Merge pull request #22 from Boehringer-Ingelheim/20-consider-includin…

…g-and-consuming-the-qc-documentation-from-dvtemplates

20 consider including and consuming the qc documentation from dv.templates

.github/workflows/test.yml

@@ -33,6 +33,43 @@ jobs:
             inst/validation
           path: templates
 
+      - name: Overwrite quality control scripts with dv.templates ones 🧹
+        shell: bash
+        run: |
+          TEMPLATE_DIR="templates/inst/validation"
+          REPO_DIR="inst/validation"
+
+          if test ! -d "${REPO_DIR}"; then
+            echo "### Quality Control documentation is not present"
+            echo "### Include quality control documentation or skip it by creating following file 'inst/validation/skip_qc'"
+            exit 1
+          fi
+
+          if test -f "${REPO_DIR}/skip_qc"; then
+            echo "skip_qc file found skipping qc documentation"
+            exit 0
+          fi
+          
+          # Conserve specs.R file
+          cp "${REPO_DIR}/specs.R" "${TEMPLATE_DIR}/specs.R"
+
+          set +e  # Disable immediate exit in conflicting parts on error for diff command
+          DIFF_OUTPUT=$(diff -qr "${TEMPLATE_DIR}" "${REPO_DIR}")
+          set -e  # Enable immediate exit on error after diff command
+
+          echo "# Quality control files" | tee -a "${GITHUB_STEP_SUMMARY}"
+          
+          if [ -n "${DIFF_OUTPUT}" ]; then
+            echo "Warning: The contents of the directories are different!" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "Modified files:" | tee -a "${GITHUB_STEP_SUMMARY}"
+            echo "$DIFF_OUTPUT" | tee -a "${GITHUB_STEP_SUMMARY}"
+          else
+            echo "The directories are identical." | tee -a "${GITHUB_STEP_SUMMARY}"
+          fi
+
+          rm -rf "${REPO_DIR}"
+          mv "${TEMPLATE_DIR}" "${REPO_DIR}"
+
       - name: Install package dependencies 📄
         uses: boehringer-ingelheim/dv.templates/.github/actions/dependencies@main     
 

NEWS.md

@@ -1,3 +1,4 @@
 # dv.templates 0.1.0
 
 - add release checks
+- qc check is done with centralized scripts from dv.templates

inst/validation/run_validation.R

@@ -1,3 +1,7 @@
+pkg_name <- read.dcf("DESCRIPTION")[, "Package"]
+pkg_version <- read.dcf("DESCRIPTION")[, "Version"]
+test_results <- tibble::as_tibble(devtools::test())
+
 local({
   # This is evaluated inside a local because, otherwise, all the variables created in the chunks of the rendered
   # document leak into the environment

inst/validation/utils-validation.R

@@ -1,32 +1,18 @@
 #' Setting up the validation
-#'
-#' 1. Add package_name
-#' 2. Copy that variable and the contents of if block to tests/testthat/setup.R
-#' (If you are using the template this may already be in place for you)
-
-package_name <- "dv.templates"
 
-if (FALSE) {
-  # validation (S)
-  vdoc <- source(
-    system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-    local = TRUE
-  )[["value"]]
-  specs <- vdoc[["specs"]]
-  # validation (F)
-}
+if (!exists("package_name")) stop("package name must be in the environment when this script is sourced")
 
-#' 2. For those tests that cover an specific spec
+#' How to link tests and specs
 
 if (FALSE) {
   test_that(
-    vdoc[["add_spec"]]("my test description", specs[["a_spec"]]),
+    vdoc[["add_spec"]]("my test description", specs$a_spec),
     {
       expect_true(TRUE)
     }
   )
 }
-#' The specs variable on the call references the one declared in point 1
+#' The specs variable on the call references the one declared in specs.R
 
 #' 3. For those tests covering more than one spec.
 #' NOTE: It must be c() and not list()
@@ -47,7 +33,11 @@ if (FALSE) {
 
 if (FALSE) {
   my_spec <- specs$my$hier$spec
-  test_that(vdoc$parse_spec(my_spec, "my test_description"), {
+  test_that(vdoc[["add_spec"]]("my test_description", my_spec), {
+    ...
+  })
+
+  test_that(vdoc[["add_spec"]]("my test_description", specs[["my"]][["hier"]][["spec"]]), {
     ...
   })
 }

inst/validation/val_report_child.Rmd

@@ -14,10 +14,14 @@
 
 ```{r setup, message = FALSE}
 # Import vdoc functions ----
-vdoc <- source(
-  system.file("validation", "utils-validation.R", package = params[["package"]], mustWork = TRUE),
-  local = TRUE
-)[["value"]]
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########  
+  package_name <- params[["package"]]
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
+})
 
 # Set required packages ----
 suppressPackageStartupMessages(stopifnot(requireNamespace("DT")))
@@ -82,6 +86,7 @@ title <- paste(result_symbol, params[["package"]], params[["version"]])
 ```
 
