docs: mark all internal functions as such

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: drugfindR
 Title: Investigate iLINCS for candidate repurposable drugs
-Version: 0.99.991
+Version: 0.99.992
 Authors@R: c(
     person(given = c("Ali", "Sajid"),
            family = "Imami",

R/utilities.R

@@ -23,7 +23,7 @@ targetRename <- function(inputNames) {
 
 #' Parameterize the base URL for the iLINCS API
 #'
-#'
+#' @keywords internal
 #' @return a fixed string URL
 .ilincsBaseUrl <- function() {
     "http://www.ilincs.org/api"
@@ -33,6 +33,7 @@ targetRename <- function(inputNames) {
 #'
 #' @param lib a string of libraries
 #'
+#' @keywords internal
 #' @return a boolean
 .validateLibrary <- function(lib) {
     lib %in% c("CP", "KD", "OE")
@@ -45,6 +46,7 @@ targetRename <- function(inputNames) {
 #'
 #' @param libs a character vector of libraries
 #'
+#' @keywords internal
 #' @return a boolean
 validateLibraries <- function(libs) {
     all(purrr::map_lgl(libs, .validateLibrary))
@@ -54,6 +56,7 @@ validateLibraries <- function(libs) {
 #'
 #' @param libs a character vector of libraries
 #'
+#' @keywords internal
 #' @return a stop if the libraries are invalid
 stopIfInvalidLibraries <- function(libs) {
     if (!validateLibraries(libs)) {
@@ -65,6 +68,7 @@ stopIfInvalidLibraries <- function(libs) {
 #'
 #' @param lib a string. One of "OE", "KD" or "CP"
 #'
+#' @keywords internal
 #' @return a tibble
 loadMetadata <- function(lib) {
     if (lib == "OE") {
@@ -83,6 +87,7 @@ loadMetadata <- function(lib) {
 #'
 #' @param lib A library name. Can be one of "OE", "KD" or "CP"
 #'
+#' @keywords internal
 #' @return A string with the associated library ID
 .return_library <- function(lib) {
     stopIfInvalidLibraries(lib)

codemeta.json

@@ -7,7 +7,7 @@
   "codeRepository": "https://github.com/CogDisResLab/drugfindR",
   "issueTracker": "https://github.com/CogDisResLab/drugfindR/issues",
   "license": "https://spdx.org/licenses/GPL-3.0",
-  "version": "0.99.991",
+  "version": "0.99.992",
   "programmingLanguage": {
     "@type": "ComputerLanguage",
     "name": "R",
@@ -17,21 +17,30 @@
   "author": [
     {
       "@type": "Person",
-      "givenName": ["Ali", "Sajid"],
+      "givenName": [
+        "Ali",
+        "Sajid"
+      ],
       "familyName": "Imami",
       "email": "[email protected]",
       "@id": "https://orcid.org/0000-0003-3684-3539"
     },
     {
       "@type": "Person",
-      "givenName": ["Justin", "Fortune"],
+      "givenName": [
+        "Justin",
+        "Fortune"
+      ],
       "familyName": "Creeden",
       "email": "[email protected]",
       "@id": "https://orcid.org/0000-0003-3123-8401"
     },
     {
       "@type": "Person",
-      "givenName": ["Evelyn", "Alden"],
+      "givenName": [
+        "Evelyn",
+        "Alden"
+      ],
       "familyName": "Bates",
       "email": "[email protected]",
       "@id": "https://orcid.org/0000-0002-4157-2481"
@@ -47,7 +56,10 @@
   "maintainer": [
     {
       "@type": "Person",
-      "givenName": ["Ali", "Sajid"],
+      "givenName": [
+        "Ali",
+        "Sajid"
+      ],
       "familyName": "Imami",
       "email": "[email protected]",
       "@id": "https://orcid.org/0000-0003-3684-3539"
@@ -349,10 +361,28 @@
   },
   "applicationCategory": "Genomics",
   "isPartOf": "https://bioconductor.org",
-  "keywords": ["LINCS", "iLINCS", "drugrepurposing", "drugdiscovery", "transcriptomics", "geneexpression", "geneknockdown", "geneoverexpression", "chemicalperturbagen", "drugfindR", "r", "ilincs", "bioinformatics", "bioinformatics-pipeline"],
+  "keywords": [
+    "LINCS",
+    "iLINCS",
+    "drugrepurposing",
+    "drugdiscovery",
+    "transcriptomics",
+    "geneexpression",
+    "geneknockdown",
+    "geneoverexpression",
+    "chemicalperturbagen",
+    "drugfindR",
+    "r",
+    "ilincs",
+    "bioinformatics",
+    "bioinformatics-pipeline"
+  ],
   "fileSize": "2087.311KB",
   "releaseNotes": "https://github.com/CogDisResLab/drugfindR/blob/master/NEWS.md",
   "readme": "https://github.com/CogDisResLab/drugfindR/blob/devel/README.md",
-  "contIntegration": ["https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml", "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"],
+  "contIntegration": [
+    "https://github.com/CogDisResLab/drugfindR/actions/workflows/rworkflows.yml",
+    "https://app.codecov.io/gh/CogDisResLab/drugfindR?branch=devel"
+  ],
   "developmentStatus": "https://lifecycle.r-lib.org/articles/stages.html#experimental"
 }