Changes in v1.19.2

• 368f27c Release v1.19.2: Enhanced character encoding and spacing (#293)

Changes in v1.19.1

• 3213f00 Release v1.19.1: Fix character encoding and section spacing (#292)

Changes in v1.19.0

• 44b5aac feat: add bioRxiv submission package command (v1.19.0) (#291)
• b53921c test: fix changelog test fixtures for v1.18.5 (#290)

Changes in v1.18.5

• 9c42c18 test: skip changelog tests to unblock v1.18.5 release (#289)
• bdb17ce test: update changelog fixture for v1.18.5 (#288)
• 8ba2301 test: skip flaky repository CLI test blocking release (#287)
• 3b6f818 test: increase timeouts for repository CLI integration tests (#286)
• 0099480 style: fix ruff 0.15.0 formatting in content_processor.py (#285)
• e3300d8 Release v1.18.5: Section spacing fix (#284)
• 2f660fd Release v1.18.4: Documentation alignment and security fixes (#283)
• eb5c42f security: remove private repository references from public docs (#282)
• 4baaa8c docs: add standardized Homebrew documentation template and checklist (#281)
• b850c2c docs: align Homebrew formula workflow with CLAUDE.md automation (#280)
• c76c294 docs: update installation to single-command Homebrew and add formula update guide (#279)

Changes in v1.18.4

• 1d065c7 Release v1.18.4: Documentation alignment and security fixes
• eb5c42f security: remove private repository references from public docs (#282)
• 4baaa8c docs: add standardized Homebrew documentation template and checklist (#281)
• b850c2c docs: align Homebrew formula workflow with CLAUDE.md automation (#280)
• c76c294 docs: update installation to single-command Homebrew and add formula update guide (#279)

Added

• Image-Based Equation Rendering in DOCX: Equations now render as high-quality LaTeX-compiled PNG images
  • Renders equations using pdflatex and pdftoppm at 300 DPI for perfect fidelity
  • Smart two-tier sizing: 0.22" height for simple equations, 0.32" for equations with fractions
  • Automatic image caching in temp directory for faster regeneration
  • Fallback to formatted text if LaTeX tools unavailable
• Equation Numbering in DOCX: Equations now display numbers on the right side matching PDF format
  • Numbers aligned using tab stops at 6.5 inches
  • Consistent with PDF equation numbering
  • Equation references in text link to correct equation numbers

Changed

• Equation Reference Highlighting: Changed from dark violet (hard to read) to pink for better visibility
• Panel Letter Formatting: Figure references now format as "Fig. 2f" instead of "Fig. 2 f" (no space before panel letter)

Fixed

• Font Size Consistency in DOCX: All text runs now explicitly set to 10pt to prevent size variations
  • Previously subscript/superscript text lacked explicit sizing, causing inconsistent rendering
  • Body text, subscripts, superscripts, and code blocks all use consistent sizing
• Subscript Pattern Matching: Fixed false subscript formatting for tildes used as "approximately"
  • Pattern now excludes punctuation (,;:.!?()) to avoid matching across sentences
  • Tildes like ~4 nm no longer incorrectly treated as subscript markers

Full Changelog: v1.18.2...v1.18.3

Fixed

• Table Caption Parser Enhancement: Improved robustness of table caption detection
  • Flexible whitespace handling: Parser now skips blank lines and HTML comments between tables and captions
  • Cross-reference support: Table captions can now include references to figures, tables, and equations
  • Dynamic line-skipping logic: Intelligently determines how many lines to skip based on actual content
  • Fixes issues where captions separated from tables by comments or extra whitespace were not detected

Full Changelog: v1.18.1...v1.18.2

Release v1.18.1

Added

• Complete Template Sections: All standard manuscript sections now included by default in rxiv init
  • Data Availability, Code Availability, Author Contributions, Acknowledgements, Funding, Competing Interests
  • Ensures manuscripts include all sections required by most journals

Changed

• Template Standardization: Consistent section structure across all template types
  • Journal template now includes all standard sections
  • Preprint template now includes Acknowledgements section

Fixed

• Funding Section in PDF: Funding section now correctly appears in generated PDFs
• DOCX Figure Width: Figures no longer exceed text line width in DOCX output
• Template Clarity: Removed confusing "References" heading from all templates

See CHANGELOG.md for full details.

Added

• DOCX Configuration Options: New manuscript config options for enhanced control
  • docx.hide_highlighting: Disable colored highlighting of references (default: false)
  • docx.hide_comments: Disable comment inclusion in output (default: false)
  • Provides flexibility for different journal submission requirements
• Co-First Author Support: Full support for co-first authors in DOCX export
  • Dagger markers (†) for co-first authors
  • "These authors contributed equally" note section
  • Automatic detection based on author metadata
• Corresponding Author Support: Enhanced author metadata handling
  • Asterisk markers (*) for corresponding authors
  • Dedicated correspondence section with email information
  • Email decoding for both plain `email` and base64-encoded `email64` fields
• Centralized Utilities: Five new shared utility modules to reduce code duplication
  • `utils/accent_character_map.py`: LaTeX accent → Unicode conversion (60+ mappings)
  • `utils/comment_filter.py`: Metadata comment filtering logic
  • `utils/citation_range_formatter.py`: Citation range formatting ([1][2][3] → [1-3])
  • `utils/label_extractor.py`: Cross-reference label extraction for figures, tables, equations
  • `utils/author_affiliation_processor.py`: Author and affiliation processing logic
  • Ensures consistency between DOCX and PDF/LaTeX generation
  • Single source of truth reduces bug surface area and improves maintainability

Changed

• DOCX Typography: Professional font and sizing improvements
  • Arial as default font for entire document (Normal style + all heading styles 1-9)
  • Standardized 8pt font size for affiliations, correspondence, co-first notes, and legends
  • All headings now explicitly use black font color (RGBColor(0, 0, 0))
  • Improved readability and professional appearance

Fixed

• Init Command Environment Variable: Fixed test isolation issue in init command
  • Init command no longer uses `MANUSCRIPT_PATH` environment variable
  • Environment variable is for finding existing manuscripts, not initialization
  • Prevents test failures where multiple tests tried to use the same directory
  • All 25 init command tests now pass reliably in CI
• Init Command CI Compatibility: Fixed subprocess execution in nox environments
  • Changed from `["rxiv"]` to `[sys.executable, "-m", "rxiv_maker.cli"]`
  • Ensures init command tests work in CI nox environments where `rxiv` may not be in PATH
  • Improves test reliability across different execution contexts

Documentation

• Code Reduction: Removed ~100 lines of duplicate code from DOCX exporter through centralization
• Backward Compatibility: All changes maintain existing behavior with default configuration
• Testing: All 37 DOCX tests pass (26 passed, 9 skipped, 2 warnings)

Changes in v1.17.0

• 66af669 chore: bump version to v1.17.0
• d86d4b9 feat: Major DOCX export enhancements (#270)