@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 +1,314 @@
1
+ """
2
+ Template for creating custom Gymnasium environments compatible with Stable Baselines3.
3
+
4
+ This template demonstrates:
5
+ - Proper Gymnasium environment structure
6
+ - Observation and action space definition
7
+ - Step and reset implementation
8
+ - Validation with SB3's env_checker
9
+ - Registration with Gymnasium
10
+ """
11
+
12
+ import gymnasium as gym
13
+ from gymnasium import spaces
14
+ import numpy as np
15
+
16
+
17
+ class CustomEnv(gym.Env):
18
+ """
19
+ Custom Gymnasium Environment Template.
20
+
21
+ This is a template for creating custom environments that work with
22
+ Stable Baselines3. Modify the observation space, action space, reward
23
+ function, and state transitions to match your specific problem.
24
+
25
+ Example:
26
+ A simple grid world where the agent tries to reach a goal position.
27
+ """
28
+
29
+ # Optional: Provide metadata for rendering modes
30
+ metadata = {"render_modes": ["human", "rgb_array"], "render_fps": 30}
31
+
32
+ def __init__(self, grid_size=5, render_mode=None):
33
+ """
34
+ Initialize the environment.
35
+
36
+ Args:
37
+ grid_size: Size of the grid world (grid_size x grid_size)
38
+ render_mode: How to render ('human', 'rgb_array', or None)
39
+ """
40
+ super().__init__()
41
+
42
+ self.grid_size = grid_size
43
+ self.render_mode = render_mode
44
+
45
+ # Define action space
46
+ # Example: 4 discrete actions (up, down, left, right)
47
+ self.action_space = spaces.Discrete(4)
48
+
49
+ # Define observation space
50
+ # Example: 2D position [x, y] in continuous space
51
+ # Note: Use np.float32 for observations (SB3 recommendation)
52
+ self.observation_space = spaces.Box(
53
+ low=0,
54
+ high=grid_size - 1,
55
+ shape=(2,),
56
+ dtype=np.float32,
57
+ )
58
+
59
+ # Alternative observation spaces:
60
+ # 1. Discrete: spaces.Discrete(n)
61
+ # 2. Multi-discrete: spaces.MultiDiscrete([n1, n2, ...])
62
+ # 3. Multi-binary: spaces.MultiBinary(n)
63
+ # 4. Box (continuous): spaces.Box(low=, high=, shape=, dtype=np.float32)
64
+ # 5. Dict: spaces.Dict({"key1": space1, "key2": space2})
65
+
66
+ # For image observations (e.g., 84x84 RGB image):
67
+ # self.observation_space = spaces.Box(
68
+ # low=0,
69
+ # high=255,
70
+ # shape=(3, 84, 84), # (channels, height, width) - channel-first
71
+ # dtype=np.uint8,
72
+ # )
73
+
74
+ # Initialize state
75
+ self._agent_position = None
76
+ self._goal_position = None
77
+
78
+ def reset(self, seed=None, options=None):
79
+ """
80
+ Reset the environment to initial state.
81
+
82
+ Args:
83
+ seed: Random seed for reproducibility
84
+ options: Additional options (optional)
85
+
86
+ Returns:
87
+ observation: Initial observation
88
+ info: Additional information dictionary
89
+ """
90
+ # Set seed for reproducibility
91
+ super().reset(seed=seed)
92
+
93
+ # Initialize agent position randomly
94
+ self._agent_position = self.np_random.integers(0, self.grid_size, size=2)
95
+
96
+ # Initialize goal position (different from agent)
97
+ self._goal_position = self.np_random.integers(0, self.grid_size, size=2)
98
+ while np.array_equal(self._agent_position, self._goal_position):
99
+ self._goal_position = self.np_random.integers(0, self.grid_size, size=2)
100
+
101
+ observation = self._get_obs()
102
+ info = self._get_info()
103
+
104
+ return observation, info
105
+
106
+ def step(self, action):
107
+ """
108
+ Execute one step in the environment.
109
+
110
+ Args:
111
+ action: Action to take
112
+
113
+ Returns:
114
+ observation: New observation
115
+ reward: Reward for this step
116
+ terminated: Whether episode has ended (goal reached)
117
+ truncated: Whether episode was truncated (time limit, etc.)
