chemicalml 0.2.0 → 0.3.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (450) hide show
  1. checksums.yaml +4 -4
  2. data/.github/workflows/release.yml +7 -1
  3. data/.rubocop.yml +23 -0
  4. data/CLAUDE.md +95 -40
  5. data/README.adoc +154 -26
  6. data/TODO.align/36-molecular-convention-coverage.md +46 -0
  7. data/TODO.align/37-compchem-convention-coverage.md +55 -0
  8. data/TODO.align/38-dictionary-convention-coverage.md +34 -0
  9. data/TODO.align/39-unit-dictionary-convention-coverage.md +33 -0
  10. data/TODO.align/40-unit-type-dictionary-convention-coverage.md +28 -0
  11. data/TODO.align/41-expand-canonical-model-layer.md +43 -0
  12. data/TODO.align/42-translator-wire-new-models.md +31 -0
  13. data/TODO.align/43-dictionary-model-no-to-h.md +39 -0
  14. data/TODO.align/44-schema3-only-and-schema24-module.md +44 -0
  15. data/TODO.align/45-documentation-and-final-verification.md +23 -0
  16. data/TODO.align/46-lattice-vector-content.md +24 -0
  17. data/TODO.align/47-molecule-crystal-spectra-property-lists.md +23 -0
  18. data/TODO.align/48-model-list-and-module-lists.md +21 -0
  19. data/TODO.align/49-more-chemistry-models.md +34 -0
  20. data/TODO.align/50-validation-report.md +29 -0
  21. data/TODO.align/51-convention-auto-detection.md +30 -0
  22. data/TODO.align/52-schema24-legacy-elements.md +28 -0
  23. data/TODO.align/53-round-trip-integration-specs.md +30 -0
  24. data/TODO.align/54-document-versioned-parser-shim.md +38 -0
  25. data/TODO.align/55-molecule-missing-attributes.md +20 -0
  26. data/TODO.align/56-geometry-models.md +24 -0
  27. data/TODO.align/57-compchem-models.md +26 -0
  28. data/TODO.align/58-remaining-models.md +24 -0
  29. data/TODO.align/59-wire-new-models-translator.md +18 -0
  30. data/TODO.align/60-docs-and-final-verification.md +19 -0
  31. data/TODO.align/61-parallel-array-attrs.md +54 -0
  32. data/TODO.align/62-per-element-attribute-gaps.md +49 -0
  33. data/TODO.align/63-universal-children-mixin.md +42 -0
  34. data/TODO.align/64-per-element-child-gaps.md +81 -0
  35. data/TODO.align/65-simple-unit-convention.md +40 -0
  36. data/TODO.align/66-schema24-legacy-children.md +32 -0
  37. data/TODO.align/67-final-verification.md +32 -0
  38. data/TODO.align/68-detection-coverage.md +33 -0
  39. data/TODO.align/69-json-yaml-roundtrip.md +27 -0
  40. data/TODO.align/70-iterative-walker.md +40 -0
  41. data/TODO.align/71-violation-value.md +25 -0
  42. data/TODO.align/72-close-child-gaps.md +66 -0
  43. data/TODO.align/73-schema24-parse-limitation.md +64 -0
  44. data/TODO.align/74-final-verification-round18.md +15 -0
  45. data/TODO.align/75-key-value-mappings.md +43 -0
  46. data/TODO.align/76-schema24-workaround.md +57 -0
  47. data/TODO.align/77-convention-coverage-matrix.md +31 -0
  48. data/TODO.align/78-fixture-audit.md +23 -0
  49. data/TODO.align/79-final-verification-round19.md +15 -0
  50. data/TODO.align/80-xsd-enum-constants.md +35 -0
  51. data/TODO.align/81-enum-validation-constraints.md +29 -0
  52. data/TODO.align/82-reference-resolver.md +33 -0
  53. data/TODO.align/83-toml-roundtrip.md +20 -0
  54. data/TODO.align/84-final-verification-round21.md +16 -0
  55. data/TODO.align/85-bond-distinct-atoms.md +25 -0
  56. data/TODO.align/86-references-should-resolve.md +20 -0
  57. data/TODO.align/87-cli-utility.md +26 -0
  58. data/TODO.align/88-diverse-fixtures.md +26 -0
  59. data/TODO.align/89-final-verification-round22.md +15 -0
  60. data/TODO.align/90-bond-stereo-completeness.md +31 -0
  61. data/TODO.align/91-atomparity-distinct.md +21 -0
  62. data/TODO.align/92-unit-dictionary-completeness.md +28 -0
  63. data/TODO.align/93-yard-docs.md +23 -0
  64. data/TODO.align/94-final-verification-round23.md +15 -0
  65. data/TODO.align/README.round17.md +28 -0
  66. data/TODO.align/README.round18.md +37 -0
  67. data/TODO.align/README.round19.md +40 -0
  68. data/TODO.align/README.round20.md +49 -0
  69. data/TODO.align/README.round21.md +35 -0
  70. data/TODO.align/README.round22.md +48 -0
  71. data/TODO.align/README.round23.md +46 -0
  72. data/TODO.align/README.round24.md +53 -0
  73. data/TODO.align/README.round25.md +66 -0
  74. data/TODO.align/README.round26.md +55 -0
  75. data/TODO.align/README.round27.md +51 -0
  76. data/TODO.align/README.round28.md +61 -0
  77. data/TODO.align/README.round29.md +64 -0
  78. data/TODO.align/README.round30.md +50 -0
  79. data/TODO.align/README.round31.md +54 -0
  80. data/TODO.align/README.round32.md +67 -0
  81. data/TODO.align/README.round33.md +62 -0
  82. data/TODO.align/README.round34.md +70 -0
  83. data/docs/constraints.md +161 -0
  84. data/docs/generate_constraint_docs.rb +44 -0
  85. data/exe/chemicalml +6 -0
  86. data/lib/chemicalml/cli/base.rb +68 -0
  87. data/lib/chemicalml/cli/command.rb +43 -0
  88. data/lib/chemicalml/cli/constraints_command.rb +27 -0
  89. data/lib/chemicalml/cli/conventions_command.rb +14 -0
  90. data/lib/chemicalml/cli/dictionaries_command.rb +14 -0
  91. data/lib/chemicalml/cli/elements_command.rb +17 -0
  92. data/lib/chemicalml/cli/enums_command.rb +17 -0
  93. data/lib/chemicalml/cli/info_command.rb +77 -0
  94. data/lib/chemicalml/cli/inspect_command.rb +39 -0
  95. data/lib/chemicalml/cli/validate_command.rb +54 -0
  96. data/lib/chemicalml/cli.rb +43 -0
  97. data/lib/chemicalml/cml/base/abundance.rb +21 -5
  98. data/lib/chemicalml/cml/base/action.rb +44 -6
  99. data/lib/chemicalml/cml/base/action_list.rb +44 -8
  100. data/lib/chemicalml/cml/base/alternative.rb +37 -0
  101. data/lib/chemicalml/cml/base/amount.rb +15 -5
  102. data/lib/chemicalml/cml/base/angle.rb +34 -7
  103. data/lib/chemicalml/cml/base/annotation.rb +38 -0
  104. data/lib/chemicalml/cml/base/any_cml.rb +12 -5
  105. data/lib/chemicalml/cml/base/appinfo.rb +40 -0
  106. data/lib/chemicalml/cml/base/arg.rb +80 -0
  107. data/lib/chemicalml/cml/base/array.rb +51 -8
  108. data/lib/chemicalml/cml/base/array_list.rb +15 -5
