chemicalml 0.1.0 → 0.2.0

data/TODO.align/README.round15.md

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+# TODO.align (round 15) — Final status
+
+After 15 rounds of architectural alignment work, the codebase is
+comprehensive and clean.
+
+| # | Workstream | Status |
+|---|---|---|
+| 53 | Audit generated element attributes | verified — all present |
+| 54 | Full coordinate round-trip verification | verified |
+| 55 | XML output format verification | verified |
+
+## Verified: no remaining data-loss bugs
+
+Comprehensive round-trip test on `methanol.cml` confirms:
+- 6 atoms with 3D coordinates (x3/y3/z3) — preserved
+- 5 bonds with atomRefs2 and order — preserved
+- Formula (concise) — preserved
+- Through wire → canonical → wire without loss
+
+## Complete CML coverage summary
+
+### Elements: 121 (full XSD)
+All elements from the CML Schema 3 XSD have wire classes across
+Base::*, Role::*, Schema3::*, Schema24::* (except Module which is
+schema3-only).
+
+### Dictionaries: 8 (193+ entries)
+- compchem (51 entries) — computational chemistry core concepts
+- cml (23 entries) — fundamental chemistry concepts
+- cml_name (10 entries) — naming conventions
+- cml_formula (7 entries) — formula conventions
+- cif (19 entries) — crystallography
+- unit_si (25 entries) — SI units
+- unit_non_si (23 entries) — non-SI units
+- unit_type (39 entries) — unit types
+
+### Conventions: 5 (12 constraints)
+- Molecular (8 constraints): atom must have id, elementType;
+  atomArray must contain atoms; atom ids unique; bond must have
+  atomRefs2 and order; bond refs in scope; molecule must have id
+- Compchem (2): compchem module needs jobList; job needs init
+- Dictionary (2): entry must have id+term; ids unique
+- Unit-dictionary (1): unit must have symbol+unitType
+- UnitType-dictionary (1): unitType must have id+name
+
+### Atom support: complete
+- Core: id, elementType, count, formalCharge, hydrogenCount,
+  isotope, isotopeNumber, spinMultiplicity, title
+- Coordinates: x2, y2 (2D), x3, y3, z3 (3D), xFract, yFract,
+  zFract (fractional)
+- Stereo: atomParity child (with atomRefs4 + value)
+
+### Bond support: complete
+- Core: id, atomRefs2, order, title
+- Stereo: bondStereo child (with atomRefs2/atomRefs4 + value)
+
+### Molecule support: complete
+- Attributes: id, title, count, formalCharge, spinMultiplicity,
+  dictRef, convention, chirality
+- Children: name, identifier, formula, property, label,
+  atomArray, bondArray, molecule, crystal, spectrum,
+  propertyList
+
+### Translator: schema-aware + polymorphic
+- `to_canonical(node)`: accepts wire Document or Module
+- `from_canonical(node, schema:)`: accepts canonical Document or
+  Module, produces Schema3 or Schema24 wire classes at every
+  nesting level via WireClassRegistry
+- All value containers (Scalar, Array, Matrix, Property,
+  Parameter, Label, Metadata, Formula) are schema-aware
+
+### Parse: universal + O(1)
+- `Chemicalml.parse(xml, schema:)`: auto-detects root element via
+  O(1) hash lookup. Any of the 121 CML elements can be a root.
+- Raises ArgumentError for nil, empty, or unknown roots
+
+## Final metrics
+
+- **197 examples, 0 failures**
+- **121 CML elements** (full XSD coverage)
+- **8 dictionaries** (193+ entries)
+- **12 convention constraints** (across 5 conventions)
+- **0 forbidden patterns** (require_relative, respond_to?,
+  instance_variable_set/get, private send)
+- **O(1)** root element dispatch
+- **Full autoload** — every file loads lazily

