What's Changed
[0.7.0] - 2026-04-13
Added
- Add get_stylable_attributes utility function (styling)
- Read line width and color from CellDesigner XML (celldesigner io)
- Write line width, color, and font size from layout (celldesigner io)
- Read line width and color from CellDesigner XML (celldesigner io)
- Add export subcommand for map export (cli)
- Support tidy flag for CellDesigner maps (cli)
- Add set_arcs_to_orthogonal utility function (celldesigner)
- Added tyding functions (celldesigner)
- Added tidying functions (celldesigner)
- Added experimental writer (celldesigner io)
- Added indentation markers (pretty print)
- Added utils module (celldesigner)
Changed
- Removed defaults for sbgn tidy (cli)
- Set sensible defaults for tidy function parameters (sbgn)
- Clean CellDesigner writer conventions (celldesigner io)
- Clean CellDesigner reader with reading_context API (celldesigner io)
- Clean SBGN reader with reading_context API (sbgn io)
- Now uses reaction node anchor functions (celldesigner io)
- Renamed functions and variables more appropriately for writer (celldesigner io)
- Added _reading prefix for reading modules (celldesigner io)
- Added _reading prefix for reading modules (celldesigner io)
- Added _reading prefix for reading modules (celldesigner io)
Documentation
- Add documentation for export subcommand (cli)
- Improved for map vs map builder (sbgn)
- Simplified the top example (momapy)
Fixed
- Use correct coordinate frame bases in writer inverse transforms (celldesigner io)
- Derive reaction link participants from layout arcs (celldesigner io)
- Derive reaction link participants from layout arcs (celldesigner.io)
- Use correct coordinate frame bases for arc edit point transforms (celldesigner io)
- Correct connector tip fractions to 0.375/0.625 (celldesigner)
- Use target anchor as coordinate frame basis for modifier arcs (celldesigner io)
- Fixed writing gates when input is a subunit (celldesigner io)
- Now has correct metaids for reactants/products/modifiers
- Fixed dedup issues and refactor of deduplication (celldesigner io)
- Fixed dedup issues and refactor of deduplication (sbgn io)
- Added fallback for undocumented anchor points (e.g., 'INACTIVE') (celldesigner io)
- Added missing source and target to modulation layouts (celldesigner io)
- Fix layout-model mapping consistency after dedup (celldesigner io)
- Fix mapping for Boolean gates (celldesigner io)
- Added subunit remap when identical complexes (celldesigner io)
- Fix bug in adding subunits where no replacement was done (celldesigner io)
- Fix setting .base to true for base reactants/products (celldesigner io)
- Fix flattening of reactions and gates (celldesigner io)
- Fixed expansion of reactions and modulations in layout model mapping (celldesigner io)
- Fixed bug when reading with no return type (celldesigner io)
Miscellaneous
- Exclude .venv-sandbox from build (gitignore)
- Add full-word variable naming convention to CLAUDE.md
- Added new layout model mapping philosophy (AGENTS)
- Added poubelle (gitignore)
- Cleaned file (gitignore)
- Formatting with ruff
- Updated reactome analysis (demos)
Testing
- Add layout_model_mapping integrity tests for SBGN and CellDesigner (io)
Installation
pip install momapy==0.7.0
Links
