@synsci/cli-darwin-x64-baseline 1.1.76 → 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 +1,277 @@
1
+ # Qiskit Primitives
2
+
3
+ Primitives are the fundamental building blocks for executing quantum circuits. Qiskit provides two main primitives: **Sampler** (for measuring bitstrings) and **Estimator** (for computing expectation values).
4
+
5
+ ## Primitive Types
6
+
7
+ ### Sampler
8
+ Calculates probabilities or quasi-probabilities of bitstrings from quantum circuits. Use when you need:
9
+ - Measurement outcomes
10
+ - Output probability distributions
11
+ - Sampling from quantum states
12
+
13
+ ### Estimator
14
+ Computes expectation values of observables for quantum circuits. Use when you need:
15
+ - Energy calculations
16
+ - Observable measurements
17
+ - Variational algorithm optimization
18
+
19
+ ## V2 Interface (Current Standard)
20
+
21
+ Qiskit uses V2 primitives (BaseSamplerV2, BaseEstimatorV2) as the current standard. V1 primitives are legacy.
22
+
23
+ ## Sampler Primitive
24
+
25
+ ### StatevectorSampler (Local Simulation)
26
+
27
+ ```python
28
+ from qiskit import QuantumCircuit
29
+ from qiskit.primitives import StatevectorSampler
30
+
31
+ # Create circuit
32
+ qc = QuantumCircuit(2)
33
+ qc.h(0)
34
+ qc.cx(0, 1)
35
+ qc.measure_all()
36
+
37
+ # Run with Sampler
38
+ sampler = StatevectorSampler()
39
+ result = sampler.run([qc], shots=1024).result()
40
+
41
+ # Access results
42
+ counts = result[0].data.meas.get_counts()
43
+ print(counts) # e.g., {'00': 523, '11': 501}
44
+ ```
45
+
46
+ ### Multiple Circuits
47
+
48
+ ```python
49
+ qc1 = QuantumCircuit(2)
50
+ qc1.h(0)
51
+ qc1.measure_all()
52
+
53
+ qc2 = QuantumCircuit(2)
54
+ qc2.x(0)
55
+ qc2.measure_all()
56
+
57
+ # Run multiple circuits
58
+ sampler = StatevectorSampler()
59
+ job = sampler.run([qc1, qc2], shots=1000)
60
+ results = job.result()
61
+
62
+ # Access individual results
63
+ counts1 = results[0].data.meas.get_counts()
64
+ counts2 = results[1].data.meas.get_counts()
65
+ ```
66
+
67
+ ### Using Parameters
68
+
69
+ ```python
70
+ from qiskit.circuit import Parameter
71
+
72
+ theta = Parameter('θ')
73
+ qc = QuantumCircuit(1)
74
+ qc.ry(theta, 0)
75
+ qc.measure_all()
76
+
77
+ # Run with parameter values
78
+ sampler = StatevectorSampler()
79
+ param_values = [[0], [np.pi/4], [np.pi/2]]
80
+ result = sampler.run([(qc, param_values)], shots=1024).result()
81
+ ```
82
+
83
+ ## Estimator Primitive
84
+
85
+ ### StatevectorEstimator (Local Simulation)
86
+
87
+ ```python
88
+ from qiskit import QuantumCircuit
89
+ from qiskit.primitives import StatevectorEstimator
90
+ from qiskit.quantum_info import SparsePauliOp
91
+
92
+ # Create circuit WITHOUT measurements
93
+ qc = QuantumCircuit(2)
94
+ qc.h(0)
95
+ qc.cx(0, 1)
96
+
97
+ # Define observable
98
+ observable = SparsePauliOp(["ZZ", "XX"])
