@synsci/cli-darwin-x64-baseline 1.1.77 → 1.1.78

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 (830) hide show
  1. package/bin/skills/adaptyv/SKILL.md +114 -0
  2. package/bin/skills/adaptyv/reference/api_reference.md +308 -0
  3. package/bin/skills/adaptyv/reference/examples.md +913 -0
  4. package/bin/skills/adaptyv/reference/experiments.md +360 -0
  5. package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
  6. package/bin/skills/aeon/SKILL.md +374 -0
  7. package/bin/skills/aeon/references/anomaly_detection.md +154 -0
  8. package/bin/skills/aeon/references/classification.md +144 -0
  9. package/bin/skills/aeon/references/clustering.md +123 -0
  10. package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
  11. package/bin/skills/aeon/references/distances.md +256 -0
  12. package/bin/skills/aeon/references/forecasting.md +140 -0
  13. package/bin/skills/aeon/references/networks.md +289 -0
  14. package/bin/skills/aeon/references/regression.md +118 -0
  15. package/bin/skills/aeon/references/segmentation.md +163 -0
  16. package/bin/skills/aeon/references/similarity_search.md +187 -0
  17. package/bin/skills/aeon/references/transformations.md +246 -0
  18. package/bin/skills/alphafold-database/SKILL.md +513 -0
  19. package/bin/skills/alphafold-database/references/api_reference.md +423 -0
  20. package/bin/skills/anndata/SKILL.md +400 -0
  21. package/bin/skills/anndata/references/best_practices.md +525 -0
  22. package/bin/skills/anndata/references/concatenation.md +396 -0
  23. package/bin/skills/anndata/references/data_structure.md +314 -0
  24. package/bin/skills/anndata/references/io_operations.md +404 -0
  25. package/bin/skills/anndata/references/manipulation.md +516 -0
  26. package/bin/skills/arboreto/SKILL.md +243 -0
  27. package/bin/skills/arboreto/references/algorithms.md +138 -0
  28. package/bin/skills/arboreto/references/basic_inference.md +151 -0
  29. package/bin/skills/arboreto/references/distributed_computing.md +242 -0
  30. package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  31. package/bin/skills/astropy/SKILL.md +331 -0
  32. package/bin/skills/astropy/references/coordinates.md +273 -0
  33. package/bin/skills/astropy/references/cosmology.md +307 -0
  34. package/bin/skills/astropy/references/fits.md +396 -0
  35. package/bin/skills/astropy/references/tables.md +489 -0
  36. package/bin/skills/astropy/references/time.md +404 -0
  37. package/bin/skills/astropy/references/units.md +178 -0
  38. package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
  39. package/bin/skills/benchling-integration/SKILL.md +480 -0
  40. package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
  41. package/bin/skills/benchling-integration/references/authentication.md +379 -0
  42. package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
  43. package/bin/skills/biopython/SKILL.md +443 -0
  44. package/bin/skills/biopython/references/advanced.md +577 -0
  45. package/bin/skills/biopython/references/alignment.md +362 -0
  46. package/bin/skills/biopython/references/blast.md +455 -0
  47. package/bin/skills/biopython/references/databases.md +484 -0
  48. package/bin/skills/biopython/references/phylogenetics.md +566 -0
  49. package/bin/skills/biopython/references/sequence_io.md +285 -0
  50. package/bin/skills/biopython/references/structure.md +564 -0
  51. package/bin/skills/biorxiv-database/SKILL.md +483 -0
  52. package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
  53. package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  54. package/bin/skills/bioservices/SKILL.md +361 -0
  55. package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
  56. package/bin/skills/bioservices/references/services_reference.md +636 -0
  57. package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
  58. package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
  59. package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  60. package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
  61. package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  62. package/bin/skills/brenda-database/SKILL.md +719 -0
  63. package/bin/skills/brenda-database/references/api_reference.md +537 -0
  64. package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
  65. package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  66. package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  67. package/bin/skills/cellxgene-census/SKILL.md +511 -0
  68. package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
  69. package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
  70. package/bin/skills/chembl-database/SKILL.md +389 -0
  71. package/bin/skills/chembl-database/references/api_reference.md +272 -0
  72. package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
  73. package/bin/skills/cirq/SKILL.md +346 -0
  74. package/bin/skills/cirq/references/building.md +307 -0
  75. package/bin/skills/cirq/references/experiments.md +572 -0
  76. package/bin/skills/cirq/references/hardware.md +515 -0
  77. package/bin/skills/cirq/references/noise.md +515 -0
  78. package/bin/skills/cirq/references/simulation.md +350 -0
  79. package/bin/skills/cirq/references/transformation.md +416 -0
  80. package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
  81. package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
  82. package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  83. package/bin/skills/clinpgx-database/SKILL.md +638 -0
  84. package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
  85. package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  86. package/bin/skills/clinvar-database/SKILL.md +362 -0
  87. package/bin/skills/clinvar-database/references/api_reference.md +227 -0
  88. package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
  89. package/bin/skills/clinvar-database/references/data_formats.md +358 -0
  90. package/bin/skills/cobrapy/SKILL.md +463 -0
  91. package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
  92. package/bin/skills/cobrapy/references/workflows.md +593 -0
  93. package/bin/skills/cosmic-database/SKILL.md +336 -0
  94. package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  95. package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  96. package/bin/skills/dask/SKILL.md +456 -0
  97. package/bin/skills/dask/references/arrays.md +497 -0
  98. package/bin/skills/dask/references/bags.md +468 -0
  99. package/bin/skills/dask/references/best-practices.md +277 -0
  100. package/bin/skills/dask/references/dataframes.md +368 -0
  101. package/bin/skills/dask/references/futures.md +541 -0
  102. package/bin/skills/dask/references/schedulers.md +504 -0
  103. package/bin/skills/datacommons-client/SKILL.md +255 -0
  104. package/bin/skills/datacommons-client/references/getting_started.md +417 -0
  105. package/bin/skills/datacommons-client/references/node.md +250 -0
  106. package/bin/skills/datacommons-client/references/observation.md +185 -0
  107. package/bin/skills/datacommons-client/references/resolve.md +246 -0
  108. package/bin/skills/datamol/SKILL.md +706 -0
  109. package/bin/skills/datamol/references/conformers_module.md +131 -0
  110. package/bin/skills/datamol/references/core_api.md +130 -0
  111. package/bin/skills/datamol/references/descriptors_viz.md +195 -0
  112. package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
  113. package/bin/skills/datamol/references/io_module.md +109 -0
  114. package/bin/skills/datamol/references/reactions_data.md +218 -0
  115. package/bin/skills/deepchem/SKILL.md +597 -0
  116. package/bin/skills/deepchem/references/api_reference.md +303 -0
  117. package/bin/skills/deepchem/references/workflows.md +491 -0
  118. package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
  119. package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
  120. package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
  121. package/bin/skills/deeptools/SKILL.md +531 -0
  122. package/bin/skills/deeptools/assets/quick_reference.md +58 -0
  123. package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
  124. package/bin/skills/deeptools/references/normalization_methods.md +410 -0
  125. package/bin/skills/deeptools/references/tools_reference.md +533 -0
  126. package/bin/skills/deeptools/references/workflows.md +474 -0
  127. package/bin/skills/deeptools/scripts/validate_files.py +195 -0
  128. package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
  129. package/bin/skills/denario/SKILL.md +215 -0
  130. package/bin/skills/denario/references/examples.md +494 -0
  131. package/bin/skills/denario/references/installation.md +213 -0
  132. package/bin/skills/denario/references/llm_configuration.md +265 -0
  133. package/bin/skills/denario/references/research_pipeline.md +471 -0
  134. package/bin/skills/diffdock/SKILL.md +483 -0
  135. package/bin/skills/diffdock/assets/batch_template.csv +4 -0
  136. package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  137. package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
  138. package/bin/skills/diffdock/references/parameters_reference.md +163 -0
  139. package/bin/skills/diffdock/references/workflows_examples.md +392 -0
  140. package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
  141. package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  142. package/bin/skills/diffdock/scripts/setup_check.py +278 -0
  143. package/bin/skills/dnanexus-integration/SKILL.md +383 -0
  144. package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
  145. package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
  146. package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
  147. package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
  148. package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
  149. package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
  150. package/bin/skills/document-skills/docx/SKILL.md +233 -0
  151. package/bin/skills/document-skills/docx/docx-js.md +350 -0
