R/info-srr.R

In ropensci-review-tools/pkgcheck: rOpenSci Package Checks

# These functions provide information derived from \pkg{srr} without
# actually being checks

#' Format the \pkg{srr} reporting section of the general editorial report.
#'
#' This is a complex multi-stage check which returns a list of sub-checks,
#' including:
#'
#' \enumerate{
#'
#' \item message: The main message from srr_stats_pre_submit confirming whether
#'     all standards have been documented or not
#' \item categories: List of statistical categories addressed in the software
#' \item missing_stds: List of any missing standards
#' \item report_file: Link to the HTML version of the `srr` report file
#' \item okay: Logical flag indicating whether or not all `srr` requirements
#'     have been met.
#'
#' }
#'
#' @param path Location of local repository to report on
#'
#' @note Unlike all other checks in this package, this one actually requires the
#' package to be loaded (because it uses \pkg{roxygen2} which only works on
#' loaded packages).
#'
#' @noRd
pkginfo_srr_report <- function (path) {

    srr <- tryCatch (
        srr::srr_stats_pre_submit (path, quiet = TRUE),
        error = function (e) e
    )

    if (is.null (srr)) {
        return (NULL)
    } # Not an srr package

    srr_okay <- !methods::is (srr, "error")
    # Warning messages for standards in single directory, or most standards in
    # single file, from srr/R/pre-submit.R:
    warn_msg <- "should be documented in"
    if (srr_okay && any (grepl (warn_msg, srr))) {
        srr [grep (warn_msg, srr)] <-
            gsub ("^S", "Statistical s", srr [grep (warn_msg, srr)])
        srr_okay <- FALSE
    }

    categories <- stds <- NULL

    # get path to report in cache dir:
    pkg_hash <- current_hash (path)
    static_dir <- fs::path (
        Sys.getenv ("PKGCHECK_CACHE_DIR"),
        "static"
    )
    if (!dir.exists (static_dir)) {
        dir.create (static_dir, recursive = TRUE)
    }

    f <- paste0 (pkg_hash [1], "_srr", pkg_hash [2])
    srr_report_file <- fs::path (static_dir, paste0 (f, ".html"))
    srr_md_file <- fs::path (static_dir, paste0 (f, ".md"))

    flist <- list.files (static_dir,
        full.names = TRUE
    )
    fnames <- vapply (
        decompose_path (flist), function (i) {
            utils::tail (i, 1)
        },
        character (1)
    )
    flist <- flist [grep (f, fnames)]

    if (srr_md_file %in% flist) {

        srr_rep <- readLines (srr_md_file)
    } else {

        if (length (flist) > 0) {
            file.remove (flist)
        }

        srr_rep <- srr::srr_report (
            path = path,
            view = FALSE
        )

        srr_file_from <- attr (srr_rep, "file")

        if (!is.null (srr_file_from)) {

            if (!file.copy (srr_file_from, srr_report_file)) {
                warning ("srr html file not copied!")
            }
            # srr_report stored the .md as a .Rmd in tempdir():
            srr_rmd <- tools::file_path_sans_ext (srr_file_from)
            srr_rmd <- paste0 (srr_rmd, ".Rmd")
            if (!file.copy (srr_rmd, srr_md_file)) {
                warning ("srr md file not copied!")
            }
        }
    }

    categories <- srr_categories_from_report (srr_rep)
    stds <- NULL # missing standards

    i <- grep ("standards \\[v.*\\] are missing from your code", srr)

    if (length (i) > 0) {

        stds <- srr [-seq (i)]
        blank <- which (nchar (stds) == 0)
        # srr_tail <- NULL
        if (length (blank) > 1) {
            stds_end <- blank [which (diff (blank) > 1) + 1]
            # srr_tail <- stds [seq (stds_end, length (stds))]
            stds <- stds [-seq (stds_end, length (stds))]
        }
        stds <- paste0 (stds [which (nchar (stds) > 0)],
            collapse = ", "
        )
    }

    if (srr_okay) {
        srr_okay <- length (i) == 0
    }

    list (
        message = srr,
        categories = categories,
        missing_stds = stds,
        report_file = srr_report_file,
        okay = srr_okay
    )
}

#' Extract the statistical categories from the `srr` report
#' @param s Result of main `srr:srr_report()` function
#' @noRd
srr_categories_from_report <- function (s) {

    cats <- regmatches (s, gregexpr ("[A-Z]+[0-9]+\\.[0-9]+([a-z]?)", s))
    cats <- sort (unique (unlist (cats)))
    cats <- unique (gsub ("[0-9].*$", "", cats))
    cats <- cats [which (!cats == "G")]

    prefixes <- c ("BS", "EA", "ML", "RE", "SP", "TS", "UL")
    categories <- c (
        "Bayesian and Monte Carlo",
        "Exploratory Data Analysis",
        "Machine Learning",
        "Regression and Supervised Learning",
        "Spatial",
        "Time Series",
        "Dimensionality Reduction, Clustering and Unsupervised Learning"
    )
    cats <- cats [which (cats %in% prefixes)]

    return (categories [match (cats, prefixes)])
}

report_file <- function (checks) {

    Sys.getenv ("PKGCHECK_SRR_REPORT_FILE", checks$info$srr$report_file)
}