Add new functions. Fix tests/examples

Author: bschilder

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: echogithub
 Type: Package
 Title: echoverse module: Extract data and metadata from GitHub
-Version: 0.99.0
+Version: 0.99.1
 Authors@R: 
     c(person(given = "Brian",
            family = "Schilder",
@@ -45,8 +45,9 @@ Suggests:
     covr,
     badger,
     hexSticker,
-    httr
-RoxygenNote: 7.2.1
+    httr,
+    rvest
+RoxygenNote: 7.2.2
 VignetteBuilder: knitr
 License: GPL-3
 Config/testthat/edition: 3

NAMESPACE

@@ -3,18 +3,25 @@
 export(description_extract)
 export(description_find)
 export(github_branches)
+export(github_commits)
+export(github_dependents)
 export(github_files)
 export(github_files_download)
 export(github_hex)
+export(github_metadata)
 export(github_pages)
 export(github_pages_files)
 export(github_pages_vignettes)
+export(github_permissions)
+export(github_traffic)
 export(readme_header)
 importFrom(data.table,":=")
 importFrom(data.table,.SD)
+importFrom(data.table,as.data.table)
 importFrom(data.table,data.table)
 importFrom(data.table,fwrite)
 importFrom(data.table,rbindlist)
+importFrom(data.table,setnafill)
 importFrom(gh,gh)
 importFrom(gh,gh_token)
 importFrom(methods,is)

NEWS.md

@@ -1,3 +1,13 @@
+# echogithub 0.99.1
+
+## New features
+
+* New functions:
+    - `github_permissions`
+    - `github_metadata`
+    - `github_commits`
+    - `github_traffic`
+    
 # echogithub 0.99.0
 
 ## New features

R/description_find.R

@@ -13,10 +13,8 @@
 #' @importFrom methods is
 #' @importFrom utils installed.packages packageDescription 
 #' @importFrom testthat is_testing
-#' @examples 
-#' \dontrun{
-#' desc_file <- description_find(repo="data.table")
-#' }
+#' @examples  
+#' desc_file <- description_find(repo="data.table") 
 description_find <- function(desc_file = NULL,
                              owner = NULL,
                              repo = NULL,

R/github_commits.R

@@ -0,0 +1,27 @@
+#' GitHub commits
+#'
+#' Get metadata for all commits to a given GitHub repo.
+#' @inheritParams github_files 
+#' @return A nested list of metadata
+#'
+#' @export 
+#' @importFrom gh gh gh_token
+#' @examples
+#' commits <- github_commits(owner="RajLabMSSM", 
+#'                           repo="echolocatoR")
+github_commits <- function(owner,
+                           repo, 
+                           token = gh::gh_token(),
+                           verbose = TRUE) {
+    # echoverseTemplate:::source_all()
+    # echoverseTemplate:::args2vars(github_commits)
+
+    endpoint <- paste("https://api.github.com","repos",
+                      owner,repo,"commits",sep="/")
+    gh_response <- gh::gh(endpoint = endpoint,
+                          .token = token,
+                          .limit = Inf,
+                          per_page = 100) 
+    dt <- gh_to_dt(gh_response)
+    return(dt)
+}

R/github_dependents.R

@@ -0,0 +1,42 @@
+#' GitHub dependents
+#'
+#' Get all GitHub repositories that are dependent on the target
+#'  GitHub repository.
+#' @inheritParams github_files 
+#' @return A \link[data.table]{data.table}.
+#'
+#' @export
+#' @importFrom data.table data.table 
+#' @importFrom stringr str_split
+#' @examples
+#' dt <- github_dependents(owner = "neurogenomics", 
+#'                         repo = "rworkflows")
+github_dependents <- function(owner,
+                              repo, 
+                              token = gh::gh_token(),
+                              verbose = TRUE) {
+    # echoverseTemplate:::source_all()
+    # echoverseTemplate:::args2vars(github_insights) 
+    
+    requireNamespace("rvest")
+    ## NOTE: GitHub API does not currently support getting deps from repo, 
+    ## so need to use webscraping instead.
+    messager("Searching for dependents of:",paste(owner,repo,sep="/"),
+             v=verbose)
+    #### Get latest commit ####
+    URL <- paste("https://github.com",owner,repo,"network/dependents",
+                 sep = "/")
+    html <- rvest::read_html(URL) 
+    box_rows <- rvest::html_elements(html,".Box-row")
+    if(length(box_rows)==0){
+        messager("WARNING: No dependents could be found. Returning NULL.",
+                 v=verbose)
+        return(NULL)
+    }
+    dt <- (rvest::html_text2(box_rows)) |> 
+        stringr::str_split(" / |\n|[ ]", simplify = TRUE) |> 
+        data.table::data.table() |> 
+        `colnames<-`(c("owner","repo","stargazers_count","forks_count"))
+    dt <- cbind(target=paste(owner,repo,sep="/"),dt)
+    return(dt)
+}