118
+ info: Additional information dictionary
119
+ """
120
+ # Map action to direction (0: up, 1: down, 2: left, 3: right)
121
+ direction = np.array([
122
+ [-1, 0], # up
123
+ [1, 0], # down
124
+ [0, -1], # left
125
+ [0, 1], # right
126
+ ])[action]
127
+
128
+ # Update agent position (clip to stay within grid)
129
+ self._agent_position = np.clip(
130
+ self._agent_position + direction,
131
+ 0,
132
+ self.grid_size - 1,
133
+ )
134
+
135
+ # Check if goal is reached
136
+ terminated = np.array_equal(self._agent_position, self._goal_position)
137
+
138
+ # Calculate reward
139
+ if terminated:
140
+ reward = 1.0 # Goal reached
141
+ else:
142
+ # Negative reward based on distance to goal (encourages efficiency)
143
+ distance = np.linalg.norm(self._agent_position - self._goal_position)
144
+ reward = -0.1 * distance
145
+
146
+ # Episode not truncated in this example (no time limit)
147
+ truncated = False
148
+
149
+ observation = self._get_obs()
150
+ info = self._get_info()
151
+
152
+ return observation, reward, terminated, truncated, info
153
+
154
+ def _get_obs(self):
155
+ """
156
+ Get current observation.
157
+
158
+ Returns:
159
+ observation: Current state as defined by observation_space
160
+ """
161
+ # Return agent position as observation
162
+ return self._agent_position.astype(np.float32)
163
+
164
+ # For dict observations:
165
+ # return {
166
+ # "agent": self._agent_position.astype(np.float32),
167
+ # "goal": self._goal_position.astype(np.float32),
168
+ # }
169
+
170
+ def _get_info(self):
171
+ """
172
+ Get additional information (for debugging/logging).
173
+
174
+ Returns:
175
+ info: Dictionary with additional information
176
+ """
177
+ return {
178
+ "agent_position": self._agent_position,
179
+ "goal_position": self._goal_position,
180
+ "distance_to_goal": np.linalg.norm(
181
+ self._agent_position - self._goal_position
182
+ ),
183
+ }
184
+
185
+ def render(self):
186
+ """
187
+ Render the environment.
188
+
189
+ Returns:
190
+ Rendered frame (if render_mode is 'rgb_array')
191
+ """
192
+ if self.render_mode == "human":
193
+ # Print simple text-based rendering
194
+ grid = np.zeros((self.grid_size, self.grid_size), dtype=str)
195
+ grid[:, :] = "."
196
+ grid[tuple(self._agent_position)] = "A"
197
+ grid[tuple(self._goal_position)] = "G"
198
+
199
+ print("\n" + "=" * (self.grid_size * 2 + 1))
200
+ for row in grid:
201
+ print(" ".join(row))
202
+ print("=" * (self.grid_size * 2 + 1) + "\n")
203
+
204
+ elif self.render_mode == "rgb_array":
205
+ # Return RGB array for video recording
206
+ # This is a placeholder - implement proper rendering as needed
207
+ canvas = np.zeros((
208
+ self.grid_size * 50,
209
+ self.grid_size * 50,
210
+ 3
211
+ ), dtype=np.uint8)
212
+ # Draw agent and goal on canvas
213
+ # ... (implement visual rendering)
214
+ return canvas
215
+
216
+ def close(self):
217
+ """
218
+ Clean up environment resources.
219
+ """
220
+ pass
221
+
222
+
223
+ # Optional: Register the environment with Gymnasium
224
+ # This allows creating the environment with gym.make("CustomEnv-v0")
225
+ gym.register(
226
+ id="CustomEnv-v0",
227
+ entry_point=__name__ + ":CustomEnv",
228
+ max_episode_steps=100,
229
+ )
230
+
231
+
232
+ def validate_environment():
233
+ """
234
+ Validate the custom environment with SB3's env_checker.
235
+ """
236
+ from stable_baselines3.common.env_checker import check_env
237
+
238
+ print("Validating custom environment...")
239
+ env = CustomEnv()
240
+ check_env(env, warn=True)
241
+ print("Environment validation passed!")
242
+
243
+
244
+ def test_environment():
245
+ """
246
+ Test the custom environment with random actions.
247
+ """
248
+ print("Testing environment with random actions...")
249
+ env = CustomEnv(render_mode="human")
250
+
251
+ obs, info = env.reset()
252
+ print(f"Initial observation: {obs}")
253
+ print(f"Initial info: {info}")
254
+
255
+ for step in range(10):
256
+ action = env.action_space.sample() # Random action
257
+ obs, reward, terminated, truncated, info = env.step(action)
258
+
259
+ print(f"\nStep {step + 1}:")
260
+ print(f" Action: {action}")
261
+ print(f" Observation: {obs}")
262
+ print(f" Reward: {reward:.3f}")
263
+ print(f" Terminated: {terminated}")
264
+ print(f" Info: {info}")
265
+
266
+ env.render()
267
+
268
+ if terminated or truncated:
269
+ print("Episode finished!")
