Prepare release v.0.5.0

What's New

Explore the latest improvements to the SynEdu documentation, talktorials,
and release infrastructure.

---

Version 0.5.0

Current development release

Version 0.5.0 strengthens the mathematical and chemical foundations of all
nine talktorials, introduces portable notebook workflows, and modernizes the
MyST website, continuous-integration pipeline, and release process.

✨ Highlights

🔬 Chemically correct graph operations

Subgraph matching now clearly distinguishes monomorphisms from
induced isomorphisms. Symmetry reduction uses complete graph
automorphisms, while formal charge, aromaticity, bond order, valence, and
hydrogen information are preserved consistently throughout graph operations.

🧭 Atom-map canonicalization

The canonicalization lesson now connects molecular parsing,
Weisfeiler--Lehman refinement, individualization--refinement search, canonical
atom ranking, and serialization in one coherent and notation-consistent
workflow.

🧪 Reliable reaction galleries

Forward and backward reaction predictions now use the same graph-native
rendering pipeline. Responsive SVG figures keep complete reactions visible and
clearly distinguish the reference reaction, matching predictions, and
alternative candidates.

📓 Portable talktorials

All nine lessons now provide deterministic notebook exports with working
Colab, Binder, direct-download, and local-execution links. Each export
is tested both inside the repository and as a standalone downloaded notebook.

🧮 Mathematical and chemical correctness

• Explicit graph semantics: Molecular graph matching now uses clearly
  defined node and edge attributes for elements, formal charges, aromaticity,
  and bond order.

• Complete symmetry handling: Orbit-based match deduplication has been
  replaced by full automorphism handling, preventing incorrect equivalence
  classes in symmetric molecular graphs.

• Chemically valid wildcard completion: Wildcard atoms are completed using
  the smallest chemically allowed open valence, including appropriate handling
  of charged and aromatic atoms. Unsupported bond orders are rejected
  explicitly.

• Safe hydrogen conversion: Explicit-to-implicit hydrogen conversion now
  preserves hydrogens that cannot be absorbed without changing the molecular
  representation.

• Consistent MCS behavior: Maximum-common-substructure helpers validate
  their inputs, retain compatibility with historical positional arguments, and
  maximize the matched atom count by default to remain consistent with the
  lesson metrics.

• Charge-aware reaction balancing: Reaction-balance validation now checks
  both elemental composition and net formal charge. Auxiliary-species
  imputation follows the direction of the detected atom imbalance.

• Unified notation and references: Definitions, symbols, equations, and
  citations have been aligned across the talktorials. Journal references and
  DOI metadata have also been updated where available.

🎓 Learning experience

• Unified visual design: The homepage, lesson cards, learning-path
  indicators, navigation, footer, dark mode, quizzes, solutions, and discussion
  sections now follow a shared visual system.

• Improved sticky navigation: After scrolling, the header displays the
  current page title and truncates long lesson names without overlapping the
  navigation controls.

• Reproducible scientific figures: The atom-map canonicalization figure is
  maintained as LaTeX/TikZ source and published as an accessible SVG.

• Expanded learning resources: The external-learning collection now
  includes TeachOpenCADD and an introductory course on artificial
  intelligence in pharmaceutical research.

⚙️ Build and release reliability

• Broader automated testing: Fast tests now cover graph semantics, MCS
  behavior, reaction balancing, visualization output, portable notebook links,
  and publication of website assets.

• Stricter documentation CI: Continuous integration propagates failures
  through logged pipelines, executes the documentation notebooks, verifies
  asset-injection idempotency, and publishes portable notebook artifacts.

• Consistent Read the Docs builds: Hosted documentation uses
  deployment-prefix-safe links and applies the same static enhancements as
  local and continuous-integration builds.

• Hardened release workflow: Release jobs install Python 3.11 explicitly,
  validate the Git tag against the project version, inspect wheel and source
  distributions with Twine, generate checksums, and attest the published
  release artifacts.

---

Prepare release v.0.2.0

v0.2.0

enhance UI

Prepare release 0.1.0

First release