99
+
100
+ # Run Estimator
101
+ estimator = StatevectorEstimator()
102
+ result = estimator.run([(qc, observable)]).result()
103
+
104
+ # Access expectation values
105
+ exp_value = result[0].data.evs
106
+ print(f"Expectation value: {exp_value}")
107
+ ```
108
+
109
+ ### Multiple Observables
110
+
111
+ ```python
112
+ from qiskit.quantum_info import SparsePauliOp
113
+
114
+ qc = QuantumCircuit(2)
115
+ qc.h(0)
116
+
117
+ obs1 = SparsePauliOp(["ZZ"])
118
+ obs2 = SparsePauliOp(["XX"])
119
+
120
+ estimator = StatevectorEstimator()
121
+ result = estimator.run([(qc, obs1), (qc, obs2)]).result()
122
+
123
+ ev1 = result[0].data.evs
124
+ ev2 = result[1].data.evs
125
+ ```
126
+
127
+ ### Parameterized Estimator
128
+
129
+ ```python
130
+ from qiskit.circuit import Parameter
131
+ import numpy as np
132
+
133
+ theta = Parameter('θ')
134
+ qc = QuantumCircuit(1)
135
+ qc.ry(theta, 0)
136
+
137
+ observable = SparsePauliOp(["Z"])
138
+
139
+ # Run with multiple parameter values
140
+ estimator = StatevectorEstimator()
141
+ param_values = [[0], [np.pi/4], [np.pi/2], [np.pi]]
142
+ result = estimator.run([(qc, observable, param_values)]).result()
143
+ ```
144
+
145
+ ## IBM Quantum Runtime Primitives
146
+
147
+ For running on real hardware, use runtime primitives:
148
+
149
+ ### Runtime Sampler
150
+
151
+ ```python
152
+ from qiskit_ibm_runtime import QiskitRuntimeService, SamplerV2 as Sampler
153
+
154
+ service = QiskitRuntimeService()
155
+ backend = service.backend("ibm_brisbane")
156
+
157
+ qc = QuantumCircuit(2)
158
+ qc.h(0)
159
+ qc.cx(0, 1)
160
+ qc.measure_all()
161
+
162
+ # Run on real hardware
163
+ sampler = Sampler(backend)
164
+ job = sampler.run([qc], shots=1024)
165
+ result = job.result()
166
+ counts = result[0].data.meas.get_counts()
167
+ ```
168
+
169
+ ### Runtime Estimator
170
+
171
+ ```python
172
+ from qiskit_ibm_runtime import QiskitRuntimeService, EstimatorV2 as Estimator
173
+ from qiskit.quantum_info import SparsePauliOp
174
+
175
+ service = QiskitRuntimeService()
176
+ backend = service.backend("ibm_brisbane")
177
+
178
+ qc = QuantumCircuit(2)
179
+ qc.h(0)
180
+ qc.cx(0, 1)
181
+
182
+ observable = SparsePauliOp(["ZZ"])
183
+
184
+ # Run on real hardware
185
+ estimator = Estimator(backend)
186
+ job = estimator.run([(qc, observable)])
187
+ result = job.result()
188
+ exp_value = result[0].data.evs
189
+ ```
190
+
191
+ ## Sessions for Iterative Workloads
192
+
193
+ Sessions group multiple jobs to reduce queue wait times:
194
+
195
+ ```python
196
+ from qiskit_ibm_runtime import Session
197
+
198
+ service = QiskitRuntimeService()
199
+ backend = service.backend("ibm_brisbane")
200
+
201
+ with Session(backend=backend) as session:
202
+ sampler = Sampler(session=session)
203
+
204
+ # Run multiple jobs in session
205
