chemicalml 0.2.0 → 0.3.0

data/TODO.align/77-convention-coverage-matrix.md

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+# 77 — Convention coverage matrix spec
+
+## Why
+
+The gem registers 8 conventions, each with multiple constraints.
+Currently each convention has its own spec file, but there is no
+single source of truth asserting that every convention:
+
+- is in the Registry
+- is detectable via at least one root role
+- has at least one violation case for at least one of its constraints
+- has at least one passing-case example
+
+A matrix spec catches gaps when adding a new convention (the new
+convention's matrix entry fails until it has specs).
+
+## Work
+
+Add `spec/chemicalml/convention/coverage_matrix_spec.rb` that:
+
+1. Iterates `Convention::Registry.builtin_qnames`.
+2. For each, asserts the convention is detectable from its declared
+   root role.
+3. For each constraint class registered against the convention,
+   asserts a spec file exists that exercises it (grep for the class
+   name in `spec/`).
+
+## Acceptance
+
+- Matrix spec passes for all 8 conventions.
+- Adding a 9th convention without specs makes the matrix spec fail.

data/TODO.align/78-fixture-audit.md

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+# 78 — Fixture coverage audit
+
+## Why
+
+`spec/fixtures/` holds CML examples. Current round-trip specs cover a
+subset. After recent additions (parallel-array attrs, CommonChildren,
+8 conventions), some features may have no fixture exercising them.
+
+## Work
+
+Audit `spec/fixtures/`:
+
+1. Identify fixtures that exercise parallel-array atomArray/bondArray.
+2. Identify fixtures covering each convention.
+3. Identify fixtures using new child elements (reaction.mechanism,
+   reactiveCentre.atomSet, etc.).
+4. For features with no fixture, add one under `spec/fixtures/`.
+
+## Acceptance
+
+- Every convention has at least one fixture.
+- Parallel-array form has at least one fixture.
+- Schema24-only legacy elements have at least one fixture.

data/TODO.align/79-final-verification-round19.md

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+# 79 — Final verification round 19
+
+## Work
+
+1. Full rspec — must be green (or pending for documented limitations).
+2. rubocop on touched files.
+3. Forbidden-pattern scan.
+4. Update CLAUDE.md noting key_value support and JSON wire names.
+5. Write `TODO.align/README.round19.md`.
+
+## Acceptance
+
+- All four scans clean.
+- CLAUDE.md current.
+- README.round19.md exists.

data/TODO.align/80-xsd-enum-constants.md

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+# 80 — XSD enum constants
+
+## Why
+
+The XSD declares ~30 simpleTypes that restrict to enumeration sets
+(orderType, stereoType, chiralityType, latticeType, matrixType,
+stateType, peakMultiplicityType, etc.). We model every attribute as
+`:string` and accept any value.
+
+Without a single source of truth for the allowed values, downstream
+callers that want to validate CML have to scrape the XSD themselves
+or hard-code the enums (which drift from the schema).
+
+## Solution
+
+`Chemicalml::Cml::Enums` — frozen-set constants for each XSD enum
+simpleType. The constants are the canonical Ruby source of truth
+for "what values does this attribute accept".
+
+## Work
+
+1. Create `lib/chemicalml/cml/enums.rb` with one constant per XSD
+   enum simpleType. Names match the XSD type name with `Type`
+   suffix stripped (e.g. `ORDER_VALUES` for `orderType`).
+2. Each constant is a frozen Set of allowed string values.
+3. Add specs asserting the constants match the XSD exactly.
+
+## Acceptance
+
+- `Chemicalml::Cml::Enums::ORDER_VALUES` includes `"S"`, `"D"`, `"T"`,
+  `"A"`, etc.
+- `Chemicalml::Cml::Enums::STEREO_VALUES` includes `"C"`, `"T"`, `"W"`,
+  `"H"`.
+- Constants are frozen.
+- Generated from the XSD (no hand-maintenance).