  152. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  153. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  154. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  155. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  156. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  157. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  158. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  159. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  160. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  161. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  162. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  163. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  164. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  165. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  166. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  167. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  168. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  169. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  170. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  171. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  172. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  173. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  174. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  175. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  176. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  177. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  178. package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  179. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  180. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  181. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  182. package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  183. package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
  184. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  185. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  186. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  187. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  188. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  189. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  190. package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  191. package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
  192. package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
  193. package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
  194. package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
  195. package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
  196. package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
  197. package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
  198. package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
  199. package/bin/skills/document-skills/docx/ooxml.md +610 -0
  200. package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
  201. package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
  202. package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
  203. package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
  204. package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  205. package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
  206. package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
  207. package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
  208. package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
  209. package/bin/skills/document-skills/pdf/SKILL.md +330 -0
  210. package/bin/skills/document-skills/pdf/forms.md +205 -0
  211. package/bin/skills/document-skills/pdf/reference.md +612 -0
  212. package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
  213. package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
  214. package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
  215. package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
  216. package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
  217. package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
  218. package/bin/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
  219. package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
  220. package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
  221. package/bin/skills/document-skills/pptx/SKILL.md +520 -0
  222. package/bin/skills/document-skills/pptx/html2pptx.md +625 -0
  223. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  224. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  225. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  226. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  227. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  228. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  229. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  230. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  231. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  232. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  233. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  234. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  235. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  236. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  237. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  238. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  239. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  240. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  241. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  242. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  243. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  244. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  245. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  246. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  247. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  248. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  249. package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  250. package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  251. package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  252. package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  253. package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  254. package/bin/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
  255. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
  256. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
  257. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
  258. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
  259. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
  260. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  261. package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
  262. package/bin/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
  263. package/bin/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
  264. package/bin/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
  265. package/bin/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
  266. package/bin/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
  267. package/bin/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
  268. package/bin/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
  269. package/bin/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
  270. package/bin/skills/document-skills/pptx/ooxml.md +427 -0
  271. package/bin/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
  272. package/bin/skills/document-skills/pptx/scripts/inventory.py +1020 -0
  273. package/bin/skills/document-skills/pptx/scripts/rearrange.py +231 -0
  274. package/bin/skills/document-skills/pptx/scripts/replace.py +385 -0
  275. package/bin/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
  276. package/bin/skills/document-skills/xlsx/LICENSE.txt +30 -0
  277. package/bin/skills/document-skills/xlsx/SKILL.md +325 -0
  278. package/bin/skills/document-skills/xlsx/recalc.py +178 -0
  279. package/bin/skills/drugbank-database/SKILL.md +190 -0
  280. package/bin/skills/drugbank-database/references/chemical-analysis.md +590 -0
  281. package/bin/skills/drugbank-database/references/data-access.md +242 -0
  282. package/bin/skills/drugbank-database/references/drug-queries.md +386 -0
  283. package/bin/skills/drugbank-database/references/interactions.md +425 -0
  284. package/bin/skills/drugbank-database/references/targets-pathways.md +518 -0
  285. package/bin/skills/drugbank-database/scripts/drugbank_helper.py +350 -0
  286. package/bin/skills/ena-database/SKILL.md +204 -0
  287. package/bin/skills/ena-database/references/api_reference.md +490 -0
  288. package/bin/skills/ensembl-database/SKILL.md +311 -0
  289. package/bin/skills/ensembl-database/references/api_endpoints.md +346 -0
  290. package/bin/skills/ensembl-database/scripts/ensembl_query.py +427 -0
  291. package/bin/skills/esm/SKILL.md +306 -0
  292. package/bin/skills/esm/references/esm-c-api.md +583 -0
  293. package/bin/skills/esm/references/esm3-api.md +452 -0
  294. package/bin/skills/esm/references/forge-api.md +657 -0
  295. package/bin/skills/esm/references/workflows.md +685 -0
  296. package/bin/skills/etetoolkit/SKILL.md +623 -0
  297. package/bin/skills/etetoolkit/references/api_reference.md +583 -0
  298. package/bin/skills/etetoolkit/references/visualization.md +783 -0
  299. package/bin/skills/etetoolkit/references/workflows.md +774 -0
  300. package/bin/skills/etetoolkit/scripts/quick_visualize.py +214 -0
  301. package/bin/skills/etetoolkit/scripts/tree_operations.py +229 -0
  302. package/bin/skills/exploratory-data-analysis/SKILL.md +446 -0
  303. package/bin/skills/exploratory-data-analysis/assets/report_template.md +196 -0
  304. package/bin/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
  305. package/bin/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
  306. package/bin/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
  307. package/bin/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
  308. package/bin/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
  309. package/bin/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
  310. package/bin/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
  311. package/bin/skills/fda-database/SKILL.md +518 -0
  312. package/bin/skills/fda-database/references/animal_veterinary.md +377 -0
  313. package/bin/skills/fda-database/references/api_basics.md +687 -0
  314. package/bin/skills/fda-database/references/devices.md +632 -0
  315. package/bin/skills/fda-database/references/drugs.md +468 -0
