Render on the desired directory (#20)

* Make it more robust

* Check quarto version that should be used

* Add the remaining code

* Render in a separate folder

* Add prefix to files

* Update quarto version

* Fix problems with prefix_output

* Add file

* Add riskmetric file as an example

* update example to not leave anything

* Set up website

* Simplify rendering steps

---------

Co-authored-by: Lluís <[email protected]>

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

@@ -32,6 +32,7 @@ jobs:
           GH_TOKEN: ${{ secrets.GITHUB_TOKEN }}
         with:
           tinytex: true
+          version: 1.7.13
 
       - uses: r-lib/actions/check-r-package@v2
         with:

.github/workflows/pkgdown.yaml

@@ -0,0 +1,49 @@
+# Workflow derived from https://github.com/r-lib/actions/tree/v2/examples
+# Need help debugging build failures? Start at https://github.com/r-lib/actions#where-to-find-help
+on:
+  push:
+    branches: [main, master]
+  pull_request:
+  release:
+    types: [published]
+  workflow_dispatch:
+
+name: pkgdown.yaml
+
+permissions: read-all
+
+jobs:
+  pkgdown:
+    runs-on: ubuntu-latest
+    # Only restrict concurrency for non-PR jobs
+    concurrency:
+      group: pkgdown-${{ github.event_name != 'pull_request' || github.run_id }}
+    env:
+      GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }}
+    permissions:
+      contents: write
+    steps:
+      - uses: actions/checkout@v4
+
+      - uses: r-lib/actions/setup-pandoc@v2
+
+      - uses: r-lib/actions/setup-r@v2
+        with:
+          use-public-rspm: true
+
+      - uses: r-lib/actions/setup-r-dependencies@v2
+        with:
+          extra-packages: any::pkgdown, local::.
+          needs: website
+
+      - name: Build site
+        run: pkgdown::build_site_github_pages(new_process = FALSE, install = FALSE)
+        shell: Rscript {0}
+
+      - name: Deploy to GitHub pages 🚀
+        if: github.event_name != 'pull_request'
+        uses: JamesIves/[email protected]
+        with:
+          clean: false
+          branch: gh-pages
+          folder: docs

DESCRIPTION

@@ -12,7 +12,7 @@ License: MIT + file LICENSE
 URL: https://github.com/pharmaR/riskreports
 BugReports: https://github.com/pharmaR/riskreports/issues
 Depends:
-    R (>= 3.5.0)
+    R (>= 4.4.0)
 Imports: 
     methods,
     quarto (>= 1.4.4)

R/reporter.R

@@ -7,16 +7,18 @@
 #' @param params A list of execute parameters passed to the template
 #' @param ... Additional arguments passed to `quarto::quarto_render()`
 #'
-#' @return A report
+#' @return A path to the reports generated, called by its side effects.
+#' @export
 #' @examples
-#' package_report(
+#' pr <- package_report(
 #'   package_name = "dplyr",
 #'   package_version = "1.1.4",
 #'   params = list(
+#'     assessment_path = system.file("assessments/dplyr.rds", package = "riskreports"),
 #'     image = "rhub/ref-image")
 #' )
-#'
-#' @export
+#' pr
+#' file.remove(pr)
 package_report <- function(
     package_name,
     package_version,
@@ -41,7 +43,7 @@ package_report <- function(
     }
 
     full_name <- paste0(package_name, "_v", package_version)
-    output_file <- paste0("validation_report_", full_name,".html")
+    output_file <- paste0("validation_report_", full_name, ".qmd")
 
     params$package_name <- package_name
     params$package_version <- package_version
@@ -57,26 +59,51 @@ package_report <- function(
       params$assessment_path <- normalizePath(params$assessment_path, mustWork = TRUE)
     }
     # 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")
+    }
+    # https://github.com/quarto-dev/quarto-r/issues/81#issuecomment-1375691267
+    # quarto rendering happens in the same place as the file/project
+    # To avoid issues copy to a different place and render there.
+    render_dir <- output_dir()
+    fc <- file.copy(from = template_path,
+                    to = file.path(render_dir, output_file), overwrite = TRUE,
+                    copy.date = TRUE)
+
+    if (any(!fc)) {
+      stop("Copying to the rendering directory failed.")
+    }
+
+    template <- list.files(render_dir, full.names = TRUE)
+    template <- template[endsWith(template, "qmd")]
+
+    if (length(template) > 1) {
+      stop("There are more than one template!\n",
+           "Please have only one quarto file on the directory.")
+    }
+
+    prefix_output <- paste0("validation_report_", full_name)
+    pre_rendering <- list.files(render_dir, full.names = TRUE)
+
     suppressMessages({suppressWarnings({
       out <- quarto::quarto_render(
-        template_path,
+        input = template,
         output_format = "all",
         execute_params = params,
         ...
       )
     })})
 