+ job1 = sampler.run([qc1], shots=1024)
206
+ result1 = job1.result()
207
+
208
+ job2 = sampler.run([qc2], shots=1024)
209
+ result2 = job2.result()
210
+ ```
211
+
212
+ ## Batch Mode for Parallel Jobs
213
+
214
+ Batch mode runs independent jobs in parallel:
215
+
216
+ ```python
217
+ from qiskit_ibm_runtime import Batch
218
+
219
+ service = QiskitRuntimeService()
220
+ backend = service.backend("ibm_brisbane")
221
+
222
+ with Batch(backend=backend) as batch:
223
+ sampler = Sampler(session=batch)
224
+
225
+ # Submit multiple independent jobs
226
+ job1 = sampler.run([qc1], shots=1024)
227
+ job2 = sampler.run([qc2], shots=1024)
228
+
229
+ # Retrieve results when ready
230
+ result1 = job1.result()
231
+ result2 = job2.result()
232
+ ```
233
+
234
+ ## Result Processing
235
+
236
+ ### Sampler Results
237
+
238
+ ```python
239
+ result = sampler.run([qc], shots=1024).result()
240
+
241
+ # Get counts
242
+ counts = result[0].data.meas.get_counts()
243
+
244
+ # Get probabilities
245
+ probs = {k: v/1024 for k, v in counts.items()}
246
+
247
+ # Get metadata
248
+ metadata = result[0].metadata
249
+ ```
250
+
251
+ ### Estimator Results
252
+
253
+ ```python
254
+ result = estimator.run([(qc, observable)]).result()
255
+
256
+ # Expectation value
257
+ exp_val = result[0].data.evs
258
+
259
+ # Standard deviation (if available)
260
+ std_dev = result[0].data.stds
261
+
262
+ # Metadata
263
+ metadata = result[0].metadata
264
+ ```
265
+
266
+ ## Differences from V1 Primitives
267
+
268
+ **V2 Improvements:**
269
+ - More flexible parameter binding
270
+ - Better result structure
271
+ - Improved performance
272
+ - Cleaner API design
273
+
274
+ **Migration from V1:**
275
+ - Use `StatevectorSampler` instead of `Sampler`
276
+ - Use `StatevectorEstimator` instead of `Estimator`
277
+ - Result access changed from `.result().quasi_dists[0]` to `.result()[0].data.meas.get_counts()`
@@ -0,0 +1,99 @@
1
+ # Qiskit Setup and Installation
2
+
3
+ ## Installation
4
+
5
+ Install Qiskit using uv:
6
+
7
+ ```bash
8
+ uv pip install qiskit
9
+ ```
10
+
11
+ For visualization capabilities:
12
+
13
+ ```bash
14
+ uv pip install "qiskit[visualization]" matplotlib
15
+ ```
16
+
17
+ ## Python Environment Setup
18
+
19
+ Create and activate a virtual environment to isolate dependencies:
20
+
21
+ ```bash
22
+ # macOS/Linux
23
+ python3 -m venv .venv
24
+ source .venv/bin/activate
25
+
26
+ # Windows
27
+ python -m venv .venv
28
+ .venv\Scripts\activate
29
+ ```
30
+
31
+ ## Supported Python Versions
32
+
33
+ Check the [Qiskit PyPI page](https://pypi.org/project/qiskit/) for currently supported Python versions. As of 2025, Qiskit typically supports Python 3.8+.
34
+
35
+ ## IBM Quantum Account Setup
36
+
37
+ To run circuits on real IBM Quantum hardware, you need an IBM Quantum account and API token.
