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Add r_repos* functions. Add github_depend* functions
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-114
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‎DESCRIPTION

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@@ -34,7 +34,8 @@ Imports:
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data.table,
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stringr,
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testthat (>= 3.0.0),
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RCurl
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RCurl,
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rvest
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Suggests:
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markdown,
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rmarkdown,
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covr,
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badger,
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hexSticker,
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httr,
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rvest,
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httr,
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BiocManager,
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githubinstall,
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UpSetR,
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grDevices
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grDevices,
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dlstats (>= 0.1.6)
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RoxygenNote: 7.2.3
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VignetteBuilder: knitr
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License: GPL-3

‎NAMESPACE

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@@ -4,6 +4,7 @@ export(description_extract)
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export(description_find)
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export(github_branches)
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export(github_commits)
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export(github_dependencies)
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export(github_dependents)
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export(github_files)
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export(github_files_download)
@@ -15,14 +16,20 @@ export(github_pages_vignettes)
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export(github_permissions)
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export(github_traffic)
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export(r_repos)
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export(r_repos_data)
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export(r_repos_downloads)
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export(r_repos_opts)
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export(readme_header)
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importFrom(data.table,":=")
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importFrom(data.table,.SD)
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importFrom(data.table,as.data.table)
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importFrom(data.table,data.table)
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importFrom(data.table,dcast)
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importFrom(data.table,fwrite)
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importFrom(data.table,merge.data.table)
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importFrom(data.table,rbindlist)
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importFrom(data.table,setnafill)
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importFrom(data.table,setnames)
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importFrom(gh,gh)
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importFrom(gh,gh_token)
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importFrom(methods,is)
@@ -31,6 +38,7 @@ importFrom(parallel,mclapply)
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importFrom(stats,setNames)
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importFrom(stringr,str_split)
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importFrom(testthat,is_testing)
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importFrom(utils,available.packages)
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importFrom(utils,download.file)
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importFrom(utils,installed.packages)
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importFrom(utils,packageDescription)

‎NEWS.md

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@@ -2,12 +2,22 @@
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## New features
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* New functions:
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* New GitHub functions:
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- `github_permissions`
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- `github_metadata`
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- `github_commits`
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- `github_traffic`
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- `github_dependents`
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- `github_dependencies`
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* New functions for finding which repos R packages are in:
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- `r_repos`
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- `r_repos_data`
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- `r_repos_downloads`
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- `r_repos_opts`
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## Bug fixes
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* Elevate `rvest` to *Imports*.
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# echogithub 0.99.0
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‎R/github_dependencies.R

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#' GitHub dependents
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#'
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#' Get all GitHub repositories that are dependent on the target
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#' GitHub repository.
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#' @inheritParams github_files
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#' @return A \link[data.table]{data.table}.
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#'
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#' @export
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#' @importFrom data.table data.table
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#' @importFrom stringr str_split
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#' @examples
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#' dt <- github_dependencies(owner = "neurogenomics",
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#' repo = "rworkflows")
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github_dependencies <- function(owner,
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repo,
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token = gh::gh_token(),
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verbose = TRUE) {
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# echoverseTemplate:::source_all()
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# echoverseTemplate:::args2vars(github_insights)
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requireNamespace("rvest")
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type <- NULL;
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## NOTE: GitHub API does not currently support getting deps from repo,
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## so need to use webscraping instead.
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messager("Searching for dependents of:",paste(owner,repo,sep="/"),
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v=verbose)
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#### Get latest commit ####
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URL <- paste("https://github.com",owner,repo,"network/dependencies",
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sep = "/")
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html <- rvest::read_html(URL)
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boxes <- rvest::html_elements(html,".Box")
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boxes <- boxes[rvest::html_attr(boxes,"class")=="Box mb-3"]
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dt <- lapply(boxes, function(box){
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#### Get workflow name ####
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workflow_url <- paste0("https://github.com",
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(rvest::html_elements(box,".Box-header") |>
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rvest::html_elements(".Link--primary") |>
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rvest::html_attr("href")))
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#### Get workflow dependencies ####
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box_rows <- rvest::html_children(box) |>
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rvest::html_elements(".Box-row")
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d <- lapply(box_rows, function(r){
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data.table::data.table(
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action = r |>
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rvest::html_elements("a") |>
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rvest::html_attr("href") |>
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trimws(whitespace = "/"),
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action_url = paste0("https://github.com",
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r |>
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rvest::html_elements("a") |>
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rvest::html_attr("href")
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),
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subaction = r |>
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rvest::html_elements("small") |>
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rvest::html_text(),
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type = r |>
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rvest::html_elements("a") |>
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rvest::html_attr("data-hovercard-type"),
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count = r |>
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rvest::html_elements(".d-flex") |>
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rvest::html_elements("code") |>
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rvest::html_text()
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)[type=="repository",][,-c("type")]
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}) |>
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data.table::rbindlist(fill=TRUE)
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cbind(
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target=paste(owner,repo,sep="/"),
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workflow=basename(workflow_url),
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workflow_url=workflow_url,
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d)
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}) |> data.table::rbindlist(fill = TRUE)
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## Unsure why some rows have the branch name instead of a number.
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#### Report ####
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messager("Found",formatC(nrow(dt),big.mark = ","),
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"dependencies across",
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formatC(dt$workflow,big.mark = ","),"workflows.",v=verbose)
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#### Return ####
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return(dt)
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}

