v0.0.1 Release Final Touches (#77)

* chore: add @returns, cran-comments.md, remove remotes suggested dependency

* fix: initial CRAN notes

* fix: add new cran-comments to buildignore

* skip reexport.srcrefs package tests on cran

* more updates for CRAN submission

.Rbuildignore

@@ -7,3 +7,4 @@
 ^\.github$
 ^doc$
 ^Meta$
+^cran-comments\.md$

.gitignore

@@ -5,3 +5,4 @@ inst/doc
 README.html
 /doc/
 /Meta/
+*\.tar\.gz

DESCRIPTION

@@ -1,24 +1,38 @@
 Package: covtracer
-Title: Tools for contextualizing tests
-Version: 0.0.0.9016
-Authors@R: c(
+Title: Contextualizing Tests
+Version: 0.0.1
+Authors@R:
+    c(
       person(
-        given = "Doug",
-        family = "Kelkhoff",
-        role = c("aut", "cre"),
-        email = "kelkhofd@gene.com"),
+        "Doug", "Kelkhoff", , 
+        "doug.kelkhoff@gmail.com", 
+        role = c("cre", "aut"),
+        comment = c(ORCID = "0009-0003-7845-4061")
+      ),
+      person(
+        given = "Szymon",
+        family = "Maksymiuk",
+        role = c("aut"),
+        email = "sz.maksymiuk@gmail.com",
+        comment = c(ORCID = "0000-0002-3120-1601")
+      ),
       person(
         given = "Andrew",
         family = "McNeil",
         role = c("aut"),
-        email = "andrew.richard.mcneil@gmail.com")
+        email = "andrew.richard.mcneil@gmail.com"
+      ),
+      person(
+	    "F. Hoffmann-La Roche AG", 
+		role = c("cph", "fnd")
+	  )
     )
 Description: 
-    Provides tools for dissecting a package namespace or "covr" coverage object
-    in order to cross reference tested code with the lines that are evaluated, as
-    well as linking those evaluated lines to the documentation that they are
-    described within. Connecting these three pieces of information provides a
-    mechanism of linking tests to documented behaviors.
+    Dissects a package environment or 'covr' coverage object in order to cross
+    reference tested code with the lines that are evaluated, as well as linking
+    those evaluated lines to the documentation that they are described within.
+    Connecting these three pieces of information provides a mechanism of 
+	linking tests to documented behaviors.
 URL: https://github.com/genentech/covtracer
 BugReports: https://github.com/genentech/covtracer/issues
 Depends:
@@ -29,7 +43,6 @@ Imports:
     methods
 Suggests:
     testthat,
-    remotes,
     covr (>= 3.5.2),
     withr,
     R6,
@@ -38,11 +51,9 @@ Suggests:
     igraph,
     knitr,
     rmarkdown
-Remotes:
-    github::r-lib/covr
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 VignetteBuilder: knitr

LICENSE

@@ -1,2 +1,2 @@
-YEAR: 2022
-COPYRIGHT HOLDER: Genentech
+YEAR: 2024
+COPYRIGHT HOLDER: F. Hoffmann-La Roche AG

NEWS.md

@@ -1,4 +1,8 @@
-# Unreleased (tentative 0.0.1)
+# covtracer 0.0.1
+
+* initial CRAN release
+
+# covtracer 0.0.0.9000
 
 * Fix handling for packages with no objects (#73, @dgkf)
 

R/Rd_df.R

@@ -37,7 +37,7 @@ Rd_df <- function(x) {
     if (length(doctype)) doctype else NA_character_
   }, character(1L))
 
-  aliases <- aliases[sort(names(aliases))]  # avoid OS-specific file sorting
+  aliases <- aliases[sort(names(aliases))] # avoid OS-specific file sorting
   naliases <- vapply(aliases, length, integer(1L))
   files <- rep(names(db), times = naliases)
   doctype <- rep(doctype, times = naliases)

R/getSrcFilepath.R

@@ -12,7 +12,9 @@ getSrcFilepath.default <- function(x) {
   path <- getSrcFilename(x, full.names = TRUE)
   wd <- attr(getSrcref(x), "srcfile")$wd
   if (!is.null(wd)) path <- file.path(wd, path)
-  if (!length(path)) return(NA_character_)
+  if (!length(path)) {
+    return(NA_character_)
+  }
   normalizePath(path, winslash = "/", mustWork = FALSE)
 }
 

