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quartify 1.1.1
New Features
- Roxygen2 Documentation Rendering:
- Roxygen2 documentation blocks (
#') are now
automatically formatted into structured callouts resembling pkgdown
reference pages
- Rendered documentation includes: title, source line reference,
description, usage with function signature, arguments, return value,
details, and examples
- LaTeX-style formatting is automatically converted to Markdown:
\href{url}{text} becomes [text](url)
\code{text} becomes `text`
\strong{text} becomes **text**
\emph{text} becomes *text*
- Multi-line parameter descriptions and details are properly
formatted
- Custom sections (via
@section) are supported and
displayed
Bug Fixes
- CRAN Compliance:
- Added
Words: qmd to DESCRIPTION to prevent spell-check
warning
- Added pattern
^CRAN_CHECKLIST_.*\.md$ to .Rbuildignore
to exclude CRAN checklist files
- Metadata Processing: Fixed issue where empty lines
and comments between metadata fields were not properly ignored, creating
unwanted empty code chunks
- Section Header Detection: Improved regex pattern
for hidden comments to correctly exclude RStudio section headers
(
##, ###, ####) from being
filtered out
Documentation
- Removed duplicate sections (Mermaid diagrams, Callouts) from
advanced-features vignettes - these topics are now only in
getting-started vignettes with correct syntax
- Added comprehensive documentation for roxygen2 rendering
feature
quartify 1.1.0
New Features
- Hidden Comments:
- Comments starting with
# immediately followed by a
non-space character (e.g., #NOTE:, #TODO:,
#DEBUG) are now completely ignored during conversion
- Allows including private development notes, debugging markers, and
internal annotations in R scripts that won’t appear in rendered
documentation
- Useful for
#TODO:, #FIXME:,
#NOTE:, #DEBUG, #INTERNAL:,
#PRIVATE:, #HACK:, #OPTIMIZE:
markers
- Only comments with a space after
# (e.g.,
# This is a comment) are converted to text in the
output
Improvements
- RStudio Snippets Installation:
install_quartify_snippets() now uses correct paths for
all platforms:
- Windows:
%APPDATA%/RStudio/snippets
- Mac/Linux:
~/.config/rstudio/snippets
- Automatically removes and replaces old quartify snippets when
re-running the function
- Opens snippets file automatically in RStudio after installation
- Snippets can be reloaded immediately by saving the file (Ctrl+S /
Cmd+S) without restarting RStudio
- Improved cross-platform compatibility for RStudio Desktop, Pro, and
Server
- Mermaid Diagram Syntax:
- Mermaid diagram content in R scripts now uses commented lines (with
# prefix) to maintain valid R syntax
- Example:
# flowchart TD,
# A[Start] --> B[End]
- The
# prefix is automatically removed during conversion
to Quarto
- Ensures R scripts remain valid and executable while containing
Mermaid diagrams
- Updated mermaid snippet to generate commented diagram lines
Bug Fixes
- Code Quality: All non-ASCII characters removed from
code to pass CRAN checks
- Comments and messages in
R/snippets.R converted to
English
Documentation
- Added comprehensive documentation for hidden comments feature in:
- Function documentation (
?rtoqmd)
- Getting Started vignettes (EN and FR)
- README files (EN and FR)
- Updated all Mermaid diagram examples to show commented syntax
- Clarified snippet installation process and immediate reload
capability
quartify 1.0.0
CRAN Release
This is the first CRAN release of quartify! The package is now fully
compliant with CRAN policies.
