v1.6.0

Added

• Tree.run() runs the search to completion and returns the tree, replacing the
  list(tree) idiom. Iterating a Tree still yields the per-iteration
  (is_solved, node_ids) for progress display or early stopping.

• An agent skill at skills/synplanner-usage/, in the
  Agent Skills open format, giving AI coding assistants
  the chython-versus-RDKit boundary, the API entry points and the recommended
  defaults. It ships with a task index mapping around thirty tasks to the calls
  each one needs; both are published in the documentation and indexed by
  llms.txt.

• "Running a search" on the MCTS page and "Two ways to map" on the
  standardization page, the latter covering when reaction mapping needs a GPU.

• Added synplan.chem.reaction.routes as the public route post-processing layer for route
  clustering, route quality, RouteCGR utilities, route I/O, analysis, depiction,
  and notebook plotting.

• Added typed RouteCGR and route-export contracts, including
  RouteCGRBuildResult, RouteExportResult, route diagnostics, and strict
  export failure handling while preserving the existing JSON and CSV shapes.

• Added synplan.chem.reaction.routes.representation to group RouteCGR builder, container,
  depiction, state, hashing, and native deconvolution helpers.

• Added route-aware RouteCGR composition with route_order metadata on dynamic
  atoms and bonds, transient bonds for bonds formed and later removed during a
  synthetic route, and compact per-step labels for reconstructing mapped route
  reactions from the RouteCGR itself.

• Added exact RouteCGR hashing in synplan.chem.reaction.routes.representation.hash, including a
  fast WL bucket hash followed by exact canonical confirmation for shared
  buckets.

• Added RouteCGR comparison helpers for identifying overlapping and unique route
  IDs across route dictionaries whose route IDs do not need to match.

• Added RouteCGR analysis helpers for selected building-block lookup and real
  versus supporting pseudo-reactant usage statistics.

• Added native RouteCGR deconvolution APIs (routes_dict_from_route_cgrs() and
  reactions_from_route_cgr()).

• Added synplan.chem.reaction.routes.clustering as a package, with clustering logic in
  synplan.chem.reaction.routes.clustering.core and route marker helpers in
  synplan.chem.reaction.routes.leaving_groups.

• Added synplan.chem.reaction.rules and synplan.chem.reaction.rules.representation
  as the public homes for rule analysis, extraction, priority rules, and Chython
  QueryCGR/Morgan rule representations.

• Added MHN ranking policy support (architecture: mhn_ranking) with QueryCGR
  rule fingerprints by default, optional QueryCGR rule-graph encoding with GPS,
  bounded runtime rule-association caches, dynamic runtime rule-set scoring, and
  checkpoint migration for the redesigned policy networks.

• Added synplan mhn_network_tuning for fine-tuning an already trained MHN
  ranking checkpoint on new rule policy data.

• Added policy/network modules for pure policy wrappers, graph embedders,
  checkpoint loading, featurization caches, and Lightning-based supervised
  training utilities.

• Added MHN ranking configuration, policy documentation, CLI documentation, and
  Tutorial 14 for MHN training/tuning workflows.

• Added strict Chython-to-RDKit SMARTS conversion with reverse diagnostics and
  semantic-loss reporting for strict round-trip validation.

• Added the mhnreact_rdkit rule-fingerprint mode for MHN ranking, using the
  original RDKit path-fingerprint template encoding.

• Added Tree.save_pickle(path) for direct tree persistence and the
  synplan-convert-protection-data command for protection source-data conversion.

• Added API documentation for synplan.chem.reaction.routes.

Changed

• Pinned chython-synplan to 1.101, which closes the interpreter-exit hang: any
  process importing chython previously finished its work and never exited.

• Raised CVE floors for eleven transitive dependencies (GitPython,
  jupyter-server, jupyterlab, pillow, mistune, aiohttp, bleach, idna, pyasn1,
  python-multipart, soupsieve) and relocked with a seven-day cooldown on newly
  published releases.

• Reorganised the maintainer documentation under docs/development/, splitting
  local setup, pull-request review and the release checklist, which now lists
  the gates CI enforces.

• Requires chython-synplan 1.100, pinned exactly. Its SMARTS parser now reads
  92% of real-world patterns instead of 57%, and three primitives follow
  Daylight rather than chython's own reading: an unmarked charge is
  unconstrained, A is any aliphatic atom where * is any atom, and x is
  ring connectivity where the heteroatom count it used to mean is now y.
  Rules written against the old meanings of A and x need updating.