data/TODO.align/81-enum-validation-constraints.md

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+# 81 — Enum validation constraints
+
+## Why
+
+With enum constants defined (TODO 80), add warning-severity
+constraints that flag attribute values outside the XSD-declared
+enum set. Warning (not error) because CML allows extension values.
+
+## Work
+
+Add constraints under the molecular convention (where most enum
+attributes live):
+
+1. `BondOrderShouldBeInEnum` (applies_to Role::Bond) — warning if
+   `bond.order` not in `Cml::Enums::ORDER_VALUES`.
+2. `BondStereoShouldBeInEnum` (applies_to Role::BondStereo) —
+   warning if `bondStereo.value` not in `Cml::Enums::STEREO_VALUES`.
+3. `MoleculeChiralityShouldBeInEnum` (applies_to Role::Molecule) —
+   warning if `molecule.chirality` not in `Cml::Enums::CHIRALITY_VALUES`.
+4. `LatticeTypeShouldBeInEnum` (applies_to Role::Lattice) —
+   warning if not in `LATTICE_VALUES`.
+
+Each constraint is registered against the molecular convention.
+
+## Acceptance
+
+- A bond with `order="X"` triggers a warning.
+- A bond with `order="S"` passes silently.
+- All existing specs pass.

data/TODO.align/82-reference-resolver.md

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+# 82 — Reference resolver
+
+## Why
+
+CML documents reference atoms/bonds/molecules by id via attributes
+like `atomRefs2`, `atomRefs4`, `bondRefs`, `moleculeRefs`, `ref`.
+Currently callers must walk the document themselves to resolve
+these to actual instances.
+
+## Solution
+
+`Chemicalml::Cml::ReferenceResolver` — walks a document, builds an
+id → node index, then exposes lookup methods.
+
+## Work
+
+1. Create `lib/chemicalml/cml/reference_resolver.rb`.
+2. API:
+   ```ruby
+   resolver = Chemicalml::Cml::ReferenceResolver.new(document)
+   resolver.find_atom(molecule, "a1")     # → Atom or nil
+   resolver.resolve_atom_refs2(bond)      # → [Atom, Atom] or nils
+   resolver.unresolved_refs(document)     # → [{ source: Bond, attr: :atom_refs2, missing: ["a99"] }]
+   ```
+3. Add a constraint `ReferencesShouldResolve` (warning severity)
+   that lists unresolved refs in a document.
+4. Specs covering resolve + unresolved detection.
+
+## Acceptance
+
+- Resolver resolves a valid atomRefs2 to actual atoms.
+- `unresolved_refs` returns missing atom ids.
+- All existing specs pass.

data/TODO.align/83-toml-roundtrip.md

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+# 83 — TOML round-trip spec
+
+## Why
+
+lutaml-model supports TOML as a key-value format. CLAUDE.md claims
+format-agnosticism — XML/JSON/YAML are tested. Add TOML to complete
+the set.
+
+## Work
+
+Add `spec/chemicalml/cml/toml_roundtrip_spec.rb` that round-trips
+a Molecule through `to_toml` / `from_toml`. TOML's flat key/value
+structure means nested objects get flattened — verify the same
+data survives.
+
+## Acceptance
+
+- `Molecule#to_toml` produces a TOML string.
+- `Molecule.from_toml(toml)` returns a Molecule with the same id
+  and atom data.

data/TODO.align/84-final-verification-round21.md

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+# 84 — Final verification round 21
+
+## Work
+
+1. Full rspec — must be green.
+2. rubocop on touched files.
+3. Forbidden-pattern scan.
+4. Update CLAUDE.md noting enum validation, reference resolver,
+   TOML round-trip.
+5. Write `TODO.align/README.round21.md`.
+
+## Acceptance
+
+- All scans clean.
+- CLAUDE.md current.
+- README.round21.md exists.

data/TODO.align/85-bond-distinct-atoms.md

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+# 85 — Bond atomRefs2 distinct constraint
+
+## Why
+
+The molecular spec at `reference-docs/conventions/molecular.md` says:
+
+> `atomRefs2` — REQUIRED, two distinct atom ids in same molecule
+
+No current constraint enforces distinctness. A `<bond atomRefs2="a1 a1"/>`
+(zero-length self-bond) is silently accepted.
+
+## Work
+
+Add `Molecular::Constraints::BondAtomRefs2ShouldBeDistinct` (warning
+severity — there are edge cases in non-classical chemistry). The
+constraint parses `node.atom_refs2`, splits on whitespace, and warns
+if the two ids are identical.
+
+Register against molecular convention.
+
+## Acceptance
+
+- `<bond atomRefs2="a1 a1"/>` triggers a warning.
+- `<bond atomRefs2="a1 a2"/>` passes silently.
+- All existing specs pass.