CRAN Compliance Fixes
- Interactive Examples:
- Replaced
\dontrun{} with
if(interactive()){} in Shiny function examples
quartify_app() and quartify_app_web()
examples now properly indicate interactive-only usage
- Users can see examples are meant for interactive sessions, not
scripts
- Working Directory Management:
- Added immediate
on.exit(setwd(old_wd), add = TRUE)
after all setwd() calls
- Ensures working directory is always restored, even if function
errors
- Fixed in
rtoqmd.R, rtoqmd_dir.R, and
quartify_app_web.R
- Removed manual
setwd() restoration in error handlers
(now handled by on.exit())
- Console Output:
- Replaced
cat() with message() in
rtoqmd_dir.R per CRAN guidelines
- Messages can now be suppressed with
suppressMessages()
if needed
- More R-like behavior for console output
- File Writing:
install_quartify_snippets() no longer writes to home
directory by default in examples
- Added
path parameter to allow custom snippet file
location
- Examples now write to
tempdir() for testing
- Interactive examples properly wrapped in
if(interactive())
- Path Handling:
- Fixed tilde (~) path expansion issue in
rtoqmd()
- Added
path.expand() for input_file,
output_file, and output_html_file
- Quarto now receives absolute paths instead of tilde shortcuts
- Resolves “No valid input files” error when using paths like
“~/file.qmd”
Documentation Improvements
- apply_styler Parameter:
- Added comprehensive documentation in vignettes (EN and FR)
- Clarified that
use_styler must be TRUE for
apply_styler to work
- Added comparison table showing parameter combinations and
results
- Included workflow example showing safe preview before applying
changes
- Listed practical use cases for permanent code formatting
- Mode Selection:
- Fixed missing mode selector in
quartify_app()
- Now matches
rtoqmd_addin() with dynamic mode selection
(single/directory)
- Mode selector properly updates with language changes
- Directory Selection UI:
- Fixed directory button display issue (no more “span…” in label)
- Directory browser now opens correctly when selecting folders
- Dynamic button rendering with proper language support
Package Readiness
- Version 1.0.0: Stable release ready for CRAN
submission
- Zero R CMD check issues: 0 errors, 0 warnings, 0
notes
- Full CRAN policy compliance: All guidelines
followed
- Comprehensive documentation: Examples, vignettes,
and help files complete
- Tested across platforms: Works on Windows, macOS,
and Linux
quartify 0.0.9
New Features
- Roxygen2 Documentation Support:
- Documentation blocks using roxygen2 syntax (
#') are now
converted to callout-note blocks
- Function name automatically extracted and added to callout title
(e.g., “Documentation - add_numbers”)
- All roxygen2 tags (
@param, @return,
@examples, etc.) preserved in callout content
- Example file available:
inst/examples/example_roxygen.R
- Works with
rtoqmd(), rtoqmd_dir() and all
Shiny applications (rtoqmd_addin(),
quartify_app(), quartify_app_web())
- Updated test suite to verify roxygen2 conversion behavior
quartify 0.0.8
CRAN Submission Fixes
- Final CRAN Compliance:
- Added
Language: en-US field in DESCRIPTION to avoid
“qmd” misspelling NOTE
- Fixed last partial argument match:
render →
render_html in rtoqmd_dir()
- Removed all non-ASCII characters: replaced accented characters (é →
e) in French messages
- Package now passes R CMD check with 0 errors, 0 warnings, 0
notes
- Documentation Compliance:
- Added ‘Quarto’ in single quotes in DESCRIPTION per CRAN policy
- Added
@return documentation for all exported functions
(rtoqmd_addin, quartify_app,
quartify_app_web)
- Changed
\dontrun{} to \donttest{} for
executable examples in rtoqmd() and
rtoqmd_dir()
- Updated all examples to write to
tempdir() instead of
current directory
- Code Quality:
- Replaced
cat() calls with message() for
user-facing messages per CRAN guidelines
- Fixed partial argument matching: changed all
render
arguments to render_html in Shiny apps
- Fixed ERROR in R CMD check: changed non-executable example in
rtoqmd_dir() back to \dontrun{}
- User Interface Improvements:
- Integrated shinyalert package for better user
notifications
- Replaced
showNotification() with elegant modal dialogs
using shinyalert()
- Success and error messages now displayed in centered modal
windows
- Bilingual support: titles and messages adapt to selected language
(EN/FR)
- Added
shinyalert to package dependencies
New Features
- Code Quality Integration: New
use_styler and use_lintr parameters for code
quality checks:
use_styler: Automatically format code using styler and
show differences in tabsets
use_lintr: Run lintr quality checks and display issues
in tabsets
- Available in both
rtoqmd() and
rtoqmd_dir() functions
- Tabsets show Original Code, Styled Code (if changes), and Lint
Issues (if found)
- Only creates tabsets when there are actual issues or changes to
report
- Example file:
inst/examples/example_code_quality.R
- RStudio Snippets Installation: New
install_quartify_snippets() function to automatically
install useful snippets:
header: R script header template with Title, Author,
Date, Description
callout: Quarto callout structure
mermaid: Mermaid diagram chunk with options
tabset: Tabset structure with tabs
Bug Fixes
- Fixed
rtoqmd_addin() error when no document is active
or unsaved (handled NULL/empty path cases)
Documentation
- Updated vignettes to reference
install_quartify_snippets() function
- Simplified tabset examples (removed “Data Structure” and “First
Rows” tabs)
- Added snippet tips for callouts, mermaid diagrams, and tabsets in
both English and French vignettes
quartify 0.0.7
New Features
- Quarto Book Creation:
create_book parameter now defaults to TRUE in
rtoqmd_dir()
- Automatically creates Quarto book structure with navigation and
index
- Books created in French now display “Sommaire” instead of “Table of
contents”
- Default output directory changed from
_documentation to
_book
- Enhanced Shiny Applications
(
rtoqmd_addin(), quartify_app(),
quartify_app_web()):
- Code Organization: Split monolithic
addins.R (2185 lines) into 3 separate files for better
maintainability
- Harmonized UI:
- GENERATE button moved to top of page (below title bar) with centered
hex logo
- Consistent button placement across all 3 applications
- Blue title bar styling (
#0073e6) with white text
- Removed Unicode symbols (checkmarks, arrows) for ASCII
compliance
- Output Directory Selection: Added selector for
custom output directory in directory mode
- Create Book Checkbox: New checkbox to
enable/disable book creation in directory mode
- Multiple File Selection: Changed from single to
multiple file selection in file mode
- Conditional UI Elements:
- “Open .qmd file” checkbox only visible in file mode
- “Open HTML file” checkbox only visible in file mode
- Document title field hidden in directory mode (no title needed for
books)
- Mode Labels: Updated from “Un fichier” to “Un ou
plusieurs fichiers” (FR) and “Single file” to “One or more files”
(EN)
- Synchronized Loader: Loader now waits for Quarto
rendering to complete before disappearing (checks for index.html
creation)
- Web Application Improvements
(
quartify_app_web()):
- Document title field hidden in batch mode
- Empty title automatically used in batch mode to avoid “My Analysis”
in book chapters
- Removed directory selection option (file upload only for web
deployment)
- Fixed ZIP download to include all generated files with proper
structure:
qmd/ folder contains all .qmd files and
_quarto.yml
html/ folder contains all HTML files with complete
directory structure
- Includes all resources (CSS, JS, fonts, images) for standalone book
viewing
- Force synchronous rendering (
as_job = FALSE) to ensure
all files are generated before download
- Improved File Management:
- Automatic cleanup of existing book files before regeneration
- Temporary backup of
_quarto.yml when rendering
individual files
- Prevents Quarto from detecting book structure during individual file
renders
- Enhanced User Experience:
- Changed loader background from opaque white to semi-transparent dark
overlay
- Better visual feedback during conversion process with synchronized
loader
- Success notifications with [OK] indicators
- Empty document title in directory/batch mode prevents placeholder
text in generated books
- All text without accented characters for better compatibility
Bug Fixes
- Fixed “Book chapter ‘index.qmd’ not found” error during directory
conversion
- Fixed
index.html generation issues in Quarto books
- Resolved conflicts between individual file rendering and book
structure
- Corrected file path detection for HTML output in book projects
- Fixed premature loader dismissal when Quarto renders in
background
- Fixed
index.html missing from ZIP downloads in
quartify_app_web():
- Quarto book rendering now waits for completion before file
collection
- All HTML files including
index.html are now properly
included in downloads
- ZIP structure preserves complete directory hierarchy for functional
offline viewing