 ## `r title`
+Date: `r format(Sys.time(), "%Y-%b-%d %H:%M:%S")`
 
 The following document generates a report for R packages, to satisfy the criteria of a "Released" status under the **Non-GxP** project. The QC report contains the following information:
 

inst/validation_templates/_pkgdown.yml

@@ -0,0 +1,18 @@
+template:
+  bootstrap: 5
+
+navbar:
+  type: inverted
+  structure:
+    left: [intro, reference, articles, tutorials, news, qc]
+  components:
+    qc:
+      text: Quality Control
+      href: articles/qc.html  
+
+articles:
+
+- title: Quality Control
+  desc: Quality Control
+  contents:
+  - qc

inst/validation_templates/tests/testthat/setup.R

@@ -0,0 +1,11 @@
+# validation (S)
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########  
+  package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
+})
+specs <- vdoc[["specs"]]
+#  validation (F)

inst/validation_templates/vignettes/qc.Rmd

@@ -0,0 +1,32 @@
+---
+title: "Quality Control"
+output:
+  rmarkdown::html_vignette
+vignette: >
+  %\VignetteIndexEntry{Quality Control}
+  %\VignetteEngine{knitr::rmarkdown}
+  %\VignetteEncoding{UTF-8}
+---
+
+```{r, include = FALSE}
+knitr::opts_chunk$set(
+  collapse = TRUE,
+  comment = "#>",
+  echo = FALSE
+)
+```
+
+```{r, params, echo = FALSE, include = FALSE}
+val_param_rds <- "../inst/validation/results/val_param.rds"
+val_param_rds_exists <- file.exists(val_param_rds)
+if (file.exists(val_param_rds)) params <- readRDS(val_param_rds)
+```
+
+```{r, results = "asis", echo = FALSE}
+if (val_param_rds_exists) {
+  res <- knitr::knit_child("../inst/validation/val_report_child.Rmd", quiet = TRUE, envir = environment())
+  cat(res, sep = "\n")
+} else {
+  "No quality control results found"
+}
+```

scripts/test_qc_pkg.R

@@ -71,6 +71,7 @@ if (!dir.exists(validation_root)) {
 }
 
 if (file.exists(validation_skip)) {
+  writeLines("", file.path(validation_results, "skipped_qc"))
   success[["valdoc"]] <- NA
 } else {
 
@@ -127,9 +128,9 @@ summary <- c(
   summary,
   purrr::imap_chr(success, ~{
     symbol <- "\U02753"
-    symbol <- if (isTRUE(.x)) "\U02705"
-    symbol <- if (isFALSE(.x)) "\U0274C"
-    symbol <- if (is.na(.x)) "\U02757"
+    if (isTRUE(.x)) symbol <- "\U02705"
+    if (isFALSE(.x)) symbol <- "\U0274C"
+    if (is.na(.x)) symbol <- "\U02757"
     paste(" - ", symbol, .y)
   })
 )
@@ -138,7 +139,7 @@ CON <- file(github_summary_file, "a")
 on.exit(close(CON))
 writeLines(summary, CON)
 
-stopifnot(isTRUE(all(success)))
+stopifnot(all(success | is.na(sucess)))
 
 message("##############################")
 message("###### BUILD RESULT (F) ######")

tests/testthat/setup.R

@@ -1,8 +1,11 @@
-package_name <- "dv.templates"
 # validation (S)
-vdoc <- source(
-  system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE),
-  local = TRUE
-)[["value"]]
+vdoc <- local({
+  #                      ##########
+  # package_name is used # INSIDE # the sourced file below
+  #                      ##########
+  package_name <- read.dcf("../../DESCRIPTION")[, "Package"]
+  utils_file_path <- system.file("validation", "utils-validation.R", package = package_name, mustWork = TRUE)
+  source(utils_file_path, local = TRUE)[["value"]]
+})
 specs <- vdoc[["specs"]]
 #  validation (F)