  109. data/lib/chemicalml/cml/base/atom.rb +93 -19
  110. data/lib/chemicalml/cml/base/atom_array.rb +77 -2
  111. data/lib/chemicalml/cml/base/atom_parity.rb +18 -2
  112. data/lib/chemicalml/cml/base/atom_set.rb +15 -5
  113. data/lib/chemicalml/cml/base/atom_type.rb +27 -7
  114. data/lib/chemicalml/cml/base/atom_type_list.rb +23 -7
  115. data/lib/chemicalml/cml/base/atomic_basis_function.rb +35 -11
  116. data/lib/chemicalml/cml/base/band.rb +22 -7
  117. data/lib/chemicalml/cml/base/band_list.rb +15 -7
  118. data/lib/chemicalml/cml/base/basis_set.rb +26 -7
  119. data/lib/chemicalml/cml/base/bond.rb +39 -7
  120. data/lib/chemicalml/cml/base/bond_array.rb +41 -2
  121. data/lib/chemicalml/cml/base/bond_set.rb +15 -5
  122. data/lib/chemicalml/cml/base/bond_stereo.rb +25 -4
  123. data/lib/chemicalml/cml/base/bond_type.rb +24 -7
  124. data/lib/chemicalml/cml/base/bond_type_list.rb +23 -7
  125. data/lib/chemicalml/cml/base/cell_parameter.rb +30 -8
  126. data/lib/chemicalml/cml/base/cml_module.rb +36 -11
  127. data/lib/chemicalml/cml/base/common_children.rb +35 -0
  128. data/lib/chemicalml/cml/base/complex_object.rb +37 -0
  129. data/lib/chemicalml/cml/base/condition_list.rb +28 -8
  130. data/lib/chemicalml/cml/base/crystal.rb +27 -9
  131. data/lib/chemicalml/cml/base/definition.rb +12 -5
  132. data/lib/chemicalml/cml/base/description.rb +15 -5
  133. data/lib/chemicalml/cml/base/dictionary.rb +30 -7
  134. data/lib/chemicalml/cml/base/dictionary_entry.rb +67 -8
  135. data/lib/chemicalml/cml/base/dimension.rb +31 -7
  136. data/lib/chemicalml/cml/base/document.rb +18 -8
  137. data/lib/chemicalml/cml/base/documentation.rb +12 -5
  138. data/lib/chemicalml/cml/base/eigen.rb +33 -7
  139. data/lib/chemicalml/cml/base/electron.rb +29 -9
  140. data/lib/chemicalml/cml/base/enumeration.rb +41 -0
  141. data/lib/chemicalml/cml/base/expression.rb +47 -0
  142. data/lib/chemicalml/cml/base/float.rb +52 -0
  143. data/lib/chemicalml/cml/base/float_array.rb +55 -0
  144. data/lib/chemicalml/cml/base/formula.rb +31 -10
  145. data/lib/chemicalml/cml/base/fragment.rb +33 -9
  146. data/lib/chemicalml/cml/base/fragment_list.rb +26 -7
  147. data/lib/chemicalml/cml/base/gradient.rb +19 -6
  148. data/lib/chemicalml/cml/base/identifier.rb +22 -4
  149. data/lib/chemicalml/cml/base/integer.rb +52 -0
  150. data/lib/chemicalml/cml/base/integer_array.rb +55 -0
  151. data/lib/chemicalml/cml/base/isotope.rb +29 -8
  152. data/lib/chemicalml/cml/base/isotope_list.rb +18 -7
  153. data/lib/chemicalml/cml/base/join.rb +28 -6
  154. data/lib/chemicalml/cml/base/kpoint.rb +17 -6
  155. data/lib/chemicalml/cml/base/kpoint_list.rb +15 -7
  156. data/lib/chemicalml/cml/base/label.rb +15 -5
  157. data/lib/chemicalml/cml/base/lattice.rb +36 -9
  158. data/lib/chemicalml/cml/base/lattice_vector.rb +17 -6
  159. data/lib/chemicalml/cml/base/length.rb +31 -7
  160. data/lib/chemicalml/cml/base/line3.rb +21 -5
  161. data/lib/chemicalml/cml/base/link.rb +51 -10
  162. data/lib/chemicalml/cml/base/list.rb +23 -9
  163. data/lib/chemicalml/cml/base/map.rb +38 -5
  164. data/lib/chemicalml/cml/base/matrix.rb +38 -9
  165. data/lib/chemicalml/cml/base/mechanism.rb +20 -7
  166. data/lib/chemicalml/cml/base/mechanism_component.rb +14 -6
  167. data/lib/chemicalml/cml/base/metadata.rb +20 -6
  168. data/lib/chemicalml/cml/base/metadata_list.rb +30 -5
  169. data/lib/chemicalml/cml/base/molecule.rb +95 -21
  170. data/lib/chemicalml/cml/base/molecule_list.rb +27 -7
  171. data/lib/chemicalml/cml/base/name.rb +11 -3
  172. data/lib/chemicalml/cml/base/object.rb +20 -6
  173. data/lib/chemicalml/cml/base/observation.rb +18 -5
  174. data/lib/chemicalml/cml/base/operator.rb +40 -0
  175. data/lib/chemicalml/cml/base/parameter.rb +38 -8
  176. data/lib/chemicalml/cml/base/parameter_list.rb +30 -5
  177. data/lib/chemicalml/cml/base/particle.rb +23 -6
  178. data/lib/chemicalml/cml/base/peak.rb +86 -11
  179. data/lib/chemicalml/cml/base/peak_group.rb +81 -7
  180. data/lib/chemicalml/cml/base/peak_list.rb +25 -8
  181. data/lib/chemicalml/cml/base/peak_structure.rb +47 -6
  182. data/lib/chemicalml/cml/base/plane3.rb +15 -5
  183. data/lib/chemicalml/cml/base/point3.rb +15 -5
  184. data/lib/chemicalml/cml/base/potential.rb +17 -6
  185. data/lib/chemicalml/cml/base/potential_form.rb +31 -6
  186. data/lib/chemicalml/cml/base/potential_list.rb +15 -7
  187. data/lib/chemicalml/cml/base/product.rb +53 -2
  188. data/lib/chemicalml/cml/base/product_list.rb +36 -2
  189. data/lib/chemicalml/cml/base/property.rb +32 -8
  190. data/lib/chemicalml/cml/base/property_list.rb +26 -5
  191. data/lib/chemicalml/cml/base/reactant.rb +53 -2
  192. data/lib/chemicalml/cml/base/reactant_list.rb +36 -2
  193. data/lib/chemicalml/cml/base/reaction.rb +82 -12
  194. data/lib/chemicalml/cml/base/reaction_list.rb +29 -2
  195. data/lib/chemicalml/cml/base/reaction_scheme.rb +48 -8
  196. data/lib/chemicalml/cml/base/reaction_step.rb +33 -9
  197. data/lib/chemicalml/cml/base/reaction_step_list.rb +34 -7
  198. data/lib/chemicalml/cml/base/reactive_centre.rb +31 -6
  199. data/lib/chemicalml/cml/base/region.rb +24 -5
  200. data/lib/chemicalml/cml/base/related_entry.rb +34 -0
  201. data/lib/chemicalml/cml/base/sample.rb +32 -5
  202. data/lib/chemicalml/cml/base/scalar.rb +41 -6
  203. data/lib/chemicalml/cml/base/spectator.rb +26 -5
  204. data/lib/chemicalml/cml/base/spectator_list.rb +20 -7
  205. data/lib/chemicalml/cml/base/spectrum.rb +63 -12
  206. data/lib/chemicalml/cml/base/spectrum_data.rb +20 -8
  207. data/lib/chemicalml/cml/base/spectrum_list.rb +30 -7
  208. data/lib/chemicalml/cml/base/sphere3.rb +15 -5
  209. data/lib/chemicalml/cml/base/stmml.rb +12 -5
  210. data/lib/chemicalml/cml/base/string.rb +40 -0
  211. data/lib/chemicalml/cml/base/string_array.rb +52 -0
  212. data/lib/chemicalml/cml/base/substance.rb +42 -8
  213. data/lib/chemicalml/cml/base/substance_list.rb +32 -7