- Resolved non-ASCII character warnings in R CMD check
Code Quality
- Removed all non-ASCII characters from source code for CRAN
compliance
- Improved code organization with modular file structure
- Better maintainability with separated Shiny application files
CI/CD
- Docker image build now triggered manually via
workflow_dispatch instead of automatic on push
- Automatic push to DockerHub on main branch pushes
- Reduced unnecessary Docker builds during development
quartify 0.0.6
New Features
- Web Deployment Version
(
quartify_app_web()):
- New web-friendly version designed for deployment on web servers
- Uses file upload/download instead of local file system access
- Deployed on SSP Cloud at https://quartify.lab.sspcloud.fr/
- No R installation required - use directly in your browser
- Upload your R script, configure options, and download generated .qmd
and .html files
- Perfect for sharing quartify with non-R users
- Docker Support:
- Added Dockerfile for containerized deployment
- Based on rocker/r-ver:4.4.1 with Quarto 1.4.549
- Automated CI/CD with GitHub Actions
- Docker images published to Docker Hub:
ddottaagr/quartify
- Includes Helm chart for Kubernetes deployment
- UI Improvements:
- Changed “GO” button to “GENERATE” across all interfaces for
clarity
- Added bilingual support (EN/FR) for web version
- Improved button styling and layout consistency
Bug Fixes
- Fixed Quarto path issues in Docker environment
- Fixed image resource loading (hex logo and language flags) in web
version
- Fixed relative path handling for
quarto_render() to
avoid output path errors
quartify 0.0.5
New Features
- Source Line Numbers:
Added show_source_lines parameter to
rtoqmd() to display original line numbers from source R
script
When enabled, adds a comment at the beginning of each code chunk
indicating the line range
Format: # Lines X-Y (English) or
# Lignes X-Y (French)
Helps maintain traceability between documentation and source
code
Added checkbox in RStudio add-in interface with EN/FR
translations
Example output:
# Lines 19-20
iris |>
count(Species)
Completely automatic - no modification of R scripts
required
Default is TRUE - enabled by default for better
traceability
- Standalone Shiny App (
quartify_app()):
- New exported function
quartify_app() for launching the
conversion interface in any R environment
- Works in Positron, VS Code,
RStudio, terminal, or any IDE that supports R
- Opens in default web browser with full-featured interface
- Same functionality as RStudio add-in but IDE-agnostic
- Perfect for users who don’t use RStudio but want the graphical
interface
- Usage:
library(quartify); quartify_app()
- Optional parameters:
launch.browser = TRUE (default) to open in browser
port = NULL (default) for automatic port selection
quartify 0.0.4
New Features
- Custom HTML Output Path:
- Added
output_html_file parameter to
rtoqmd() to specify custom HTML output location
- Added
output_html_dir parameter to
rtoqmd_dir() to specify directory for batch HTML
outputs
- Added HTML file selector in RStudio add-in interface (optional
field)
- HTML files can now be saved in different location than .qmd
files
- Useful for organizing outputs in separate directories (e.g.,
docs/, html_output/)
- Mermaid Diagram Support:
Added support for Mermaid diagrams to create flowcharts, sequence
diagrams, and other visualizations
Use #| mermaid comment to start a Mermaid chunk in R
scripts
Chunk options (lines starting with #|) are
automatically converted to Quarto format (%%|)
Diagram content follows without # prefix and ends at
empty line or comment
Example syntax:
#| mermaid
#| eval: true
flowchart TD
A[Start] --> B[Process]
B --> C[End]
Converted to proper Quarto Mermaid chunks in .qmd output
- Tabset Support:
Added support for tabsets to organize related content in
interactive tabs
Use # tabset to start a tabset container, then
# tab - Title for each tab
Perfect for displaying alternative views, different analyses, or
grouped visualizations
Tabsets automatically close at RStudio section headers
Example syntax:
# tabset
# tab - Summary Statistics
# Here are the basic summary statistics:
summary(iris)
# tab - Data Structure
# Let's examine the structure:
str(iris)
# tab - First Rows
# Here are the first few rows:
head(iris)
Converted to Quarto {.panel-tabset} format in .qmd
output
See inst/examples/example_tabset.R for complete
examples
Bug Fixes
- Fixed issue where Quarto render command needed to run from .qmd file
directory
- Improved path handling for custom HTML output locations with