data/TODO.align/86-references-should-resolve.md

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+# 86 — References-should-resolve constraint
+
+## Why
+
+With `Cml::ReferenceResolver` (TODO 82), we can now detect bonds
+whose `atomRefs2` reference atoms that don't exist in the parent
+molecule. Currently no constraint flags this — typos like
+`atomRefs2="a1 a99"` (where `a99` doesn't exist) pass silently.
+
+## Work
+
+Add `Molecular::Constraints::ReferencesShouldResolve` as a
+`DocumentConstraint`. It instantiates a `ReferenceResolver` and
+reports each unresolved reference as a warning violation.
+
+## Acceptance
+
+- A bond referencing a missing atom triggers a warning.
+- A bond referencing existing atoms passes silently.
+- All existing specs pass.

data/TODO.align/87-cli-utility.md

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+# 87 — CLI utility for validation
+
+## Why
+
+A user-facing CLI makes the gem immediately useful for command-line
+validation of CML files. Without a CLI, users have to write Ruby
+to use the gem.
+
+## Work
+
+Create `exe/chemicalml` (executable) with subcommands:
+
+- `chemicalml validate <file>` — auto-detect convention, print
+  violations to stderr, exit non-zero if errors.
+- `chemicalml conventions` — list registered conventions.
+- `chemicalml dictionaries` — list builtin dictionaries.
+
+Wire it through `Chemicalml::Cli` module under
+`lib/chemicalml/cli.rb` so the logic is reusable.
+
+## Acceptance
+
+- `bundle exec chemicalml validate spec/fixtures/schema3/molecular/water.cml`
+  parses, detects convention:molecular, prints nothing, exits 0.
+- `chemicalml conventions` lists all 8 conventions.
+- `chemicalml dictionaries` lists all built-in dictionaries.

data/TODO.align/88-diverse-fixtures.md

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+# 88 — Diverse real-world fixtures
+
+## Why
+
+Current fixtures cover basic structures (water, methanol, ethanol,
+compchem, dictionary). Real CML documents have richer features:
+bond stereo (wedge/hash), propertyList nesting, reaction mechanisms,
+formulas, crystallographic lattices. Adding fixtures that exercise
+these ensures the gem handles real-world CML.
+
+## Work
+
+Add fixtures under `spec/fixtures/schema3/`:
+- `molecular/chiral_center_with_bond_stereo.cml` — bondStereo W/H
+- `molecular/ethanol_with_properties.cml` — propertyList with scalars
+- `molecular/ethanol_with_formula.cml` — formula concise
+- `crystal/nacl_with_lattice.cml` — crystal + lattice + symmetry
+- `reactions/diels_alder.cml` — reactionScheme with reactantList/productList
+
+Round-trip each in a spec.
+
+## Acceptance
+
+- Each fixture parses without raising.
+- The features it exercises (bondStereo, property, formula, lattice,
+  reaction) round-trip.

data/TODO.align/89-final-verification-round22.md

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+# 89 — Final verification round 22
+
+## Work
+
+1. Full rspec — must be green.
+2. rubocop on touched files.
+3. Forbidden-pattern scan.
+4. Update CLAUDE.md noting CLI + new constraints.
+5. Write `TODO.align/README.round22.md`.
+
+## Acceptance
+
+- All scans clean.
+- CLAUDE.md current.
+- README.round22.md exists.

data/TODO.align/90-bond-stereo-completeness.md

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+# 90 — BondStereo completeness constraints
+
+## Why
+
+The molecular spec at `reference-docs/conventions/molecular.md` says:
+
+> If value is `C` or `T` — MUST have `atomRefs4` (four distinct atom
+> ids; two MUST be the parent bond's atoms). MUST NOT have `atomRefs2`.
+> If value is `W` or `H` — MUST have `atomRefs2` (two distinct atom
+> ids ... both MUST be in the parent bond).
+
+We have `BondStereoCisTransMustHaveAtomRefs4` and
+`BondStereoWedgeHashMustHaveAtomRefs2` but not the distinctness or
+parent-bond-membership rules.
+
+## Work
+
+Add to molecular convention:
+- `BondStereoAtomRefs4ShouldBeDistinct` (warning) — atomRefs4 has 4 distinct ids
+- `BondStereoAtomsShouldBeInParentBond` (warning) — atomRefs2/4
+  references should be a subset of the parent bond's atoms (the
+  walker doesn't track parents, so this is approximate — checks
+  against the document's atoms).
+
+Register both against molecular.
+
+## Acceptance
+
+- `<bondStereo atomRefs4="a1 a2 a3 a3">C</bondStereo>` triggers warning.
+- `<bondStereo atomRefs4="a1 a2 a3 a4">C</bondStereo>` passes.
+- All existing specs pass.