  316. package/bin/skills/fda-database/references/foods.md +374 -0
  317. package/bin/skills/fda-database/references/other.md +472 -0
  318. package/bin/skills/fda-database/scripts/fda_examples.py +335 -0
  319. package/bin/skills/fda-database/scripts/fda_query.py +440 -0
  320. package/bin/skills/flowio/SKILL.md +608 -0
  321. package/bin/skills/flowio/references/api_reference.md +372 -0
  322. package/bin/skills/fluidsim/SKILL.md +349 -0
  323. package/bin/skills/fluidsim/references/advanced_features.md +398 -0
  324. package/bin/skills/fluidsim/references/installation.md +68 -0
  325. package/bin/skills/fluidsim/references/output_analysis.md +283 -0
  326. package/bin/skills/fluidsim/references/parameters.md +198 -0
  327. package/bin/skills/fluidsim/references/simulation_workflow.md +172 -0
  328. package/bin/skills/fluidsim/references/solvers.md +94 -0
  329. package/bin/skills/fred-economic-data/SKILL.md +433 -0
  330. package/bin/skills/fred-economic-data/references/api_basics.md +212 -0
  331. package/bin/skills/fred-economic-data/references/categories.md +442 -0
  332. package/bin/skills/fred-economic-data/references/geofred.md +588 -0
  333. package/bin/skills/fred-economic-data/references/releases.md +642 -0
  334. package/bin/skills/fred-economic-data/references/series.md +584 -0
  335. package/bin/skills/fred-economic-data/references/sources.md +423 -0
  336. package/bin/skills/fred-economic-data/references/tags.md +485 -0
  337. package/bin/skills/fred-economic-data/scripts/fred_examples.py +354 -0
  338. package/bin/skills/fred-economic-data/scripts/fred_query.py +590 -0
  339. package/bin/skills/gene-database/SKILL.md +179 -0
  340. package/bin/skills/gene-database/references/api_reference.md +404 -0
  341. package/bin/skills/gene-database/references/common_workflows.md +428 -0
  342. package/bin/skills/gene-database/scripts/batch_gene_lookup.py +298 -0
  343. package/bin/skills/gene-database/scripts/fetch_gene_data.py +277 -0
  344. package/bin/skills/gene-database/scripts/query_gene.py +251 -0
  345. package/bin/skills/geniml/SKILL.md +318 -0
  346. package/bin/skills/geniml/references/bedspace.md +127 -0
  347. package/bin/skills/geniml/references/consensus_peaks.md +238 -0
  348. package/bin/skills/geniml/references/region2vec.md +90 -0
  349. package/bin/skills/geniml/references/scembed.md +197 -0
  350. package/bin/skills/geniml/references/utilities.md +385 -0
  351. package/bin/skills/geo-database/SKILL.md +815 -0
  352. package/bin/skills/geo-database/references/geo_reference.md +829 -0
  353. package/bin/skills/geopandas/SKILL.md +251 -0
  354. package/bin/skills/geopandas/references/crs-management.md +243 -0
  355. package/bin/skills/geopandas/references/data-io.md +165 -0
  356. package/bin/skills/geopandas/references/data-structures.md +70 -0
  357. package/bin/skills/geopandas/references/geometric-operations.md +221 -0
  358. package/bin/skills/geopandas/references/spatial-analysis.md +184 -0
  359. package/bin/skills/geopandas/references/visualization.md +243 -0
  360. package/bin/skills/get-available-resources/SKILL.md +277 -0
  361. package/bin/skills/get-available-resources/scripts/detect_resources.py +401 -0
  362. package/bin/skills/gget/SKILL.md +871 -0
  363. package/bin/skills/gget/references/database_info.md +300 -0
  364. package/bin/skills/gget/references/module_reference.md +467 -0
  365. package/bin/skills/gget/references/workflows.md +814 -0
  366. package/bin/skills/gget/scripts/batch_sequence_analysis.py +191 -0
  367. package/bin/skills/gget/scripts/enrichment_pipeline.py +235 -0
  368. package/bin/skills/gget/scripts/gene_analysis.py +161 -0
  369. package/bin/skills/gtars/SKILL.md +285 -0
  370. package/bin/skills/gtars/references/cli.md +222 -0
  371. package/bin/skills/gtars/references/coverage.md +172 -0
  372. package/bin/skills/gtars/references/overlap.md +156 -0
  373. package/bin/skills/gtars/references/python-api.md +211 -0
  374. package/bin/skills/gtars/references/refget.md +147 -0
  375. package/bin/skills/gtars/references/tokenizers.md +103 -0
  376. package/bin/skills/gwas-database/SKILL.md +608 -0
  377. package/bin/skills/gwas-database/references/api_reference.md +793 -0
  378. package/bin/skills/histolab/SKILL.md +678 -0
  379. package/bin/skills/histolab/references/filters_preprocessing.md +514 -0
  380. package/bin/skills/histolab/references/slide_management.md +172 -0
  381. package/bin/skills/histolab/references/tile_extraction.md +421 -0
  382. package/bin/skills/histolab/references/tissue_masks.md +251 -0
  383. package/bin/skills/histolab/references/visualization.md +547 -0
  384. package/bin/skills/hmdb-database/SKILL.md +196 -0
  385. package/bin/skills/hmdb-database/references/hmdb_data_fields.md +267 -0
  386. package/bin/skills/hypogenic/SKILL.md +655 -0
  387. package/bin/skills/hypogenic/references/config_template.yaml +150 -0
  388. package/bin/skills/imaging-data-commons/SKILL.md +1182 -0
  389. package/bin/skills/imaging-data-commons/references/bigquery_guide.md +556 -0
  390. package/bin/skills/imaging-data-commons/references/cli_guide.md +272 -0
  391. package/bin/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
  392. package/bin/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
  393. package/bin/skills/infographics/SKILL.md +563 -0
  394. package/bin/skills/infographics/references/color_palettes.md +496 -0
  395. package/bin/skills/infographics/references/design_principles.md +636 -0
  396. package/bin/skills/infographics/references/infographic_types.md +907 -0
  397. package/bin/skills/infographics/scripts/generate_infographic.py +234 -0
  398. package/bin/skills/infographics/scripts/generate_infographic_ai.py +1290 -0
  399. package/bin/skills/iso-13485-certification/SKILL.md +680 -0
  400. package/bin/skills/iso-13485-certification/assets/templates/procedures/CAPA-procedure-template.md +453 -0
  401. package/bin/skills/iso-13485-certification/assets/templates/procedures/document-control-procedure-template.md +567 -0
  402. package/bin/skills/iso-13485-certification/assets/templates/quality-manual-template.md +521 -0
  403. package/bin/skills/iso-13485-certification/references/gap-analysis-checklist.md +568 -0
  404. package/bin/skills/iso-13485-certification/references/iso-13485-requirements.md +610 -0
  405. package/bin/skills/iso-13485-certification/references/mandatory-documents.md +606 -0
  406. package/bin/skills/iso-13485-certification/references/quality-manual-guide.md +688 -0
  407. package/bin/skills/iso-13485-certification/scripts/gap_analyzer.py +440 -0
  408. package/bin/skills/kegg-database/SKILL.md +377 -0
  409. package/bin/skills/kegg-database/references/kegg_reference.md +326 -0
  410. package/bin/skills/kegg-database/scripts/kegg_api.py +251 -0
  411. package/bin/skills/labarchive-integration/SKILL.md +268 -0
  412. package/bin/skills/labarchive-integration/references/api_reference.md +342 -0
  413. package/bin/skills/labarchive-integration/references/authentication_guide.md +357 -0
  414. package/bin/skills/labarchive-integration/references/integrations.md +425 -0
  415. package/bin/skills/labarchive-integration/scripts/entry_operations.py +334 -0
  416. package/bin/skills/labarchive-integration/scripts/notebook_operations.py +269 -0
  417. package/bin/skills/labarchive-integration/scripts/setup_config.py +205 -0
  418. package/bin/skills/lamindb/SKILL.md +390 -0
  419. package/bin/skills/lamindb/references/annotation-validation.md +513 -0
  420. package/bin/skills/lamindb/references/core-concepts.md +380 -0
  421. package/bin/skills/lamindb/references/data-management.md +433 -0
  422. package/bin/skills/lamindb/references/integrations.md +642 -0
  423. package/bin/skills/lamindb/references/ontologies.md +497 -0
  424. package/bin/skills/lamindb/references/setup-deployment.md +733 -0
  425. package/bin/skills/latchbio-integration/SKILL.md +353 -0
  426. package/bin/skills/latchbio-integration/references/data-management.md +427 -0
  427. package/bin/skills/latchbio-integration/references/resource-configuration.md +429 -0
  428. package/bin/skills/latchbio-integration/references/verified-workflows.md +487 -0
  429. package/bin/skills/latchbio-integration/references/workflow-creation.md +254 -0
  430. package/bin/skills/matchms/SKILL.md +203 -0
  431. package/bin/skills/matchms/references/filtering.md +288 -0
  432. package/bin/skills/matchms/references/importing_exporting.md +416 -0
  433. package/bin/skills/matchms/references/similarity.md +380 -0
  434. package/bin/skills/matchms/references/workflows.md +647 -0
  435. package/bin/skills/matlab/SKILL.md +376 -0
  436. package/bin/skills/matlab/references/data-import-export.md +479 -0
  437. package/bin/skills/matlab/references/executing-scripts.md +444 -0
  438. package/bin/skills/matlab/references/graphics-visualization.md +579 -0
  439. package/bin/skills/matlab/references/mathematics.md +553 -0
  440. package/bin/skills/matlab/references/matrices-arrays.md +349 -0
  441. package/bin/skills/matlab/references/octave-compatibility.md +544 -0
  442. package/bin/skills/matlab/references/programming.md +672 -0
  443. package/bin/skills/matlab/references/python-integration.md +433 -0
  444. package/bin/skills/matplotlib/SKILL.md +361 -0
  445. package/bin/skills/matplotlib/references/api_reference.md +412 -0
  446. package/bin/skills/matplotlib/references/common_issues.md +563 -0
  447. package/bin/skills/matplotlib/references/plot_types.md +476 -0
  448. package/bin/skills/matplotlib/references/styling_guide.md +589 -0
  449. package/bin/skills/matplotlib/scripts/plot_template.py +401 -0
  450. package/bin/skills/matplotlib/scripts/style_configurator.py +409 -0
  451. package/bin/skills/medchem/SKILL.md +406 -0
  452. package/bin/skills/medchem/references/api_guide.md +600 -0
  453. package/bin/skills/medchem/references/rules_catalog.md +604 -0
  454. package/bin/skills/medchem/scripts/filter_molecules.py +418 -0
  455. package/bin/skills/metabolomics-workbench-database/SKILL.md +259 -0
  456. package/bin/skills/metabolomics-workbench-database/references/api_reference.md +494 -0
  457. package/bin/skills/modal-research-gpu/SKILL.md +238 -0
  458. package/bin/skills/molfeat/SKILL.md +511 -0
  459. package/bin/skills/molfeat/references/api_reference.md +428 -0
  460. package/bin/skills/molfeat/references/available_featurizers.md +333 -0
