chemicalml 0.1.0

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 (248) hide show
  1. checksums.yaml +7 -0
  2. data/.gitignore +11 -0
  3. data/.rubocop.yml +20 -0
  4. data/CHANGELOG.md +21 -0
  5. data/CLAUDE.md +198 -0
  6. data/Gemfile +14 -0
  7. data/LICENSE +24 -0
  8. data/NOTICES.adoc +115 -0
  9. data/README.adoc +87 -0
  10. data/Rakefile +8 -0
  11. data/TODO.align/01-cml-base-mixins.md +122 -0
  12. data/TODO.align/02-real-schema-hierarchies.md +88 -0
  13. data/TODO.align/03-configuration.md +50 -0
  14. data/TODO.align/04-parse-entry-points.md +59 -0
  15. data/TODO.align/05-schema-aware-translator.md +33 -0
  16. data/TODO.align/06-no-respond-to.md +44 -0
  17. data/TODO.align/07-canon-xml-comparison.md +43 -0
  18. data/TODO.align/08-expand-fixtures.md +37 -0
  19. data/TODO.align/09-final-spec-lint.md +29 -0
  20. data/TODO.align/10-role-marker-modules.md +54 -0
  21. data/TODO.align/11-dry-configuration.md +63 -0
  22. data/TODO.align/12-wire-class-macro.md +51 -0
  23. data/TODO.align/13-wire-namespace.md +44 -0
  24. data/TODO.align/14-schema24-correctness.md +37 -0
  25. data/TODO.align/15-canon-fixture-roundtrip.md +38 -0
  26. data/TODO.align/16-schema24-convention-coverage.md +33 -0
  27. data/TODO.align/17-final-spec-lint.md +28 -0
  28. data/TODO.align/README.md +27 -0
  29. data/TODO.align/README.round2.md +24 -0
  30. data/TODO.cml-full/01-reference-docs.md +43 -0
  31. data/TODO.cml-full/02-schema-versioned-model.md +70 -0
  32. data/TODO.cml-full/03-fixtures-scrape.md +52 -0
  33. data/TODO.cml-full/04-convention-framework.md +69 -0
  34. data/TODO.cml-full/05-dictionary-layer.md +77 -0
  35. data/TODO.cml-full/06-extend-canonical-translator.md +60 -0
  36. data/TODO.cml-full/07-attribution-notices.md +42 -0
  37. data/TODO.cml-full/08-autoload-only.md +48 -0
  38. data/TODO.cml-full/09-spec-coverage.md +38 -0
  39. data/TODO.cml-full/README.md +23 -0
  40. data/chemicalml.gemspec +35 -0
  41. data/data/dictionaries/_index.yaml +14 -0
  42. data/data/dictionaries/compchem.yaml +481 -0
  43. data/data/dictionaries/unit_non_si.yaml +53 -0
  44. data/data/dictionaries/unit_si.yaml +87 -0
  45. data/data/dictionaries/unit_type.yaml +113 -0
  46. data/lib/chemicalml/cml/array.rb +10 -0
  47. data/lib/chemicalml/cml/atom.rb +10 -0
  48. data/lib/chemicalml/cml/atom_array.rb +10 -0
  49. data/lib/chemicalml/cml/atom_parity.rb +10 -0
  50. data/lib/chemicalml/cml/base/array.rb +36 -0
  51. data/lib/chemicalml/cml/base/atom.rb +38 -0
  52. data/lib/chemicalml/cml/base/atom_array.rb +22 -0
  53. data/lib/chemicalml/cml/base/atom_parity.rb +24 -0
  54. data/lib/chemicalml/cml/base/bond.rb +28 -0
  55. data/lib/chemicalml/cml/base/bond_array.rb +22 -0
  56. data/lib/chemicalml/cml/base/bond_stereo.rb +28 -0
  57. data/lib/chemicalml/cml/base/cml_module.rb +40 -0
  58. data/lib/chemicalml/cml/base/dictionary.rb +32 -0
  59. data/lib/chemicalml/cml/base/dictionary_entry.rb +34 -0
  60. data/lib/chemicalml/cml/base/document.rb +26 -0
  61. data/lib/chemicalml/cml/base/formula.rb +38 -0
  62. data/lib/chemicalml/cml/base/identifier.rb +26 -0
  63. data/lib/chemicalml/cml/base/label.rb +28 -0
  64. data/lib/chemicalml/cml/base/list.rb +36 -0
  65. data/lib/chemicalml/cml/base/matrix.rb +38 -0
  66. data/lib/chemicalml/cml/base/metadata.rb +30 -0
  67. data/lib/chemicalml/cml/base/metadata_list.rb +28 -0
  68. data/lib/chemicalml/cml/base/molecule.rb +40 -0
  69. data/lib/chemicalml/cml/base/name.rb +26 -0