R/list_of_srcref.R

@@ -1,6 +1,7 @@
 #' Create an S3 list of srcref objects
 #'
-#' @param x A list or single srcref to coerce to a list_of_srcref
+#' @param x A list or single srcref to coerce to a `list_of_srcref`
+#' @return A `list_of_srcref` class object
 #'
 #' @rdname as_list_of_srcref
 as_list_of_srcref <- function(x) {
@@ -41,15 +42,20 @@ as_list_of_srcref.list <- function(x) {
 #'   paths when formatting `srcref`s.
 #' @param full.num A \code{logical} value indicating whether to use all numeric
 #'   `srcref` components when formatting `srcref`s.
+#' @return A `character` vector of formatted strings
 #'
 #' @export
 format.list_of_srcref <- function(x, ..., full.names = FALSE, full.num = FALSE) {
   out <- rep_len(NA_character_, length(x))
-  if (!length(x)) return(out)
+  if (!length(x)) {
+    return(out)
+  }
   xnull <- vapply(x, is.null, logical(1L))
   srcnull <- vapply(x, function(i) is.null(getSrcref(i)), logical(1L))
   isnull <- xnull | srcnull
-  if (all(isnull)) return(out)
+  if (all(isnull)) {
+    return(out)
+  }
   fps <- if (full.names) getSrcFilepath(x[!isnull]) else vapply(x[!isnull], getSrcFilename, character(1L))
   srcref_num_rep_len <- length(as.numeric(x[!isnull][[1]]))
   nums <- t(vapply(x[!isnull], as.numeric, numeric(srcref_num_rep_len)))
@@ -71,7 +77,8 @@ print.list_of_srcref <- function(x, ...) {
     sprintf("$%s", ifelse(
       grepl("^[a-zA-Z0-9_.]*$", names(x)),
       names(x),
-      sprintf("`%s`", names(x))))
+      sprintf("`%s`", names(x))
+    ))
   )
   xfmt <- sprintf(
     "%s\n%s\n\n",

R/obj_namespace_name.R

@@ -1,5 +1,7 @@
 env_ns_name <- function(e) {
-  if (is.null(e) || !isNamespace(e)) return(NA_character_)
+  if (is.null(e) || !isNamespace(e)) {
+    return(NA_character_)
+  }
   unname(getNamespaceName(e))
 }
 
@@ -24,6 +26,7 @@ env_name <- function(e) {
 #'
 #' @param x A value to find within namespace `ns`
 #' @param ns A package namespace
+#' @return A `character` string representing a namespace or similar
 #'
 obj_namespace_name <- function(x, ns) {
   UseMethod("obj_namespace_name")
@@ -37,7 +40,9 @@ obj_namespace_name.default <- function(x, ns) {
 #' @exportS3Method
 obj_namespace_name.character <- function(x, ns) {
   is_exported <- x %in% getNamespaceExports(ns)
-  if (!is_exported) return(NA_character_)
+  if (!is_exported) {
+    return(NA_character_)
+  }
   env_ns_name(environment(getExportedValue(ns, x)))
 }
 

R/pseudo_srcref.R

@@ -12,10 +12,12 @@
 #' @param call Any code object, most often a `call` object
 #' @param file A filepath to bind as a `srcfile` object
 #' @param lloc A `srcef`-like `lloc` numeric vector
+#' @return A `with_pseudo_srcref` object, mimicking the structure of `srcref`
 #'
 with_pseudo_srcref <- function(call, file, lloc) {
-  if (!is.null(srcfile) && !is.null(lloc))
+  if (!is.null(srcfile) && !is.null(lloc)) {
     attr(call, "srcref") <- structure(lloc, srcfile = srcfile(file), class = "pseudo_srcref")
+  }
   structure(call, class = c("with_pseudo_srcref", class(call)))
 }
 

