Merge pull request #7 from LiNk-NY/commit-stats

Add summary statistics for commits in repositories

DESCRIPTION

@@ -17,10 +17,14 @@ Imports: tibble,
 	utils,
 	dplyr,
 	ggplot2,
+	gh,
 	httr,
-	lubridate, rorcid
+	lubridate,
+	purrr,
+	rorcid,
+	tibble
 Suggests: knitr, testthat
 LazyData: true
 VignetteBuilder: knitr
 biocViews: Infrastructure
-RoxygenNote: 7.2.1
+RoxygenNote: 7.3.2

NAMESPACE

@@ -1,13 +1,26 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(print,bioc_support_stats)
+S3method(print,commit_summary)
+export(filter_r_repos)
+export(get_repositories)
 export(get_support_site_stats)
 export(orcid_table)
+export(repository_commits)
+export(repository_summary)
+export(summarize_account_activity)
 export(summarize_software_downloads)
 import(dplyr)
 import(ggplot2)
 import(httr)
 import(lubridate)
 import(rorcid)
 import(tibble)
+importFrom(gh,gh)
+importFrom(gh,gh_token)
+importFrom(purrr,map)
+importFrom(purrr,map_chr)
+importFrom(purrr,map_dbl)
+importFrom(purrr,map_df)
+importFrom(tibble,tibble)
 importFrom(utils,read.table)