‎R/github_dependents.R

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@@ -38,5 +38,9 @@ github_dependents <- function(owner,
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data.table::data.table() |>
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`colnames<-`(c("owner","repo","stargazers_count","forks_count"))
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dt <- cbind(target=paste(owner,repo,sep="/"),dt)
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#### Report ####
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messager("Found",formatC(nrow(dt),big.mark = ","),
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"dependents.",v=verbose)
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#### Return ####
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return(dt)
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}

‎R/github_metadata.R

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@@ -13,10 +13,10 @@
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#' dt <- github_metadata(owner="RajLabMSSM",
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#' repo="echolocatoR")
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github_metadata <- function(owner,
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repo,
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add_traffic = FALSE,
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token = gh::gh_token(),
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verbose = TRUE) {
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repo,
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add_traffic = FALSE,
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token = gh::gh_token(),
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verbose = TRUE) {
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# echoverseTemplate:::source_all()
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# echoverseTemplate:::args2vars(github_metadata)
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‎R/r_repos.R

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#' R repositories
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#'
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#' Report on which repositories R packages are distributed through
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#' (e.g. CRAN, Bioc, rOpenSci, and/or GitHub).
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#' (i.e. base R, CRAN, Bioc, rOpenSci, R-Forge, and/or GitHub).
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#' @param which Which R repositories to extract data from.
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#' @param upset_plot Whether to create an upset plot
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#' showing R package overlap between repositories.
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#' @param show_plot Print the plot.
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#' @param save_path Path to save upset plot to.
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#' @param verbose Print messages.
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#' @inheritParams BiocManager::repositories
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#' @returns Named list.
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#'
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#' @export
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#' @importFrom data.table data.table
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#' @examples
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#' report <- r_repos()
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r_repos <- function(save_path=tempfile(pattern = "upsetr.pdf"),
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r_repos <- function(which=r_repos_opts(),
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version=NULL,
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upset_plot=TRUE,
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show_plot=TRUE,
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save_path=tempfile(fileext = "upsetr.pdf"),
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verbose=TRUE){
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16-
requireNamespace("UpSetR")
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if(isTRUE(upset_plot)) requireNamespace("UpSetR")
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total <- percent_all <- percent_exclusive <-
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count_exclusive <- count_all <- count_exclusive <- NULL;
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#### Gather data ####
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pkgs <- r_repos_data(verbose = verbose)
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pkgs <- r_repos_data(which = which,
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version = version,
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verbose = verbose)
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#### Upset plot ####
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upset <- r_repos_upset(pkgs = pkgs,
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save_path = save_path,
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verbose = verbose,
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sets.bar.color = "slategrey",
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main.bar.color = "slategrey",
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text.scale = 1.5,
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queries = list(list(query = UpSetR::intersects,
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params = list("GitHub"),
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color = "darkred",
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active = TRUE))
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)
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upset_data <- upset$data
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#### Compute percentages ####
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stats_1repo <- colSums(upset_data[rowSums(upset_data)==1,])
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repo_stats <- data.table::data.table(
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repo=names(stats_1repo),
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total=length(unique(pkgs$package)),
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count_all=colSums(upset_data),
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count_exclusive=stats_1repo
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)[,percent_all:=(
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count_all/total*100)][,percent_exclusive:=(
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count_exclusive/total*100)]
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#### Return ####
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return(list(pkgs=pkgs,
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repo_stats=repo_stats,
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upset=upset))
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if(isTRUE(upset_plot)){
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upset <- r_repos_upset(pkgs = pkgs,
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save_path = save_path,
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show_plot = show_plot,
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verbose = verbose,
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sets.bar.color = "slategrey",
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main.bar.color = "slategrey",
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text.scale = 1.5,
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queries = list(list(query = UpSetR::intersects,
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params = list("GitHub"),
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color = "darkred",
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active = TRUE))
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)
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upset_data <- upset$data
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#### Compute percentages ####
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stats_1repo <- colSums(upset_data[rowSums(upset_data)==1,])
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repo_stats <- data.table::data.table(
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r_repo=names(stats_1repo),
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total=length(unique(pkgs$package)),
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count_all=colSums(upset_data),
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count_exclusive=stats_1repo
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)[,percent_all:=(
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count_all/total*100)][,percent_exclusive:=(
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count_exclusive/total*100)]
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#### Return ####
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return(list(pkgs=pkgs,
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repo_stats=repo_stats,
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upset=upset))
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} else {
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return(pkgs)
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}
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}

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