Fixes package (#3)

Author: llrs-roche

.github/workflows/R-CMD-check.yaml

@@ -25,7 +25,7 @@ jobs:
 
       - uses: r-lib/actions/setup-r-dependencies@v2
         with:
-          extra-packages: any::rcmdcheck
+          extra-packages: any::rcmdcheck, any::pak
           needs: check
 
       - uses: quarto-dev/quarto-actions/setup@v2

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: val.report
 Title: Validation Reports
-Version: 0.0.0.9006
+Version: 0.0.0.9007
 Authors@R: c(
     person("Lluís", "Revilla Sancho", , "lluis.revilla_sancho@roche.com", role = c("aut", "cre"),
            comment = c(ORCID = "0000-0001-9747-2570")),

R/render_table.R

@@ -3,17 +3,16 @@
 #' @param riskmetric_assessment object coming from rismetric::pkg_assess function
 #' @keywords internal
 prepare_namespace_table <- function(riskmetric_assessment) {
-  namespace_table <- riskmetric_assessment$export_help[sort(riskmetric_assessment$exported_namespace)] |>
-  as.data.frame()
-  colnames(namespace_table) <- "value"
-
+  namespace_vector <- riskmetric_assessment$export_help[sort(riskmetric_assessment$exported_namespace)]
+  namespace_table <- data.frame(object = names(namespace_vector), value = namespace_vector)
+  rownames(namespace_table) <- NULL
   namespace_table |>
     reactable::reactable(
       columns = list(
         value = reactable::colDef(
           cell = function(value) {
             # Please to update icons search for unicodes here: https://icons.getbootstrap.com/
-            if (value) {
+            if (isTRUE(value)) {
               # Green checkmark
               htmltools::tags$i(class = "bi bi-check-square", style = "background-color: var(--bs-success); font-weight: bold;")
             } else {

R/reporter.R

@@ -3,7 +3,7 @@
 #' @param package_name Package name.
 #' @param package_version Package version number.
 #' @param package Path where to find a package source to retrieve name and version number.
-#' @param template_path Path to a custom quarto template file
+#' @param template_path Path to a directory with one quarto template file (and the files required for rendering it).
 #' @param output_format Output format for the report. Default is "all".
 #' @param params A list of execute parameters passed to the template
 #' @param ... Additional arguments passed to `quarto::quarto_render()`
@@ -13,12 +13,14 @@
 #' calling function `riskmetric::pkg_ref` before the risk assessment is executed
 #' @export
 #' @examples
+#' options("valreport_output_dir" = tempdir())
 #' pr <- package_report(
 #'   package_name = "dplyr",
 #'   package_version = "1.1.4",
 #'   params = list(
 #'     assessment_path = system.file("assessments/dplyr.rds", package = "val.report"),
-#'     image = "rhub/ref-image")
+#'     image = "rhub/ref-image"),
+#'     quiet = FALSE
 #' )
 #' pr
 #' file.remove(pr)
@@ -53,17 +55,19 @@ package_report <- function(
     params$package_version <- package_version
     params$image <- get_image_name(params)
 
-    if (is.null(template_path)) {
-        template_path <- system.file("report/pkg_template.qmd",
+    if (is.null(template_path) || !nzchar(template_path)) {
+        template_path <- system.file("report/package",
                                      package = "val.report")
+    } else if (!dir.exists(template_path)) {
+        stop("Template directory is not available")
     }
 
-    params$package <- normalizePath(params$package, mustWork = FALSE)
-    if (!is.null(params$assessment_path)) {
-      params$assessment_path <- normalizePath(params$assessment_path, mustWork = TRUE)
+    params$package <- normalizePath(params$package, mustWork = FALSE, winslash = "/")
+    if (length(params$assessment_path) == 1L && !nzchar(params$assessment_path)) {
+      params$assessment_path <- normalizePath(params$assessment_path, mustWork = TRUE, winslash = "/")
     }
-    # Bug on https://github.com/quarto-dev/quarto-cli/issues/5765
 
+    # Bug on https://github.com/quarto-dev/quarto-cli/issues/5765
     v <- quarto::quarto_version()
     if (v < package_version("1.7.13")) {
       warning("Please install the latest (devel) version of Quarto")

R/utils.R

@@ -23,10 +23,11 @@ fill_in <- function(list, names) {
 }
 
 output_dir <- function() {
-  opt <- getOption("valreport_output_dir", default = NULL)
-  env <- Sys.getenv("VALREPORT_OUTPUT_DIR", unset = getwd())
-
-  opt %||% env
+  getOption("valreport_output_dir",
+            default = Sys.getenv("VALREPORT_OUTPUT_DIR",
+                                 unset = getwd()
+            )
+  )
 }
 
 rendering_dir <- function() {

inst/assessments/dplyr.rds

@@ -22,13 +22,17 @@ format:
       light: [default, custom.scss, custom_light.scss]
   gfm:
     html-math-method: webtex    
-  typst:
+  pdf:
     toc: true
-    section-numbering: 1.1.1
-    df-print: default
-    margin:
-      x: 2cm
-      y: 2cm
+    number-depth: 3
+  # FIXME: Typst didn't handle well the relative paths to images
+  #  typst:
+  #   toc: true
+  #   section-numbering: 1.1.1
+  #   df-print: default
+  #   margin:
+  #     x: 2cm
+  #     y: 2cm
 filters:
   - foldable_code.lua
 ---
@@ -126,8 +130,6 @@ namespace_table <- val.report:::prepare_namespace_table(d_riskmetric)
 ```
 
 
-::: {.content-visible when-format="html"}
-
 ```{r prepare_tables_dependencies}
 deps <- d_riskmetric$dependencies
 deps$package <- gsub("\\n", " ", deps$package)
@@ -143,8 +145,6 @@ dependencies_table <- htmltools::div(
 )
 ```
 
-:::
-
 ```{r prepare_tables_reverse_dependencies}
 reverse_dependencies <- paste(d_riskmetric$reverse_dependencies, collapse = ", ")
 ```
@@ -253,7 +253,6 @@ The package uses `r if ("license" %in% names(d_riskmetric) && !is.null(d_riskmet
 
 ## Code checks
 
-Code checks for this package are: 
 
 ```{r r_cmd_check, eval=!is_risk_error(d_riskmetric[["r_cmd_check"]])}
 d_riskmetric[["r_cmd_check"]]

inst/report/package/pkg_template.qmd

@@ -1,4 +1,4 @@
-# Card is created with the expected components depending on arguments: only has title if no other argument is set
+# Card is created with the expected components depending on arguments / only has title if no other argument is set
 
     Code
       create_info_card("test title")
@@ -7,7 +7,7 @@
         <h3 class="card-title">test title</h3>
       </div>
 
-# Card is created with the expected components depending on arguments: has title and header
+# Card is created with the expected components depending on arguments / has title and header
 
     Code
       create_info_card(title = "test title", header = "Information header")
@@ -17,7 +17,7 @@
         <h3 class="card-title">test title</h3>
       </div>
 
-# Card is created with the expected components depending on arguments: has all arguments set
+# Card is created with the expected components depending on arguments / has all arguments set
 
     Code
       create_info_card(title = "test title", header = "Information header", text = "Extra test")

man/package_report.Rd

@@ -1,4 +1,4 @@
-# Namespace table is created: It is created by without error from existing example package assessment
+# Namespace table is created / It is created by without error from existing example package assessment
 
     Code
       prepare_namespace_table(example_assessment)