270
+ break
271
+
272
+ env.close()
273
+
274
+
275
+ def train_on_custom_env():
276
+ """
277
+ Train a PPO agent on the custom environment.
278
+ """
279
+ from stable_baselines3 import PPO
280
+
281
+ print("Training PPO agent on custom environment...")
282
+
283
+ # Create environment
284
+ env = CustomEnv()
285
+
286
+ # Validate first
287
+ from stable_baselines3.common.env_checker import check_env
288
+ check_env(env, warn=True)
289
+
290
+ # Train agent
291
+ model = PPO("MlpPolicy", env, verbose=1)
292
+ model.learn(total_timesteps=10000)
293
+
294
+ # Test trained agent
295
+ obs, info = env.reset()
296
+ for _ in range(20):
297
+ action, _states = model.predict(obs, deterministic=True)
298
+ obs, reward, terminated, truncated, info = env.step(action)
299
+ if terminated or truncated:
300
+ print(f"Goal reached! Final reward: {reward}")
301
+ break
302
+
303
+ env.close()
304
+
305
+
306
+ if __name__ == "__main__":
307
+ # Validate the environment
308
+ validate_environment()
309
+
310
+ # Test with random actions
311
+ # test_environment()
312
+
313
+ # Train an agent
314
+ # train_on_custom_env()
@@ -0,0 +1,245 @@
1
+ """
2
+ Template script for evaluating trained RL agents with Stable Baselines3.
3
+
4
+ This template demonstrates:
5
+ - Loading trained models
6
+ - Evaluating performance with statistics
7
+ - Recording videos of agent behavior
8
+ - Visualizing agent performance
9
+ """
10
+
11
+ import gymnasium as gym
12
+ import numpy as np
13
+ from stable_baselines3 import PPO
14
+ from stable_baselines3.common.evaluation import evaluate_policy
15
+ from stable_baselines3.common.vec_env import DummyVecEnv, VecVideoRecorder, VecNormalize
16
+ import os
17
+
18
+
19
+ def evaluate_agent(
20
+ model_path,
21
+ env_id="CartPole-v1",
22
+ n_eval_episodes=10,
23
+ deterministic=True,
24
+ render=False,
25
+ record_video=False,
26
+ video_folder="./videos/",
27
+ vec_normalize_path=None,
28
+ ):
29
+ """
30
+ Evaluate a trained RL agent.
31
+
32
+ Args:
33
+ model_path: Path to the saved model
34
+ env_id: Gymnasium environment ID
35
+ n_eval_episodes: Number of episodes to evaluate
36
+ deterministic: Use deterministic actions
37
+ render: Render the environment during evaluation
38
+ record_video: Record videos of the agent
39
+ video_folder: Folder to save videos
40
+ vec_normalize_path: Path to VecNormalize statistics (if used during training)
41
+
42
+ Returns:
43
+ mean_reward: Mean episode reward
44
+ std_reward: Standard deviation of episode rewards
45
+ """
46
+ # Load the trained model
47
+ print(f"Loading model from {model_path}...")
48
+ model = PPO.load(model_path)
49
+
50
+ # Create evaluation environment
51
+ if render:
52
+ env = gym.make(env_id, render_mode="human")
53
+ else:
54
+ env = gym.make(env_id)
55
+
56
+ # Wrap in DummyVecEnv for consistency
57
+ env = DummyVecEnv([lambda: env])
58
+
59
+ # Load VecNormalize statistics if they were used during training
60
+ if vec_normalize_path and os.path.exists(vec_normalize_path):
61
+ print(f"Loading VecNormalize statistics from {vec_normalize_path}...")
62
+ env = VecNormalize.load(vec_normalize_path, env)
63
+ env.training = False # Don't update statistics during evaluation
64
+ env.norm_reward = False # Don't normalize rewards during evaluation
65
+
66
+ # Set up video recording if requested
67
+ if record_video:
68
+ os.makedirs(video_folder, exist_ok=True)
69
+ env = VecVideoRecorder(
70
+ env,
71
+ video_folder,
72
+ record_video_trigger=lambda x: x == 0, # Record all episodes
73
+ video_length=1000, # Max video length
74
+ name_prefix=f"eval-{env_id}",
75
+ )
76
+ print(f"Recording videos to {video_folder}...")