  70. data/lib/chemicalml/cml/base/parameter.rb +34 -0
  71. data/lib/chemicalml/cml/base/parameter_list.rb +28 -0
  72. data/lib/chemicalml/cml/base/product.rb +22 -0
  73. data/lib/chemicalml/cml/base/product_list.rb +22 -0
  74. data/lib/chemicalml/cml/base/property.rb +34 -0
  75. data/lib/chemicalml/cml/base/property_list.rb +28 -0
  76. data/lib/chemicalml/cml/base/reactant.rb +22 -0
  77. data/lib/chemicalml/cml/base/reactant_list.rb +22 -0
  78. data/lib/chemicalml/cml/base/reaction.rb +32 -0
  79. data/lib/chemicalml/cml/base/reaction_list.rb +22 -0
  80. data/lib/chemicalml/cml/base/scalar.rb +32 -0
  81. data/lib/chemicalml/cml/base/substance.rb +30 -0
  82. data/lib/chemicalml/cml/base/unit.rb +38 -0
  83. data/lib/chemicalml/cml/base/unit_list.rb +30 -0
  84. data/lib/chemicalml/cml/base/unit_type.rb +28 -0
  85. data/lib/chemicalml/cml/base/unit_type_list.rb +30 -0
  86. data/lib/chemicalml/cml/base.rb +51 -0
  87. data/lib/chemicalml/cml/bond.rb +10 -0
  88. data/lib/chemicalml/cml/bond_array.rb +10 -0
  89. data/lib/chemicalml/cml/bond_stereo.rb +10 -0
  90. data/lib/chemicalml/cml/cml_module.rb +10 -0
  91. data/lib/chemicalml/cml/dictionary.rb +10 -0
  92. data/lib/chemicalml/cml/dictionary_entry.rb +10 -0
  93. data/lib/chemicalml/cml/document.rb +10 -0
  94. data/lib/chemicalml/cml/elements.rb +58 -0
  95. data/lib/chemicalml/cml/formula.rb +10 -0
  96. data/lib/chemicalml/cml/identifier.rb +10 -0
  97. data/lib/chemicalml/cml/label.rb +10 -0
  98. data/lib/chemicalml/cml/list.rb +10 -0
  99. data/lib/chemicalml/cml/matrix.rb +10 -0
  100. data/lib/chemicalml/cml/metadata.rb +10 -0
  101. data/lib/chemicalml/cml/metadata_list.rb +10 -0
  102. data/lib/chemicalml/cml/molecule.rb +10 -0
  103. data/lib/chemicalml/cml/name.rb +10 -0
  104. data/lib/chemicalml/cml/namespace.rb +17 -0
  105. data/lib/chemicalml/cml/parameter.rb +10 -0
  106. data/lib/chemicalml/cml/parameter_list.rb +10 -0
  107. data/lib/chemicalml/cml/product.rb +10 -0
  108. data/lib/chemicalml/cml/product_list.rb +10 -0
  109. data/lib/chemicalml/cml/property.rb +10 -0
  110. data/lib/chemicalml/cml/property_list.rb +10 -0
  111. data/lib/chemicalml/cml/reactant.rb +10 -0
  112. data/lib/chemicalml/cml/reactant_list.rb +10 -0
  113. data/lib/chemicalml/cml/reaction.rb +10 -0
  114. data/lib/chemicalml/cml/reaction_list.rb +10 -0
  115. data/lib/chemicalml/cml/role/array.rb +13 -0
  116. data/lib/chemicalml/cml/role/atom.rb +13 -0
  117. data/lib/chemicalml/cml/role/atom_array.rb +13 -0
  118. data/lib/chemicalml/cml/role/atom_parity.rb +13 -0
  119. data/lib/chemicalml/cml/role/bond.rb +13 -0
  120. data/lib/chemicalml/cml/role/bond_array.rb +13 -0
  121. data/lib/chemicalml/cml/role/bond_stereo.rb +13 -0
  122. data/lib/chemicalml/cml/role/cml_module.rb +14 -0
  123. data/lib/chemicalml/cml/role/dictionary.rb +13 -0
  124. data/lib/chemicalml/cml/role/dictionary_entry.rb +13 -0
  125. data/lib/chemicalml/cml/role/document.rb +13 -0
  126. data/lib/chemicalml/cml/role/formula.rb +13 -0
  127. data/lib/chemicalml/cml/role/identifier.rb +13 -0
  128. data/lib/chemicalml/cml/role/label.rb +13 -0
  129. data/lib/chemicalml/cml/role/list.rb +13 -0
  130. data/lib/chemicalml/cml/role/matrix.rb +13 -0
  131. data/lib/chemicalml/cml/role/metadata.rb +13 -0
  132. data/lib/chemicalml/cml/role/metadata_list.rb +13 -0
  133. data/lib/chemicalml/cml/role/molecule.rb +13 -0
  134. data/lib/chemicalml/cml/role/name.rb +13 -0
