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.

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

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.

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.

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.

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