38
+
39
+ ### Creating an Account
40
+
41
+ 1. Visit [IBM Quantum Platform](https://quantum.ibm.com/)
42
+ 2. Sign up for a free account
43
+ 3. Navigate to your account settings to retrieve your API token
44
+
45
+ ### Configuring Authentication
46
+
47
+ Save your IBM Quantum credentials:
48
+
49
+ ```python
50
+ from qiskit_ibm_runtime import QiskitRuntimeService
51
+
52
+ # Save credentials (first time only)
53
+ QiskitRuntimeService.save_account(
54
+ channel="ibm_quantum",
55
+ token="YOUR_IBM_QUANTUM_TOKEN"
56
+ )
57
+
58
+ # Later sessions - load saved credentials
59
+ service = QiskitRuntimeService()
60
+ ```
61
+
62
+ ### Environment Variable Method
63
+
64
+ Alternatively, set the API token as an environment variable:
65
+
66
+ ```bash
67
+ export QISKIT_IBM_TOKEN="YOUR_IBM_QUANTUM_TOKEN"
68
+ ```
69
+
70
+ ## Local Development (No Account Required)
71
+
72
+ You can build and test quantum circuits locally without an IBM Quantum account using simulators:
73
+
74
+ ```python
75
+ from qiskit import QuantumCircuit
76
+ from qiskit.primitives import StatevectorSampler
77
+
78
+ qc = QuantumCircuit(2)
79
+ qc.h(0)
80
+ qc.cx(0, 1)
81
+ qc.measure_all()
82
+
83
+ # Run locally with simulator
84
+ sampler = StatevectorSampler()
85
+ result = sampler.run([qc], shots=1024).result()
86
+ ```
87
+
88
+ ## Verifying Installation
89
+
90
+ Test your installation:
91
+
92
+ ```python
93
+ import qiskit
94
+ print(qiskit.__version__)
95
+
96
+ from qiskit import QuantumCircuit
97
+ qc = QuantumCircuit(2)
98
+ print("Qiskit installed successfully!")
99
+ ```
@@ -0,0 +1,286 @@
1
+ # Circuit Transpilation and Optimization
2
+
3
+ Transpilation is the process of rewriting a quantum circuit to match the topology and gate set of a specific quantum device, while optimizing for execution on noisy quantum computers.
4
+
5
+ ## Why Transpilation?
6
+
7
+ **Problem**: Abstract quantum circuits may use gates not available on hardware and assume all-to-all qubit connectivity.
8
+
9
+ **Solution**: Transpilation transforms circuits to:
10
+ 1. Use only hardware-native gates (basis gates)
11
+ 2. Respect physical qubit connectivity
12
+ 3. Minimize circuit depth and gate count
13
+ 4. Optimize for reduced errors on noisy devices
14
+
15
+ ## Basic Transpilation
16
+
17
+ ### Simple Transpile
18
+
19
+ ```python
20
+ from qiskit import QuantumCircuit, transpile
21
+
22
+ qc = QuantumCircuit(3)
23
+ qc.h(0)
24
+ qc.cx(0, 1)
25
+ qc.cx(1, 2)
26
+
27
+ # Transpile for a specific backend
28
+ transpiled_qc = transpile(qc, backend=backend)
29
+ ```
30
+
31
+ ### Optimization Levels
32
+
33
+ Choose optimization level 0-3:
34
+
35
+ ```python
36
+ # Level 0: No optimization (fastest)
37
+ qc_0 = transpile(qc, backend=backend, optimization_level=0)
38
+
39
+ # Level 1: Light optimization
40
+ qc_1 = transpile(qc, backend=backend, optimization_level=1)
41
+
42
+ # Level 2: Moderate optimization (default)
43
+ qc_2 = transpile(qc, backend=backend, optimization_level=2)
44
+
45
+ # Level 3: Heavy optimization (slowest, best results)
46
+ qc_3 = transpile(qc, backend=backend, optimization_level=3)
47
+ ```
48
+
49
+ **Qiskit SDK v2.2** provides **83x faster transpilation** compared to competitors.