  214. data/lib/chemicalml/cml/base/symmetry.rb +33 -7
  215. data/lib/chemicalml/cml/base/system.rb +23 -8
  216. data/lib/chemicalml/cml/base/table.rb +43 -8
  217. data/lib/chemicalml/cml/base/table_cell.rb +12 -5
  218. data/lib/chemicalml/cml/base/table_content.rb +20 -8
  219. data/lib/chemicalml/cml/base/table_header.rb +15 -7
  220. data/lib/chemicalml/cml/base/table_header_cell.rb +27 -5
  221. data/lib/chemicalml/cml/base/table_row.rb +15 -7
  222. data/lib/chemicalml/cml/base/table_row_list.rb +15 -7
  223. data/lib/chemicalml/cml/base/tcell.rb +43 -0
  224. data/lib/chemicalml/cml/base/torsion.rb +34 -7
  225. data/lib/chemicalml/cml/base/transform3.rb +12 -5
  226. data/lib/chemicalml/cml/base/transition_state.rb +23 -5
  227. data/lib/chemicalml/cml/base/trow.rb +48 -0
  228. data/lib/chemicalml/cml/base/unit.rb +45 -10
  229. data/lib/chemicalml/cml/base/unit_list.rb +40 -6
  230. data/lib/chemicalml/cml/base/unit_type.rb +32 -5
  231. data/lib/chemicalml/cml/base/unit_type_list.rb +34 -6
  232. data/lib/chemicalml/cml/base/vector3.rb +15 -5
  233. data/lib/chemicalml/cml/base/xaxis.rb +33 -7
  234. data/lib/chemicalml/cml/base/yaxis.rb +33 -7
  235. data/lib/chemicalml/cml/base/z_matrix.rb +26 -5
  236. data/lib/chemicalml/cml/base.rb +139 -121
  237. data/lib/chemicalml/cml/canonical_comparison.rb +54 -0
  238. data/lib/chemicalml/cml/elements.rb +168 -124
  239. data/lib/chemicalml/cml/enums.rb +55 -0
  240. data/lib/chemicalml/cml/namespace.rb +2 -3
  241. data/lib/chemicalml/cml/patterns.rb +33 -0
  242. data/lib/chemicalml/cml/reference_resolver.rb +137 -0
  243. data/lib/chemicalml/cml/role/alternative.rb +10 -0
  244. data/lib/chemicalml/cml/role/annotation.rb +10 -0
  245. data/lib/chemicalml/cml/role/appinfo.rb +10 -0
  246. data/lib/chemicalml/cml/role/arg.rb +10 -0
  247. data/lib/chemicalml/cml/role/cml_module.rb +2 -3
  248. data/lib/chemicalml/cml/role/complex_object.rb +10 -0
  249. data/lib/chemicalml/cml/role/enumeration.rb +10 -0
  250. data/lib/chemicalml/cml/role/expression.rb +10 -0
  251. data/lib/chemicalml/cml/role/float.rb +10 -0
  252. data/lib/chemicalml/cml/role/float_array.rb +10 -0
  253. data/lib/chemicalml/cml/role/integer.rb +10 -0
  254. data/lib/chemicalml/cml/role/integer_array.rb +10 -0
  255. data/lib/chemicalml/cml/role/operator.rb +10 -0
  256. data/lib/chemicalml/cml/role/related_entry.rb +10 -0
  257. data/lib/chemicalml/cml/role/string.rb +10 -0
  258. data/lib/chemicalml/cml/role/string_array.rb +10 -0
  259. data/lib/chemicalml/cml/role/tcell.rb +10 -0
  260. data/lib/chemicalml/cml/role/trow.rb +10 -0
  261. data/lib/chemicalml/cml/role.rb +138 -121
  262. data/lib/chemicalml/cml/schema24/alternative.rb +14 -0
  263. data/lib/chemicalml/cml/schema24/annotation.rb +15 -0
  264. data/lib/chemicalml/cml/schema24/appinfo.rb +15 -0
  265. data/lib/chemicalml/cml/schema24/arg.rb +14 -0
  266. data/lib/chemicalml/cml/schema24/cml_module.rb +18 -0
  267. data/lib/chemicalml/cml/schema24/complex_object.rb +14 -0
  268. data/lib/chemicalml/cml/schema24/configuration.rb +15 -2
  269. data/lib/chemicalml/cml/schema24/enumeration.rb +16 -0
  270. data/lib/chemicalml/cml/schema24/expression.rb +14 -0
  271. data/lib/chemicalml/cml/schema24/float.rb +14 -0
  272. data/lib/chemicalml/cml/schema24/float_array.rb +14 -0
  273. data/lib/chemicalml/cml/schema24/integer.rb +14 -0
  274. data/lib/chemicalml/cml/schema24/integer_array.rb +14 -0
  275. data/lib/chemicalml/cml/schema24/operator.rb +14 -0
  276. data/lib/chemicalml/cml/schema24/related_entry.rb +14 -0
  277. data/lib/chemicalml/cml/schema24/string.rb +14 -0
  278. data/lib/chemicalml/cml/schema24/string_array.rb +14 -0
  279. data/lib/chemicalml/cml/schema24/tcell.rb +14 -0
  280. data/lib/chemicalml/cml/schema24/trow.rb +14 -0
  281. data/lib/chemicalml/cml/schema24.rb +154 -126
  282. data/lib/chemicalml/cml/schema3.rb +123 -123
  283. data/lib/chemicalml/cml/visitable.rb +77 -3
  284. data/lib/chemicalml/cml/wire_class_registry.rb +3 -3
  285. data/lib/chemicalml/cml.rb +164 -132
  286. data/lib/chemicalml/context_configuration.rb +12 -4
  287. data/lib/chemicalml/convention/base.rb +17 -3
  288. data/lib/chemicalml/convention/cascade/constraints/reaction_scheme_must_have_content.rb +33 -0
  289. data/lib/chemicalml/convention/cascade/constraints/reaction_step_list_must_contain_steps.rb +31 -0
  290. data/lib/chemicalml/convention/cascade/constraints/reaction_step_must_have_reaction_or_lists.rb +33 -0
  291. data/lib/chemicalml/convention/cascade/constraints/reactive_centre_atom_refs_should_be_present.rb +34 -0
  292. data/lib/chemicalml/convention/cascade/constraints.rb +18 -0
  293. data/lib/chemicalml/convention/cascade.rb +43 -0
  294. data/lib/chemicalml/convention/compchem/constraints/array_rules.rb +44 -0
  295. data/lib/chemicalml/convention/compchem/constraints/calculation_requires_finalization.rb +28 -0
  296. data/lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.rb +5 -4
  297. data/lib/chemicalml/convention/compchem/constraints/environment_at_most_one_property_list.rb +26 -0
  298. data/lib/chemicalml/convention/compchem/constraints/environment_must_not_contain_parameter.rb +28 -0
  299. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_molecule.rb +26 -0
  300. data/lib/chemicalml/convention/compchem/constraints/finalization_at_most_one_property_list.rb +26 -0
  301. data/lib/chemicalml/convention/compchem/constraints/finalization_must_have_content.rb +44 -0
  302. data/lib/chemicalml/convention/compchem/constraints/finalization_must_not_contain_parameter.rb +27 -0
  303. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_molecule.rb +26 -0
  304. data/lib/chemicalml/convention/compchem/constraints/initialization_at_most_one_parameter_list.rb +26 -0
  305. data/lib/chemicalml/convention/compchem/constraints/initialization_must_have_content.rb +54 -0