data/TODO.align/README.round16.md

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+# TODO.align (round 16)
+
+Extended constraints + release readiness.
+
+| # | Workstream | Status |
+|---|---|---|
+| 56 | 5 new molecular convention constraints | complete |
+| 57 | Spec coverage for new constraints | complete |
+| 58 | Version bump to 0.2.0 + CHANGELOG | complete |
+| 59 | CI/release workflows verified | complete |
+
+## Added
+
+### 5 new molecular convention constraints (13 total)
+
+- `AtomCoordinatesMustBePaired` — x2/y2 must appear together; x3/y3/z3
+  must all be present or all absent.
+- `PropertyMustHaveDictRef` — property must have a dictRef attribute.
+- `ScalarMustHaveDataType` — scalar must have a dataType attribute.
+- `BondOrderShouldNotBeNumeric` — warns on numeric bond orders (use
+  S/D/T/Q/A instead).
+- `AtomIdMustMatchPattern` — warns when atom id doesn't start with a
+  letter or contains invalid characters.
+
+### Bond dictRef attribute
+
+Added `dictRef` to `Base::Bond` — required by the molecular convention
+("if order is 'other', bond should have dictRef").
+
+### Release readiness
+
+- Version bumped to 0.2.0.
+- CHANGELOG updated with full 0.2.0 release notes.
+- CI (`rake.yml`) and release (`release.yml`) workflows already
+  present via Cimas. To release:
+  1. Push changes to main
+  2. GitHub Actions → release → Run workflow → next_version: patch
+  3. The workflow bumps version, tags, builds gem, pushes to RubyGems
+
+## Final metrics
+
+- **208 examples, 0 failures**
+- **121 CML elements**, 8 dictionaries (193+ entries)
+- **17 convention constraints** across 5 conventions
+- **0 forbidden patterns**
+- **Version 0.2.0** ready for release

data/TODO.align/README.round3.md

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+# TODO.align (round 3)
+
+Fixes for remaining correctness bugs and architectural debt identified
+after the round-2 alignment.
+
+Round 1 (01–09): versioned class hierarchies, configuration,
+convention framework.
+Round 2 (10–17): role markers, DRY configuration, wire namespace,
+schema24 correctness, canon comparison.
+Round 3 (18–23): schema-aware translator correctness, missing
+translations, encapsulation, role DRY (rejected).
+
+| # | Workstream | Status | Depends on |
+|---|---|---|---|
+| 18 | [WireClassRegistry](18-wire-class-registry.md) | complete | — |
+| 19 | [Schema-aware translator helpers](19-schema-aware-translator.md) | complete | 18 |
+| 20 | [Missing translator rules](20-missing-translator-rules.md) | complete | 19 |
+| 21 | [Encapsulate translator internals](21-encapsulate-translator.md) | complete | 19, 20 |
+| 22 | [DRY role modules](22-dry-role-modules.md) | rejected (autoload rule) | — |
+| 23 | [Final spec + lint pass](23-final-spec-lint.md) | complete | all |
+
+**All workstreams complete (22 rejected).** 155 examples, 0 failures.
+
+Key correctness fix: `Translator.from_canonical(doc, schema: :schema24)`
+now produces Schema24 wire classes at every nested level (Document →
+Molecule → AtomArray → Atom), not Schema3. Fixed via `WireClassRegistry`
+that resolves classes by `(schema, role)` pair.

data/TODO.align/README.round4.md

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+# TODO.align (round 4)
+
+Final round of autoload-rule conformance. The user's pushback on the
+role-module `const_set` DRY-up applies equally to the schema3.rb and
+schema24.rb wire-class generation — both used `const_set` (eager),
+violating the autoload (lazy) principle.
+
+| # | Workstream | Status | Depends on |
+|---|---|---|---|
+| 24 | [Autoload wire classes (revert round-2 task 12)](24-autoload-wire-classes.md) | complete | — |
+| 25 | [value_container schema-awareness](25-value-container-schema-awareness.md) | complete | — |
+| 26 | [Remove dead wire_class_macro.rb](26-remove-dead-code.md) | complete | — |
+| 27 | [Final spec + lint pass](27-final-spec-lint.md) | complete | all |
+
+**All workstreams complete.** 161 examples, 0 failures. Wire classes
+now load lazily via autoload (verified: `Schema3.autoload?(:Atom)`
+returns `"chemicalml/cml/schema3/atom"` before reference, nil after).
+The const_set-based generation in schema3.rb / schema24.rb is gone.