R/github_files.R

@@ -3,7 +3,7 @@
 #' Search for files within a GitHub repository and filter them 
 #' by a regex \code{query}. Optionally, can download these selected files to 
 #' your local computer using the original folder structure.
-#' \emph{NOTET}: To search your private repos, make sure you
+#' \emph{NOTE}: To search your private repos, make sure you
 #' GitHub token is supplied to the \code{token} argument, or is saved as in your
 #' \emph{~.Renviron} file, e.g.: \code{GITHUB_TOKEN=<token_here>}
 #' @param owner Repo owner name

R/github_metadata.R

@@ -0,0 +1,56 @@
+#' GitHub metadata
+#'
+#' Get metadata on a GitHub repository.
+#' @param add_traffic Add traffic metadata 
+#' with \link[echogithub]{github_traffic}.
+#' @inheritParams github_files 
+#' @return A \link[data.table]{data.table}.
+#'
+#' @export
+#' @importFrom data.table as.data.table   
+#' @importFrom gh gh gh_token
+#' @examples
+#' dt <- github_metadata(owner="RajLabMSSM", 
+#'                       repo="echolocatoR")
+github_metadata <- function(owner,
+                           repo, 
+                           add_traffic = FALSE,
+                           token = gh::gh_token(),
+                           verbose = TRUE) { 
+    # echoverseTemplate:::source_all()
+    # echoverseTemplate:::args2vars(github_metadata)
+    
+    messager(paste0(
+        "Gathering metadata",
+        if(isTRUE(add_traffic))" (with traffic data)" else NULL
+    ),"for repo:",paste(owner,repo,sep="/"),v=verbose)
+    endpoint <- paste("https://api.github.com","repos",
+                      owner,repo,sep="/")
+    gh_response <- gh::gh(endpoint = endpoint,
+                          .token = token, 
+                          per_page = 100)
+    dt <- cbind(
+        owner=owner,
+        repo=repo,
+        data.table::as.data.table(gh_response[!sapply(gh_response, is.list)])   
+    )
+    for(x in names(gh_response[sapply(gh_response, is.list)])){
+        if(x %in% c("owner","repo")){
+            x2 <- paste(x,"info",sep="_")
+        }else {
+            x2 <- x
+        }
+        dt[[x2]] <- list(gh_response[[x]])
+    }
+    #### Add traffic metadata ####
+    if(isTRUE(add_traffic)){
+        traffic <- github_traffic(owner = owner,
+                                  repo = repo, 
+                                  token = token,
+                                  verbose = FALSE) 
+        if(!is.null(traffic)){
+            dt <- merge(dt,traffic,by=c("owner","repo"))
+        } 
+    }
+    return(dt)
+}

R/github_pages.R

@@ -8,8 +8,9 @@
 #' 
 #' @export
 #' @importFrom gh gh gh_token
-#' @examples 
-#' link <- github_pages(owner="RajLabMSSM", repo="echolocatoR")
+#' @examples
+#' link <- github_pages(owner="RajLabMSSM",
+#'                      repo="echolocatoR")
 github_pages <- function(owner, 
                          repo,
                          error = TRUE,

R/github_permissions.R

@@ -0,0 +1,26 @@
+#' GitHub permissions
+#'
+#' Get permissions metadat on a GitHub repository.
+#' @inheritParams github_files 
+#' @return A \link[data.table]{data.table}.
+#'
+#' @export
+#' @importFrom data.table as.data.table   
+#' @importFrom gh gh gh_token
+#' @examples
+#' permissions <- github_permissions(owner="RajLabMSSM", 
+#'                                   repo="echolocatoR")
+github_permissions <- function(owner,
+                               repo, 
+                               token = gh::gh_token(),
+                               verbose = TRUE) { 
+    
+    messager("Gathering permissions metadata for repo:",
+             paste(owner,repo,sep="/"),
+             v=verbose)
+    dt <- github_metadata(owner = owner, 
+                          repo = repo, 
+                          token = token, 
+                          verbose = verbose)
+    return(dt$permissions[[1]])
+}