data/TODO.align/91-atomparity-distinct.md

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+# 91 — AtomParity atomRefs4 distinct constraint
+
+## Why
+
+`<atomParity atomRefs4="a b c d">1</atomParity>` references 4 atoms
+around a chiral center. Per CML semantics, all 4 must be distinct
+(duplicates make the parity meaningless). No constraint enforces
+this today.
+
+## Work
+
+Add `Molecular::Constraints::AtomParityAtomRefs4ShouldBeDistinct`
+(applies_to Role::AtomParity). Warning severity. Parses
+`node.atom_refs4` and warns if not 4 distinct ids.
+
+Register against molecular.
+
+## Acceptance
+
+- AtomParity with `atomRefs4="a1 a2 a3 a3"` triggers warning.
+- AtomParity with `atomRefs4="a1 a2 a3 a4"` passes.

data/TODO.align/92-unit-dictionary-completeness.md

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+# 92 — Unit-dictionary completeness
+
+## Why
+
+`reference-docs/conventions/unit-dictionary.md` says unit MUST have:
+- `id` (already covered)
+- `title` — typically the full name
+- `symbol` (already covered alongside unitType)
+- `parentSI` — QName referencing an SI unit
+- at least one of `multiplierToSI` or `constantToSI`
+- `unitType` (already covered)
+- single `definition` child (already covered)
+
+Missing constraints: title, parentSI, multiplierTo/constantToSI.
+
+## Work
+
+Add three constraints to unit-dictionary convention:
+- `UnitMustHaveTitle`
+- `UnitMustHaveParentSI`
+- `UnitMustHaveMultiplierOrConstantToSI`
+
+## Acceptance
+
+- A `<unit>` without `title` triggers an error.
+- A `<unit>` with `parentSI="si:m"` passes.
+- A `<unit>` without both `multiplierToSI` and `constantToSI` triggers error.
+- All existing specs pass.

data/TODO.align/93-yard-docs.md

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+# 93 — YARD docs for public API
+
+## Why
+
+The public API (`Chemicalml.parse`, `Chemicalml.serialize`,
+`Chemicalml::Cli.run`, `Chemicalml::Convention.validate`,
+`Chemicalml::Dictionary.load`) lacks YARD docstrings. Without
+docs, `yard doc` produces empty output and users have to read source.
+
+## Work
+
+Add concise YARD docstrings to:
+- `Chemicalml.parse`, `Chemicalml.serialize`, `Chemicalml.parser_for`
+- `Chemicalml::Cli.run` and subcommand methods
+- `Chemicalml::Convention.validate`, `validate_report`, `detect_and_validate`
+- `Chemicalml::Dictionary.load`
+- `Chemicalml::Cml::ReferenceResolver` public methods
+- `Chemicalml::Cml::Enums` module
+
+## Acceptance
+
+- `bundle exec yard doc` succeeds with no errors.
+- `bundle exec yard server` serves documented API.

data/TODO.align/94-final-verification-round23.md

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+# 94 — Final verification round 23
+
+## Work
+
+1. Full rspec — must be green.
+2. rubocop on touched files.
+3. Forbidden-pattern scan.
+4. Update CLAUDE.md noting new constraints + YARD.
+5. Write `TODO.align/README.round23.md`.
+
+## Acceptance
+
+- All scans clean.
+- CLAUDE.md current.
+- README.round23.md exists.

data/TODO.align/README.round17.md

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+# Round 17 — XSD gap closure
+
+This round closes the remaining XSD-declared feature gaps in the gem.
+Started from a clean XSD-vs-Ruby comparison and worked through each
+cluster.
+
+## Files
+
+- [61 — Parallel-array attrs for atomArray/bondArray](61-parallel-array-attrs.md)
+- [62 — Per-element attribute gaps](62-per-element-attribute-gaps.md)
+- [63 — Universal children mixin](63-universal-children-mixin.md)
+- [64 — Per-element child element gaps (Schema 2.4)](64-per-element-child-gaps.md)
+- [65 — SimpleUnit convention](65-simple-unit-convention.md)
+- [66 — Schema24-only legacy element children](66-schema24-legacy-children.md)
+- [67 — Final spec/lint/docs verification](67-final-verification.md)
+
+## Outcomes
+
+- Schema3 XSD: **0 attribute gaps, 0 child gaps** (excluding `<anyCml>`
+  wildcard, which is intentionally not modelled as a concrete child).
+- Schema24 XSD: **0 attribute gaps**; child gaps reduced from 235 to
+  ~140 element-specific declarations, with ~80% of the universal
+  children (metadataList/label/name/description) absorbed by the new
+  `CommonChildren` mixin.
+- 8 conventions now registered (was 5 at start of round): molecular,
+  compchem, dictionary, unit-dictionary, unitType-dictionary,
+  spectroscopy, cascade, simpleUnit.
+- 300 specs total, 0 failures, 0 forbidden patterns.

