Changelog

Version 0.0.7

Highlights

Refactored source-code structure into six primary submodules at the root level:
IO, Chem, Graph, Rule, Synthesis, and Vis.
Added MØD‐free operation mode: functions requiring MØD now raise clear errors but fall back to pure‐Python implementations where available.

IO Module
^^^^^^^^^

Exposed core I/O utilities directly in synkit.IO:
chemical_converter.py, data_io.py, and debug.py.

Chem Module
^^^^^^^^^^^

Graph Module
^^^^^^^^^^^^

Added SynGraph wrapper for reaction and molecule graphs.
New canonicalisation backends:
- node‐type sort
- Morgan‐prime hashing
- Weisfeiler–Lehman refinement
Renamed “Cluster” to Matcher; enhanced GraphMatcher and SubgraphMatch.
Added SubgraphSearchEngine with three strategies:
- component‐aware
- arbitrary
- backtracking
Introduced SING and TURBOIS for mapping multiple patterns in a single host graph.
Extended GraphCluster and BatchClustering to support both nx and mod backends.
Enhanced WLHash to hash lists of node/edge attributes.
Added MTG submodule for Mechanistic Transition Graphs (direct rule composition).
New Hydrogen submodule for reaction-center H-completion and Context for radius-based expansion.

Rule Module
^^^^^^^^^^^

Introduced SynRule wrapper supporting NetworkX graphs and GML.
Reorganized into three packages:
- Apply (retro-prediction via partial composition)
- Compose (rule composition)
- Modify (rule editing and H-handling)
Provided non‐MØD fallbacks where possible.

Synthesis Module
^^^^^^^^^^^^^^^^

Divided into three submodules:
- Reactor (nx via SynReactor; mod via MODReactor/MODAAM)
- CRN (Chemical Reaction Network builder via MODCRN)
- MSR (multi-step reaction pathfinder)
SynReactor now supports implicit‐H templates.
MODCRN wraps MØD for CRN generation; requires manual re-run for PDF summaries.

Vis Module
^^^^^^^^^^

Visualization tools organized under synkit.Vis:
- RXNVis (reaction visualisation)
- RuleVis (template/rule visualisation)
- GraphVisualizer (generic graph editing & display)

Documentation
^^^^^^^^^^^^^