50
+
51
+ ## Transpilation Stages
52
+
53
+ The transpiler pipeline consists of six stages:
54
+
55
+ ### 1. Init Stage
56
+ - Validates circuit instructions
57
+ - Translates multi-qubit gates to standard form
58
+
59
+ ### 2. Layout Stage
60
+ - Maps virtual qubits to physical qubits
61
+ - Considers qubit connectivity and error rates
62
+
63
+ ```python
64
+ from qiskit.transpiler import CouplingMap
65
+
66
+ # Define custom coupling
67
+ coupling = CouplingMap([(0, 1), (1, 2), (2, 3)])
68
+ qc_transpiled = transpile(qc, coupling_map=coupling)
69
+ ```
70
+
71
+ ### 3. Routing Stage
72
+ - Inserts SWAP gates to satisfy connectivity constraints
73
+ - Minimizes additional SWAP overhead
74
+
75
+ ### 4. Translation Stage
76
+ - Converts gates to hardware basis gates
77
+ - Typical basis: {RZ, SX, X, CX}
78
+
79
+ ```python
80
+ # Specify basis gates
81
+ basis_gates = ['cx', 'id', 'rz', 'sx', 'x']
82
+ qc_transpiled = transpile(qc, basis_gates=basis_gates)
83
+ ```
84
+
85
+ ### 5. Optimization Stage
86
+ - Reduces gate count and circuit depth
87
+ - Applies gate cancellation and commutation rules
88
+ - Uses **virtual permutation elision** (levels 2-3)
89
+ - Finds separable operations to decompose
90
+
91
+ ### 6. Scheduling Stage
92
+ - Adds timing information for pulse-level control
93
+
94
+ ## Advanced Optimization Features
95
+
96
+ ### Virtual Permutation Elision
97
+
98
+ At optimization levels 2-3, Qiskit analyzes commutation structure to eliminate unnecessary SWAP gates by tracking virtual qubit permutations.
99
+
100
+ ### Gate Cancellation
101
+
102
+ Identifies and removes pairs of gates that cancel:
103
+ - X-X → I
104
+ - H-H → I
105
+ - CNOT-CNOT → I
106
+
107
+ ### Numerical Decomposition
108
+
109
+ Splits two-qubit gates that can be expressed as separable one-qubit operations.
110
+
111
+ ## Common Transpilation Parameters
112
+
113
+ ### Initial Layout
114
+
115
+ Specify which physical qubits to use:
116
+
117
+ ```python
118
+ # Use specific physical qubits
119
+ initial_layout = [0, 2, 4] # Maps circuit qubits 0,1,2 to physical qubits 0,2,4
120
+ qc_transpiled = transpile(qc, backend=backend, initial_layout=initial_layout)
121
+ ```
122
+
123
+ ### Approximation Degree
124
+
125
+ Trade accuracy for fewer gates (0.0 = max approximation, 1.0 = no approximation):
126
+
127
+ ```python
128
+ # Allow 5% approximation error for fewer gates
129
+ qc_transpiled = transpile(qc, backend=backend, approximation_degree=0.95)
130
+ ```
131
+
132
+ ### Seed for Reproducibility
133
+
134
+ ```python
135
+ qc_transpiled = transpile(qc, backend=backend, seed_transpiler=42)
136
+ ```
137
+
138
+ ### Scheduling Method
139
+
140
+ ```python
141
+ # Add timing constraints
142
+ qc_transpiled = transpile(
143
+ qc,
144
+ backend=backend,
145
+ scheduling_method='alap' # As Late As Possible
146
+ )
147
+ ```
148
+
149
+ ## Transpiling for Simulators
150
+
151
+ Even for simulators, transpilation can optimize circuits:
152
+
153
+ ```python
154
+ from qiskit_aer import AerSimulator
155
+
156
+ simulator = AerSimulator()
157
+ qc_optimized = transpile(qc, backend=simulator, optimization_level=3)
158
+
159
+ # Compare gate counts
160
+ print(f"Original: {qc.size()} gates")
161
+ print(f"Optimized: {qc_optimized.size()} gates")
162
+ ```
163
+
164
+ ## Target-Aware Transpilation
165
+
166
+ Use `Target` objects for detailed backend specifications:
167
+
168
+ ```python
169
+ from qiskit.transpiler import Target
170
+
171
+ # Transpile with target specification
172
+ qc_transpiled = transpile(qc, target=backend.target)
173
+ ```
174
+
175
+ ## Circuit Analysis After Transpilation
176
+
177
+ ```python
178
+ qc_transpiled = transpile(qc, backend=backend, optimization_level=3)
179
+
180
+ # Analyze results
181
+ print(f"Depth: {qc_transpiled.depth()}")
182
+ print(f"Gate count: {qc_transpiled.size()}")
183
+ print(f"Operations: {qc_transpiled.count_ops()}")
184
+
185
+ # Check two-qubit gate count (major error source)
186
+ two_qubit_gates = qc_transpiled.count_ops().get('cx', 0)
187
+ print(f"Two-qubit gates: {two_qubit_gates}")
188
+ ```
189
+
190
+ **Qiskit produces circuits with 29% fewer two-qubit gates** than leading alternatives, significantly reducing errors.
