Merge pull request #203 from phuse-org/release_0.4.0

Release 0.4.0

.Rbuildignore

@@ -11,3 +11,4 @@ CONTRIBUTING.md
 ^validation\.yml$
 
 vignettes/validation/validation.yml
+^man/figures/cheatsheets/*

.gitignore

@@ -1,3 +1,4 @@
 valtools.Rproj
 .Rproj.user
 .Rhistory
+inst/doc

DESCRIPTION

@@ -1,12 +1,12 @@
 Package: valtools
 Title: Automate Validated Package Creation
-Version: 0.3.0
+Version: 0.4.0
 Authors@R: 
     c(
     person(given = "Ellis",
            family = "Hughes",
            role = c("aut","cre"),
-           email = "ehhughes@scharp.org",
+           email = "ellishughes@live.com",
            comment = c(ORCID = "0000-0003-0637-4436")),
     person(given = "Eli",
            family = "Miller",
@@ -23,6 +23,11 @@ Authors@R:
            role = "aut",
            email = "peymaan.es@gmail.com",
            comment = c(ORCID = "0000-0003-1613-2705")),
+    person(given = "Maya",
+           family = "Gans",
+           role = "ctb",
+           email = "maya.gans@atorusresearch.com",
+           comment = c(ORCID = "0000-0002-5452-6089")),
     person(given = "PHUSE",
            role = "cph")
     )
@@ -35,7 +40,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.1.1
+RoxygenNote: 7.1.2
 Suggests: 
     covr,
     XML,

NAMESPACE

@@ -18,6 +18,7 @@ S3method(roxy_tag_rd,roxy_tag_riskAssessment)
 export(vt_add_file_to_config)
 export(vt_add_user_to_config)
 export(vt_create_package)
+export(vt_create_packet)
 export(vt_drop_file_from_config)
 export(vt_drop_user_from_config)
 export(vt_dynamic_referencer)
@@ -87,6 +88,7 @@ importFrom(kableExtra,kable_styling)
 importFrom(knitr,asis_output)
 importFrom(knitr,current_input)
 importFrom(knitr,kable)
+importFrom(knitr,knit)
 importFrom(knitr,knit_child)
 importFrom(knitr,opts_knit)
 importFrom(lubridate,parse_date_time)
@@ -128,9 +130,12 @@ importFrom(tools,file_ext)
 importFrom(tools,file_path_sans_ext)
 importFrom(usethis,create_package)
 importFrom(usethis,edit_file)
+importFrom(usethis,local_project)
+importFrom(usethis,proj_activate)
 importFrom(usethis,ui_stop)
 importFrom(usethis,ui_value)
 importFrom(usethis,use_git_ignore)
+importFrom(usethis,use_rstudio)
 importFrom(usethis,write_union)
 importFrom(utils,capture.output)
 importFrom(utils,getFromNamespace)

R/case.R

@@ -40,7 +40,7 @@
 vt_use_test_case <- function(name, username = vt_username(), title = NULL, open = interactive(),
                              add_before = NULL, add_after = NULL) {
 
-  name <- vt_set_ext(name, ext = "md")
+  name <- vt_set_ext(name, ext = c("md","rmd"))
 
   is_valid_name(name)
 
@@ -60,14 +60,17 @@ vt_use_test_case <- function(name, username = vt_username(), title = NULL, open
                        username = username,
                        editDate = as.character(Sys.Date())
                      ))
-
+
+    # Add file to validation configuration
+    vt_add_file_to_config(
+      filename = name,
+      after = {{add_after}},
+      before = {{add_before}}
+      )
   }
 
-  # Add file to validation configuration
-  vt_add_file_to_config(filename = name, after = {{add_after}}, before = {{add_before}})
-
   if(open){
-    edit_file(case_name)
+    edit_file(case_name) # nocov
   }
 
   invisible(case_name)

R/code.R

@@ -20,14 +20,19 @@ vt_use_test_code <- function(name, username = vt_username(), open = interactive(
                       username = username,
                       editDate = as.character(Sys.Date())
                     ))
+
+    # Add file to validation configuration
+    vt_add_file_to_config(
+      filename = name,
+      after = {{add_after}},
+      before = {{add_before}}
+      )
   }
 
-  # Add file to validation configuration
-  vt_add_file_to_config(filename = name, after = {{add_after}},
-                        before = {{add_before}})
+
 
   if(open){
-    edit_file(code_name)
+    edit_file(code_name) # nocov
   }
 
   invisible(code_name)