R/commit-stats.R

@@ -0,0 +1,290 @@
+#' @name commit_stats
+#'
+#' @title Get and summarize repository statistics from GitHub
+#'
+#' @description These functions allow the user to query the GitHub API and
+#'   produce a comprehensive summary of commit activity for each R package
+#'   repository. The main workhorse function is `summarize_account_activity`
+#'   which calls all other functions internally to produce a summary of GitHub R
+#'   repository activity.
+#'
+#' @param username `character(1)` The GitHub username
+#'
+#' @param org `character(1)` optional. The organization account for which to
+#'   search repositories for.
+#'
+#' @param github_token `gh_pat` The personal access token obtained from GitHub.
+#'   By default, `gh::gh_token()` is used.
+#'
+#' @returns `get_repositories`: A list of repositories for the corresponding
+#'   account or organization
+#'
+#' @examples
+#' if (interactive()) {
+#'     gitcreds::gitcreds_set()
+#'     summarize_account_activity(
+#'         username = "LiNk-NY",
+#'         org = "waldronlab",
+#'         start_date = "2023-08-31",
+#'         end_date = "2024-09-01"
+#'     )
+#' }
+#' @export
+get_repositories <- function(username, org, github_token = gh::gh_token()) {
+    message("Finding repositories for ", username, "...")
+    repos <- list()
+    page <- 1
+    has_more <- TRUE
+
+    while (has_more) {
+        if (!missing(org)) {
+            endpoint <- "GET /orgs/{org}/repos"
+            username <- org
+        } else {
+            endpoint <- "GET /users/{username}/repos"
+        }
+        new_repos <- gh::gh(
+            endpoint,
+            username = username,
+            org = username,
+            page = page,
+            .token = github_token
+        )
+        if (length(new_repos)) {
+            repos <- c(repos, new_repos)
+            page <- page + 1
+        } else {
+            has_more <- FALSE
+        }
+    }
+    repos
+}
+
+#' @rdname commit_stats
+#'
+#' @param repo_list `list` A list as obtained from `get_repositories`
+#'
+#' @returns `filter_r_repos`: A list of filtered repositories containing R code
+#'
+#' @export
+filter_r_repos <-
+    function(repo_list, username, org, github_token = gh::gh_token())
+{
+    message("Identifying R repositories...")
+    purrr::map_df(repo_list, function(repo, username, org, github_token) {
+        if (!missing(org))
+            username <- org
+        languages <- gh::gh(
+            "GET /repos/{owner}/{repo}/languages",
+            owner = username,
+            repo = repo$name,
+            .token = github_token
+        )
+        if ("R" %in% names(languages)) {
+            tibble::tibble(
+                full_name = repo$full_name,
+                name = repo$name,
+                description =
+                    ifelse(is.null(repo$description), NA, repo$description),
+                stars = repo$stargazers_count,
+                forks = repo$forks_count,
+                last_updated = repo$updated_at,
+                is_fork = repo$fork,
+                default_branch = repo$default_branch,
+                r_percentage =
+                    round(languages$R / sum(unlist(languages)) * 100, 1)
+            )
+        }
+    }, username = username, org = org, github_token = github_token)
+}
+
+#' @rdname commit_stats
+#'
+#' @param repos_df `tibble` A tibble of filtered R repositories as obtained from
+#'   `filter_r_repos`
+#'
+#' @param start_date,end_date `character(1)` The start and end dates delimiting
+#'   commit searches in the `YYYY-MM-DD` format
+#'
+#' @returns `repository_commits`: A `list` of commits for each row in the
+#'   `repos_df` input
+#'
+#' @export
+repository_commits <- function(
+    repos_df, username, org, github_token = gh::gh_token(),
+    start_date, end_date
+) {
+    message("Fetching commits for ", nrow(repos_df), " R repositories...")
+    all_commits <- list()
+    if (missing(org))
+        org <- username
+    for (i in seq_len(nrow(repos_df))) {
+        repo <- repos_df$full_name[i]
+        message("Processing ", repo, " (", i, "/", nrow(repos_df), ")")
+        commits <- tryCatch({
+            gh::gh(
+                "GET /repos/{owner}/{repo}/commits",
+                author = username,
+                owner = org,
+                repo = repos_df$name[i],
+                since = start_date,
+                until = end_date,
+                .token = github_token
+            )
+        }, error = function(e) {
+            warning("Error fetching commits for ", repo, ": ", e$message)
+            return(list())
+        })
+        repo_commits <- purrr::map(commits, function(commit) {
+            list(
+                repository = repo,
+                sha = commit$sha,
+                author = commit$commit$author$name,
+                date = commit$commit$author$date,
+                message = commit$commit$message,
+                changes = tryCatch({
+                    commit_detail <- gh::gh(
+                        "GET /repos/{owner}/{repo}/commits/{sha}",
+                        owner = org,
+                        repo = repos_df$name[i],
+                        sha = commit$sha,
+                        since = start_date,
+                        until = end_date,
+                        .token = github_token
+                    )
+                    list(
+                        additions = commit_detail$stats$additions,
+                        deletions = commit_detail$stats$deletions,
+                        files_changed = length(commit_detail$files)
+                    )
+                }, error = function(e) {
+                    list(additions = NA, deletions = NA, files_changed = NA)
+                })
+            )
+        })
+        all_commits <- c(all_commits, repo_commits)
+    }
+    all_commits
+}
+
+#' @rdname commit_stats
+#'
+#' @param commits_list `list` The output of `repository_commits` that contains
+#'   commit details for each repository
+#'
+#' @returns `repository_summary`: A `list` of `tibbles` that summarize activity
+#'   in the associated `repositories` for the `username` / `org` account
+#'
+#' @export
+repository_summary <- function(
+    commits_list, repositories, username, org, start_date, end_date
+) {
+    if (missing(org))
+        org <- username
+    commit_stats <- tibble::tibble(
+        repository = map_chr(commits_list, "repository"),
+        author = map_chr(commits_list, "author"),
+        date = map_chr(commits_list, "date"),
+        additions = map_dbl(commits_list, function(x) x$changes$additions),
+        deletions = map_dbl(commits_list, function(x) x$changes$deletions),
+        files_changed =
+            map_dbl(commits_list, function(x) x$changes$files_changed)
+    )
+    repo_summary <- commit_stats |>
+        group_by(repository) |>
+        summarise(
+            total_commits = n(),
+            unique_authors = n_distinct(author),
+            total_additions = sum(additions, na.rm = TRUE),
+            total_deletions = sum(deletions, na.rm = TRUE),
+            total_files_changed = sum(files_changed, na.rm = TRUE)
+        )
+    summary <- list(
+        account_info = tibble::tibble(
+            name = username, org = org, start = start_date, end = end_date
+        ),
+        repositories = repositories,
+        repository_stats = repo_summary,
+        commit_details = commit_stats,
+        overall_stats = tibble::tibble(
+            total_repositories = nrow(repositories),
+            total_commits = nrow(commit_stats),
+            unique_authors = n_distinct(commit_stats$author),
+            total_additions = sum(commit_stats$additions, na.rm = TRUE),
+            total_deletions = sum(commit_stats$deletions, na.rm = TRUE),
+            total_files_changed = sum(commit_stats$files_changed, na.rm = TRUE)
+        )
+    )
+    class(summary) <- c("commit_summary", class(summary))
+    summary
+}
+
+#' @rdname commit_stats
+#'
+#' @importFrom tibble tibble
+#' @importFrom gh gh gh_token
+#' @importFrom purrr map_df map_chr map_dbl map
+#'
+#' @returns `summarize_account_activity`: A `list` of `tibbles` that summarize
+#'   activity in the associated `repositories` for the `username` / `org`
+#'   account
+#'
+#' @export
+summarize_account_activity <- function(
+    username,
+    org,
+    start_date,
+    end_date,
+    github_token = gh::gh_token()
+) {
+    start_date <- as.POSIXct(start_date) |> format("%Y-%m-%dT%H:%M:%SZ")
+    end_date <- as.POSIXct(end_date) |> format("%Y-%m-%dT%H:%M:%SZ")
+    # Step 1: Find all repositories for the account
+    repos <- get_repositories(
+        username = username, org = org, github_token = github_token
+    )
+    # Step 2: Filter for R repositories
+    r_repos <- filter_r_repos(
+        repos, username = username, org = org, github_token = github_token
+    )
+    if (!nrow(r_repos))
+        stop("No R package repositories found in 'username' / 'org' account")
+    # Step 3: Fetch commits for each R repository
+    commits_list <- repository_commits(
+        repos_df = r_repos, username = username, org = org,
+        github_token = github_token,
+        start_date = start_date, end_date = end_date
+    )
+    # Step 4: Summarize statistics
+    repository_summary(
+        commits_list = commits_list,
+        repositories = r_repos, username = username, org = org,
+        start_date = start_date, end_date = end_date
+    )
+}
+
+# Print method for nice output
+
+#' @rdname commit_stats
+#'
+#' @export
+print.commit_summary <- function(x) {
+    cat("\nR Development Activity Analysis\n")
+    cat("============================\n")
+    cat("Username:",x$account_info$name, "\n")
+    if (length(x$account_info$org))
+        cat("Org:", x$account_info$org, "\n")
+    cat(
+        "Period:", x$account_info$start, "to", x$account_info$end, "\n\n"
+    )
+    cat("Overall Statistics:\n")
+    cat(sprintf("- R Repositories: %d\n", x$overall_stats$total_repositories))
+    cat(sprintf("- Total Commits: %d\n", x$overall_stats$total_commits))
+    cat(sprintf("- Unique Contributors: %d\n", x$overall_stats$unique_authors))
+    cat(sprintf("- Lines Added: %d\n", x$overall_stats$total_additions))
+    cat(sprintf("- Lines Deleted: %d\n", x$overall_stats$total_deletions))
+    cat(sprintf("- Files Changed: %d\n\n", x$overall_stats$total_files_changed))
+
+    cat("Repository Summary:\n")
+    print(x$repository_stats)
+}

