @@ setMethod(
 #' @param .Object an object of \code{"\linkS4class{Project}"}
 #' @param stIndex character string indicating a constructor-specified sample table index
 #' @param sstIndex character string indicating a constructor-specified subsample table index
+#' @keywords internal
 .getTableIndexes <- function(.Object, stIndex, sstIndex) {
     .getIndexVal <- function(spec, config, default, key) {
         if (!is.null(spec))

diff --git a/R/utils.R b/R/utils.R
@@ -16,6 +16,7 @@
 #' path = "$HOME/my/path/string.txt"
 #' .expandPath(path)
 #' @export
+#' @keywords internal
 .expandPath = function(path) {
   # helper function
   removeNonWords = function(str) {
@@ -90,6 +91,7 @@
 #' @examples
 #' .strformat("~/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))
 #' .strformat("$HOME/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"))
+#' @keywords internal
 .strformat = function(string, args, parent = NULL) {
   result = c()
   # if parent provided, make the path absolute and expand it.
@@ -130,6 +132,7 @@
 #'
 #' @export
 #' @return Target itself if already absolute, else target nested within parent.
+#' @keywords internal
 .makeAbsPath = function(perhapsRelative, parent) {
   res = c()
   for (pR in perhapsRelative) {
@@ -155,6 +158,7 @@
 
 # Must test for is.null first, since is.na(NULL) returns a logical(0) which is
 # not a boolean
+#' @keywords internal
 .isDefined = function(var) {
   !(is.null(var) || is.na(var))
 }
@@ -163,6 +167,7 @@
 #'
 #' @param path The path to check for seeming absolute-ness.
 #' @return Flag indicating whether the \code{path} appears to be absolute.
+#' @keywords internal
 .isAbsolute = function(path) {
   if (!is.character(path))
     stop("The path must be character")
@@ -176,6 +181,7 @@
 #' @import RCurl
 #'
 #' @return logical indicating whether a string is a valid URL
+#' @keywords internal
 .isValidUrl = function(str) {
   ans = FALSE
   if (grepl("www.|http:|https:", str)) {
@@ -189,6 +195,7 @@
 #' @param path string to be checked
 #'
 #' @return a logical indicating whether it's an existing path or valid URL
+#' @keywords internal
 .safeFileExists = function(path) {
   (.isValidUrl(path) || (!is.null(path) && file.exists(path)))
 }
@@ -205,6 +212,7 @@
 #' dataFrame=mtcars
 #' listifiedDataFrame=.listifyDF(dataFrame)
 #' @export
+#' @keywords internal
 .listifyDF = function(DF) {
   if (!is.data.frame(DF))
     stop("The input object must be a data.frame.")
@@ -296,6 +304,7 @@ fetchSamples = function(samples,
 #' @param rgx string to expand in the system
 #'
 #' @return a list of all the elements after possible expansion
+#' @keywords internal
 .matchesAndRegexes = function(rgx) {
   res = c()
   for (i in rgx) {
@@ -327,6 +336,7 @@ fetchSamples = function(samples,
 #' p = Project(file = projectConfig)
 #' .printNestedList(config(p),level=2)
 #' @export
+#' @keywords internal
 .printNestedList = function(lst, level = 0) {
   if (!is.list(lst))
     stop("The input is not a list, cannot be displayed.")
@@ -358,6 +368,7 @@ fetchSamples = function(samples,
 #' l = list(a=list(b="test"))
 #' .checkSection(l,c("a","b"))
 #' .checkSection(l,c("c","b"))
+#' @keywords internal
 .checkSection = function(object, sectionNames) {
   tryToNum = function(x) {
     convertedX = suppressWarnings(as.numeric(x))
@@ -382,6 +393,7 @@ fetchSamples = function(samples,
 #' @param config an object of \code{"\linkS4class{Config}"}
 #'
 #' @return a string which specifies a path to the sample table file
+#' @keywords internal
 .getSampleTablePathFromConfig = function(config) {
   if (!CFG_SAMPLE_TABLE_KEY %in% names(config))
     stop("Sample table not defined in config")
@@ -393,6 +405,7 @@ fetchSamples = function(samples,
 #' @param config an object of \code{"\linkS4class{Config}"}
 #'
 #' @return  string/vector of strings/NULL depending on the configuration
+#' @keywords internal
 .getSubSampleTablePathFromConfig = function(config) {
   if (!CFG_SUBSAMPLE_TABLE_KEY %in% names(config))
     return(NULL)
@@ -408,6 +421,7 @@ fetchSamples = function(samples,
 #'
 #' @return a boolean, TRUE if indicating the path seems to be pointing to a config,
 #'  or FALSE if the path seems to be pointing to an annotation file.
+#' @keywords internal
 .isCfg = function(filePath) {
   if (endsWith(tolower(filePath), ".yaml") ||
       endsWith(tolower(filePath), ".yml"))