R/srcref_df.R

@@ -21,34 +21,40 @@
 #'
 #' @examples
 #' pkg <- system.file("examplepkg", package = "covtracer")
-#' remotes::install_local(
+#' install.packages(
 #'   pkg,
-#'   force = TRUE,
+#'   type = "source",
+#'   repos = NULL,
 #'   quiet = TRUE,
 #'   INSTALL_opts = "--with-keep.source"
 #' )
 #' as.data.frame(pkg_srcrefs("examplepkg"))
 #' @export
-as.data.frame.list_of_srcref <- function(x, ..., use.names = TRUE,
+as.data.frame.list_of_srcref <- function(
+    x, ..., use.names = TRUE,
     expand.srcref = FALSE, row.names = NULL) {
-
   if (expand.srcref) {
     df <- data.frame(
       srcfile = getSrcFilepath(x),
       matrix(
         t(vapply(lapply(x, as.numeric), `[`, numeric(8L), 1:8)),
         ncol = 8L,
-        dimnames = list(c(), c("line1", "byte1", "line2",
-          "byte2", "col1", "col2", "parsed1", "parsed2"))),
+        dimnames = list(c(), c(
+          "line1", "byte1", "line2",
+          "byte2", "col1", "col2", "parsed1", "parsed2"
+        ))
+      ),
       stringsAsFactors = FALSE,
       row.names = row.names,
-      ...)
+      ...
+    )
   } else {
     df <- data.frame(
       srcref = I(x),
       stringsAsFactors = FALSE,
       row.names = row.names,
-      ...)
+      ...
+    )
     class(df$srcref) <- setdiff(class(df$srcref), "AsIs")
   }
 
@@ -74,9 +80,10 @@ as.data.frame.list_of_srcref <- function(x, ..., use.names = TRUE,
 #'
 #' @examples
 #' pkg <- system.file("examplepkg", package = "covtracer")
-#' remotes::install_local(
+#' install.packages(
 #'   pkg,
-#'   force = TRUE,
+#'   type = "source",
+#'   repos = NULL,
 #'   quiet = TRUE,
 #'   INSTALL_opts = "--with-keep.source"
 #' )
@@ -246,8 +253,9 @@ test_trace_mapping <- function(x) {
     logical(1L)
   )
 
-  if (!any(has_tests))
+  if (!any(has_tests)) {
     return(new_empty_test_trace_tally())
+  }
 
   mat <- do.call(
     rbind,
@@ -259,7 +267,7 @@ test_trace_mapping <- function(x) {
     )
   )
 
-  mat <- mat[order(mat[, "test"], mat[, "i"]),, drop = FALSE]
+  mat <- mat[order(mat[, "test"], mat[, "i"]), , drop = FALSE]
   mat
 }
 
@@ -273,6 +281,8 @@ test_trace_mapping <- function(x) {
 #'
 #' @param l A `list_of_srcref` object
 #' @param r A `list_of_srcref` object
+#' @return A `integer` vector of the first index in `r` that fully encapsulate
+#'   the respective element in `l`
 #'
 match_containing_srcrefs <- function(l, r) {
   # NOTE:
@@ -311,11 +321,11 @@ match_containing_srcrefs <- function(l, r) {
 
     l_start_gte_r_start <- (ldf[[li, "line1"]] > rdf[[ri, "line1"]]) ||
       (ldf[[li, "line1"]] == rdf[[ri, "line1"]] &&
-       ldf[[li, "col1"]] >= rdf[[ri, "col1"]])
+        ldf[[li, "col1"]] >= rdf[[ri, "col1"]])
 
     l_end_lte_r_end <- (ldf[[li, "line2"]] < rdf[[ri, "line2"]]) ||
       (ldf[[li, "line2"]] == rdf[[ri, "line2"]] &&
-       ldf[[li, "col2"]] <= rdf[[ri, "col2"]])
+        ldf[[li, "col2"]] <= rdf[[ri, "col2"]])
 
     if (!is.na(l_start_gte_r_start) && l_start_gte_r_start) {
       if (!is.na(l_end_lte_r_end) && l_end_lte_r_end) {
@@ -358,12 +368,14 @@ match_containing_srcrefs <- function(l, r) {
 #'   The name should be the name of the column from the left `data.frame`
 #'   containing a `list_of_srcref` column, and the value should be the name of a
 #'   column from the right `data.frame` containing a `list_of_srcref` column.
+#' @return A `data.frame` of `x` joined on `y` by spanning `srcref`
 #'
 #' @export
 join_on_containing_srcrefs <- function(x, y, by = c("srcref" = "srcref")) {
   by <- by[1L]
-  if (!names(by) %in% names(x) || !by %in% names(y))
+  if (!names(by) %in% names(x) || !by %in% names(y)) {
     stop("joining columns defined in `by` not found in provided data.frames")
+  }
 
   idx <- match_containing_srcrefs(x[[names(by)[[1L]]]], y[[by[[1L]]]])
   if (any(names(y) %in% names(x))) {