  461. package/bin/skills/molfeat/references/examples.md +723 -0
  462. package/bin/skills/networkx/SKILL.md +437 -0
  463. package/bin/skills/networkx/references/algorithms.md +383 -0
  464. package/bin/skills/networkx/references/generators.md +378 -0
  465. package/bin/skills/networkx/references/graph-basics.md +283 -0
  466. package/bin/skills/networkx/references/io.md +441 -0
  467. package/bin/skills/networkx/references/visualization.md +529 -0
  468. package/bin/skills/neurokit2/SKILL.md +356 -0
  469. package/bin/skills/neurokit2/references/bio_module.md +417 -0
  470. package/bin/skills/neurokit2/references/complexity.md +715 -0
  471. package/bin/skills/neurokit2/references/ecg_cardiac.md +355 -0
  472. package/bin/skills/neurokit2/references/eda.md +497 -0
  473. package/bin/skills/neurokit2/references/eeg.md +506 -0
  474. package/bin/skills/neurokit2/references/emg.md +408 -0
  475. package/bin/skills/neurokit2/references/eog.md +407 -0
  476. package/bin/skills/neurokit2/references/epochs_events.md +471 -0
  477. package/bin/skills/neurokit2/references/hrv.md +480 -0
  478. package/bin/skills/neurokit2/references/ppg.md +413 -0
  479. package/bin/skills/neurokit2/references/rsp.md +510 -0
  480. package/bin/skills/neurokit2/references/signal_processing.md +648 -0
  481. package/bin/skills/neuropixels-analysis/SKILL.md +350 -0
  482. package/bin/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
  483. package/bin/skills/neuropixels-analysis/references/AI_CURATION.md +345 -0
  484. package/bin/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
  485. package/bin/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +358 -0
  486. package/bin/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
  487. package/bin/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
  488. package/bin/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
  489. package/bin/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
  490. package/bin/skills/neuropixels-analysis/references/api_reference.md +415 -0
  491. package/bin/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
  492. package/bin/skills/neuropixels-analysis/references/standard_workflow.md +385 -0
  493. package/bin/skills/neuropixels-analysis/scripts/compute_metrics.py +178 -0
  494. package/bin/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
  495. package/bin/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
  496. package/bin/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +432 -0
  497. package/bin/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
  498. package/bin/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
  499. package/bin/skills/offer-k-dense-web/SKILL.md +21 -0
  500. package/bin/skills/omero-integration/SKILL.md +251 -0
  501. package/bin/skills/omero-integration/references/advanced.md +631 -0
  502. package/bin/skills/omero-integration/references/connection.md +369 -0
  503. package/bin/skills/omero-integration/references/data_access.md +544 -0
  504. package/bin/skills/omero-integration/references/image_processing.md +665 -0
  505. package/bin/skills/omero-integration/references/metadata.md +688 -0
  506. package/bin/skills/omero-integration/references/rois.md +648 -0
  507. package/bin/skills/omero-integration/references/scripts.md +637 -0
  508. package/bin/skills/omero-integration/references/tables.md +532 -0
  509. package/bin/skills/openalex-database/SKILL.md +494 -0
  510. package/bin/skills/openalex-database/references/api_guide.md +371 -0
  511. package/bin/skills/openalex-database/references/common_queries.md +381 -0
  512. package/bin/skills/openalex-database/scripts/openalex_client.py +337 -0
  513. package/bin/skills/openalex-database/scripts/query_helpers.py +306 -0
  514. package/bin/skills/opentargets-database/SKILL.md +373 -0
  515. package/bin/skills/opentargets-database/references/api_reference.md +249 -0
  516. package/bin/skills/opentargets-database/references/evidence_types.md +306 -0
  517. package/bin/skills/opentargets-database/references/target_annotations.md +401 -0
  518. package/bin/skills/opentargets-database/scripts/query_opentargets.py +403 -0
  519. package/bin/skills/opentrons-integration/SKILL.md +573 -0
  520. package/bin/skills/opentrons-integration/references/api_reference.md +366 -0
  521. package/bin/skills/opentrons-integration/scripts/basic_protocol_template.py +67 -0
  522. package/bin/skills/opentrons-integration/scripts/pcr_setup_template.py +154 -0
  523. package/bin/skills/opentrons-integration/scripts/serial_dilution_template.py +96 -0
  524. package/bin/skills/pathml/SKILL.md +166 -0
  525. package/bin/skills/pathml/references/data_management.md +742 -0
  526. package/bin/skills/pathml/references/graphs.md +653 -0
  527. package/bin/skills/pathml/references/image_loading.md +448 -0
  528. package/bin/skills/pathml/references/machine_learning.md +725 -0
  529. package/bin/skills/pathml/references/multiparametric.md +686 -0
  530. package/bin/skills/pathml/references/preprocessing.md +722 -0
  531. package/bin/skills/pdb-database/SKILL.md +309 -0
  532. package/bin/skills/pdb-database/references/api_reference.md +617 -0
  533. package/bin/skills/pennylane/SKILL.md +226 -0
  534. package/bin/skills/pennylane/references/advanced_features.md +667 -0
  535. package/bin/skills/pennylane/references/devices_backends.md +596 -0
  536. package/bin/skills/pennylane/references/getting_started.md +227 -0
  537. package/bin/skills/pennylane/references/optimization.md +671 -0
  538. package/bin/skills/pennylane/references/quantum_chemistry.md +567 -0
  539. package/bin/skills/pennylane/references/quantum_circuits.md +437 -0
  540. package/bin/skills/pennylane/references/quantum_ml.md +571 -0
  541. package/bin/skills/perplexity-search/SKILL.md +448 -0
  542. package/bin/skills/perplexity-search/assets/.env.example +16 -0
  543. package/bin/skills/perplexity-search/references/model_comparison.md +386 -0
  544. package/bin/skills/perplexity-search/references/openrouter_setup.md +454 -0
  545. package/bin/skills/perplexity-search/references/search_strategies.md +258 -0
  546. package/bin/skills/perplexity-search/scripts/perplexity_search.py +277 -0
  547. package/bin/skills/perplexity-search/scripts/setup_env.py +171 -0
  548. package/bin/skills/plotly/SKILL.md +267 -0
  549. package/bin/skills/plotly/references/chart-types.md +488 -0
  550. package/bin/skills/plotly/references/export-interactivity.md +453 -0
  551. package/bin/skills/plotly/references/graph-objects.md +302 -0
  552. package/bin/skills/plotly/references/layouts-styling.md +457 -0
  553. package/bin/skills/plotly/references/plotly-express.md +213 -0
  554. package/bin/skills/polars/SKILL.md +387 -0
  555. package/bin/skills/polars/references/best_practices.md +649 -0
  556. package/bin/skills/polars/references/core_concepts.md +378 -0
  557. package/bin/skills/polars/references/io_guide.md +557 -0
  558. package/bin/skills/polars/references/operations.md +602 -0
  559. package/bin/skills/polars/references/pandas_migration.md +417 -0
  560. package/bin/skills/polars/references/transformations.md +549 -0
  561. package/bin/skills/protocolsio-integration/SKILL.md +421 -0
  562. package/bin/skills/protocolsio-integration/references/additional_features.md +387 -0
  563. package/bin/skills/protocolsio-integration/references/authentication.md +100 -0
  564. package/bin/skills/protocolsio-integration/references/discussions.md +225 -0
  565. package/bin/skills/protocolsio-integration/references/file_manager.md +412 -0
  566. package/bin/skills/protocolsio-integration/references/protocols_api.md +294 -0
  567. package/bin/skills/protocolsio-integration/references/workspaces.md +293 -0
  568. package/bin/skills/pubchem-database/SKILL.md +574 -0
  569. package/bin/skills/pubchem-database/references/api_reference.md +440 -0
  570. package/bin/skills/pubchem-database/scripts/bioactivity_query.py +367 -0
  571. package/bin/skills/pubchem-database/scripts/compound_search.py +297 -0
  572. package/bin/skills/pubmed-database/SKILL.md +460 -0
  573. package/bin/skills/pubmed-database/references/api_reference.md +298 -0
  574. package/bin/skills/pubmed-database/references/common_queries.md +453 -0
  575. package/bin/skills/pubmed-database/references/search_syntax.md +436 -0
  576. package/bin/skills/pufferlib/SKILL.md +436 -0
  577. package/bin/skills/pufferlib/references/environments.md +508 -0
  578. package/bin/skills/pufferlib/references/integration.md +621 -0
  579. package/bin/skills/pufferlib/references/policies.md +653 -0
  580. package/bin/skills/pufferlib/references/training.md +360 -0
  581. package/bin/skills/pufferlib/references/vectorization.md +557 -0
  582. package/bin/skills/pufferlib/scripts/env_template.py +340 -0
  583. package/bin/skills/pufferlib/scripts/train_template.py +239 -0
  584. package/bin/skills/pydeseq2/SKILL.md +559 -0
  585. package/bin/skills/pydeseq2/references/api_reference.md +228 -0
  586. package/bin/skills/pydeseq2/references/workflow_guide.md +582 -0
  587. package/bin/skills/pydeseq2/scripts/run_deseq2_analysis.py +353 -0
  588. package/bin/skills/pydicom/SKILL.md +434 -0
  589. package/bin/skills/pydicom/references/common_tags.md +228 -0
  590. package/bin/skills/pydicom/references/transfer_syntaxes.md +352 -0
  591. package/bin/skills/pydicom/scripts/anonymize_dicom.py +137 -0
  592. package/bin/skills/pydicom/scripts/dicom_to_image.py +172 -0
  593. package/bin/skills/pydicom/scripts/extract_metadata.py +173 -0
  594. package/bin/skills/pyhealth/SKILL.md +491 -0
  595. package/bin/skills/pyhealth/references/datasets.md +178 -0
  596. package/bin/skills/pyhealth/references/medical_coding.md +284 -0
  597. package/bin/skills/pyhealth/references/models.md +594 -0
  598. package/bin/skills/pyhealth/references/preprocessing.md +638 -0
  599. package/bin/skills/pyhealth/references/tasks.md +379 -0
  600. package/bin/skills/pyhealth/references/training_evaluation.md +648 -0
  601. package/bin/skills/pylabrobot/SKILL.md +185 -0
  602. package/bin/skills/pylabrobot/references/analytical-equipment.md +464 -0
  603. package/bin/skills/pylabrobot/references/hardware-backends.md +480 -0
  604. package/bin/skills/pylabrobot/references/liquid-handling.md +403 -0
  605. package/bin/skills/pylabrobot/references/material-handling.md +620 -0
