Skip to content
Permalink

Comparing changes

Choose two branches to see what’s changed or to start a new pull request. If you need to, you can also or learn more about diff comparisons.

Open a pull request

Create a new pull request by comparing changes across two branches. If you need to, you can also . Learn more about diff comparisons here.
base repository: HenriquesLab/rxiv-maker
Failed to load repositories. Confirm that selected base ref is valid, then try again.
Loading
base: main
Choose a base ref
...
head repository: HenriquesLab/rxiv-maker
Failed to load repositories. Confirm that selected head ref is valid, then try again.
Loading
compare: feat/underlined-text-formatting
Choose a head ref
Checking mergeability… Don’t worry, you can still create the pull request.
  • 4 commits
  • 18 files changed
  • 1 contributor

Commits on Sep 26, 2025

  1. feat: implement underlined text formatting support 

    Add native markdown syntax for underlined text that converts to LaTeX \underline{} commands.

## Features Added
- `__text__` markdown syntax converts to `\underline{text}` LaTeX commands
- Smart environment protection: works in regular text and lists, protected in code blocks and math environments
- Comprehensive integration with existing text formatting pipeline
- Full compatibility with bold, italic, subscript, and superscript formatting

## Implementation Details
- Added `protect_underline_outside_texttt()` function with selective LaTeX environment protection
- Enhanced `_process_text_formatting()` pipeline to include underline processing
- Improved environment protection to allow formatting in lists while protecting code/math environments

## Testing
- Added 14 comprehensive unit tests covering all use cases and edge cases
- Verified integration with full markdown-to-LaTeX conversion pipeline
- Confirmed compatibility with existing text formatting features
- Updated EXAMPLE_MANUSCRIPT documentation and demonstration

## Documentation Updates
- Added underline formatting to syntax reference table in EXAMPLE_MANUSCRIPT
- Included practical demonstration in main manuscript text
- Updated formatting capabilities description

Closes: Support for underlined text formatting in markdown
    @paxcalpt
    paxcalpt committed Sep 26, 2025
    Configuration menu
    Copy the full SHA
    f272002 View commit details
    Browse the repository at this point in the history

  2. feat: implement underlined text formatting with comprehensive improve… 

    …ments and test fixes

This commit implements underlined text formatting using `__text__` markdown syntax that converts to LaTeX `\underline{text}` commands, along with comprehensive performance optimizations, code refactoring, and test suite fixes.

## Core Implementation

### Underlined Text Feature
- Added `__text__` markdown syntax support converting to LaTeX `\underline{text}`
- Implemented selective LaTeX environment protection (protects math/code/tables, allows formatting in lists)
- Added comprehensive unit tests covering all edge cases and formatting combinations

### Performance Optimizations
- Implemented pre-compiled regex patterns at module level for all text formatting operations
- Added performance benchmarking tests to validate optimization effectiveness
- Optimized pattern matching for better compilation speed

### Code Architecture Improvements
- Created generic `_apply_formatting_outside_protected_environments()` function
- Eliminated code duplication across protection functions
- Fixed regex backreference bug in environment protection pattern
- Refactored text formatting pipeline for better maintainability

## Test Suite Fixes

### E2E Test Updates
- Fixed deprecated `engine="local"` parameter usage in BuildManager/FigureGenerator calls
- Updated figure path expectations from `Figures/` to `../FIGURES/` format
- Replaced deprecated `copy_figures()` method calls with current workflow methods
- Updated LaTeX output expectations (`\FloatBarrier` instead of `\clearpage`)
- Fixed Guillaume issue tests for current implementation behavior

### Comprehensive Test Coverage
- Added 19+ new unit tests for underlined formatting with edge cases
- Updated integration tests to match current system architecture
- All E2E tests now pass (21 passed, 2 skipped)

## Documentation Updates
- Enhanced EXAMPLE_MANUSCRIPT with comprehensive formatting interaction examples
- Updated syntax reference table with underlined text and nested formatting examples

## Impact

### Performance
- Significant improvement in text formatting compilation speed through pre-compiled regex
- Reduced redundant pattern compilation during document processing

### Code Quality
- Eliminated code duplication through generic helper functions
- Improved maintainability with cleaner architecture
- Enhanced test coverage with comprehensive edge case validation

### User Experience
- New underlined text formatting capability with `__text__` syntax
- Seamless integration with existing formatting (bold, italic, subscript, superscript)
- Full support for nested formatting combinations

## Validation
- All existing functionality preserved (no breaking changes)
- Comprehensive test suite passes
- Performance benchmarks validate optimization effectiveness
    @paxcalpt
    paxcalpt committed Sep 26, 2025
    Configuration menu
    Copy the full SHA
    e9e4d68 View commit details
    Browse the repository at this point in the history

  3. chore: bump version to 1.7.8 

    - Updated version to 1.7.8 in __version__.py
- Added comprehensive changelog entry for v1.7.8 including:
  - Underlined text formatting feature
  - Performance optimizations with pre-compiled regex
  - Code quality improvements and architecture refactoring
  - E2E test suite overhaul and fixes
  - Enhanced documentation and examples
    @paxcalpt
    paxcalpt committed Sep 26, 2025
    Configuration menu
    Copy the full SHA
    b97ba45 View commit details
    Browse the repository at this point in the history

  4. fix: resolve workflow failures and documentation issues 

    - Fix release workflow to handle deprecated repository triggers gracefully
- Remove references to removed homebrew/apt repositories from config
- Fix broken documentation links in API documentation
- Fix malformed link syntax in EXAMPLE_MANUSCRIPT
    @paxcalpt
    paxcalpt committed Sep 26, 2025
    Configuration menu
    Copy the full SHA
    41e20d1 View commit details
    Browse the repository at this point in the history
Loading