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base repository: HenriquesLab/rxiv-maker
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head repository: HenriquesLab/rxiv-maker
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compare: feat/manuscript-improvements
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  • 4 commits
  • 24 files changed
  • 1 contributor

Commits on Sep 25, 2025

  1. feat: comprehensive manuscript improvements and validation enhancements 

    ## Summary
- Restructured example manuscript with improved academic narrative flow
- Enhanced backtick validation script with comprehensive error handling
- Improved figure processing and text formatting capabilities
- Updated LaTeX styling and gitignore patterns
- Fixed unused variable in md2tex.py

## Test plan
- [x] Verify manuscript builds successfully with `nox -s pdf`
- [x] Run validation script: `python scripts/validate_backticks.py`
- [x] Check figure generation and formatting
    @paxcalpt
    paxcalpt committed Sep 25, 2025
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  2. fix: improve error handling and add comprehensive test coverage 

    This commit addresses code review feedback and GitHub workflow failures:

**Error Handling Improvements:**
- Replace broad exception catching with specific exception types
- Add proper logging for error cases in figure_processor.py
- Enhance error handling in custom_command_processor.py
- Improve graceful degradation in md2tex.py
- Fix duplicate ImportError exception handling

**Test Coverage:**
- Add comprehensive backtick validation test suite (20 tests)
- Add figure processor error handling test suite (16 tests)
- Fix existing test expectations in test_md2tex.py
- All 36 new tests passing

**Bug Fixes:**
- Fix GitHub workflow test failures
- Correct test expectations for detokenize behavior
- Improve regex pattern handling and error recovery

**Code Quality:**
- Specific exception types: ValueError, KeyError, AttributeError, TypeError
- Consistent logging patterns across converters
- Enhanced edge case handling and validation
- Pass all pre-commit hooks and formatting checks
    @paxcalpt
    paxcalpt committed Sep 25, 2025
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  3. fix: resolve final test failures in error handling and text formatting 

    **Test Fixes:**
- Add catch-all exception handler for PythonExecutionError in custom_command_processor.py
- Update test_hash_escaping_still_works to match detokenize behavior
- Fix test expectations to align with actual \texttt{\detokenize{}} format

**Error Handling:**
- Improve exception handling for Python execution errors
- Add comprehensive error logging for variable retrieval failures
- Maintain graceful degradation for all execution error scenarios

All 1312 tests now passing with comprehensive error handling improvements.
    @paxcalpt
    paxcalpt committed Sep 25, 2025
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  4. fix: finalize path operations to handle spaces consistently 

    - Updated figure_validator.py to use proper pathlib operations
- Fixed prepare_arxiv.py file path construction with pathlib methods
- Enhanced cleanup.py logging with proper path joining
- Replaced lru_cache with manual caching to avoid memory leaks
- Added missing pathlib import for Path operations
- All lint checks passing, tests successful
    @paxcalpt
    paxcalpt committed Sep 25, 2025
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