• Supports Python 3.14, which chython 1.100 is the first release to ship wheels
  for. Python 3.15 is out of reach until torch, rdkit, numpy and chytorch
  publish cp315 wheels.

• Verifies chython ring-connectivity queries against RDKit's AtomRingBondCount
  during rule conversion instead of passing them through unchecked; only
  rings_count and heteroatom queries stay unverifiable.

• Dropped the exclude-newer resolution cutoff; the exact chython-synplan pin
  is what holds the lock steady now.

• Moved route clustering, route analysis, route depiction, route I/O, notebook
  plotting, route-quality scoring, and RouteCGR implementation to
  synplan.chem.reaction.routes.

• Moved reaction-rule analysis, extraction, priority-rule parsing, and rule
  representation helpers under synplan.chem.reaction.rules.

• Moved MCTS expansion wrappers into synplan.mcts.policy, separating generic
  policy selection from MHN-specific dynamic rule-association preparation.

• Split ML graph embedders, policy networks, checkpoint loading, featurization,
  and training helpers into focused submodules under synplan.ml.

• Updated internal imports, tests, tutorials, Colab notebooks, API docs, and
  migration notes to use the new route, rule, policy, and ML module layout.

• Centralized route parent-chain traversal for tree, visualisation, and RDKit
  route conversion while preserving their existing output formats.

• compose_route_cgr() now uses a fast default path that returns the RouteCGR
  without eagerly reconstructing reactions; callers that need the debug
  reactions_dict can request it explicitly or deconvolute from the RouteCGR.

• RouteCGR composition now assumes route-level atom mapping: the same atom-map
  number must identify the same atom throughout a route, while independently
  mapped local reaction steps are outside the supported input contract.

• MHN light prediction keeps the rollout-friendly integer rule-count API; dynamic
  MHN rule associations are prepared by the full predict_reaction_rules() path.

Fixed

• Removed the force-exit hook from tests/conftest.py. It worked around the
  chython exit hang and is unnecessary with 1.101; pytest now gets its normal
  teardown instead of being terminated before it can flush.

• Four shipped configuration files could not be loaded at all, because every
  config model forbids unknown keys and nothing checked that the files parse:
  the two combined-policy configs carried priority_rules_fraction, which
  belongs to a different model, mhn_ranking_policy_training.yaml used
  rule_encoder_type where the field is rule_embedding_type, and
  planning_value.yaml was unreachable because the planning CLI merged the
  node_evaluation section into the tree config. Loading every shipped config
  is now a test.

• Protecting-group selection cannot protect aldehydes, ketones, alpha-halo
  ketones or phthalimide-protected amines. Nine of the twenty-five published
  templates attach at two points, which acetals and dithianes need because they
  replace the carbonyl double bond rather than substituting onto it, and the
  product builder adds a single bond and deletes nothing. Eighteen reactive
  functions allow only those templates, so they have no protection option at
  all. The table is unchanged and the loader now says this once at startup
  rather than failing quietly at each call.

• The functional-group patterns in extraction_functional_groups.yaml used A
  to mean any atom, which chython 1.100 reads as any aliphatic atom, so they
  silently stopped matching aromatic neighbours such as benzaldehyde and
  styrene. They now use *.

• Route JSON export now recovers precursor nodes whose producing fragment is
  structurally identical to the consuming reactant even when atom-number overlap
  with the final target is absent, and drops malformed routes instead of emitting
  JSON null children.

• QueryCGR rule fingerprints and QueryCGR rule graphs preserve important query
  constraints, including degree, hydrogen-count, ring-size, set-valued atom
  labels, and dynamic bond semantics.

• Runtime MHN rule-association caches are bounded and keyed by the ordered rule
  SMARTS plus the rule representation contract.

Removed

• Removed deprecated route compatibility namespaces: synplan.routes,
  synplan.routes.quality, and synplan.route_quality.
• Retained synplan.chem.reaction_routes as a deprecated forwarding namespace
  for the historical main-branch route module paths.
• Removed TreeWrapper; use Tree.save_pickle(path) instead.
• Removed the old flat synplan.mcts.expansion and synplan.ml.networks.policy
  modules in favor of the new policy/network package layout.