custom report #39

Zhenglei-BCS · 2025-07-10T14:37:46Z

added a custom_report folder, will be merged into report folder
added a custo _report function, will be mergerd into the main function.

Co-authored-by: Alvaro Sanchez <71273913+svalvaro@users.noreply.github.com> Co-authored-by: svalvaro <sanchezvillalba.alvaro@gmail.com> Co-authored-by: osenan <oriol@praenoscere.com>

Co-authored-by: osenan <oriol@praenoscere.com> Co-authored-by: Rabii Bouhestine <rabiibouhestine@outlook.com>

Zhenglei-BCS · 2025-07-10T19:01:23Z

Summary of Changes from Original `package_report()` Function

Here’s a brief overview of the key modifications made to the original package_report() function to support customized R package risk assessment reporting:

New Parameters for Branding: Added logo_path, logo_path_dark, and r_validation_logo_path to support custom logos for light/dark modes (header) and R Validation Hub branding (footer), with defaults set to "r_validation_logo.png".
Dual-Logo Setup: Modified top_page.html to include both light and dark mode logos in a container <div>, with CSS to toggle visibility based on theme.
R Validation Hub Footer: Created footer.html in the template directory to add the R Validation Hub logo and text ("Generated by R-Validation Hub workflow") at the bottom of HTML reports.
File Accessibility: Added logic to copy all logo files to the rendering directory with unique filenames (e.g., logo_light.png) to ensure accessibility during rendering, addressing potential path resolution issues.

In addition to changes in the package_report() function, the Quarto template has been updated to include the new parameters in the YAML front matter, ensuring they are accessible during rendering.

PDF issues

Unlike HTML, PDF output via Typst does not support dynamic CSS-based theme switching for light/dark logos. Maybe We should also explore Typst-specific customization in the Quarto YAML (header-includes or footer-includes?) to automate footer inclusion for PDF output.

Currently tried using ::: {.content-visible when-format="pdf"} syntax for including logos in PDF/Typst output, added the following to the template but did not work

::: {.content-visible when-format="pdf"}
#figure(image("logo_light.png", width: 30%), caption: "Logo")
:::



::: {.content-visible when-format="pdf"}
#figure(image("r_validation_logo.png", width: 30%), caption: "Generated by R-Validation Hub workflow")
:::

Copilot

Pull Request Overview

This PR introduces a new custom report feature—allowing light/dark logos and future color theming—by adding a custom_report folder, updating templates, and extending package_report() with new parameters.

Added logo_path, logo_path_dark, r_validation_logo_path, primary_color, and secondary_color to the report API
Updated Quarto templates and HTML/CSS to render dual‐mode logos and a footer
Expanded documentation (.Rd and vignettes) and included example R functions

Reviewed Changes

Copilot reviewed 15 out of 16 changed files in this pull request and generated 2 comments.

Show a summary per file

File	Description
vignettes/articles/Generate-Customized-Report.Rmd	Spelling fix and updated usage example for custom logos
man/package_report.Rd	Documented new logo and color arguments
man/custom_package_report.Rd	Added custom report Rd and arguments; example usage mismatch
inst/report/package/top_page.html	Replaced single logo with dual‐logo container and dynamic title
inst/report/package/pkg_template.qmd	Injected new params and PDF fallback logo
inst/report/package/footer.html	Introduced a footer with R Validation Hub logo
R/utils.R	Duplicate `is.empty` definition
R/reporter.R	Copying logos and CSS removal logic

Comments suppressed due to low confidence (3)

inst/dev/custom_report.R:10

The @param block documents primary_color and secondary_color but is missing @param logo_path_dark; please add documentation for the logo_path_dark argument to keep the Rd in sync with the function signature.

#' @param primary_color Hex color code for primary styling (e.g., links, headers). Defaults to "#007BFF" (blue). Currently not applied; reserved for future customization.

man/custom_package_report.Rd:59

The example calls package_report() instead of custom_package_report(); update this to reflect the correct function name for the custom report.

pr <- package_report(

R/reporter.R:135

The new logo‐copying and CSS removal logic isn’t covered by tests; consider adding unit or integration tests for logo_path/logo_path_dark handling to prevent regressions.

  logo_to_remove <- c()

Copilot · 2025-07-10T19:27:26Z

R/utils.R

+is.empty <- function(x) {
+  is.null(x) || is.na(x) || !nzchar(x)
+}


You’ve introduced is.empty which duplicates is_empty; consider consolidating to a single helper to avoid confusion and reduce code duplication.