  306. data/lib/chemicalml/convention/compchem/constraints/initialization_must_not_contain_property.rb +28 -0
  307. data/lib/chemicalml/convention/compchem/constraints/job_list_module_must_have_id.rb +25 -0
  308. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_environment.rb +25 -0
  309. data/lib/chemicalml/convention/compchem/constraints/job_module_at_most_one_finalization.rb +25 -0
  310. data/lib/chemicalml/convention/compchem/constraints/job_module_must_have_id.rb +25 -0
  311. data/lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb +7 -9
  312. data/lib/chemicalml/convention/compchem/constraints/matrix_rules.rb +48 -0
  313. data/lib/chemicalml/convention/compchem/constraints/module_predicates.rb +50 -0
  314. data/lib/chemicalml/convention/compchem/constraints/scalar_units.rb +42 -0
  315. data/lib/chemicalml/convention/compchem/constraints.rb +40 -2
  316. data/lib/chemicalml/convention/compchem.rb +20 -2
  317. data/lib/chemicalml/convention/constraint.rb +68 -24
  318. data/lib/chemicalml/convention/coordinator.rb +90 -0
  319. data/lib/chemicalml/convention/detection.rb +39 -0
  320. data/lib/chemicalml/convention/dictionary/constraints/dictionary_must_have_namespace.rb +29 -0
  321. data/lib/chemicalml/convention/dictionary/constraints/dictionary_namespace_should_end_with_slash_or_hash.rb +32 -0
  322. data/lib/chemicalml/convention/dictionary/constraints/entry_id_must_match_pattern.rb +33 -0
  323. data/lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb +4 -4
  324. data/lib/chemicalml/convention/dictionary/constraints/entry_must_contain_definition.rb +29 -0
  325. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb +6 -6
  326. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_unit_type.rb +31 -0
  327. data/lib/chemicalml/convention/dictionary/constraints/entry_units_co_constraints.rb +44 -0
  328. data/lib/chemicalml/convention/dictionary/constraints.rb +14 -2
  329. data/lib/chemicalml/convention/dictionary.rb +8 -2
  330. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_be_child_of_molecule_or_formula.rb +41 -0
  331. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb +18 -9
  332. data/lib/chemicalml/convention/molecular/constraints/atom_coordinates_must_be_paired.rb +6 -6
  333. data/lib/chemicalml/convention/molecular/constraints/atom_element_type_should_be_in_periodic_table.rb +39 -0
  334. data/lib/chemicalml/convention/molecular/constraints/atom_id_must_match_pattern.rb +7 -6
  335. data/lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb +3 -2
  336. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_element_type.rb +4 -4
  337. data/lib/chemicalml/convention/molecular/constraints/atom_must_have_id.rb +5 -4
  338. data/lib/chemicalml/convention/molecular/constraints/atom_parity_atom_refs4_should_be_distinct.rb +44 -0
  339. data/lib/chemicalml/convention/molecular/constraints/atom_parity_should_include_parent_atom.rb +65 -0
  340. data/lib/chemicalml/convention/molecular/constraints/bond_array_must_be_child_of_molecule.rb +37 -0
  341. data/lib/chemicalml/convention/molecular/constraints/bond_atom_refs2_should_be_distinct.rb +44 -0
  342. data/lib/chemicalml/convention/molecular/constraints/bond_id_should_match_pattern.rb +38 -0
  343. data/lib/chemicalml/convention/molecular/constraints/bond_ids_unique_within_molecule.rb +44 -0
  344. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_atom_refs2.rb +4 -4
  345. data/lib/chemicalml/convention/molecular/constraints/bond_must_have_order.rb +5 -4
  346. data/lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb +4 -3
  347. data/lib/chemicalml/convention/molecular/constraints/bond_order_other_must_have_dict_ref.rb +34 -0
  348. data/lib/chemicalml/convention/molecular/constraints/bond_order_should_be_in_enum.rb +39 -0
  349. data/lib/chemicalml/convention/molecular/constraints/bond_order_should_not_be_numeric.rb +3 -3
  350. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_atom_refs4_should_be_distinct.rb +43 -0
  351. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_cis_trans_must_have_atom_refs4.rb +45 -0
  352. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_other_must_have_dict_ref.rb +33 -0
  353. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_should_be_in_enum.rb +38 -0
  354. data/lib/chemicalml/convention/molecular/constraints/bond_stereo_wedge_hash_must_have_atom_refs2.rb +45 -0
  355. data/lib/chemicalml/convention/molecular/constraints/dict_ref_should_resolve.rb +59 -0
  356. data/lib/chemicalml/convention/molecular/constraints/molecule_atom_array_mutually_exclusive_with_children.rb +33 -0
  357. data/lib/chemicalml/convention/molecular/constraints/molecule_bond_array_mutually_exclusive_with_children.rb +32 -0
  358. data/lib/chemicalml/convention/molecular/constraints/molecule_chirality_should_be_in_enum.rb +38 -0
  359. data/lib/chemicalml/convention/molecular/constraints/molecule_count_must_not_appear_on_top_level.rb +35 -0
  360. data/lib/chemicalml/convention/molecular/constraints/molecule_id_should_match_pattern.rb +38 -0
  361. data/lib/chemicalml/convention/molecular/constraints/molecule_must_have_id.rb +4 -4
  362. data/lib/chemicalml/convention/molecular/constraints/property_must_have_dict_ref.rb +4 -4
  363. data/lib/chemicalml/convention/molecular/constraints/property_scalar_data_type_matches_dictionary.rb +58 -0
  364. data/lib/chemicalml/convention/molecular/constraints/references_should_resolve.rb +37 -0
  365. data/lib/chemicalml/convention/molecular/constraints/scalar_must_have_data_type.rb +4 -4
  366. data/lib/chemicalml/convention/molecular/constraints.rb +59 -13
  367. data/lib/chemicalml/convention/molecular.rb +25 -2
  368. data/lib/chemicalml/convention/registry.rb +95 -10
  369. data/lib/chemicalml/convention/simple_unit/constraints/root_must_be_unit_list.rb +24 -0
  370. data/lib/chemicalml/convention/simple_unit/constraints/unit_must_have_power.rb +32 -0