data/TODO.align/README.round18.md

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+# Round 18 — Convention detection, format coverage, robustness
+
+This round closes convention-detection gaps, proves format-agnosticism
+beyond XML, hardens the constraint walker, and enriches the violation
+value-object.
+
+## Files
+
+- [68 — Detection coverage for all 8 conventions](68-detection-coverage.md)
+- [69 — JSON / YAML round-trip proof](69-json-yaml-roundtrip.md)
+- [70 — Iterative tree walker](70-iterative-walker.md)
+- [71 — Enrich Violation with offending value](71-violation-value.md)
+- [72 — Close remaining Schema24 child gaps](72-close-child-gaps.md)
+- [73 — Document Schema24 nested-parse limitation](73-schema24-parse-limitation.md)
+- [74 — Final verification round 18](74-final-verification-round18.md)
+
+## Outcomes
+
+- `Convention::Detection` recognises Spectrum, SpectrumList,
+  ReactionScheme, ReactionList as convention-bearing roots.
+- JSON and YAML round-trip specs prove the format-agnostic claim
+  (lutaml-model applies XML mappings only to XML; JSON/YAML use Ruby
+  snake_case names).
+- The recursive walker in `Constraint#walk_nodes` is now an iterative
+  worklist (DFS pre-order preserved) — a 200-deep Module chain walks
+  without stack overflow.
+- `Violation` carries an optional `value` field with the offending
+  literal; three constraints populate it (AtomIdMustMatchPattern,
+  PeakShouldHaveValues, UnitMustHavePower).
+- ~25 additional Base modules gained element-specific children
+  (reactiveCentre, sample, spectator, transitionState, substance,
+  lattice, table, trow, zMatrix, symmetry, map, eigen, xaxis, yaxis)
+  plus self-references on 10 recursive containers.
+- Schema24 nested-XML parse limitation documented with a pending
+  spec that will auto-resolve when lutaml-model fixes its
+  TypeResolver context handling.
+- 342 specs total, 0 failures, 2 pending. Zero forbidden patterns.

data/TODO.align/README.round19.md

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+# Round 19 — JSON wire names, Schema24 workaround attempts, matrix coverage
+
+This round directly addresses the user's question about `key_value`
+blocks for JSON/YAML, and continues closing coverage gaps.
+
+## Files
+
+- [75 — key_value mappings for JSON/YAML wire names](75-key-value-mappings.md)
+- [76 — Schema24 parse workaround attempts](76-schema24-workaround.md)
+- [77 — Convention coverage matrix spec](77-convention-coverage-matrix.md)
+- [78 — Fixture coverage audit](78-fixture-audit.md)
+- [79 — Final verification round 19](79-final-verification-round19.md)
+
+## Outcomes
+
+- **Answer to user's question**: previously NO, JSON output used
+  Ruby snake_case names because no `key_value do ... end` blocks
+  were declared. Added `Base::WireMappings` mixin with
+  `auto_key_value_mapping!` class method — generates a parallel
+  key_value mapping from the existing XML mappings. JSON now
+  carries CML wire names (`elementType`, `atomArray`, `formalCharge`).
+  Single source of truth — one wire name per attribute.
+- **Schema24 nested-XML parse**: ROOT CAUSE FOUND AND FIXED in
+  subsequent round (see TODO 76). The bug was a type-name collision:
+  Schema24's legacy `<string>`/`<integer>`/`<float>` CML elements
+  shadowed lutaml-model's primitive types in the schema24 context.
+  Fixed by excluding these from type registration while keeping
+  them as wire classes.
+- **Convention coverage matrix spec**: 49 specs asserting all 8
+  conventions have QName, namespace, >=1 constraint, a spec file,
+  a Detection root role, and run detect_and_validate without
+  raising. Adding a new convention without full coverage makes
+  the matrix spec fail.
+- **Fixed bug**: `CompchemModuleMustContainJobList` assumed
+  `node.modules` was non-nil; now defensively handles nil.
+- **New fixtures**: ethanol IR (spectroscopy), methane combustion
+  (cascade), basic SI units (simpleUnit), ethanol parallel-array
+  form (parallel_array), standard unit types (unitType-dictionary).
+- **422 examples, 0 failures, 0 pending**. Zero forbidden patterns.
+  (After TODO 76 fix: 423 examples, 0 failures.)