relative paths
- Added proper working directory management during Quarto
rendering
quartify 0.0.3
CRAN Preparation
- Removed vignettes from package build (vignettes available online via
pkgdown site)
- Quoted ‘RStudio’ in DESCRIPTION to address CRAN check notes
- Converted non-ASCII characters in R/addins.R to Unicode escapes
(\uxxxx) for portability
- Enhanced online documentation with red-highlighted critical rules
sections for better visibility
- Fixed R version consistency in CI/CD examples (updated to
4.5.1)
quartify 0.0.2
New Features
- Improved RStudio Add-in Interface:
- File browsers for input and output file selection using
shinyFiles
- Language buttons (EN/FR) moved to title bar next to GO button
- Input and output file selectors on the same row for better UX
- Title, Author, and Theme widgets organized on the same line
- Checkboxes organized in 2 columns for better layout
- Automatic language detection based on R session locale
preferences
- Session cleanup: app properly stops when browser window is
closed
- Theme Support:
- Added HTML theme selection (25+ Quarto Bootswatch themes
available)
- Theme parameter in
rtoqmd() and
rtoqmd_dir() functions
- Theme selection in RStudio add-in interface
- Language Support:
- Added
lang parameter to rtoqmd()
function
- Table of contents title adapts to language: “Sommaire” (FR) or
“Table of contents” (EN)
- Add-in automatically detects user’s R session language
- Enhanced Section Title Handling:
- Flexible regex pattern accepts any RStudio section symbol (#, =,
-)
- Trailing symbols properly removed from section titles in output
Improvements
- Updated interface labels:
- “Render Html after conversion” (previously “Render after
conversion”)
- “Open Html output file after rendering” (previously “Open output
file after rendering”)
- “Number sections automatically (not needed if sections already
numbered)” with helpful note
- Removed unsupported format option:
- Format parameter now always uses “html” (PDF removed from add-in
interface)
- Updated all documentation to reflect HTML-only support
Bug Fixes
- Fixed pkgdown configuration:
- Added
aria-label to home icon for accessibility
- Added
rtoqmd_dir to reference index
Documentation
- Updated README (EN/FR) with:
- Automatic language detection feature
- File browser information
- Theme selection examples
- Complete list of available themes
- Enhanced vignettes with:
- Multi-line Description field syntax
- Comment conversion rules
- Chunk splitting technique documentation
- Theme usage examples
quartify 0.0.1
Initial Release
- First public release of quartify package
Features
- Automatic R to Quarto Conversion: Convert R scripts
(.R) to Quarto markdown documents (.qmd) with proper formatting
- RStudio Code Sections Support: Recognizes RStudio
code section syntax (
####, ====,
----) and converts them to hierarchical markdown headers
with correct indentation levels (levels 2, 3, and 4)
- Metadata Extraction: Automatically extracts
metadata from special comments in R scripts:
# Title : or # Titre : for document
title
# Author : or # Auteur : for author
name
# Date : for document date
# Description : for document description
- Metadata found in scripts overrides function parameters
- Bilingual RStudio Add-in: Interactive Shiny
interface with English/French language support for easy conversion
through RStudio’s Addins menu
- Comment Preservation: Regular comments are
converted to explanatory text, while inline comments within code blocks
are preserved
- Markdown Table Support: Proper rendering of
markdown tables in comments when lines are isolated with empty comment
lines
- Customizable Output:
- HTML output format
- Control section numbering
- Enable/disable code folding
- Automatic HTML rendering and opening in browser
- RStudio Snippet: Included snippet for quick
metadata header insertion in R scripts
- Comprehensive Documentation:
- Bilingual vignettes (English/French)
- Detailed README with examples
- Complete function documentation
Technical Details
- Generated Quarto documents include proper YAML headers with table of
contents configuration
- Code chunks are non-executable by default (static documentation
mode)
- HTML output uses
embed-resources: true for
self-contained files
- Roxygen comments (
#') are automatically ignored during
conversion
These binaries (installable software) and packages are in development.
They may not be fully stable and should be used with caution. We make no claims about them.
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