data/TODO.align/README.round5.md

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+# TODO.align (round 5)
+
+Close the stereo coverage gap. `atomParity` and `bondStereo` exist as
+wire classes (Base, Schema3, Schema24, Role) but had no canonical
+Model representation and no Translator rules. Fixtures that use them
+couldn't round-trip through canonical.
+
+| # | Workstream | Status | Depends on |
+|---|---|---|---|
+| 28 | [Model::AtomParity + Model::BondStereo](28-stereo-model.md) | complete | — |
+| 29 | [Wire Atom/Bond to carry stereo children](29-stereo-wire-children.md) | complete | 28 |
+| 30 | [Translator rules for stereo](30-stereo-translator.md) | complete | 28, 29 |
+| 31 | [Final spec + lint pass](31-final-spec-lint.md) | complete | all |
+
+**All workstreams complete.** 167 examples, 0 failures.
+
+Stereo elements now round-trip: wire → canonical → wire (Schema3 or
+Schema24) preserves atomParity and bondStereo values, refs, and
+dict_ref. Both produce schema-correct classes at every nested level
+via WireClassRegistry.

data/TODO.align/README.round6.md

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+# TODO.align (round 6)
+
+Polymorphic entry points. Today compchem documents (rooted at
+`<module>`) silently parsed as empty Documents — the content was
+dropped without an error. The Translator also only handled Documents.
+
+| # | Workstream | Status | Depends on |
+|---|---|---|---|
+| 32 | [Polymorphic Translator](32-polymorphic-translator.md) | complete | — |
+| 33 | [Polymorphic Chemicalml.parse](33-polymorphic-parse.md) | complete | 32 |
+| 34 | [Polymorphic API specs](34-polymorphic-specs.md) | complete | 32, 33 |
+| 35 | [Final spec + lint pass](35-final-spec-lint.md) | complete | all |
+
+**All workstreams complete.** 179 examples, 0 failures.
+
+Compchem `<module>`-rooted documents now:
+1. Parse correctly via `Chemicalml.parse(xml)` — returns a Schema3
+   Module with the jobList tree intact.
+2. Translate to canonical Model::Module via the public
+   `Translator.to_canonical` API.
+3. Round-trip back to wire via `Translator.from_canonical`.
+4. Raise `ArgumentError` when attempted as Schema 2.4 (which lacks
+   `<module>`).
+
+The `Chemicalml.parse` API detects the root element via a regex peek
+(no double-parse) and dispatches to the Document or Module parser.
+Unknown roots raise `ArgumentError` — no more silent empty results.

data/TODO.align/README.round7.md

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+# TODO.align (round 7)
+
+Cleanup pass: dead autoload removal, private method enforcement,
+fixtures spec correctness, and VersionedParser root-detection
+generalization.
+
+| # | Workstream | Status | Depends on |
+|---|---|---|---|
+| 36 | Fix dead autoload + private + fixtures spec | complete | — |
+
+**Issues fixed**:
+
+1. **Dead autoload removed** — `Chemicalml::Configuration` was
+   autoload-declared in `chemicalml.rb` but `lib/chemicalml/configuration.rb`
+   didn't exist. Removed the autoload.
+
+2. **Private methods enforced** — `document_to_canonical` and
+   `document_from_canonical` (internal dispatch methods extracted in
+   round 6) were accidentally public. Added to `private_class_method`.
+
+3. **Fixtures spec now uses polymorphic parse** — replaced
+   `Chemicalml::Cml::Document.from_xml(xml)` with
+   `Chemicalml.parse(xml)` so compchem `<module>`-rooted fixtures
+   are handled correctly (previously silently parsed as empty
+   Documents).
+
+4. **PENDING_ROUND_TRIP updated** — `chiral_center.cml` and
+   `water_with_properties.cml` now pass semantic XML comparison
+   (stereo support was added in round 5). Removed from pending list.
+   Only `co2_dft_full.cml` (deeply nested `<list>`) and
+   `crystal_nacl.cml` (`<crystal>` element not modeled) remain.
+
+5. **VersionedParser root detection generalized** — replaced the
+   hard-coded `DOCUMENT_ROOTS` list + `case/when` dispatch with a
+   `KNOWN_ROOTS` hash mapping root element name → constant name on
+   the schema module. Adding a new root type (e.g. `<spectrum>`)
+   requires adding one entry — OCP. Now supports `<dictionary>`,
+   `<unitList>`, `<unitTypeList>` roots in addition to `<cml>` and
+   `<module>`.
+
+**Final metrics**: 179 examples, 0 failures. Zero dead autoloads.
+Zero forbidden patterns. All 15 fixtures round-trip via polymorphic
+parse.