  606. package/bin/skills/pylabrobot/references/resources.md +489 -0
  607. package/bin/skills/pylabrobot/references/visualization.md +532 -0
  608. package/bin/skills/pymatgen/SKILL.md +691 -0
  609. package/bin/skills/pymatgen/references/analysis_modules.md +530 -0
  610. package/bin/skills/pymatgen/references/core_classes.md +318 -0
  611. package/bin/skills/pymatgen/references/io_formats.md +469 -0
  612. package/bin/skills/pymatgen/references/materials_project_api.md +517 -0
  613. package/bin/skills/pymatgen/references/transformations_workflows.md +591 -0
  614. package/bin/skills/pymatgen/scripts/phase_diagram_generator.py +233 -0
  615. package/bin/skills/pymatgen/scripts/structure_analyzer.py +266 -0
  616. package/bin/skills/pymatgen/scripts/structure_converter.py +169 -0
  617. package/bin/skills/pymc/SKILL.md +572 -0
  618. package/bin/skills/pymc/assets/hierarchical_model_template.py +333 -0
  619. package/bin/skills/pymc/assets/linear_regression_template.py +241 -0
  620. package/bin/skills/pymc/references/distributions.md +320 -0
  621. package/bin/skills/pymc/references/sampling_inference.md +424 -0
  622. package/bin/skills/pymc/references/workflows.md +526 -0
  623. package/bin/skills/pymc/scripts/model_comparison.py +387 -0
  624. package/bin/skills/pymc/scripts/model_diagnostics.py +350 -0
  625. package/bin/skills/pymoo/SKILL.md +571 -0
  626. package/bin/skills/pymoo/references/algorithms.md +180 -0
  627. package/bin/skills/pymoo/references/constraints_mcdm.md +417 -0
  628. package/bin/skills/pymoo/references/operators.md +345 -0
  629. package/bin/skills/pymoo/references/problems.md +265 -0
  630. package/bin/skills/pymoo/references/visualization.md +353 -0
  631. package/bin/skills/pymoo/scripts/custom_problem_example.py +181 -0
  632. package/bin/skills/pymoo/scripts/decision_making_example.py +161 -0
  633. package/bin/skills/pymoo/scripts/many_objective_example.py +72 -0
  634. package/bin/skills/pymoo/scripts/multi_objective_example.py +63 -0
  635. package/bin/skills/pymoo/scripts/single_objective_example.py +59 -0
  636. package/bin/skills/pyopenms/SKILL.md +217 -0
  637. package/bin/skills/pyopenms/references/data_structures.md +497 -0
  638. package/bin/skills/pyopenms/references/feature_detection.md +410 -0
  639. package/bin/skills/pyopenms/references/file_io.md +349 -0
  640. package/bin/skills/pyopenms/references/identification.md +422 -0
  641. package/bin/skills/pyopenms/references/metabolomics.md +482 -0
  642. package/bin/skills/pyopenms/references/signal_processing.md +433 -0
  643. package/bin/skills/pysam/SKILL.md +265 -0
  644. package/bin/skills/pysam/references/alignment_files.md +280 -0
  645. package/bin/skills/pysam/references/common_workflows.md +520 -0
  646. package/bin/skills/pysam/references/sequence_files.md +407 -0
  647. package/bin/skills/pysam/references/variant_files.md +365 -0
  648. package/bin/skills/pytdc/SKILL.md +460 -0
  649. package/bin/skills/pytdc/references/datasets.md +246 -0
  650. package/bin/skills/pytdc/references/oracles.md +400 -0
  651. package/bin/skills/pytdc/references/utilities.md +684 -0
  652. package/bin/skills/pytdc/scripts/benchmark_evaluation.py +327 -0
  653. package/bin/skills/pytdc/scripts/load_and_split_data.py +214 -0
  654. package/bin/skills/pytdc/scripts/molecular_generation.py +404 -0
  655. package/bin/skills/qiskit/SKILL.md +275 -0
  656. package/bin/skills/qiskit/references/algorithms.md +607 -0
  657. package/bin/skills/qiskit/references/backends.md +433 -0
  658. package/bin/skills/qiskit/references/circuits.md +197 -0
  659. package/bin/skills/qiskit/references/patterns.md +533 -0
  660. package/bin/skills/qiskit/references/primitives.md +277 -0
  661. package/bin/skills/qiskit/references/setup.md +99 -0
  662. package/bin/skills/qiskit/references/transpilation.md +286 -0
  663. package/bin/skills/qiskit/references/visualization.md +415 -0
  664. package/bin/skills/qutip/SKILL.md +318 -0
  665. package/bin/skills/qutip/references/advanced.md +555 -0
  666. package/bin/skills/qutip/references/analysis.md +523 -0
  667. package/bin/skills/qutip/references/core_concepts.md +293 -0
  668. package/bin/skills/qutip/references/time_evolution.md +348 -0
  669. package/bin/skills/qutip/references/visualization.md +431 -0
  670. package/bin/skills/rdkit/SKILL.md +780 -0
  671. package/bin/skills/rdkit/references/api_reference.md +432 -0
  672. package/bin/skills/rdkit/references/descriptors_reference.md +595 -0
  673. package/bin/skills/rdkit/references/smarts_patterns.md +668 -0
  674. package/bin/skills/rdkit/scripts/molecular_properties.py +243 -0
  675. package/bin/skills/rdkit/scripts/similarity_search.py +297 -0
  676. package/bin/skills/rdkit/scripts/substructure_filter.py +386 -0
  677. package/bin/skills/reactome-database/SKILL.md +278 -0
  678. package/bin/skills/reactome-database/references/api_reference.md +465 -0
  679. package/bin/skills/reactome-database/scripts/reactome_query.py +286 -0
  680. package/bin/skills/rowan/SKILL.md +427 -0
  681. package/bin/skills/rowan/references/api_reference.md +413 -0
  682. package/bin/skills/rowan/references/molecule_handling.md +429 -0
  683. package/bin/skills/rowan/references/proteins_and_organization.md +499 -0
  684. package/bin/skills/rowan/references/rdkit_native.md +438 -0
  685. package/bin/skills/rowan/references/results_interpretation.md +481 -0
  686. package/bin/skills/rowan/references/workflow_types.md +591 -0
  687. package/bin/skills/scanpy/SKILL.md +386 -0
  688. package/bin/skills/scanpy/assets/analysis_template.py +295 -0
  689. package/bin/skills/scanpy/references/api_reference.md +251 -0
  690. package/bin/skills/scanpy/references/plotting_guide.md +352 -0
  691. package/bin/skills/scanpy/references/standard_workflow.md +206 -0
  692. package/bin/skills/scanpy/scripts/qc_analysis.py +200 -0
  693. package/bin/skills/scientific-brainstorming/SKILL.md +191 -0
  694. package/bin/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
  695. package/bin/skills/scientific-visualization/SKILL.md +779 -0
  696. package/bin/skills/scientific-visualization/assets/color_palettes.py +197 -0
  697. package/bin/skills/scientific-visualization/assets/nature.mplstyle +63 -0
  698. package/bin/skills/scientific-visualization/assets/presentation.mplstyle +61 -0
  699. package/bin/skills/scientific-visualization/assets/publication.mplstyle +68 -0
  700. package/bin/skills/scientific-visualization/references/color_palettes.md +348 -0
  701. package/bin/skills/scientific-visualization/references/journal_requirements.md +320 -0
  702. package/bin/skills/scientific-visualization/references/matplotlib_examples.md +620 -0
  703. package/bin/skills/scientific-visualization/references/publication_guidelines.md +205 -0
  704. package/bin/skills/scientific-visualization/scripts/figure_export.py +343 -0
  705. package/bin/skills/scientific-visualization/scripts/style_presets.py +416 -0
  706. package/bin/skills/scikit-bio/SKILL.md +437 -0
  707. package/bin/skills/scikit-bio/references/api_reference.md +749 -0
  708. package/bin/skills/scikit-learn/SKILL.md +521 -0
  709. package/bin/skills/scikit-learn/references/model_evaluation.md +592 -0
  710. package/bin/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
  711. package/bin/skills/scikit-learn/references/preprocessing.md +606 -0
  712. package/bin/skills/scikit-learn/references/quick_reference.md +433 -0
  713. package/bin/skills/scikit-learn/references/supervised_learning.md +378 -0
  714. package/bin/skills/scikit-learn/references/unsupervised_learning.md +505 -0
  715. package/bin/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
  716. package/bin/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
  717. package/bin/skills/scikit-survival/SKILL.md +399 -0
  718. package/bin/skills/scikit-survival/references/competing-risks.md +397 -0
  719. package/bin/skills/scikit-survival/references/cox-models.md +182 -0
  720. package/bin/skills/scikit-survival/references/data-handling.md +494 -0
  721. package/bin/skills/scikit-survival/references/ensemble-models.md +327 -0
  722. package/bin/skills/scikit-survival/references/evaluation-metrics.md +378 -0
  723. package/bin/skills/scikit-survival/references/svm-models.md +411 -0
  724. package/bin/skills/scvi-tools/SKILL.md +190 -0
  725. package/bin/skills/scvi-tools/references/differential-expression.md +581 -0
  726. package/bin/skills/scvi-tools/references/models-atac-seq.md +321 -0
  727. package/bin/skills/scvi-tools/references/models-multimodal.md +367 -0
  728. package/bin/skills/scvi-tools/references/models-scrna-seq.md +330 -0
  729. package/bin/skills/scvi-tools/references/models-spatial.md +438 -0
  730. package/bin/skills/scvi-tools/references/models-specialized.md +408 -0
  731. package/bin/skills/scvi-tools/references/theoretical-foundations.md +438 -0
  732. package/bin/skills/scvi-tools/references/workflows.md +546 -0
  733. package/bin/skills/seaborn/SKILL.md +673 -0
  734. package/bin/skills/seaborn/references/examples.md +822 -0
  735. package/bin/skills/seaborn/references/function_reference.md +770 -0
  736. package/bin/skills/seaborn/references/objects_interface.md +964 -0
  737. package/bin/skills/shap/SKILL.md +566 -0
  738. package/bin/skills/shap/references/explainers.md +339 -0
  739. package/bin/skills/shap/references/plots.md +507 -0
  740. package/bin/skills/shap/references/theory.md +449 -0
  741. package/bin/skills/shap/references/workflows.md +605 -0
  742. package/bin/skills/simpy/SKILL.md +429 -0
  743. package/bin/skills/simpy/references/events.md +374 -0
  744. package/bin/skills/simpy/references/monitoring.md +475 -0
  745. package/bin/skills/simpy/references/process-interaction.md +424 -0
  746. package/bin/skills/simpy/references/real-time.md +395 -0
  747. package/bin/skills/simpy/references/resources.md +275 -0
  748. package/bin/skills/simpy/scripts/basic_simulation_template.py +193 -0
  749. package/bin/skills/simpy/scripts/resource_monitor.py +345 -0
  750. package/bin/skills/stable-baselines3/SKILL.md +299 -0
  751. package/bin/skills/stable-baselines3/references/algorithms.md +333 -0
  752. package/bin/skills/stable-baselines3/references/callbacks.md +556 -0
  753. package/bin/skills/stable-baselines3/references/custom_environments.md +526 -0