  371. data/lib/chemicalml/convention/simple_unit/constraints/unit_must_have_symbol.rb +31 -0
  372. data/lib/chemicalml/convention/simple_unit/constraints.rb +16 -0
  373. data/lib/chemicalml/convention/simple_unit.rb +37 -0
  374. data/lib/chemicalml/convention/spectroscopy/constraints/peak_list_must_contain_peaks.rb +31 -0
  375. data/lib/chemicalml/convention/spectroscopy/constraints/peak_should_have_values.rb +34 -0
  376. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_content.rb +31 -0
  377. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_convention.rb +32 -0
  378. data/lib/chemicalml/convention/spectroscopy/constraints/spectrum_must_have_format.rb +31 -0
  379. data/lib/chemicalml/convention/spectroscopy/constraints.rb +20 -0
  380. data/lib/chemicalml/convention/spectroscopy.rb +41 -0
  381. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_contain_at_least_one_unit.rb +29 -0
  382. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_list_must_have_namespace.rb +36 -0
  383. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_contain_definition.rb +28 -0
  384. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_id.rb +28 -0
  385. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_multiplier_or_constant_to_si.rb +34 -0
  386. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_parent_si.rb +32 -0
  387. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb +4 -4
  388. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_title.rb +32 -0
  389. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_parent_si_should_resolve.rb +45 -0
  390. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_unit_type_should_resolve.rb +46 -0
  391. data/lib/chemicalml/convention/unit_dictionary/constraints.rb +19 -1
  392. data/lib/chemicalml/convention/unit_dictionary.rb +11 -2
  393. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_id_must_match_pattern.rb +31 -0
  394. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_contain_at_least_one_unit_type.rb +28 -0
  395. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_list_must_have_namespace.rb +35 -0
  396. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_contain_definition.rb +28 -0
  397. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb +6 -6
  398. data/lib/chemicalml/convention/unit_type_dictionary/constraints.rb +9 -1
  399. data/lib/chemicalml/convention/unit_type_dictionary.rb +6 -2
  400. data/lib/chemicalml/convention/validation_report.rb +90 -0
  401. data/lib/chemicalml/convention/violation.rb +9 -3
  402. data/lib/chemicalml/convention.rb +49 -11
  403. data/lib/chemicalml/dictionary/entry.rb +6 -6
  404. data/lib/chemicalml/dictionary/enum.rb +1 -1
  405. data/lib/chemicalml/dictionary/link.rb +3 -3
  406. data/lib/chemicalml/dictionary/loader.rb +19 -19
  407. data/lib/chemicalml/dictionary/model.rb +5 -5
  408. data/lib/chemicalml/dictionary/registry.rb +9 -9
  409. data/lib/chemicalml/dictionary.rb +13 -9
  410. data/lib/chemicalml/logger.rb +47 -0
  411. data/lib/chemicalml/schema/definition.rb +2 -2
  412. data/lib/chemicalml/schema.rb +7 -7
  413. data/lib/chemicalml/version.rb +1 -1
  414. data/lib/chemicalml/versioned_parser.rb +28 -10
  415. data/lib/chemicalml.rb +79 -17
  416. data/lib/tasks/reference_fetch.rake +30 -31
  417. data/lib/tasks/scrape_fixtures.rake +23 -24
  418. metadata +235 -35
  419. data/lib/chemicalml/cml/child_mappings.rb +0 -168
  420. data/lib/chemicalml/cml/translator/value_translations.rb +0 -270
  421. data/lib/chemicalml/cml/translator.rb +0 -484
  422. data/lib/chemicalml/model/atom.rb +0 -64
  423. data/lib/chemicalml/model/atom_parity.rb +0 -21
  424. data/lib/chemicalml/model/bond.rb +0 -39
  425. data/lib/chemicalml/model/bond_stereo.rb +0 -29
  426. data/lib/chemicalml/model/cml_array.rb +0 -27
  427. data/lib/chemicalml/model/cml_module.rb +0 -45
  428. data/lib/chemicalml/model/document.rb +0 -29
  429. data/lib/chemicalml/model/formula.rb +0 -34
  430. data/lib/chemicalml/model/identifier.rb +0 -21
  431. data/lib/chemicalml/model/label.rb +0 -21
  432. data/lib/chemicalml/model/matrix.rb +0 -29
  433. data/lib/chemicalml/model/metadata.rb +0 -23
  434. data/lib/chemicalml/model/metadata_list.rb +0 -25
  435. data/lib/chemicalml/model/molecule.rb +0 -45
  436. data/lib/chemicalml/model/name.rb +0 -21
  437. data/lib/chemicalml/model/node.rb +0 -45
  438. data/lib/chemicalml/model/parameter.rb +0 -27
  439. data/lib/chemicalml/model/parameter_list.rb +0 -25
  440. data/lib/chemicalml/model/product.rb +0 -21
  441. data/lib/chemicalml/model/product_list.rb +0 -21
  442. data/lib/chemicalml/model/property.rb +0 -28
  443. data/lib/chemicalml/model/property_list.rb +0 -25
  444. data/lib/chemicalml/model/reactant.rb +0 -21
  445. data/lib/chemicalml/model/reactant_list.rb +0 -21
  446. data/lib/chemicalml/model/reaction.rb +0 -41
  447. data/lib/chemicalml/model/reaction_list.rb +0 -23
  448. data/lib/chemicalml/model/scalar.rb +0 -25
  449. data/lib/chemicalml/model/substance.rb +0 -25
  450. data/lib/chemicalml/model.rb +0 -40
data/lib/chemicalml/cml/role/integer.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module Integer
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/integer_array.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module IntegerArray
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/operator.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module Operator
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/related_entry.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module RelatedEntry
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/string.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module String
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/string_array.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module StringArray
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/tcell.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module Tcell