  135. data/lib/chemicalml/cml/role/parameter.rb +13 -0
  136. data/lib/chemicalml/cml/role/parameter_list.rb +13 -0
  137. data/lib/chemicalml/cml/role/product.rb +13 -0
  138. data/lib/chemicalml/cml/role/product_list.rb +13 -0
  139. data/lib/chemicalml/cml/role/property.rb +13 -0
  140. data/lib/chemicalml/cml/role/property_list.rb +13 -0
  141. data/lib/chemicalml/cml/role/reactant.rb +13 -0
  142. data/lib/chemicalml/cml/role/reactant_list.rb +13 -0
  143. data/lib/chemicalml/cml/role/reaction.rb +13 -0
  144. data/lib/chemicalml/cml/role/reaction_list.rb +13 -0
  145. data/lib/chemicalml/cml/role/scalar.rb +13 -0
  146. data/lib/chemicalml/cml/role/substance.rb +13 -0
  147. data/lib/chemicalml/cml/role/unit.rb +13 -0
  148. data/lib/chemicalml/cml/role/unit_list.rb +13 -0
  149. data/lib/chemicalml/cml/role/unit_type.rb +13 -0
  150. data/lib/chemicalml/cml/role/unit_type_list.rb +13 -0
  151. data/lib/chemicalml/cml/role.rb +54 -0
  152. data/lib/chemicalml/cml/scalar.rb +10 -0
  153. data/lib/chemicalml/cml/schema24/configuration.rb +19 -0
  154. data/lib/chemicalml/cml/schema24.rb +40 -0
  155. data/lib/chemicalml/cml/schema3/configuration.rb +17 -0
  156. data/lib/chemicalml/cml/schema3.rb +40 -0
  157. data/lib/chemicalml/cml/substance.rb +10 -0
  158. data/lib/chemicalml/cml/translator/value_translations.rb +265 -0
  159. data/lib/chemicalml/cml/translator.rb +233 -0
  160. data/lib/chemicalml/cml/unit.rb +10 -0
  161. data/lib/chemicalml/cml/unit_list.rb +10 -0
  162. data/lib/chemicalml/cml/unit_type.rb +10 -0
  163. data/lib/chemicalml/cml/unit_type_list.rb +10 -0
  164. data/lib/chemicalml/cml/visitable.rb +65 -0
  165. data/lib/chemicalml/cml/wire_class_macro.rb +45 -0
  166. data/lib/chemicalml/cml.rb +55 -0
  167. data/lib/chemicalml/context_configuration.rb +127 -0
  168. data/lib/chemicalml/convention/base.rb +48 -0
  169. data/lib/chemicalml/convention/compchem/constraints/compchem_module_must_contain_job_list.rb +33 -0
  170. data/lib/chemicalml/convention/compchem/constraints/job_must_contain_initialization.rb +38 -0
  171. data/lib/chemicalml/convention/compchem/constraints.rb +14 -0
  172. data/lib/chemicalml/convention/compchem.rb +28 -0
  173. data/lib/chemicalml/convention/constraint.rb +79 -0
  174. data/lib/chemicalml/convention/dictionary/constraints/entry_ids_unique_within_dictionary.rb +33 -0
  175. data/lib/chemicalml/convention/dictionary/constraints/entry_must_have_id_and_term.rb +34 -0
  176. data/lib/chemicalml/convention/dictionary/constraints.rb +14 -0
  177. data/lib/chemicalml/convention/dictionary.rb +28 -0
  178. data/lib/chemicalml/convention/molecular/constraints/atom_array_must_contain_atoms.rb +30 -0
  179. data/lib/chemicalml/convention/molecular/constraints/atom_ids_unique_within_molecule.rb +42 -0
  180. data/lib/chemicalml/convention/molecular/constraints/bond_must_reference_atoms_in_same_molecule.rb +54 -0
  181. data/lib/chemicalml/convention/molecular/constraints.rb +19 -0
  182. data/lib/chemicalml/convention/molecular.rb +29 -0
  183. data/lib/chemicalml/convention/registry.rb +50 -0
  184. data/lib/chemicalml/convention/unit_dictionary/constraints/unit_must_have_symbol_and_unit_type.rb +46 -0
  185. data/lib/chemicalml/convention/unit_dictionary/constraints.rb +12 -0
  186. data/lib/chemicalml/convention/unit_dictionary.rb +27 -0
  187. data/lib/chemicalml/convention/unit_type_dictionary/constraints/unit_type_must_have_id_and_name.rb +34 -0