  754. package/bin/skills/stable-baselines3/references/vectorized_envs.md +568 -0
  755. package/bin/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
  756. package/bin/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
  757. package/bin/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
  758. package/bin/skills/statistical-analysis/SKILL.md +632 -0
  759. package/bin/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
  760. package/bin/skills/statistical-analysis/references/bayesian_statistics.md +661 -0
  761. package/bin/skills/statistical-analysis/references/effect_sizes_and_power.md +581 -0
  762. package/bin/skills/statistical-analysis/references/reporting_standards.md +469 -0
  763. package/bin/skills/statistical-analysis/references/test_selection_guide.md +129 -0
  764. package/bin/skills/statistical-analysis/scripts/assumption_checks.py +539 -0
  765. package/bin/skills/statsmodels/SKILL.md +614 -0
  766. package/bin/skills/statsmodels/references/discrete_choice.md +669 -0
  767. package/bin/skills/statsmodels/references/glm.md +619 -0
  768. package/bin/skills/statsmodels/references/linear_models.md +447 -0
  769. package/bin/skills/statsmodels/references/stats_diagnostics.md +859 -0
  770. package/bin/skills/statsmodels/references/time_series.md +716 -0
  771. package/bin/skills/string-database/SKILL.md +534 -0
  772. package/bin/skills/string-database/references/string_reference.md +455 -0
  773. package/bin/skills/string-database/scripts/string_api.py +369 -0
  774. package/bin/skills/sympy/SKILL.md +500 -0
  775. package/bin/skills/sympy/references/advanced-topics.md +635 -0
  776. package/bin/skills/sympy/references/code-generation-printing.md +599 -0
  777. package/bin/skills/sympy/references/core-capabilities.md +348 -0
  778. package/bin/skills/sympy/references/matrices-linear-algebra.md +526 -0
  779. package/bin/skills/sympy/references/physics-mechanics.md +592 -0
  780. package/bin/skills/torch_geometric/SKILL.md +676 -0
  781. package/bin/skills/torch_geometric/references/datasets_reference.md +574 -0
  782. package/bin/skills/torch_geometric/references/layers_reference.md +485 -0
  783. package/bin/skills/torch_geometric/references/transforms_reference.md +679 -0
  784. package/bin/skills/torch_geometric/scripts/benchmark_model.py +309 -0
  785. package/bin/skills/torch_geometric/scripts/create_gnn_template.py +529 -0
  786. package/bin/skills/torch_geometric/scripts/visualize_graph.py +313 -0
  787. package/bin/skills/torchdrug/SKILL.md +450 -0
  788. package/bin/skills/torchdrug/references/core_concepts.md +565 -0
  789. package/bin/skills/torchdrug/references/datasets.md +380 -0
  790. package/bin/skills/torchdrug/references/knowledge_graphs.md +320 -0
  791. package/bin/skills/torchdrug/references/models_architectures.md +541 -0
  792. package/bin/skills/torchdrug/references/molecular_generation.md +352 -0
  793. package/bin/skills/torchdrug/references/molecular_property_prediction.md +169 -0
  794. package/bin/skills/torchdrug/references/protein_modeling.md +272 -0
  795. package/bin/skills/torchdrug/references/retrosynthesis.md +436 -0
  796. package/bin/skills/transformers/SKILL.md +164 -0
  797. package/bin/skills/transformers/references/generation.md +467 -0
  798. package/bin/skills/transformers/references/models.md +361 -0
  799. package/bin/skills/transformers/references/pipelines.md +335 -0
  800. package/bin/skills/transformers/references/tokenizers.md +447 -0
  801. package/bin/skills/transformers/references/training.md +500 -0
  802. package/bin/skills/umap-learn/SKILL.md +479 -0
  803. package/bin/skills/umap-learn/references/api_reference.md +532 -0
  804. package/bin/skills/uniprot-database/SKILL.md +195 -0
  805. package/bin/skills/uniprot-database/references/api_examples.md +413 -0
  806. package/bin/skills/uniprot-database/references/api_fields.md +275 -0
  807. package/bin/skills/uniprot-database/references/id_mapping_databases.md +285 -0
  808. package/bin/skills/uniprot-database/references/query_syntax.md +256 -0
  809. package/bin/skills/uniprot-database/scripts/uniprot_client.py +341 -0
  810. package/bin/skills/uspto-database/SKILL.md +607 -0
  811. package/bin/skills/uspto-database/references/additional_apis.md +394 -0
  812. package/bin/skills/uspto-database/references/patentsearch_api.md +266 -0
  813. package/bin/skills/uspto-database/references/peds_api.md +212 -0
  814. package/bin/skills/uspto-database/references/trademark_api.md +358 -0
  815. package/bin/skills/uspto-database/scripts/patent_search.py +290 -0
  816. package/bin/skills/uspto-database/scripts/peds_client.py +285 -0
  817. package/bin/skills/uspto-database/scripts/trademark_client.py +311 -0
  818. package/bin/skills/vaex/SKILL.md +182 -0
  819. package/bin/skills/vaex/references/core_dataframes.md +367 -0
  820. package/bin/skills/vaex/references/data_processing.md +555 -0
  821. package/bin/skills/vaex/references/io_operations.md +703 -0
  822. package/bin/skills/vaex/references/machine_learning.md +728 -0
  823. package/bin/skills/vaex/references/performance.md +571 -0
  824. package/bin/skills/vaex/references/visualization.md +613 -0
  825. package/bin/skills/zarr-python/SKILL.md +779 -0
  826. package/bin/skills/zarr-python/references/api_reference.md +515 -0
  827. package/bin/skills/zinc-database/SKILL.md +404 -0
  828. package/bin/skills/zinc-database/references/api_reference.md +692 -0
  829. package/bin/synsc +0 -0
  830. package/package.json +1 -1
@@ -0,0 +1,250 @@
1
+ # Node Endpoint - Knowledge Graph Exploration
2
+
3
+ ## Purpose
4
+
5
+ The Node endpoint retrieves property relationships and values from the Data Commons knowledge graph. It returns information about directed edges (properties) connecting nodes, enabling discovery of connections within the graph structure.
6
+
7
+ ## Core Capabilities
8
+
9
+ The Node API performs three primary functions:
10
+ 1. Retrieve property labels associated with nodes
11
+ 2. Obtain values for specific properties across nodes
12
+ 3. Discover all connected nodes linked through relationships
13
+
14
+ ## Available Methods
15
+
16
+ ### 1. fetch()
17
+
18
+ Retrieve properties using relation expressions with arrow notation.
19
+
20
+ **Key Parameters:**
21
+ - `node_dcids`: Target node identifier(s)
22
+ - `expression`: Relation syntax using arrows (`->`, `<-`, `<-*`)
23
+ - `all_pages`: Enable pagination (default: True)
24
+ - `next_token`: Continue paginated results
25
+
26
+ **Arrow Notation:**
27
+ - `->`: Outgoing property (from node to value)
28
+ - `<-`: Incoming property (from value to node)
29
+ - `<-*`: Multi-hop incoming traversal
30
+
31
+ **Example Usage:**
32
+ ```python
33
+ from datacommons_client import DataCommonsClient
34
+
35
+ client = DataCommonsClient()
36
+
37
+ # Get outgoing properties from California
38
+ response = client.node.fetch(
39
+ node_dcids=["geoId/06"],
40
+ expression="->name"
41
+ )
42
+
43
+ # Get incoming properties (what points to this node)
44
+ response = client.node.fetch(
45
+ node_dcids=["geoId/06"],
46
+ expression="<-containedInPlace"
47
+ )
48
+ ```
49
+
50
+ ### 2. fetch_property_labels()
51
+
52
+ Get property labels without retrieving values—useful for discovering what properties exist.
53
+
54
+ **Parameters:**
55
+ - `node_dcids`: Node identifier(s)
56
+ - `out`: Boolean—True for outgoing properties, False for incoming
57
+
58
+ **Example Usage:**
59
+ ```python
60
+ # Get all outgoing property labels for California
61
+ labels = client.node.fetch_property_labels(
62
+ node_dcids=["geoId/06"],
63
+ out=True
64
+ )
65
+
66
+ # Get all incoming property labels
67
+ labels = client.node.fetch_property_labels(
68
+ node_dcids=["geoId/06"],
69
+ out=False
70
+ )
71
+ ```
72
+
73
+ ### 3. fetch_property_values()
74
+
75
+ Obtain specific property values with optional filters.
76
+
77
+ **Parameters:**
78
+ - `node_dcids`: Node identifier(s)
79
+ - `property`: Property name to query
80
+ - `out`: Direction (True for outgoing, False for incoming)
81
+ - `limit`: Maximum number of values to return
82
+
83
+ **Example Usage:**
84
+ ```python
85
+ # Get name property for California
86
+ values = client.node.fetch_property_values(
87
+ node_dcids=["geoId/06"],
88
+ property="name",
89
+ out=True
90
+ )
91
+ ```
92
+
93
+ ### 4. fetch_all_classes()
94
+
95
+ List all entity types (Class nodes) in the Data Commons graph.
96
+
97
+ **Example Usage:**
98
+ ```python
99
+ classes = client.node.fetch_all_classes()
100
+ ```
101
+
102
+ ### 5. fetch_entity_names()
103
+
104
+ Look up entity names by DCID in selected languages.
105
+
106
+ **Parameters:**
107
+ - `node_dcids`: Entity identifier(s)
108
+ - `language`: Language code (default: "en")
109
+
110
+ **Example Usage:**
111
+ ```python
112
+ names = client.node.fetch_entity_names(
113
+ node_dcids=["geoId/06", "country/USA"],
114
+ language="en"
115
+ )
116
+ # Returns: {"geoId/06": "California", "country/USA": "United States"}
117
+ ```
118
+
119
+ ### 6. Place Hierarchy Methods
120
+
121
+ These methods navigate geographic relationships:
122
+
123
+ #### fetch_place_children()
124
+ Get direct child places.
125
+
126
+ **Example Usage:**
127
+ ```python
128
+ # Get all states in USA
129
+ children = client.node.fetch_place_children(
130
+ node_dcids=["country/USA"]
131
+ )
132
+ ```
133
+
134
+ #### fetch_place_descendants()
135
+ Retrieve full child hierarchies (recursive).
136
+
137
+ **Example Usage:**
138
+ ```python
139
+ # Get all descendants of California (counties, cities, etc.)
140
+ descendants = client.node.fetch_place_descendants(
141
+ node_dcids=["geoId/06"]
142
+ )
143
+ ```
144
+
145
+ #### fetch_place_parents()
146
+ Get direct parent places.
147
+
148
+ **Example Usage:**
149
+ ```python
150
+ # Get parent of San Francisco
151
+ parents = client.node.fetch_place_parents(
152
+ node_dcids=["geoId/0667000"]
153
+ )
154
+ ```
155
+
156
+ #### fetch_place_ancestors()
157
+ Retrieve complete parent lineages.
158
+
159
+ **Example Usage:**
160
+ ```python
161
+ # Get all ancestors of San Francisco (CA, USA, etc.)
162
+ ancestors = client.node.fetch_place_ancestors(
163
+ node_dcids=["geoId/0667000"]
164
+ )
165
+ ```
166
+
167
+ ### 7. fetch_statvar_constraints()
168
+
169
+ Access constraint properties for statistical variables—useful for understanding variable definitions and constraints.