diff --git a/_pkgdown.yaml b/_pkgdown.yaml
@@ -31,16 +31,5 @@ articles:
     contents:
       - starts_with("feature")
 
-reference:
-  - title: "pepr API"
-    desc: "Exported functions of `pepr`."
-    contents:
-      - -matches("\\.")
-  - title: "utilities"
-    desc: "Extra non-exported utility functions."
-    contents:
-      - .strformat
-      - .expandPath
-      - .printNestedList
 news:
 - one_page: true
diff --git a/man/dot-appendAttrs.Rd b/man/dot-appendAttrs.Rd
diff --git a/man/dot-applyAmendments.Rd b/man/dot-applyAmendments.Rd
diff --git a/man/dot-applyImports.Rd b/man/dot-applyImports.Rd
diff --git a/man/dot-autoMergeDuplicatedNames.Rd b/man/dot-autoMergeDuplicatedNames.Rd
diff --git a/man/dot-checkSection.Rd b/man/dot-checkSection.Rd
diff --git a/man/dot-deriveAttrs.Rd b/man/dot-deriveAttrs.Rd
diff --git a/man/dot-duplicateAttrs.Rd b/man/dot-duplicateAttrs.Rd
diff --git a/man/dot-expandList.Rd b/man/dot-expandList.Rd
diff --git a/man/dot-expandPath.Rd b/man/dot-expandPath.Rd
diff --git a/man/dot-getSampleTablePathFromConfig.Rd b/man/dot-getSampleTablePathFromConfig.Rd
diff --git a/man/dot-getSubSampleTablePathFromConfig.Rd b/man/dot-getSubSampleTablePathFromConfig.Rd
diff --git a/man/dot-getSubscript.Rd b/man/dot-getSubscript.Rd
diff --git a/man/dot-getTableIndexes.Rd b/man/dot-getTableIndexes.Rd
diff --git a/man/dot-implyAttrs.Rd b/man/dot-implyAttrs.Rd
diff --git a/man/dot-inferProjectName.Rd b/man/dot-inferProjectName.Rd
diff --git a/man/dot-isAbsolute.Rd b/man/dot-isAbsolute.Rd
diff --git a/man/dot-isCfg.Rd b/man/dot-isCfg.Rd
diff --git a/man/dot-isValidUrl.Rd b/man/dot-isValidUrl.Rd
diff --git a/man/dot-listifyDF.Rd b/man/dot-listifyDF.Rd
diff --git a/man/dot-loadConfig.Rd b/man/dot-loadConfig.Rd
diff --git a/man/dot-loadSampleAnnotation.Rd b/man/dot-loadSampleAnnotation.Rd
diff --git a/man/dot-loadSubsampleAnnotation.Rd b/man/dot-loadSubsampleAnnotation.Rd
diff --git a/man/dot-makeAbsPath.Rd b/man/dot-makeAbsPath.Rd
diff --git a/man/dot-matchesAndRegexes.Rd b/man/dot-matchesAndRegexes.Rd
diff --git a/man/dot-mergeAttrs.Rd b/man/dot-mergeAttrs.Rd