data/TODO.align/README.round20.md

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+# Round 20 — Schema24 parse bug FIXED
+
+This round found and fixed the long-standing Schema24 nested-XML
+parse bug that had been documented as a "limitation" since round 18.
+
+## Root cause
+
+`Cml::Elements::SCHEMA24_ONLY` included CML's legacy `<string>`,
+`<integer>`, `<float>` elements, and Schema24::Configuration
+registered them as types in the schema24 context. Their XML names
+collided with lutaml-model's primitive type names. Every
+`attribute :foo, :string` cast in any Schema24 wire class resolved
+`:string` to `Chemicalml::Cml::Schema24::String` (a Serializable)
+instead of `Lutaml::Model::Type::String` (the primitive).
+
+The Serializable.cast path on a String value tried to deserialize
+it as a CML `<string>` element, which failed. Schema3 was
+unaffected because Schema 3 doesn't declare these elements.
+
+## Fix
+
+Added `Cml::Elements::SCHEMA24_TYPE_COLLISIONS = %i[Float Integer
+String].freeze`. Schema24::Configuration now passes this list as
+`except:` when registering SCHEMA24_ONLY. The three wire classes
+remain defined (parseable as document roots) but are no longer
+registered as types.
+
+## Files
+
+- [76 — Schema24 parse bug FIXED](76-schema24-workaround.md)
+
+## Outcomes
+
+- `Chemicalml::Cml::Schema24::Document.from_xml` parses nested
+  content. Schema24 finally works the same as Schema3.
+- `spec/chemicalml/cml/schema24_nested_parse_spec.rb` has 3
+  passing specs including one with parallel-array atomArray and
+  nested molecule.
+- Removed the pending spec.
+- Updated CLAUDE.md (limitation replaced with collision note).
+- Updated TODO 76 with the real root cause and fix.
+- Full suite: **423 examples, 0 failures, 0 pending**.
+
+## Lesson
+
+When a bug seems to be in upstream but only one of two parallel
+implementations is affected, look for **what's different** about
+that implementation's setup. The bug wasn't in lutaml-model's
+caching — it was in our registration of type-colliding names.

data/TODO.align/README.round21.md

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+# Round 21 — XSD enums, reference resolution, TOML probe
+
+This round adds the canonical enum source of truth, three
+enum-validation constraints, a reference resolver for id-based
+links, and a TOML round-trip probe.
+
+## Files
+
+- [80 — XSD enum constants](80-xsd-enum-constants.md)
+- [81 — Enum validation constraints](81-enum-validation-constraints.md)
+- [82 — Reference resolver](82-reference-resolver.md)
+- [83 — TOML round-trip spec](83-toml-roundtrip.md)
+- [84 — Final verification round 21](84-final-verification-round21.md)
+
+## Outcomes
+
+- `Chemicalml::Cml::Enums` — 31 frozen-Set constants matching every
+  XSD simpleType that restricts to enumerations (orderType,
+  stereoType, chiralityType, latticeType, matrixType, stateType,
+  peakMultiplicityType, etc.). A spec parses the XSD and asserts
+  every constant matches — drift is caught automatically.
+- Three enum-validation constraints in the molecular convention
+  (bond order, bond stereo, molecule chirality). Warning severity
+  so extension values are flagged but not rejected. Each populates
+  `Violation.value` with the offending literal.
+- `Chemicalml::Cml::ReferenceResolver` walks a document, builds an
+  id-index, and resolves `atomRefs2`/`atomRefs4`/`bondRefs`/`ref`
+  to actual wire instances. `unresolved_refs` lists every missing
+  target — a programmatic alternative to the constraint walker.
+- TOML round-trip spec added (3 pending specs because the tomlib
+  adapter isn't installed; will auto-resolve when tomlib is added
+  to the Gemfile).
+- Molecular convention now registers 26 constraints (up from 23).
+- **452 examples, 0 failures, 3 pending** (TOML adapter pending).
+  Zero forbidden patterns.