170
+
171
+ **Example Usage:**
172
+ ```python
173
+ constraints = client.node.fetch_statvar_constraints(
174
+ node_dcids=["Count_Person"]
175
+ )
176
+ ```
177
+
178
+ ## Response Format
179
+
180
+ Methods return either:
181
+ - **NodeResponse objects** with `.to_dict()`, `.to_json()`, and `.nextToken` properties
182
+ - **Dictionaries** for entity names and place hierarchy methods
183
+
184
+ ## Pagination
185
+
186
+ For large responses:
187
+ 1. Set `all_pages=False` to receive data in chunks
188
+ 2. Response includes a `nextToken` value
189
+ 3. Re-query using that token to fetch subsequent pages
190
+
191
+ **Example:**
192
+ ```python
193
+ # First page
194
+ response = client.node.fetch(
195
+ node_dcids=["country/USA"],
196
+ expression="<-containedInPlace",
197
+ all_pages=False
198
+ )
199
+
200
+ # Get next page if available
201
+ if response.nextToken:
202
+ next_response = client.node.fetch(
203
+ node_dcids=["country/USA"],
204
+ expression="<-containedInPlace",
205
+ next_token=response.nextToken
206
+ )
207
+ ```
208
+
209
+ ## Common Use Cases
210
+
211
+ ### Use Case 1: Explore Available Properties
212
+
213
+ ```python
214
+ # Discover what properties an entity has
215
+ labels = client.node.fetch_property_labels(
216
+ node_dcids=["geoId/06"],
217
+ out=True
218
+ )
219
+ print(labels) # Shows all outgoing properties like 'name', 'latitude', etc.
220
+ ```
221
+
222
+ ### Use Case 2: Navigate Geographic Hierarchies
223
+
224
+ ```python
225
+ # Get all counties in California
226
+ counties = client.node.fetch_place_children(
227
+ node_dcids=["geoId/06"]
228
+ )
229
+
230
+ # Filter for specific type if needed
231
+ county_dcids = [child for child in counties["geoId/06"]
232
+ if "County" in child]
233
+ ```
234
+
235
+ ### Use Case 3: Build Entity Relationships
236
+
237
+ ```python
238
+ # Find all entities that reference a specific node
239
+ references = client.node.fetch(
240
+ node_dcids=["geoId/06"],
241
+ expression="<-location"
242
+ )
243
+ ```
244
+
245
+ ## Important Notes
246
+
247
+ - Use `fetch_property_labels()` first to discover available properties
248
+ - The Node API cannot resolve complex relation expressions—use simpler expressions or break into multiple queries
249
+ - For linked entity properties with arc relationships, combine Node API queries with Observation API
250
+ - Place hierarchy methods return dictionaries, not NodeResponse objects
@@ -0,0 +1,185 @@
1
+ # Observation Endpoint - Statistical Data Queries
2
+
3
+ ## Purpose
4
+
5
+ The Observation API retrieves statistical observations—data points linking entities, variables, and specific dates. Examples include:
6
+ - "USA population in 2020"
7
+ - "California GDP over time"
8
+ - "Unemployment rate for all counties in a state"
9
+
10
+ ## Core Methods
11
+
12
+ ### 1. fetch()
13
+
14
+ Primary method for retrieving observations with flexible entity specification.
15
+
16
+ **Key Parameters:**
17
+ - `variable_dcids` (required): List of statistical variable identifiers
18
+ - `entity_dcids` or `entity_expression` (required): Specify entities by ID or relation expression
19
+ - `date` (optional): Defaults to "latest". Accepts:
20
+ - ISO-8601 format (e.g., "2020", "2020-01", "2020-01-15")
21
+ - "all" for complete time series
22
+ - "latest" for most recent data
23
+ - `select` (optional): Controls returned fields
24
+ - Default: `["date", "entity", "variable", "value"]`
25
+ - Alternative: `["entity", "variable", "facet"]` to check availability without data
26
+ - `filter_facet_domains`: Filter by data source domain
27
+ - `filter_facet_ids`: Filter by specific facet IDs
28
+
29
+ **Response Structure:**
30
+ Data organized hierarchically by variable → entity, with metadata about "facets" (data sources) including:
31
+ - Provenance URLs
32
+ - Measurement methods
33
+ - Observation periods
34
+ - Import names
35
+
36
+ **Example Usage:**
37
+ ```python
38
+ from datacommons_client import DataCommonsClient
39
+
40
+ client = DataCommonsClient()
41
+
42
+ # Get latest population for multiple entities
43
+ response = client.observation.fetch(
44
+ variable_dcids=["Count_Person"],
45
+ entity_dcids=["geoId/06", "geoId/48"], # California and Texas
46
+ date="latest"
47
+ )
48
+
49
+ # Get complete time series
50
+ response = client.observation.fetch(
51
+ variable_dcids=["Count_Person"],
52
+ entity_dcids=["country/USA"],
53
+ date="all"
54
+ )
55
+
56
+ # Use relation expressions to query hierarchies
57
+ response = client.observation.fetch(
58
+ variable_dcids=["Count_Person"],
59
+ entity_expression="geoId/06<-containedInPlace+{typeOf:County}",
60
+ date="2020"
61
+ )
62
+ ```
63
+
64
+ ### 2. fetch_available_statistical_variables()
65
+
66
+ Discovers which statistical variables contain data for given entities.
67
+
68
+ **Input:** Entity DCIDs only
69
+ **Output:** Dictionary of available variables organized by entity
70
+
71
+ **Example Usage:**
72
+ ```python
73
+ # Check what variables are available for California
74
+ available = client.observation.fetch_available_statistical_variables(
75
+ entity_dcids=["geoId/06"]
76
+ )
77
+ ```
78
+
79
+ ### 3. fetch_observations_by_entity_dcid()
80
+
81
+ Explicit method targeting specific entities by DCID (functionally equivalent to `fetch()` with entity_dcids).
82
+
83
+ ### 4. fetch_observations_by_entity_type()
84
+
85
+ Retrieves observations for multiple entities grouped by parent and type—useful for querying all countries in a region or all counties within a state.
86
+
87
+ **Parameters:**
88
+ - `parent_entity`: Parent entity DCID
89
+ - `entity_type`: Type of child entities
90
+ - `variable_dcids`: Statistical variables to query
91
+ - `date`: Time specification
92
+ - `select` and filter options
93
+
94
+ **Example Usage:**
95
+ ```python
96
+ # Get population for all counties in California
97
+ response = client.observation.fetch_observations_by_entity_type(
98
+ parent_entity="geoId/06",
99
+ entity_type="County",
100
+ variable_dcids=["Count_Person"],
101
+ date="2020"
102
+ )
103
+ ```
104
+
105
+ ## Response Object Methods
106
+
107
+ All response objects support:
108
+ - `to_json()`: Format as JSON string
109
+ - `to_dict()`: Return as dictionary
110
+ - `get_data_by_entity()`: Reorganize by entity instead of variable
111
+ - `to_observations_as_records()`: Flatten into individual records
112
+
113
+ ## Common Use Cases
114
+
115
+ ### Use Case 1: Check Data Availability Before Querying
116
+
117
+ Use `select=["entity", "variable"]` to confirm entities have observations without retrieving actual data:
118
+ ```python
119
+ response = client.observation.fetch(
120
+ variable_dcids=["Count_Person"],
121
+ entity_dcids=["geoId/06"],
122
+ select=["entity", "variable"]
123
+ )
124
+ ```
125
+
126
+ ### Use Case 2: Access Complete Time Series
127
+
128
+ Request `date="all"` to obtain complete historical observations for trend analysis:
129
+ ```python
130
+ response = client.observation.fetch(
131
+ variable_dcids=["Count_Person", "UnemploymentRate_Person"],
132
+ entity_dcids=["country/USA"],
133
+ date="all"
134
+ )
135
+ ```
136
+
137
+ ### Use Case 3: Filter by Data Source
138
+
139
+ Specify `filter_facet_domains` to retrieve data from specific sources for consistency:
140
+ ```python
141
+ response = client.observation.fetch(
142
+ variable_dcids=["Count_Person"],
143
+ entity_dcids=["country/USA"],
144
+ filter_facet_domains=["census.gov"]
145
+ )
146
+ ```
147
+
148
+ ### Use Case 4: Query Hierarchical Relationships
149
+
150
+ Use relation expressions to fetch observations for related entities:
151
+ ```python
152
+ # Get data for all counties within California
153
+ response = client.observation.fetch(
154
+ variable_dcids=["MedianIncome_Household"],
155
+ entity_expression="geoId/06<-containedInPlace+{typeOf:County}",
156
+ date="2020"
157
+ )
158
+ ```
159
+
160
+ ## Working with Pandas
161
+
162
+ The API integrates seamlessly with Pandas. Install with Pandas support:
163
+ ```bash
164
+ pip install "datacommons-client[Pandas]"
165
+ ```
166
+
167
+ Response objects can be converted to DataFrames for analysis:
168
+ ```python
169
+ response = client.observation.fetch(
170
+ variable_dcids=["Count_Person"],
171
+ entity_dcids=["geoId/06", "geoId/48"],
172
+ date="all"
173
+ )
174
+
175
+ # Convert to DataFrame
176
+ df = response.to_observations_as_records()
177
+ # Returns DataFrame with columns: date, entity, variable, value
178
+ ```
179
+
180
+ ## Important Notes
181
+
182
+ - **facets** represent data sources and include provenance metadata
183
+ - **orderedFacets** are sorted by reliability/recency
184
+ - Use relation expressions for complex graph queries
185
+ - The `fetch()` method is the most flexible—use it for most queries
@@ -0,0 +1,246 @@
1
+ # Resolve Endpoint - Entity Identification
2
+
3
+ ## Purpose
4
+
5
+ The Resolve API identifies Data Commons IDs (DCIDs) for entities in the knowledge graph. DCIDs are required for most queries in the Data Commons API, so resolution is typically the first step in any workflow.