  188. data/lib/chemicalml/convention/unit_type_dictionary/constraints.rb +12 -0
  189. data/lib/chemicalml/convention/unit_type_dictionary.rb +27 -0
  190. data/lib/chemicalml/convention/violation.rb +36 -0
  191. data/lib/chemicalml/convention.rb +39 -0
  192. data/lib/chemicalml/dictionary/entry.rb +59 -0
  193. data/lib/chemicalml/dictionary/enum.rb +51 -0
  194. data/lib/chemicalml/dictionary/link.rb +32 -0
  195. data/lib/chemicalml/dictionary/loader.rb +60 -0
  196. data/lib/chemicalml/dictionary/model.rb +64 -0
  197. data/lib/chemicalml/dictionary/registry.rb +75 -0
  198. data/lib/chemicalml/dictionary.rb +26 -0
  199. data/lib/chemicalml/errors.rb +7 -0
  200. data/lib/chemicalml/model/atom.rb +40 -0
  201. data/lib/chemicalml/model/bond.rb +33 -0
  202. data/lib/chemicalml/model/cml_array.rb +27 -0
  203. data/lib/chemicalml/model/cml_module.rb +45 -0
  204. data/lib/chemicalml/model/document.rb +29 -0
  205. data/lib/chemicalml/model/formula.rb +34 -0
  206. data/lib/chemicalml/model/identifier.rb +21 -0
  207. data/lib/chemicalml/model/label.rb +21 -0
  208. data/lib/chemicalml/model/matrix.rb +29 -0
  209. data/lib/chemicalml/model/metadata.rb +23 -0
  210. data/lib/chemicalml/model/metadata_list.rb +25 -0
  211. data/lib/chemicalml/model/molecule.rb +38 -0
  212. data/lib/chemicalml/model/name.rb +21 -0
  213. data/lib/chemicalml/model/node.rb +45 -0
  214. data/lib/chemicalml/model/parameter.rb +27 -0
  215. data/lib/chemicalml/model/parameter_list.rb +25 -0
  216. data/lib/chemicalml/model/product.rb +21 -0
  217. data/lib/chemicalml/model/product_list.rb +21 -0
  218. data/lib/chemicalml/model/property.rb +28 -0
  219. data/lib/chemicalml/model/property_list.rb +25 -0
  220. data/lib/chemicalml/model/reactant.rb +21 -0
  221. data/lib/chemicalml/model/reactant_list.rb +21 -0
  222. data/lib/chemicalml/model/reaction.rb +41 -0
  223. data/lib/chemicalml/model/reaction_list.rb +23 -0
  224. data/lib/chemicalml/model/scalar.rb +25 -0
  225. data/lib/chemicalml/model/substance.rb +25 -0
  226. data/lib/chemicalml/model.rb +38 -0
  227. data/lib/chemicalml/schema/definition.rb +41 -0
  228. data/lib/chemicalml/schema/registry.rb +30 -0
  229. data/lib/chemicalml/schema.rb +35 -0
  230. data/lib/chemicalml/version.rb +5 -0
  231. data/lib/chemicalml/versioned_parser.rb +43 -0
  232. data/lib/chemicalml.rb +47 -0
  233. data/lib/tasks/reference_fetch.rake +105 -0
  234. data/lib/tasks/scrape_fixtures.rake +133 -0
  235. data/reference-docs/conventions/compchem.md +141 -0
  236. data/reference-docs/conventions/dictionary.md +119 -0
  237. data/reference-docs/conventions/index.md +56 -0
  238. data/reference-docs/conventions/molecular.md +115 -0
  239. data/reference-docs/conventions/unit-dictionary.md +92 -0
  240. data/reference-docs/conventions/unitType-dictionary.md +51 -0
  241. data/reference-docs/dictionaries/compchem.md +335 -0
  242. data/reference-docs/dictionaries/index.md +52 -0
  243. data/reference-docs/examples/schema24-index.md +50 -0
  244. data/reference-docs/examples/schema3-compchem-index.md +14 -0
  245. data/reference-docs/examples/schema3-molecular-index.md +28 -0
  246. data/reference-docs/schemas/schema24/schema.xsd +10624 -0
  247. data/reference-docs/schemas/schema3/schema.xsd +11459 -0
  248. metadata +306 -0

There are too many changes on this page to be displayed.

The amount of changes on this page would crash your brower.

You can still verify the content by downloading the gem file manually.