Release Notes for Version 0.4.0

Summary

Version 0.4.0 includes bug fixes, new features, and enhancements aimed at improving functionality and usability.

New Features

Species Glyph Management:
- Added the ability to associate species glyphs with reactions using their index (suggested by @dalbabur).
- Added functionality to retrieve the index of a species reference in a reaction using the ID of the connected species (suggested by @sanast22 and @mkcook).
- Introduced visibility controls for species glyphs, allowing them to be hidden or shown as needed (suggested by @mkcook).
Reaction Aliasing:
- Implemented a feature to create alias reactions, including alias nodes for reaction centroids and species, as well as alias edges for species references (suggested by @sanast22, @mkcook, and @dalbabur).
Species Aliasing Enhancement:
- Introduced a new function to create alias nodes for specific species within specific reactions (suggested by @sanast22, @mkcook, and @dalbabur).
Curve Segment Locking:
- Introduced a new feature that locks all curve segments of a species reference glyph when the user sets any of the curve segment features (suggested by @luciansmith).
Error Logging Improvements:
- Added getErrorLog and clearErrorLog functions for improved error tracking and management (suggested by @luciansmith).
- Errors are no longer printed directly; instead, they are now logged, allowing users to review and manage them more effectively (suggested by @luciansmith).
Dynamic Autolayout Adjustments:
- Autolayout parameters (gravity and stiffness) are now dynamically adjustable to meet desired layout dimensions (reported by @luciansmith).
- User-defined compartment extents are retained during autolayout operations, with optional resetting (reported by @luciansmith).
Documentation Updates:
- Newly added API functions have been documented for better user guidance.

Bug Fixes

Resolved several minor bugs related to:
- Storing user data correctly.
- Setting stroke and fill colors for graphical objects.
- Handling the stroke color to differentiate between font and border colors (reported by @luciansmith).
- Line color/width settings for reactions and species references (Reported by @luciansmith and @hsauro).
- Fixed issues with the interpretation of SBML Layout specifications, particularly concerning the misinterpretation of the order of the start and end points of the curve segments in species roles (reported by @luciansmith).
- Addressed issues with setting hex color codes for visual elements (reported by @mkcook).

Other Improvements

Header files are now organized in the /include/sbmlnetwork directory for cleaner integration in third-party projects.
The getText function implementation has been optimized by moving it from the C layer to the C++ layer, enhancing performance and maintainability (reported by @luciansmith).

Deprecations

Functions and parameters related to SpeciesReferenceGlyph have been replaced by SpeciesReference. Both are now treated as equivalent in functionality.