191
+
192
+ ## Multiple Circuit Transpilation
193
+
194
+ Transpile multiple circuits efficiently:
195
+
196
+ ```python
197
+ circuits = [qc1, qc2, qc3]
198
+ transpiled_circuits = transpile(
199
+ circuits,
200
+ backend=backend,
201
+ optimization_level=3
202
+ )
203
+ ```
204
+
205
+ ## Pre-transpilation Best Practices
206
+
207
+ ### 1. Design with Hardware Topology in Mind
208
+
209
+ Consider backend coupling map when designing circuits:
210
+
211
+ ```python
212
+ # Check backend coupling
213
+ print(backend.coupling_map)
214
+
215
+ # Design circuits that align with coupling
216
+ ```
217
+
218
+ ### 2. Use Native Gates When Possible
219
+
220
+ Some backends support gates beyond {CX, RZ, SX, X}:
221
+
222
+ ```python
223
+ # Check available basis gates
224
+ print(backend.configuration().basis_gates)
225
+ ```
226
+
227
+ ### 3. Minimize Two-Qubit Gates
228
+
229
+ Two-qubit gates have significantly higher error rates:
230
+ - Design algorithms to minimize CNOT gates
231
+ - Use gate identities to reduce counts
232
+
233
+ ### 4. Test with Simulators First
234
+
235
+ ```python
236
+ from qiskit_aer import AerSimulator
237
+
238
+ # Test transpilation locally
239
+ sim_backend = AerSimulator.from_backend(backend)
240
+ qc_test = transpile(qc, backend=sim_backend, optimization_level=3)
241
+ ```
242
+
243
+ ## Transpilation for Different Providers
244
+
245
+ ### IBM Quantum
246
+
247
+ ```python
248
+ from qiskit_ibm_runtime import QiskitRuntimeService
249
+
250
+ service = QiskitRuntimeService()
251
+ backend = service.backend("ibm_brisbane")
252
+ qc_transpiled = transpile(qc, backend=backend)
253
+ ```
254
+
255
+ ### IonQ
256
+
257
+ ```python
258
+ # IonQ has all-to-all connectivity, different basis gates
259
+ basis_gates = ['gpi', 'gpi2', 'ms']
260
+ qc_transpiled = transpile(qc, basis_gates=basis_gates)
261
+ ```
262
+
263
+ ### Amazon Braket
264
+
265
+ Transpilation depends on specific device (Rigetti, IonQ, etc.)
266
+
267
+ ## Performance Tips
268
+
269
+ 1. **Cache transpiled circuits** - Transpilation is expensive, reuse when possible
270
+ 2. **Use appropriate optimization level** - Level 3 is slow but best for production
271
+ 3. **Leverage v2.2 speed improvements** - Update to latest Qiskit for 83x speedup
272
+ 4. **Parallelize transpilation** - Qiskit automatically parallelizes when transpiling multiple circuits
273
+
274
+ ## Common Issues and Solutions
275
+
276
+ ### Issue: Circuit too deep after transpilation
277
+ **Solution**: Use higher optimization level or redesign circuit with fewer layers
278
+
279
+ ### Issue: Too many SWAP gates inserted
280
+ **Solution**: Adjust initial_layout to better match qubit topology
281
+
282
+ ### Issue: Transpilation takes too long
283
+ **Solution**: Reduce optimization level or update to Qiskit v2.2+ for speed improvements
284
+
285
+ ### Issue: Unexpected gate decompositions
286
+ **Solution**: Check basis_gates and consider specifying custom decomposition rules