-    # Move reports after creation (work around issue https://github.com/quarto-dev/quarto-cli/issues/5765)
-    lf <- list.files(dirname(template_path), full.names = TRUE)
-    files_template <- lf[!dir.exists(lf)]
-    file_name <- tools::file_path_sans_ext(basename(template_path))
-    files_template <- files_template[startsWith(basename(files_template),
-                                                file_name)]
-    files_template <- files_template[!endsWith(files_template, ".qmd")]
-    output_file = paste0("validation_report_", full_name,
-                         ".", tools::file_ext(files_template))
-    file.rename(files_template, output_file)
-    invisible(output_file)
+    fr <- file.remove(file.path(render_dir, output_file))
+    if (any(!fr)) {
+      warning("Failed to remove the quarto template used from the directory.")
+    }
+
+    post_rendering <- list.files(render_dir, full.names = TRUE)
+    output_files <- setdiff(post_rendering, pre_rendering)
+    invisible(output_files)
 }
 
 is.empty <- function(x) {

R/utils.R

@@ -17,3 +17,18 @@ fill_in <- function(list, names) {
   list[missing_names] <- NA
   list
 }
+
+
+output_dir <- function() {
+  opt <- getOption("riskreports_output_dir", default = NULL)
+  env <- Sys.getenv("RISKREPORTS_OUTPUT_DIR", unset = getwd())
+
+  opt %||% env
+}
+
+rendering_dir <- function() {
+  opt <- getOption("riskreports_rendering_dir", default = NULL)
+  env <- Sys.getenv("RISKREPORTS_RENDERING_DIR", unset = tempdir())
+
+  opt %||% env
+}

_pkgdown.yml

@@ -0,0 +1,4 @@
+url: ~
+template:
+  bootstrap: 5
+

inst/report/pkg_template.qmd

@@ -1,6 +1,5 @@
 ---
 title: "Validation Report - `r paste0(params$package_name, '@', params$package_version)`"
-date: "`r Sys.time()`"
 date-format: "ddd MMM DD hh:mm:ss A YYYY"
 params:
   package_name: dplyr
@@ -83,7 +82,7 @@ d_riskmetric <- readRDS(risk_path)
 
 # Assesment produces a data.frame with one row
 r_riskmetric <- riskreports::assessment(d_riskmetric)
-is_na <- sapply(r_riskmetric, is.na)
+is_na <- sapply(r_riskmetric, function(x){is.na(x) || (is.character(x) && startsWith(x, "no applicable"))})
 knitr::kable(r_riskmetric[, !is_na]) # Use this to have some summary text and report it.
 # d_riskmetric
 ```
@@ -120,15 +119,15 @@ d_riskmetric$export_help[sort(d_riskmetric$exported_namespace)]
 
 ### Examples
 
-There are `r sum(d_riskmetric$has_examples)` help pages with examples, from `r length(d_riskmetric$has_examples)` (`r sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100) ` %).
+There are `r if (!is_na["has_examples"]) sum(d_riskmetric$has_examples)` help pages with examples, from `r if (!is_na["has_examples"]) {length(d_riskmetric$has_examples)}` (`r if (!is_na["has_examples"]) {sprintf("%0.2f", sum(d_riskmetric$has_examples)/length(d_riskmetric$has_examples)*100)} else {"?"} ` %).
 
 ### NEWS
 
-The package has `r d_riskmetric$has_news` NEWS file and it is `r if(!d_riskmetric$news_current) "not"` current.
+The package has `r if ("has_news" %in% names(d_riskmetric) && !is.null(d_riskmetric$has_news)) print(d_riskmetric$has_news)` NEWS file and it is `r if (is.null(d_riskmetric$news_current) && !d_riskmetric$news_current) "not"` current.
 
 ### License
 
-The package uses `r d_riskmetric$license`.
+The package uses `r if ("license" %in% names(d_riskmetric) && !is.null(d_riskmetric$license)) print(d_riskmetric$license)`.