Suggested change

is.empty <- function(x) {

is.null(x) || is.na(x) || !nzchar(x)

}

# Removed the duplicate is.empty function. Use is_empty instead.

Not sure if this is used somewhere else, @llrs-roche , I copied the original reporter.R and there is an is.empty function, and I put it to the utils.R, Copilot says it is redundant, can you confirm? I also kept the original function in orig_reporter.R, if you agree, we can also delete that.

This is a real issue, I duplicated the functions. Maybe initially they did different things but now they have the same body. This should be fixed in all files of the package (not just on the ones you modified). So maybe we can left it as is and we address it later, or we can address it here for custom_report.R, orig_reporter.R, ...
We should replace is_empty by is.empty (in tests too) this would be the minimal diff.

vignettes/articles/Generate-Customized-Report.Rmd

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

llrs-roche

I like the idea of having a specific vignette for customizing the report.
However, how the packages provides this customization is not clear yet to me.
Adding a new function for each customization doesn't look sustainable in light of the _brand.yaml file (but that hasn't been tested). See the specific comments. In addition, this PR adds some folders inst/dev that I am not sure what they are.

This PR can be the base to write more robust code for customization.

llrs-roche · 2025-07-15T12:09:56Z

R/utils.R

+is.empty <- function(x) {
+  is.null(x) || is.na(x) || !nzchar(x)
+}


This is a real issue, I duplicated the functions. Maybe initially they did different things but now they have the same body. This should be fixed in all files of the package (not just on the ones you modified). So maybe we can left it as is and we address it later, or we can address it here for custom_report.R, orig_reporter.R, ...
We should replace is_empty by is.empty (in tests too) this would be the minimal diff.

R/custom_report.R

llrs-roche · 2025-07-15T13:00:16Z

R/custom_report.R

+  params$package_name <- package_name
+  params$package_version <- package_version
+  params$image <- get_image_name(params)
+  params$logo_path <- logo_path
+  params$logo_path_dark <- logo_path_dark
+  params$primary_color <- primary_color
+  params$secondary_color <- secondary_color


I see that the arguments are then added to params. Good catch! I think it would make more sense to directly pass them as params, as I don't see any transformation or interaction before adding them to the parameters.

llrs-roche · 2025-07-15T13:09:10Z

R/custom_report.R

+  # Placeholder for custom CSS or SCSS styling
+  # Note: Add custom styling here in the future. Options include:
+  # - Inline CSS by appending a <style> block to top_page_file with custom styles using params$primary_color and params$secondary_color.
+  # - Creating a separate custom CSS file in render_dir and ensuring it's referenced in the Quarto template YAML under format:html:include-in-header.
+  # - Dynamically updating SCSS files like custom.scss or custom_light.scss with color variables before rendering, if supported by the build process.
+  # Minimal CSS for dual-logo visibility in light and dark modes:
+  custom_style <- c(
+    "<style>",
+    "  /* Dual-logo styling for light and dark modes */",
+    "  .logo-container { position: relative; display: inline-block; }",
+    "  .logo-light { display: block; }",
+    "  .logo-dark { display: none; }",
+    "  @media (prefers-color-scheme: dark) {",
+    "    .logo-light { display: none; }",
+    "    .logo-dark { display: block; }",
+    "  }",
+    "</style>"
+  )


This custom_style variable is not sustainable for all styles different organizations will like. The _brand.yaml file supported by quarto, allows to customize light and dark logos too:

logo: small: logos/icon.png medium: light: logos/header-logo-light.png dark: logos/header-logo-dark.png large: logos/full-logo.svg

Difficulties in using this approach:

Quarto up to 1.6 did not clearly support dark mode branding (such as different logos or themes for dark mode) through the _brand.yml configuration. There are many ways to tweak it to work. Also it serves more for website project or project based, rather than single html file rendering. (Seems that the top.html need to be reconstructed in this case.)

1.7 supports dark and light both, but I don't have enough time to test it out yet as my RStudio does not pick up the newly installed quarto automatically but keeps using the quarto.exe under RStudio. I will have to try under Ubuntu environment instead. I will leave it here and get back to this after my vacation.

Yes, with the reports we are on the edge of what quarto can provide. But I don't think we have other options that would have this. Rmarkdown can't provide this integration with multiple themes and the customizations we want as easily.