6
+
7
+ ## Key Capabilities
8
+
9
+ The endpoint currently supports **place entities only** and allows resolution through multiple methods:
10
+ - **By name**: Search using descriptive terms like "San Francisco, CA"
11
+ - **By Wikidata ID**: Lookup using external identifiers (e.g., "Q30" for USA)
12
+ - **By coordinates**: Locate places via latitude/longitude
13
+ - **By relation expressions**: Advanced searches using synthetic attributes
14
+
15
+ ## Available Methods
16
+
17
+ ### 1. fetch()
18
+
19
+ General resolution using relation expressions—most flexible method.
20
+
21
+ **Parameters:**
22
+ - `nodes`: List of search terms or identifiers
23
+ - `property`: Property to search (e.g., "name", "wikidataId")
24
+
25
+ **Example Usage:**
26
+ ```python
27
+ from datacommons_client import DataCommonsClient
28
+
29
+ client = DataCommonsClient()
30
+
31
+ # Resolve by name
32
+ response = client.resolve.fetch(
33
+ nodes=["California", "Texas"],
34
+ property="name"
35
+ )
36
+ ```
37
+
38
+ ### 2. fetch_dcids_by_name()
39
+
40
+ Name-based lookup with optional type filtering—most commonly used method.
41
+
42
+ **Parameters:**
43
+ - `names`: List of place names to resolve
44
+ - `entity_type`: Optional type filter (e.g., "City", "State", "County")
45
+
46
+ **Returns:** `ResolveResponse` object with candidates for each name
47
+
48
+ **Example Usage:**
49
+ ```python
50
+ # Basic name resolution
51
+ response = client.resolve.fetch_dcids_by_name(
52
+ names=["San Francisco, CA", "Los Angeles"]
53
+ )
54
+
55
+ # With type filtering
56
+ response = client.resolve.fetch_dcids_by_name(
57
+ names=["San Francisco"],
58
+ entity_type="City"
59
+ )
60
+
61
+ # Access results
62
+ for name, result in response.to_dict().items():
63
+ print(f"{name}: {result['candidates']}")
64
+ ```
65
+
66
+ ### 3. fetch_dcids_by_wikidata_id()
67
+
68
+ Wikidata ID resolution for entities with known Wikidata identifiers.
69
+
70
+ **Parameters:**
71
+ - `wikidata_ids`: List of Wikidata IDs (e.g., "Q30", "Q99")
72
+
73
+ **Example Usage:**
74
+ ```python
75
+ # Resolve Wikidata IDs
76
+ response = client.resolve.fetch_dcids_by_wikidata_id(
77
+ wikidata_ids=["Q30", "Q99"] # USA and California
78
+ )
79
+ ```
80
+
81
+ ### 4. fetch_dcid_by_coordinates()
82
+
83
+ Geographic coordinate lookup to find the place at specific lat/long coordinates.
84
+
85
+ **Parameters:**
86
+ - `latitude`: Latitude coordinate
87
+ - `longitude`: Longitude coordinate
88
+
89
+ **Returns:** Single DCID string for the place at those coordinates
90
+
91
+ **Example Usage:**
92
+ ```python
93
+ # Find place at coordinates
94
+ dcid = client.resolve.fetch_dcid_by_coordinates(
95
+ latitude=37.7749,
96
+ longitude=-122.4194
97
+ )
98
+ # Returns DCID for San Francisco
99
+ ```
100
+
101
+ ## Response Structure
102
+
103
+ All methods (except `fetch_dcid_by_coordinates`) return a `ResolveResponse` object containing:
104
+ - **node**: The search term provided
105
+ - **candidates**: List of matching DCIDs with optional metadata
106
+ - Each candidate may include `dominantType` field for disambiguation
107
+ - **Helper methods**:
108
+ - `to_dict()`: Full response as dictionary
109
+ - `to_json()`: JSON string format
110
+ - `to_flat_dict()`: Simplified format with just DCIDs
111
+
112
+ **Example Response:**
113
+ ```python
114
+ response = client.resolve.fetch_dcids_by_name(names=["Springfield"])
115
+
116
+ # May return multiple candidates since many cities named Springfield exist
117
+ # {
118
+ # "Springfield": {
119
+ # "candidates": [
120
+ # {"dcid": "geoId/1767000", "dominantType": "City"}, # Springfield, IL
121
+ # {"dcid": "geoId/2567000", "dominantType": "City"}, # Springfield, MA
122
+ # ...
123
+ # ]
124
+ # }
125
+ # }
126
+ ```
127
+
128
+ ## Common Use Cases
129
+
130
+ ### Use Case 1: Resolve Place Names Before Querying
131
+
132
+ Most workflows start by resolving names to DCIDs:
133
+ ```python
134
+ # Step 1: Resolve names
135
+ resolve_response = client.resolve.fetch_dcids_by_name(
136
+ names=["California", "Texas"]
137
+ )
138
+
139
+ # Step 2: Extract DCIDs
140
+ dcids = []
141
+ for name, result in resolve_response.to_dict().items():
142
+ if result["candidates"]:
143
+ dcids.append(result["candidates"][0]["dcid"])
144
+
145
+ # Step 3: Query data using DCIDs
146
+ data_response = client.observation.fetch(
147
+ variable_dcids=["Count_Person"],
148
+ entity_dcids=dcids,
149
+ date="latest"
150
+ )
151
+ ```
152
+
153
+ ### Use Case 2: Handle Ambiguous Names
154
+
155
+ When multiple candidates exist, use `dominantType` or be more specific:
156
+ ```python
157
+ # Ambiguous name
158
+ response = client.resolve.fetch_dcids_by_name(names=["Springfield"])
159
+ candidates = response.to_dict()["Springfield"]["candidates"]
160
+
161
+ # Filter by type or choose based on context
162
+ city_candidates = [c for c in candidates if c.get("dominantType") == "City"]
163
+
164
+ # Or be more specific in the query
165
+ response = client.resolve.fetch_dcids_by_name(
166
+ names=["Springfield, Illinois"],
167
+ entity_type="City"
168
+ )
169
+ ```
170
+
171
+ ### Use Case 3: Batch Resolution
172
+
173
+ Resolve multiple entities efficiently:
174
+ ```python
175
+ places = [
176
+ "San Francisco, CA",
177
+ "Los Angeles, CA",
178
+ "San Diego, CA",
179
+ "Sacramento, CA"
180
+ ]
181
+
182
+ response = client.resolve.fetch_dcids_by_name(names=places)
183
+
184
+ # Build mapping of name to DCID
185
+ name_to_dcid = {}
186
+ for name, result in response.to_dict().items():
187
+ if result["candidates"]:
188
+ name_to_dcid[name] = result["candidates"][0]["dcid"]
189
+ ```
190
+
191
+ ### Use Case 4: Coordinate-Based Queries
192
+
193
+ Find the administrative place for a location:
194
+ ```python
195
+ # User provides coordinates, find the place
196
+ latitude, longitude = 37.7749, -122.4194
197
+ dcid = client.resolve.fetch_dcid_by_coordinates(
198
+ latitude=latitude,
199
+ longitude=longitude
200
+ )
201
+
202
+ # Now query data for that place
203
+ response = client.observation.fetch(
204
+ variable_dcids=["Count_Person", "MedianIncome_Household"],
205
+ entity_dcids=[dcid],
206
+ date="latest"
207
+ )
208
+ ```
209
+
210
+ ### Use Case 5: External ID Integration
211
+
212
+ When working with external datasets that use Wikidata IDs:
213
+ ```python
214
+ # External dataset has Wikidata IDs
215
+ wikidata_ids = ["Q30", "Q99", "Q1384"] # USA, California, New York
216
+
217
+ # Convert to Data Commons DCIDs
218
+ response = client.resolve.fetch_dcids_by_wikidata_id(
219
+ wikidata_ids=wikidata_ids
220
+ )
221
+
222
+ # Extract DCIDs for further queries
223
+ dcids = []
224
+ for wid, result in response.to_dict().items():
225
+ if result["candidates"]:
226
+ dcids.append(result["candidates"][0]["dcid"])
227
+ ```
228
+
229
+ ## Important Limitations
230
+
231
+ 1. **Place entities only**: The Resolve API currently supports only place entities (countries, states, cities, counties, etc.). For other entity types, DCIDs must be obtained through other means (e.g., Node API exploration).
232
+
233
+ 2. **Cannot resolve linked entity properties**: For queries involving relationships like `containedInPlace`, use the Node API instead.
234
+
235
+ 3. **Ambiguity handling**: When multiple candidates exist, the API returns all matches. The application must decide which is correct based on context or additional filtering.
236
+
237
+ ## Best Practices
238
+
239
+ 1. **Always resolve names first**: Never assume DCID format—always use the Resolve API
240
+ 2. **Cache resolutions**: If querying the same places repeatedly, cache name→DCID mappings
241
+ 3. **Handle ambiguity**: Check for multiple candidates and use `entity_type` filtering or more specific names
242
+ 4. **Validate results**: Always check that `candidates` list is not empty before accessing DCIDs
243
+ 5. **Use appropriate method**:
244
+ - Names → `fetch_dcids_by_name()`
245
+ - Coordinates → `fetch_dcid_by_coordinates()`
246
+ - Wikidata IDs → `fetch_dcids_by_wikidata_id()`