R/coverage-matrix.R

@@ -13,12 +13,10 @@ vt_scrape_coverage_matrix <- function(type = c("long", "wide"),
     do.call("rbind", apply(vals, 1, FUN = function(x){
 
       this_row <- strsplit(x[["coverage"]], split = ":")[[1]]
-      if(length(this_row) == 1){
-        this_row <- rep(this_row, 2)
 
-      } else if(length(this_row) != 2){
-        rlang::abort(paste("Coverage details must follow format Test_Case:Requirement.",
-                           "See", x[["tc_title"]]),
+      if(length(this_row) != 2){
+        rlang::abort(paste0("Coverage details must follow format Test_Case:Requirement.",
+                           " See ", x[["tc_title"]], ", Coverage Entry: ",trimws(x[["coverage"]])),
                      class = "vt.coverage_format")
       }
       names(this_row) <- c("tc_id", "req_id")
@@ -31,19 +29,31 @@ vt_scrape_coverage_matrix <- function(type = c("long", "wide"),
   }
 
   split_req <- function(vals){
-    do.call("rbind", apply(vals, 1, FUN = function(x){
+    out <- do.call("rbind", apply(vals, 1, FUN = function(x){
 
 
       req_one_row <- data.frame(tc_title = x[["tc_title"]],
                                 tc_id = x[["tc_id"]],
-                                req_id = strsplit(trimws(x[["req_id"]]), split = ", ")[[1]],
+                                req_id = trimws(strsplit(trimws(x[["req_id"]]), split = ", ")[[1]]),
                                 deprecate = x[["deprecate"]],
                                 stringsAsFactors = FALSE)
+
+
+
       req_one_row$req_title <- paste0("Requirement ", gsub(req_one_row$req_id,
                                                            pattern = "^(\\d+)\\.*.*",
                                                            replacement = "\\1"))
+
       req_one_row
     }))
+
+    # req_title uses only first numeric position
+    out$req_title <- factor(out$req_title,
+                            levels = paste0("Requirement ", 
+                                            sort(as.numeric(unique(unlist(lapply(strsplit(out$req_title, split = " "), 
+                                                        function(x){x[2]})))))))
+    out[order(out$req_title),]
+
   }
 
   # avoids dependency on tidyr::pivot_wider
@@ -64,6 +74,7 @@ vt_scrape_coverage_matrix <- function(type = c("long", "wide"),
       x
     })
     out <- do.call("rbind", list_all_x)
+
     row.names(out) <- 1:nrow(out)
     out[, c("req_title", "req_id", sort(names(out)[-1:-2]))]
   }
@@ -91,7 +102,7 @@ vt_scrape_coverage_matrix <- function(type = c("long", "wide"),
   vals_all <- split_req(numbered_cov_vals)
 
   if(type[1] == "long"){
-    out_data <- vals_all[order(vals_all$req_id),]
+    out_data <- vals_all[order(vals_all$req_title),]
     row.names(out_data) <- 1:nrow(out_data)
     out_data <- out_data[, c("req_title", "req_id", "tc_title", "tc_id", "deprecate")]
     attr(out_data, "table_type") <- "long"

R/dynamic_referencing.R

@@ -50,9 +50,12 @@ vt_dynamic_referencer <- R6::R6Class("vt_dynamic_referencer",
           #' ref$list_references()
 
           scrape_references = function(text){
-
+            
             ## Drop roxygen comment headers from text for scraping references.
             text <- unname(unlist(text[!grepl("^#'", text)]))
+
+            ## drop NA text from scraping
+            text <- text[!is.na(text)]
 
             reference_locations <-
               gregexpr(

R/file_and_path_utils.R

@@ -58,8 +58,18 @@ vt_path <- function(...){
 #'
 #' @export
 vt_find_config <- function(){
-
-  root <- find_root(has_file(".here") | is_rstudio_project | is_r_package | is_vcs_root)
+
+  tryCatch({
+    root <- find_root(has_file(".here") | is_rstudio_project | is_r_package | is_vcs_root)
+  }, error = function(e){
+    abort(
+      paste0(
+      "Could not find root directory. ",
+      "Is your working directory inside a package, validation packet, or project?\n"
+      ),
+      class = "vt.validation_root_missing"
+    )
+  })
 
   tryCatch({
 

R/init.R

@@ -54,7 +54,7 @@ vt_use_validation <- function( pkg = ".", working_dir, ...) {
 #' @inheritParams usethis::create_package
 #'
 #' @importFrom usethis create_package
-#' @importFrom rlang inform abort
+#' @importFrom rlang inform abort is_interactive
 #'
 #' @rdname val_init
 #'
@@ -89,6 +89,62 @@ vt_create_package <- function(pkg = ".", ..., fields = list(), rstudio = rstudio
 