I too think that working with a single file is easier with Rmarkdown than with quarto. But ideally that drawback is reduced as the reports are generated for multiple packages.

About the problems with the quarto version picked on your computer I found a discussion. Which suggest this approach:

The version used in RStudio can also be forced by setting RSTUDIO_QUARTO env var

I hope this helps

…, something is wrong.

Make it more compatible with older packages

…utput directory to inst/dev/TMP_tests

…n your local machine.

llrs-roche and others added 12 commits February 20, 2025 15:45

Add files for webstie

1bc856d

Remove PATS

c04c9bd

Add new test

18ed893

Update

2f8345c

Close #27

bb6835c

Update links

d2a47bd

Add email for R validation hub

ea8d723

Improve the looks of the report (#19)

84d4c96

Co-authored-by: Alvaro Sanchez <71273913+svalvaro@users.noreply.github.com> Co-authored-by: svalvaro <sanchezvillalba.alvaro@gmail.com> Co-authored-by: osenan <oriol@praenoscere.com>

Fix html format and content (#35)

bb6ff8a

Co-authored-by: osenan <oriol@praenoscere.com> Co-authored-by: Rabii Bouhestine <rabiibouhestine@outlook.com>

Update documentation

df30dbb

Add manual trigger to verify it works well

5cec8b3

custom report

f8d4781

Zhenglei-BCS mentioned this pull request Jul 10, 2025

Adding branding resources #23

Open

2 tasks

Zhenglei Gao added 4 commits July 10, 2025 19:31

merge custom report to report

2d62ed6

update example

55fa00c

change R version to 4.5.1 to pass the build check

37ce5d4

change R version to 4.5.0 to pass the build check

721dd9c

added logo remove to clean up the rendering folder.

6b26d2d

Zhenglei-BCS marked this pull request as ready for review July 10, 2025 19:26

Zhenglei-BCS requested review from Copilot and llrs-roche July 10, 2025 19:26

Copilot AI reviewed Jul 10, 2025

View reviewed changes

Update vignettes/articles/Generate-Customized-Report.Rmd

3961796

Co-authored-by: Copilot <175728472+Copilot@users.noreply.github.com>

Zhenglei-BCS mentioned this pull request Jul 11, 2025

Brand updates: add permanent R Validation Hub acknowledgement #40

Open

llrs-roche mentioned this pull request Jul 15, 2025

Consider having a template #13

Open

llrs-roche reviewed Jul 15, 2025

View reviewed changes

llrs-roche and others added 3 commits July 17, 2025 13:01

Fix typo

2898e81

If missing field is attempted return FALSE

99fe0a3

try the branding.yml approach

fb19bf0

Zhenglei Gao and others added 13 commits August 11, 2025 14:35

Merge branch 'main' into branding

0b56952

copy all includeing logo subfolder

2c20ddb

revert back to custom_package_report and original package_report

504524f

there are still warning of missing .js resources for the react tables…

42bbffa

…, something is wrong.

Use private function if not available

c4b1d01

Lower R requirements to 4.3

9d674ca

Merge pull request #42 from pharmaR/increase_back_compatibility

390e205

Make it more compatible with older packages

added devcontainer configuration for VS Code

1ce7f8d

modify vignettes/articles/Generate-Customized-Report.Rmd to set the o…

bf1ac56

…utput directory to inst/dev/TMP_tests

Merge branch 'main' into branding

1cd97f7

Example generation

f0add03

ignore all dev/TMP_tests

5e5321f

delete the files in dev/TMP_tests from the repository but keep them o…

5547d38

…n your local machine.

Zhenglei-BCS force-pushed the branding branch from 75a8fcc to 4f534d0 Compare October 9, 2025 14:41

Zhenglei-BCS force-pushed the main branch from e250fe5 to 6871856 Compare October 9, 2025 14:44

Zhenglei-BCS force-pushed the branding branch 2 times, most recently from 39e28db to 5547d38 Compare October 9, 2025 15:23

llrs-roche mentioned this pull request Nov 20, 2025

Add branding features pharmaR/val.report#2

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custom report #39

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custom report #39

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Zhenglei-BCS commented Jul 10, 2025

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Summary of Changes from Original package_report() Function

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Zhenglei-BCS commented Jul 10, 2025 •

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Summary of Changes from Original `package_report()` Function

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