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

Full Changelog: v1.1.0...v1.1.1

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

Full Changelog: v1.0.0...v1.1.0

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

Full Changelog: v0.0.9...v1.0.0

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

Full Changelog: v0.0.8...v0.0.9

quartify 0.0.8

CRAN Submission Fixes

• 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

Full Changelog: v0.0.7...v0.0.8

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

Full Changelog: v0.0.6...v0.0.7

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

Full Changelog: v0.0.5...v0.0.6

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

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

Full Changelog: v0.0.3...v0.0.4

quartify 0.0.3

CRAN Preparation

• Added VignetteBuilder: knitr to DESCRIPTION
• Added knitr and rmarkdown to Suggests for vignette building
• Quoted 'RStudio' in DESCRIPTION to address CRAN check notes
• Converted non-ASCII characters in R/addins.R to Unicode escapes (\uxxxx) for portability
• Enhanced vignettes with red-highlighted critical rules sections for better visibility
• Fixed R version consistency in CI/CD examples (updated to 4.5.1)