 }
 
+#' @description Create the validation packet infrastructure. Intended to create
+#' validation infrastructure external to an R package.
+#'
+#' @param target target of validation. Character name of package or scope validation packet is being performed for.
+#' @param ... Additional argument passed to `vt_use_config()`
+#' @inheritParams usethis::create_project
+#'
+#' @importFrom usethis use_rstudio local_project proj_activate
+#' @importFrom rlang inform abort is_interactive
+#'
+#' @rdname val_init
+#'
+#' @export
+vt_create_packet <- function(path = ".", target, ..., rstudio = rstudioapi::isAvailable(), open = rlang::is_interactive()) {
+
+  if(is_package(path)){
+      abort(paste0(
+        "`vt_create_packet()` is not intended to add validation infrastructure",
+        " to an existing package. Use `vt_use_validation()` instead."
+        ))
+  }
+
+  tryCatch({
+
+    if(!dir.exists(path)){
+      dir.create(path = path, recursive = TRUE, showWarnings = FALSE)
+      usethis::with_project(path = path,force = TRUE,{
+        if(rstudio){
+          usethis::use_rstudio()
+        }else{
+          file.create(".here")
+        }
+      })
+    }
+
+    ## set up validation structure in package & create basic config for validation
+    vt_use_validation(pkg = path, working_dir = ".", package = target, ...)
+
+    inform("Created validation packet",
+           class = "vt.initPacket")
+
+  }, error = function(e) {
+    abort(paste0("Failed to create validation packet.\n",   #nocov
+                 e, sep = "\n"),                            #nocov
+          class = "vt.initPacketFail")                      #nocov
+
+  })
+
+  if(open){
+    usethis::proj_activate(path = path)
+  }
+
+  invisible()
+
+}
+
 #' Internal wrapper function to call vt_create_package().
 #' To be used by RStudio project wizard, preventing opening the project twice.
 #'
@@ -99,5 +155,14 @@ vt_create_package_wizard <- function(path, ...){
   vt_create_package(pkg= path, open= FALSE, ...)   # nocov
 }
 
+#' Internal wrapper function to call vt_create_packet().
+#' To be used by RStudio project wizard, preventing opening the project twice.
+#'
+#' @param path Project directory, collected through project wizard
+#'
+#' @noRd
+vt_create_packet_wizard <- function(path, ...){
+  vt_create_packet(path = path, open= FALSE, ...)   # nocov
+}
 
 

R/req.R

@@ -8,7 +8,7 @@ vt_use_req <- function(name, username = vt_username(), title = NULL, open = inte
                        add_before = NULL, add_after = NULL){
 
   # ensure file extensions are of the acceptable type
-  name <- vt_set_ext(name, ext = "md")
+  name <- vt_set_ext(name, ext = c("md", "rmd"))
 
   is_valid_name(name)
 
@@ -29,12 +29,17 @@ vt_use_req <- function(name, username = vt_username(), title = NULL, open = inte
                       title = title,
                       editDate = as.character(Sys.Date())
                     ))
+
+    vt_add_file_to_config(
+      filename = name,
+      after = {{add_after}},
+      before = {{add_before}}
+      )
   }
 
-  vt_add_file_to_config(filename = name, after = {{add_after}}, before = {{add_before}})
 
   if(open){
-    edit_file(req_name)
+    edit_file(req_name) # nocov
   }
 
   invisible(req_name)

R/roxygen_extension.R

@@ -30,6 +30,8 @@ roxy_tag_parse.roxy_tag_deprecate <- function(x) {
   tag_markdown(x)
 }
 
+# nocov start
+
 #' @export
 #' @importFrom roxygen2 rd_section roxy_tag_rd
 roxy_tag_rd.roxy_tag_editor <- function(x, base_path, env) {
@@ -97,6 +99,7 @@ format.rd_section_deprecate <- function(x, ...) {
   )
 }
 
+# nocov end
 
 format_coverage_text <- function(x){