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role/trow.rb ADDED
@@ -0,0 +1,10 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Role
6
+ module Trow
7
+ end
8
+ end
9
+ end
10
+ end
data/lib/chemicalml/cml/role.rb CHANGED
@@ -13,127 +13,144 @@ module Chemicalml
13
13
  #
14
14
  # Each Role module is empty — it's a pure type marker, no methods.
15
15
  module Role
16
- autoload :Array, "chemicalml/cml/role/array"
17
- autoload :Atom, "chemicalml/cml/role/atom"
18
- autoload :AtomArray, "chemicalml/cml/role/atom_array"
19
- autoload :AtomParity, "chemicalml/cml/role/atom_parity"
20
- autoload :Bond, "chemicalml/cml/role/bond"
21
- autoload :BondArray, "chemicalml/cml/role/bond_array"
22
- autoload :BondStereo, "chemicalml/cml/role/bond_stereo"
23
- autoload :Dictionary, "chemicalml/cml/role/dictionary"
24
- autoload :DictionaryEntry, "chemicalml/cml/role/dictionary_entry"
25
- autoload :Document, "chemicalml/cml/role/document"
26
- autoload :Formula, "chemicalml/cml/role/formula"
27
- autoload :Identifier, "chemicalml/cml/role/identifier"
28
- autoload :Label, "chemicalml/cml/role/label"
29
- autoload :List, "chemicalml/cml/role/list"
30
- autoload :Matrix, "chemicalml/cml/role/matrix"
31
- autoload :Metadata, "chemicalml/cml/role/metadata"
32
- autoload :MetadataList, "chemicalml/cml/role/metadata_list"
33
- autoload :Module, "chemicalml/cml/role/cml_module"
34
- autoload :Molecule, "chemicalml/cml/role/molecule"
35
- autoload :Name, "chemicalml/cml/role/name"
36
- autoload :Parameter, "chemicalml/cml/role/parameter"
37
- autoload :ParameterList, "chemicalml/cml/role/parameter_list"
38
- autoload :Product, "chemicalml/cml/role/product"
39
- autoload :ProductList, "chemicalml/cml/role/product_list"
40
- autoload :Property, "chemicalml/cml/role/property"
41
- autoload :PropertyList, "chemicalml/cml/role/property_list"
42
- autoload :Reaction, "chemicalml/cml/role/reaction"
43
- autoload :ReactionList, "chemicalml/cml/role/reaction_list"
44
- autoload :Reactant, "chemicalml/cml/role/reactant"
45
- autoload :ReactantList, "chemicalml/cml/role/reactant_list"
46
- autoload :Scalar, "chemicalml/cml/role/scalar"
47
- autoload :Substance, "chemicalml/cml/role/substance"
48
- autoload :Unit, "chemicalml/cml/role/unit"
49
- autoload :UnitList, "chemicalml/cml/role/unit_list"
50
- autoload :UnitType, "chemicalml/cml/role/unit_type"
51
- autoload :UnitTypeList, "chemicalml/cml/role/unit_type_list"
52
- autoload :Abundance, "chemicalml/cml/role/abundance"
53
- autoload :Action, "chemicalml/cml/role/action"
54
- autoload :ActionList, "chemicalml/cml/role/action_list"
55
- autoload :Amount, "chemicalml/cml/role/amount"
56
- autoload :Angle, "chemicalml/cml/role/angle"
57
- autoload :AnyCml, "chemicalml/cml/role/any_cml"
58
- autoload :ArrayList, "chemicalml/cml/role/array_list"
59
- autoload :AtomSet, "chemicalml/cml/role/atom_set"
60
- autoload :AtomType, "chemicalml/cml/role/atom_type"
61
- autoload :AtomTypeList, "chemicalml/cml/role/atom_type_list"
62
- autoload :AtomicBasisFunction, "chemicalml/cml/role/atomic_basis_function"
63
- autoload :Band, "chemicalml/cml/role/band"
64
- autoload :BandList, "chemicalml/cml/role/band_list"
65
- autoload :BasisSet, "chemicalml/cml/role/basis_set"
66
- autoload :BondSet, "chemicalml/cml/role/bond_set"
67
- autoload :BondType, "chemicalml/cml/role/bond_type"
68
- autoload :BondTypeList, "chemicalml/cml/role/bond_type_list"
69
- autoload :CellParameter, "chemicalml/cml/role/cell_parameter"
70
- autoload :ConditionList, "chemicalml/cml/role/condition_list"
71
- autoload :Crystal, "chemicalml/cml/role/crystal"
72
- autoload :Definition, "chemicalml/cml/role/definition"
73
- autoload :Description, "chemicalml/cml/role/description"
74
- autoload :Dimension, "chemicalml/cml/role/dimension"
75
- autoload :Documentation, "chemicalml/cml/role/documentation"
76
- autoload :Eigen, "chemicalml/cml/role/eigen"
77
- autoload :Electron, "chemicalml/cml/role/electron"
78
- autoload :Fragment, "chemicalml/cml/role/fragment"
79
- autoload :FragmentList, "chemicalml/cml/role/fragment_list"
80
- autoload :Gradient, "chemicalml/cml/role/gradient"
81
- autoload :Isotope, "chemicalml/cml/role/isotope"
82
- autoload :IsotopeList, "chemicalml/cml/role/isotope_list"
83
- autoload :Join, "chemicalml/cml/role/join"
84
- autoload :Kpoint, "chemicalml/cml/role/kpoint"
85
- autoload :KpointList, "chemicalml/cml/role/kpoint_list"
86
- autoload :Lattice, "chemicalml/cml/role/lattice"
87
- autoload :LatticeVector, "chemicalml/cml/role/lattice_vector"
88
- autoload :Length, "chemicalml/cml/role/length"
89
- autoload :Line3, "chemicalml/cml/role/line3"
90
- autoload :Link, "chemicalml/cml/role/link"
91
- autoload :Map, "chemicalml/cml/role/map"
92
- autoload :Mechanism, "chemicalml/cml/role/mechanism"
93
- autoload :MechanismComponent, "chemicalml/cml/role/mechanism_component"
94
- autoload :MoleculeList, "chemicalml/cml/role/molecule_list"
95
- autoload :Object, "chemicalml/cml/role/object"
96
- autoload :Observation, "chemicalml/cml/role/observation"
97
- autoload :Particle, "chemicalml/cml/role/particle"
98
- autoload :Peak, "chemicalml/cml/role/peak"
99
- autoload :PeakGroup, "chemicalml/cml/role/peak_group"
100
- autoload :PeakList, "chemicalml/cml/role/peak_list"
101
- autoload :PeakStructure, "chemicalml/cml/role/peak_structure"
102
- autoload :Plane3, "chemicalml/cml/role/plane3"
103
- autoload :Point3, "chemicalml/cml/role/point3"
104
- autoload :Potential, "chemicalml/cml/role/potential"
105
- autoload :PotentialForm, "chemicalml/cml/role/potential_form"
106
- autoload :PotentialList, "chemicalml/cml/role/potential_list"
107
- autoload :ReactionScheme, "chemicalml/cml/role/reaction_scheme"
108
- autoload :ReactionStep, "chemicalml/cml/role/reaction_step"
109
- autoload :ReactionStepList, "chemicalml/cml/role/reaction_step_list"
110
- autoload :ReactiveCentre, "chemicalml/cml/role/reactive_centre"
111
- autoload :Region, "chemicalml/cml/role/region"
112
- autoload :Sample, "chemicalml/cml/role/sample"
113
- autoload :Spectator, "chemicalml/cml/role/spectator"
114
- autoload :SpectatorList, "chemicalml/cml/role/spectator_list"
115
- autoload :Spectrum, "chemicalml/cml/role/spectrum"
116
- autoload :SpectrumData, "chemicalml/cml/role/spectrum_data"
117
- autoload :SpectrumList, "chemicalml/cml/role/spectrum_list"
118
- autoload :Sphere3, "chemicalml/cml/role/sphere3"
119
- autoload :Stmml, "chemicalml/cml/role/stmml"
120
- autoload :SubstanceList, "chemicalml/cml/role/substance_list"
121
- autoload :Symmetry, "chemicalml/cml/role/symmetry"
122
- autoload :System, "chemicalml/cml/role/system"
123
- autoload :Table, "chemicalml/cml/role/table"
124
- autoload :TableCell, "chemicalml/cml/role/table_cell"
125
- autoload :TableContent, "chemicalml/cml/role/table_content"
126
- autoload :TableHeader, "chemicalml/cml/role/table_header"
127
- autoload :TableHeaderCell, "chemicalml/cml/role/table_header_cell"
