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/model.rb DELETED
@@ -1,40 +0,0 @@
1
- # frozen_string_literal: true
2
-
3
- module Chemicalml
4
- # Canonical chemistry representation model. Format-agnostic plain
5
- # Ruby classes; not tied to any wire format.
6
- #
7
- # Every adapter (CML XML, AsciiChem text, future SMILES/InChI/MOL)
8
- # speaks the canonical model. Adapters never talk to each other
9
- # directly — only through these classes.
10
- module Model
11
- autoload :Array, "chemicalml/model/cml_array"
12
- autoload :Atom, "chemicalml/model/atom"
13
- autoload :AtomParity, "chemicalml/model/atom_parity"
14
- autoload :Bond, "chemicalml/model/bond"
15
- autoload :BondStereo, "chemicalml/model/bond_stereo"
16
- autoload :Document, "chemicalml/model/document"
17
- autoload :Formula, "chemicalml/model/formula"
18
- autoload :Identifier, "chemicalml/model/identifier"
19
- autoload :Label, "chemicalml/model/label"
20
- autoload :Matrix, "chemicalml/model/matrix"
21
- autoload :Metadata, "chemicalml/model/metadata"
22
- autoload :MetadataList, "chemicalml/model/metadata_list"
23
- autoload :Module, "chemicalml/model/cml_module"
24
- autoload :Molecule, "chemicalml/model/molecule"
25
- autoload :Name, "chemicalml/model/name"
26
- autoload :Node, "chemicalml/model/node"
27
- autoload :Parameter, "chemicalml/model/parameter"
28
- autoload :ParameterList, "chemicalml/model/parameter_list"
29
- autoload :Product, "chemicalml/model/product"
30
- autoload :ProductList, "chemicalml/model/product_list"
31
- autoload :Property, "chemicalml/model/property"
32
- autoload :PropertyList, "chemicalml/model/property_list"
33
- autoload :Reaction, "chemicalml/model/reaction"
34
- autoload :ReactionList, "chemicalml/model/reaction_list"
35
- autoload :Reactant, "chemicalml/model/reactant"
36
- autoload :ReactantList, "chemicalml/model/reactant_list"
37
- autoload :Scalar, "chemicalml/model/scalar"
38
- autoload :Substance, "chemicalml/model/substance"
39
- end
40
- end