From f85b8e02ffe87922e331f0f1bf184450b039db73 Mon Sep 17 00:00:00 2001 From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> Date: Sat, 21 Sep 2024 21:20:58 -0400 Subject: [PATCH 1/2] docs: mark all internal functions as such --- DESCRIPTION | 2 +- R/utilities.R | 7 +++++- codemeta.json | 44 +++++++++++++++++++++++++++++------ man/dot-ilincsBaseUrl.Rd | 1 + man/dot-return_library.Rd | 1 + man/dot-validateLibrary.Rd | 1 + man/loadMetadata.Rd | 1 + man/stopIfInvalidLibraries.Rd | 1 + man/validateLibraries.Rd | 1 + 9 files changed, 50 insertions(+), 9 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index e10fbe6..7afb30f 100644 --- a/DESCRIPTION +++ b/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", diff --git a/R/utilities.R b/R/utilities.R index 998d5cb..8a38e77 100644 --- a/R/utilities.R +++ b/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) diff --git a/codemeta.json b/codemeta.json index ae93eba..de53074 100644 --- a/codemeta.json +++ b/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": "Ali.Sajid.Imami@gmail.com", "@id": "https://orcid.org/0000-0003-3684-3539" }, { "@type": "Person", - "givenName": ["Justin", "Fortune"], + "givenName": [ + "Justin", + "Fortune" + ], "familyName": "Creeden", "email": "Justin.Creeden@rockets.utoledo.edu", "@id": "https://orcid.org/0000-0003-3123-8401" }, { "@type": "Person", - "givenName": ["Evelyn", "Alden"], + "givenName": [ + "Evelyn", + "Alden" + ], "familyName": "Bates", "email": "Evelyn.Bates@rockets.utoledo.edu", "@id": "https://orcid.org/0000-0002-4157-2481" @@ -47,7 +56,10 @@ "maintainer": [ { "@type": "Person", - "givenName": ["Ali", "Sajid"], + "givenName": [ + "Ali", + "Sajid" + ], "familyName": "Imami", "email": "Ali.Sajid.Imami@gmail.com", "@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" } diff --git a/man/dot-ilincsBaseUrl.Rd b/man/dot-ilincsBaseUrl.Rd index 6aa1baa..14dbf41 100644 --- a/man/dot-ilincsBaseUrl.Rd +++ b/man/dot-ilincsBaseUrl.Rd @@ -12,3 +12,4 @@ a fixed string URL \description{ Parameterize the base URL for the iLINCS API } +\keyword{internal} diff --git a/man/dot-return_library.Rd b/man/dot-return_library.Rd index e983258..45010b1 100644 --- a/man/dot-return_library.Rd +++ b/man/dot-return_library.Rd @@ -15,3 +15,4 @@ A string with the associated library ID \description{ Return the internal iLINCS Library ID for a given library } +\keyword{internal} diff --git a/man/dot-validateLibrary.Rd b/man/dot-validateLibrary.Rd index e4fe9d2..7077043 100644 --- a/man/dot-validateLibrary.Rd +++ b/man/dot-validateLibrary.Rd @@ -15,3 +15,4 @@ a boolean \description{ Check if the library is valid } +\keyword{internal} diff --git a/man/loadMetadata.Rd b/man/loadMetadata.Rd index 62ebbae..7df3c33 100644 --- a/man/loadMetadata.Rd +++ b/man/loadMetadata.Rd @@ -15,3 +15,4 @@ a tibble \description{ Load the correct metadata table } +\keyword{internal} diff --git a/man/stopIfInvalidLibraries.Rd b/man/stopIfInvalidLibraries.Rd index fed2d23..73e7869 100644 --- a/man/stopIfInvalidLibraries.Rd +++ b/man/stopIfInvalidLibraries.Rd @@ -15,3 +15,4 @@ a stop if the libraries are invalid \description{ Stop if the libraries are invalid } +\keyword{internal} diff --git a/man/validateLibraries.Rd b/man/validateLibraries.Rd index ce0f69a..2c06aae 100644 --- a/man/validateLibraries.Rd +++ b/man/validateLibraries.Rd @@ -16,3 +16,4 @@ a boolean This function confirms that the library parameter is one of the allowed ones. } +\keyword{internal} From 5bcd9565b4877501dfb5e52d8a259e5573eaef69 Mon Sep 17 00:00:00 2001 From: Ali Sajid Imami <395482+AliSajid@users.noreply.github.com> Date: Sat, 21 Sep 2024 21:25:15 -0400 Subject: [PATCH 2/2] build: add `always_run` to the create_tag script --- .pre-commit-config.yaml | 1 + DESCRIPTION | 2 +- codemeta.json | 2 +- 3 files changed, 3 insertions(+), 2 deletions(-) diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml index 0d9818c..360cc15 100644 --- a/.pre-commit-config.yaml +++ b/.pre-commit-config.yaml @@ -133,5 +133,6 @@ repos: ./utilities/create_tag.sh language: system pass_filenames: false + always_run: true stages: - post-commit diff --git a/DESCRIPTION b/DESCRIPTION index 7afb30f..8a1499c 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,6 +1,6 @@ Package: drugfindR Title: Investigate iLINCS for candidate repurposable drugs -Version: 0.99.992 +Version: 0.99.993 Authors@R: c( person(given = c("Ali", "Sajid"), family = "Imami", diff --git a/codemeta.json b/codemeta.json index de53074..4ad6aae 100644 --- a/codemeta.json +++ b/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": "0.99.992", + "version": "0.99.993", "programmingLanguage": { "@type": "ComputerLanguage", "name": "R",