128
- autoload :TableRow, "chemicalml/cml/role/table_row"
129
- autoload :TableRowList, "chemicalml/cml/role/table_row_list"
130
- autoload :Torsion, "chemicalml/cml/role/torsion"
131
- autoload :Transform3, "chemicalml/cml/role/transform3"
132
- autoload :TransitionState, "chemicalml/cml/role/transition_state"
133
- autoload :Vector3, "chemicalml/cml/role/vector3"
134
- autoload :Xaxis, "chemicalml/cml/role/xaxis"
135
- autoload :Yaxis, "chemicalml/cml/role/yaxis"
136
- autoload :ZMatrix, "chemicalml/cml/role/z_matrix"
16
+ autoload :Array, 'chemicalml/cml/role/array'
17
+ autoload :Atom, 'chemicalml/cml/role/atom'
18
+ autoload :AtomArray, 'chemicalml/cml/role/atom_array'
19
+ autoload :AtomParity, 'chemicalml/cml/role/atom_parity'
20
+ autoload :Bond, 'chemicalml/cml/role/bond'
21
+ autoload :BondArray, 'chemicalml/cml/role/bond_array'
22
+ autoload :BondStereo, 'chemicalml/cml/role/bond_stereo'
23
+ autoload :Dictionary, 'chemicalml/cml/role/dictionary'
24
+ autoload :DictionaryEntry, 'chemicalml/cml/role/dictionary_entry'
25
+ autoload :Document, 'chemicalml/cml/role/document'
26
+ autoload :Formula, 'chemicalml/cml/role/formula'
27
+ autoload :Identifier, 'chemicalml/cml/role/identifier'
28
+ autoload :Label, 'chemicalml/cml/role/label'
29
+ autoload :List, 'chemicalml/cml/role/list'
30
+ autoload :Matrix, 'chemicalml/cml/role/matrix'
31
+ autoload :Metadata, 'chemicalml/cml/role/metadata'
32
+ autoload :MetadataList, 'chemicalml/cml/role/metadata_list'
33
+ autoload :Module, 'chemicalml/cml/role/cml_module'
34
+ autoload :Molecule, 'chemicalml/cml/role/molecule'
35
+ autoload :Name, 'chemicalml/cml/role/name'
36
+ autoload :Parameter, 'chemicalml/cml/role/parameter'
37
+ autoload :ParameterList, 'chemicalml/cml/role/parameter_list'
38
+ autoload :Product, 'chemicalml/cml/role/product'
39
+ autoload :ProductList, 'chemicalml/cml/role/product_list'
40
+ autoload :Property, 'chemicalml/cml/role/property'
41
+ autoload :PropertyList, 'chemicalml/cml/role/property_list'
42
+ autoload :Reaction, 'chemicalml/cml/role/reaction'
43
+ autoload :ReactionList, 'chemicalml/cml/role/reaction_list'
44
+ autoload :Reactant, 'chemicalml/cml/role/reactant'
45
+ autoload :ReactantList, 'chemicalml/cml/role/reactant_list'
46
+ autoload :Scalar, 'chemicalml/cml/role/scalar'
47
+ autoload :Substance, 'chemicalml/cml/role/substance'
48
+ autoload :Unit, 'chemicalml/cml/role/unit'
49
+ autoload :UnitList, 'chemicalml/cml/role/unit_list'
50
+ autoload :UnitType, 'chemicalml/cml/role/unit_type'
51
+ autoload :UnitTypeList, 'chemicalml/cml/role/unit_type_list'
52
+ autoload :Abundance, 'chemicalml/cml/role/abundance'
53
+ autoload :Action, 'chemicalml/cml/role/action'
54
+ autoload :ActionList, 'chemicalml/cml/role/action_list'
55
+ autoload :Amount, 'chemicalml/cml/role/amount'
56
+ autoload :Angle, 'chemicalml/cml/role/angle'
57
+ autoload :AnyCml, 'chemicalml/cml/role/any_cml'
58
+ autoload :ArrayList, 'chemicalml/cml/role/array_list'
59
+ autoload :AtomSet, 'chemicalml/cml/role/atom_set'
60
+ autoload :AtomType, 'chemicalml/cml/role/atom_type'
61
+ autoload :AtomTypeList, 'chemicalml/cml/role/atom_type_list'
62
+ autoload :AtomicBasisFunction, 'chemicalml/cml/role/atomic_basis_function'
63
+ autoload :Band, 'chemicalml/cml/role/band'
64
+ autoload :BandList, 'chemicalml/cml/role/band_list'
65
+ autoload :BasisSet, 'chemicalml/cml/role/basis_set'
66
+ autoload :BondSet, 'chemicalml/cml/role/bond_set'
67
+ autoload :BondType, 'chemicalml/cml/role/bond_type'
68
+ autoload :BondTypeList, 'chemicalml/cml/role/bond_type_list'
69
+ autoload :CellParameter, 'chemicalml/cml/role/cell_parameter'
70
+ autoload :ConditionList, 'chemicalml/cml/role/condition_list'
71
+ autoload :Crystal, 'chemicalml/cml/role/crystal'
72
+ autoload :Definition, 'chemicalml/cml/role/definition'
73
+ autoload :Description, 'chemicalml/cml/role/description'
74
+ autoload :Dimension, 'chemicalml/cml/role/dimension'
75
+ autoload :Documentation, 'chemicalml/cml/role/documentation'
76
+ autoload :Eigen, 'chemicalml/cml/role/eigen'
77
+ autoload :Electron, 'chemicalml/cml/role/electron'
78
+ autoload :Fragment, 'chemicalml/cml/role/fragment'
79
+ autoload :FragmentList, 'chemicalml/cml/role/fragment_list'
80
+ autoload :Gradient, 'chemicalml/cml/role/gradient'
81
+ autoload :Isotope, 'chemicalml/cml/role/isotope'
82
+ autoload :IsotopeList, 'chemicalml/cml/role/isotope_list'
83
+ autoload :Join, 'chemicalml/cml/role/join'
84
+ autoload :Kpoint, 'chemicalml/cml/role/kpoint'
85
+ autoload :KpointList, 'chemicalml/cml/role/kpoint_list'
86
+ autoload :Lattice, 'chemicalml/cml/role/lattice'
87
+ autoload :LatticeVector, 'chemicalml/cml/role/lattice_vector'
88
+ autoload :Length, 'chemicalml/cml/role/length'
89
+ autoload :Line3, 'chemicalml/cml/role/line3'
90
+ autoload :Link, 'chemicalml/cml/role/link'
91
+ autoload :Map, 'chemicalml/cml/role/map'
92
+ autoload :Mechanism, 'chemicalml/cml/role/mechanism'
93
+ autoload :MechanismComponent, 'chemicalml/cml/role/mechanism_component'
94
+ autoload :MoleculeList, 'chemicalml/cml/role/molecule_list'
95
+ autoload :Object, 'chemicalml/cml/role/object'
96
+ autoload :Observation, 'chemicalml/cml/role/observation'
97
+ autoload :Particle, 'chemicalml/cml/role/particle'
98
+ autoload :Peak, 'chemicalml/cml/role/peak'
99
+ autoload :PeakGroup, 'chemicalml/cml/role/peak_group'
100
+ autoload :PeakList, 'chemicalml/cml/role/peak_list'
101
+ autoload :PeakStructure, 'chemicalml/cml/role/peak_structure'
102
+ autoload :Plane3, 'chemicalml/cml/role/plane3'
103
+ autoload :Point3, 'chemicalml/cml/role/point3'
104
+ autoload :Potential, 'chemicalml/cml/role/potential'
105
+ autoload :PotentialForm, 'chemicalml/cml/role/potential_form'
106
+ autoload :PotentialList, 'chemicalml/cml/role/potential_list'
107
+ autoload :ReactionScheme, 'chemicalml/cml/role/reaction_scheme'
108
+ autoload :ReactionStep, 'chemicalml/cml/role/reaction_step'
109
+ autoload :ReactionStepList, 'chemicalml/cml/role/reaction_step_list'
110
+ autoload :ReactiveCentre, 'chemicalml/cml/role/reactive_centre'
111
+ autoload :Region, 'chemicalml/cml/role/region'
112
+ autoload :Sample, 'chemicalml/cml/role/sample'
113
+ autoload :Spectator, 'chemicalml/cml/role/spectator'
114
+ autoload :SpectatorList, 'chemicalml/cml/role/spectator_list'
115
+ autoload :Spectrum, 'chemicalml/cml/role/spectrum'
116
+ autoload :SpectrumData, 'chemicalml/cml/role/spectrum_data'
117
+ autoload :SpectrumList, 'chemicalml/cml/role/spectrum_list'
118
+ autoload :Sphere3, 'chemicalml/cml/role/sphere3'
119
+ autoload :Stmml, 'chemicalml/cml/role/stmml'
120
+ autoload :SubstanceList, 'chemicalml/cml/role/substance_list'
121
+ autoload :Symmetry, 'chemicalml/cml/role/symmetry'
122
+ autoload :System, 'chemicalml/cml/role/system'
123
+ autoload :Table, 'chemicalml/cml/role/table'
124
+ autoload :TableCell, 'chemicalml/cml/role/table_cell'