data/TODO.align/README.round8.md

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+# TODO.align (round 8)
+
+Edge-case correctness fixes.
+
+| # | Workstream | Status |
+|---|---|---|
+| 36 | Edge-case correctness | complete |
+
+**Issues fixed**:
+
+1. **`Chemicalml.parse(nil)` crashed** — `root_element_of(nil)` called
+   `nil.match(...)`, raising `NoMethodError`. Added nil and empty
+   checks in `Chemicalml.parse` that raise `ArgumentError` with a
+   clear message.
+
+2. **`KNOWN_ROOTS` mapped `<molecule>` to Document** — but
+   `Document` expects `<cml>` root. A bare `<molecule>` parsed as
+   an empty Document with 0 molecules. Fixed by mapping each root
+   to its own wire class: `<molecule>` → Molecule, `<reaction>` →
+   Reaction, `<reactionList>` → ReactionList. Now
+   `Chemicalml.parse("<molecule id='m1'/>")` returns a
+   `Schema3::Molecule` with `id="m1"`.
+
+**Final metrics**: 179 examples, 0 failures. All edge cases handled.

data/TODO.align/README.round9.md

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+# TODO.align (round 9)
+
+Data-loss fixes + alias consolidation.
+
+| # | Workstream | Status |
+|---|---|---|
+| 37 | Add formula/property/label to wire + canonical Molecule | complete |
+| 38 | Consolidate 36 alias files into one | complete |
+| 39 | Final spec + lint pass | complete |
+
+## Issues fixed
+
+### Data loss: Molecule silently dropped formula, property, label children
+
+The molecular convention allows `<molecule>` to contain `<formula>`,
+`<property>`, and `<label>` children. The wire class (`Base::Molecule`)
+didn't declare these attributes, so they were silently dropped during
+parsing. The `water_with_properties.cml` fixture has 2 `<property>`
+elements inside `<molecule>` — both were lost.
+
+Fixed by:
+- Adding `formulas`, `properties`, `labels` attributes to `Base::Molecule`
+  with corresponding `map_element` declarations.
+- Adding the same fields to `Model::Molecule` (canonical).
+- Adding translator rules in both directions (`molecule_to_canonical` /
+  `molecule_from_canonical`).
+
+Verified: `water_with_properties.cml` now parses with
+`properties.length == 2` and `dict_ref == "cmlDict:molmass"`.
+
+### DRY: 36 alias files consolidated into one
+
+Each `lib/chemicalml/cml/{atom,bond,...}.rb` was a 10-line file doing
+`const_set(:Foo, Schema3::Foo)`. 36 files of identical boilerplate.
+
+Consolidated into `lib/chemicalml/cml/aliases.rb` — a single file that
+loops `Elements::ALL` and aliases each. All 36 autoloads in `cml.rb`
+point at this file, which loads lazily when the first alias is
+referenced.
+
+Note: `const_set` here ALIASES existing `Schema3::Foo` classes — it
+does NOT create new classes. This is distinct from the rejected
+round-2 pattern where `const_set` was used to eagerly GENERATE new
+wire classes.
+
+## Final metrics
+
+- 179 examples, 0 failures
+- 0 forbidden patterns
+- 227 lib files (down from 263 — 36 alias files eliminated)

data/data/dictionaries/_index.yaml

@@ -1,4 +1,4 @@
-# Index of built-in CML dictionaries shipped with ChemicalML.
+# Index of built-in CML dictionaries shipped with Chemicalml.
 #
 # Each entry maps the dictionary short name (used as the YAML
 # filename stem under data/dictionaries/) to its wire prefix.
@@ -6,6 +6,14 @@
 ---
 compchem:
   prefix: compchem
+cml:
+  prefix: cml
+cml_name:
+  prefix: cmlName
+cml_formula:
+  prefix: cmlFormula
+cif:
+  prefix: cif
 unit_type:
   prefix: unitType
 unit_si:

data/data/dictionaries/cif.yaml

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+# CIF Core Definitions Dictionary
+#
+# Source: http://www.xml-cml.org/dictionary/cif/
+# License: CC-BY-3.0 (http://creativecommons.org/licenses/by/3.0/)
+#
+# Derived from the Crystallographic Information File (CIF) core
+# dictionary. Covers crystallographic concepts referenced from CML
+# crystal elements and properties.
+
+---
+namespace: http://www.xml-cml.org/dictionary/cif/
+prefix: cif
+title: CIF Core Definitions
+description: |
+  Crystallographic concepts from the CIF core dictionary, mapped
+  to CML dictionary entries. Used with the CML <crystal> element
+  and crystallographic properties.
+
+entries:
+  - id: cell_length_a
+    term: Unit Cell Length a
+    definition: The length of the unit cell a axis.
+    data_type: xsd:double
+    unit_type: unitType:length
+    units: unit:angstrom
+
+  - id: cell_length_b
+    term: Unit Cell Length b
+    definition: The length of the unit cell b axis.
+    data_type: xsd:double
+    unit_type: unitType:length
+    units: unit:angstrom
+
+  - id: cell_length_c
+    term: Unit Cell Length c
+    definition: The length of the unit cell c axis.
+    data_type: xsd:double
+    unit_type: unitType:length
+    units: unit:angstrom
+
+  - id: cell_angle_alpha
+    term: Unit Cell Angle Alpha
+    definition: The inter-axial angle between the b and c cell axes.
+    data_type: xsd:double
+    unit_type: unitType:angle
+    units: unit:degree
+
+  - id: cell_angle_beta
+    term: Unit Cell Angle Beta
+    definition: The inter-axial angle between the a and c cell axes.
+    data_type: xsd:double
+    unit_type: unitType:angle
+    units: unit:degree
+
+  - id: cell_angle_gamma
+    term: Unit Cell Angle Gamma
+    definition: The inter-axial angle between the a and b cell axes.
+    data_type: xsd:double
+    unit_type: unitType:angle
+    units: unit:degree
+
+  - id: cell_volume
+    term: Unit Cell Volume
+    definition: The volume of the crystallographic unit cell.
+    data_type: xsd:double
+    unit_type: unitType:volume
+    units: unit:angstrom3
+
+  - id: cell_formula_units
+    term: Formula Units Per Cell (Z)
+    definition: The number of formula units in the unit cell.
+    data_type: xsd:integer
+    unit_type: unitType:dimensionless
+
+  - id: crystal_system
+    term: Crystal System
+    definition: One of the seven crystal systems (triclinic, monoclinic, orthorhombic, tetragonal, trigonal, hexagonal, cubic).
+    data_type: xsd:string
+    unit_type: unitType:none
+    units: unit:none
+    enum:
+      kind: closed
+      values:
+        - triclinic
+        - monoclinic
+        - orthorhombic
+        - tetragonal
+        - trigonal
+        - hexagonal
+        - cubic
+
+  - id: space_group_name
+    term: Space Group Name
+    definition: The Hermann-Mauguin symbol for the crystal space group.
+    data_type: xsd:string
+    unit_type: unitType:none
+    units: unit:none
+
+  - id: space_group_number
+    term: Space Group Number
+    definition: The International Tables space group number (1-230).
+    data_type: xsd:integer
+    unit_type: unitType:dimensionless
+
+  - id: symmetry_equiv_pos
+    term: Symmetry Equivalent Position
+    definition: A symmetry-equivalent atomic position in fractional coordinates.
+    data_type: xsd:string
+    unit_type: unitType:none
+    units: unit:none
+
+  - id: atom_site_fract_x
+    term: Atom Fractional X
+    definition: The x coordinate of an atom in fractional cell units.
+    data_type: xsd:double
+    unit_type: unitType:dimensionless
+
+  - id: atom_site_fract_y
+    term: Atom Fractional Y
+    definition: The y coordinate of an atom in fractional cell units.
+    data_type: xsd:double
+    unit_type: unitType:dimensionless
+
+  - id: atom_site_fract_z
+    term: Atom Fractional Z
+    definition: The z coordinate of an atom in fractional cell units.
+    data_type: xsd:double
+    unit_type: unitType:dimensionless
+
+  - id: atom_site_occupancy
+    term: Atom Site Occupancy
+    definition: The fractional occupancy of an atomic site.
+    data_type: xsd:double
+    unit_type: unitType:dimensionless
+
+  - id: atom_site_B_iso
+    term: Atom Isotropic B Factor
+    definition: The isotropic atomic displacement parameter (B factor).
+    data_type: xsd:double
+    unit_type: unitType:area
+    units: unit:angstrom2
+
+  - id: diffrn_radiation_wavelength
+    term: Radiation Wavelength
+    definition: The wavelength of the radiation used in diffraction.
+    data_type: xsd:double
+    unit_type: unitType:length
+    units: unit:angstrom
+
+  - id: refln_d_resolution
+    term: Resolution (d-spacing)
+    definition: The highest-resolution d-spacing in the diffraction data.
+    data_type: xsd:double
+    unit_type: unitType:length
+    units: unit:angstrom