R/download-stats.R

@@ -8,37 +8,38 @@
 #' @note Modified from BiocReports script to give raw data on download activities per month.
 #' There may be effects in 2022 of modified distribution channels.
 #' @return a list with components ipplot, dlplot with ggplot elements, and a tibble with all stats.
-#' @examples 
+#' @examples
 #' pls = summarize_software_downloads()
 #' opar = par(no.readonly=TRUE)
 #' par(ask=TRUE)
 #' pls$ipplot
 #' pls$dlplot
 #' par(opar)
 #' @export
-summarize_software_downloads = function( years = 2018:2022, final = "2022-08-16" ) {
+summarize_software_downloads <-
+    function(years = 2018:2022, final = "2022-08-16")
+{
+    urls <- sprintf(
+        "http://bioconductor.org/packages/stats/bioc/bioc_%d_stats.tab",
+        years
+    )
 
-  urls <- sprintf(
-    "http://bioconductor.org/packages/stats/bioc/bioc_%d_stats.tab",
-    years
-  )
+    tbl <- Map(read.table, urls, MoreArgs=list(header=TRUE))
+    tbl0 <- as_tibble(do.call(rbind, unname(tbl)))
+    tbl0 = tbl0 |> filter(Month != "all")
+    dd = paste(tbl0$Year, tbl0$Month, "15", sep="-")
+    dld = as_date(dd)
+    tbl0$Date = dld
+    tbl0 = tbl0 |> dplyr::filter(Date < as_date(final))
 
- tbl <- Map(read.table, urls, MoreArgs=list(header=TRUE))
- tbl0 <- as_tibble(do.call(rbind, unname(tbl)))
- tbl0 = tbl0 |> filter(Month != "all")
- dd = paste(tbl0$Year, tbl0$Month, "15", sep="-")
- dld = as_date(dd)
- tbl0$Date = dld
- tbl0 = tbl0 |> dplyr::filter(Date < as_date(final))
-
- ipplot = ggplot(tbl0, aes(x=Date, y=Nb_of_distinct_IPs)) +
-    geom_point(size=5) +
-    ylab("# Unique IP addresses") +
-    ggtitle("Unique IPs requesting downloads")
- dlplot = ggplot(tbl0, aes(x=Date, y=Nb_of_downloads)) +
-    geom_point(size=5) +
-    ylab("# downloads") +
-    ggtitle("Number of downloads requested")
- list(ipplot=ipplot, dlplot=dlplot, table=tbl0)
-} 
+    ipplot = ggplot(tbl0, aes(x=Date, y=Nb_of_distinct_IPs)) +
+        geom_point(size=5) +
+        ylab("# Unique IP addresses") +
+        ggtitle("Unique IPs requesting downloads")
+    dlplot = ggplot(tbl0, aes(x=Date, y=Nb_of_downloads)) +
+        geom_point(size=5) +
+        ylab("# downloads") +
+        ggtitle("Number of downloads requested")
+    list(ipplot=ipplot, dlplot=dlplot, table=tbl0)
+}