125
+ autoload :TableContent, 'chemicalml/cml/role/table_content'
126
+ autoload :TableHeader, 'chemicalml/cml/role/table_header'
127
+ autoload :TableHeaderCell, 'chemicalml/cml/role/table_header_cell'
128
+ autoload :TableRow, 'chemicalml/cml/role/table_row'
129
+ autoload :TableRowList, 'chemicalml/cml/role/table_row_list'
130
+ autoload :Torsion, 'chemicalml/cml/role/torsion'
131
+ autoload :Transform3, 'chemicalml/cml/role/transform3'
132
+ autoload :TransitionState, 'chemicalml/cml/role/transition_state'
133
+ autoload :Vector3, 'chemicalml/cml/role/vector3'
134
+ autoload :Xaxis, 'chemicalml/cml/role/xaxis'
135
+ autoload :Yaxis, 'chemicalml/cml/role/yaxis'
136
+ autoload :ZMatrix, 'chemicalml/cml/role/z_matrix'
137
+ autoload :Alternative, 'chemicalml/cml/role/alternative'
138
+ autoload :Arg, 'chemicalml/cml/role/arg'
139
+ autoload :ComplexObject, 'chemicalml/cml/role/complex_object'
140
+ autoload :Expression, 'chemicalml/cml/role/expression'
141
+ autoload :Float, 'chemicalml/cml/role/float'
142
+ autoload :FloatArray, 'chemicalml/cml/role/float_array'
143
+ autoload :Integer, 'chemicalml/cml/role/integer'
144
+ autoload :IntegerArray, 'chemicalml/cml/role/integer_array'
145
+ autoload :Operator, 'chemicalml/cml/role/operator'
146
+ autoload :RelatedEntry, 'chemicalml/cml/role/related_entry'
147
+ autoload :String, 'chemicalml/cml/role/string'
148
+ autoload :StringArray, 'chemicalml/cml/role/string_array'
149
+ autoload :Tcell, 'chemicalml/cml/role/tcell'
150
+ autoload :Trow, 'chemicalml/cml/role/trow'
151
+ autoload :Annotation, 'chemicalml/cml/role/annotation'
152
+ autoload :Appinfo, 'chemicalml/cml/role/appinfo'
153
+ autoload :Enumeration, 'chemicalml/cml/role/enumeration'
137
154
  end
138
155
  end
139
156
  end
data/lib/chemicalml/cml/schema24/alternative.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Alternative < Lutaml::Model::Serializable
8
+ include Base::Alternative
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/annotation.rb ADDED
@@ -0,0 +1,15 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. `<annotation>` wraps documentation for an
7
+ # entry or element. Not in Schema 3.
8
+ class Annotation < Lutaml::Model::Serializable
9
+ include Base::Annotation
10
+ include Visitable
11
+ extend Context
12
+ end
13
+ end
14
+ end
15
+ end
data/lib/chemicalml/cml/schema24/appinfo.rb ADDED
@@ -0,0 +1,15 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. `<appinfo>` carries application-specific
7
+ # metadata. Not in Schema 3.
8
+ class Appinfo < Lutaml::Model::Serializable
9
+ include Base::Appinfo
10
+ include Visitable
11
+ extend Context
12
+ end
13
+ end
14
+ end
15
+ end
data/lib/chemicalml/cml/schema24/arg.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Arg < Lutaml::Model::Serializable
8
+ include Base::Arg
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/cml_module.rb ADDED
@@ -0,0 +1,18 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # CML <module> wire class. Schema 2.4 declares <module> in its
7
+ # XSD (verified against `reference-docs/schemas/schema24/`), so
8
+ # this class exists and is registered by `Schema24::Configuration`.
9
+ # See `Chemicalml::Cml::Base::Module` for the shared attribute
10
+ # + xml-mapping declarations.
11
+ class Module < Lutaml::Model::Serializable
12
+ include Base::Module
13
+ include Visitable
14
+ extend Context
15
+ end
16
+ end
17
+ end
18
+ end
data/lib/chemicalml/cml/schema24/complex_object.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class ComplexObject < Lutaml::Model::Serializable
8
+ include Base::ComplexObject
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/configuration.rb CHANGED
@@ -8,10 +8,23 @@ module Chemicalml
8
8
 
9
9
  CONTEXT_ID = :chemicalml_schema24
10
10
 
11
- # Schema 2.4 lacks the generic <module> element (introduced
12
- # in Schema 3) — skip its registration.
11
+ # Schema 2.4 lacks <anyCml> (Schema 3 only) — skip its
12
+ # registration. Schema 2.4 also declares three legacy
13
+ # elements (<annotation>, <appinfo>, <enumeration>) not in
14
+ # Schema 3; register those explicitly from SCHEMA24_ONLY.
15
+ #
16
+ # Also skip registering <float>, <integer>, <string> as
17
+ # types — their ids collide with lutaml-model primitives
18
+ # (:float, :integer, :string), and registering them would
19
+ # shadow the primitive, breaking every attribute typed as
20
+ # :string in any Schema24 wire class. They remain defined
21
+ # as wire classes and parseable as document roots.
13
22
  def self.register_models!
14
23
  register_elements!(except: Chemicalml::Cml::Elements::SCHEMA3_ONLY)
24
+ register_elements!(
25
+ only: true,
26
+ except: Chemicalml::Cml::Elements::SCHEMA24_TYPE_COLLISIONS
27
+ )
15
28
  end
16
29
  end
17
30
  end
data/lib/chemicalml/cml/schema24/enumeration.rb ADDED
@@ -0,0 +1,16 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. `<enumeration>` declares a closed/open set of
7
+ # values for a dictionary entry. Not in Schema 3 (Schema 3 uses
8
+ # the `enum` attribute on `<entry>`).
9
+ class Enumeration < Lutaml::Model::Serializable
10
+ include Base::Enumeration
11
+ include Visitable
12
+ extend Context
13
+ end
14
+ end
15
+ end
16
+ end
data/lib/chemicalml/cml/schema24/expression.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Expression < Lutaml::Model::Serializable
8
+ include Base::Expression
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/float.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Float < Lutaml::Model::Serializable
8
+ include Base::Float
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/float_array.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class FloatArray < Lutaml::Model::Serializable
8
+ include Base::FloatArray
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/integer.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Integer < Lutaml::Model::Serializable
8
+ include Base::Integer
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/integer_array.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class IntegerArray < Lutaml::Model::Serializable
8
+ include Base::IntegerArray
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/operator.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class Operator < Lutaml::Model::Serializable
8
+ include Base::Operator
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/related_entry.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class RelatedEntry < Lutaml::Model::Serializable
8
+ include Base::RelatedEntry
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end
data/lib/chemicalml/cml/schema24/string.rb ADDED
@@ -0,0 +1,14 @@
1
+ # frozen_string_literal: true
2
+
3
+ module Chemicalml
4
+ module Cml
5
+ module Schema24
6
+ # Schema 2.4 only. Not in Schema 3.
7
+ class String < Lutaml::Model::Serializable
8
+ include Base::String
9
+ include Visitable
10
+ extend Context
11
+ end
12
+ end
13
+ end
14
+ end