77
+
78
+ # Evaluate the agent
79
+ print(f"Evaluating for {n_eval_episodes} episodes...")
80
+ mean_reward, std_reward = evaluate_policy(
81
+ model,
82
+ env,
83
+ n_eval_episodes=n_eval_episodes,
84
+ deterministic=deterministic,
85
+ render=False, # VecEnv doesn't support render parameter
86
+ return_episode_rewards=False,
87
+ )
88
+
89
+ print(f"Mean reward: {mean_reward:.2f} +/- {std_reward:.2f}")
90
+
91
+ # Cleanup
92
+ env.close()
93
+
94
+ return mean_reward, std_reward
95
+
96
+
97
+ def watch_agent(
98
+ model_path,
99
+ env_id="CartPole-v1",
100
+ n_episodes=5,
101
+ deterministic=True,
102
+ vec_normalize_path=None,
103
+ ):
104
+ """
105
+ Watch a trained agent play (with rendering).
106
+
107
+ Args:
108
+ model_path: Path to the saved model
109
+ env_id: Gymnasium environment ID
110
+ n_episodes: Number of episodes to watch
111
+ deterministic: Use deterministic actions
112
+ vec_normalize_path: Path to VecNormalize statistics (if used during training)
113
+ """
114
+ # Load the trained model
115
+ print(f"Loading model from {model_path}...")
116
+ model = PPO.load(model_path)
117
+
118
+ # Create environment with rendering
119
+ env = gym.make(env_id, render_mode="human")
120
+
121
+ # Load VecNormalize statistics if needed
122
+ obs_normalization = None
123
+ if vec_normalize_path and os.path.exists(vec_normalize_path):
124
+ print(f"Loading VecNormalize statistics from {vec_normalize_path}...")
125
+ # For rendering, we'll manually apply normalization
126
+ dummy_env = DummyVecEnv([lambda: gym.make(env_id)])
127
+ vec_env = VecNormalize.load(vec_normalize_path, dummy_env)
128
+ obs_normalization = vec_env
129
+ dummy_env.close()
130
+
131
+ # Run episodes
132
+ for episode in range(n_episodes):
133
+ obs, info = env.reset()
134
+ episode_reward = 0
135
+ done = False
136
+ step = 0
137
+
138
+ print(f"\nEpisode {episode + 1}/{n_episodes}")
139
+
140
+ while not done:
141
+ # Apply observation normalization if needed
142
+ if obs_normalization:
143
+ obs_normalized = obs_normalization.normalize_obs(obs)
144
+ else:
145
+ obs_normalized = obs
146
+
147
+ # Get action from model
148
+ action, _states = model.predict(obs_normalized, deterministic=deterministic)
149
+
150
+ # Take step in environment
151
+ obs, reward, terminated, truncated, info = env.step(action)
152
+ done = terminated or truncated
153
+
154
+ episode_reward += reward
155
+ step += 1
156
+
157
+ print(f"Episode reward: {episode_reward:.2f} ({step} steps)")
158
+
159
+ env.close()
160
+
161
+
162
+ def compare_models(
163
+ model_paths,
164
+ env_id="CartPole-v1",
165
+ n_eval_episodes=10,
166
+ deterministic=True,
167
+ ):
168
+ """
169
+ Compare performance of multiple trained models.
170
+
171
+ Args:
172
+ model_paths: List of paths to saved models
173
+ env_id: Gymnasium environment ID
174
+ n_eval_episodes: Number of episodes to evaluate each model
175
+ deterministic: Use deterministic actions
176
+ """
177
+ results = {}
178
+
179
+ for model_path in model_paths:
180
+ print(f"\nEvaluating {model_path}...")
181
+ mean_reward, std_reward = evaluate_agent(
182
+ model_path,
183
+ env_id=env_id,
184
+ n_eval_episodes=n_eval_episodes,
185
+ deterministic=deterministic,
186
+ )
187
+ results[model_path] = {"mean": mean_reward, "std": std_reward}
188
+
189
+ # Print comparison
190
+ print("\n" + "=" * 60)
191
+ print("Model Comparison Results")
192
+ print("=" * 60)
193
+ for model_path, stats in results.items():
194
+ print(f"{model_path}: {stats['mean']:.2f} +/- {stats['std']:.2f}")
195
+ print("=" * 60)
196
+
197
+ return results
198
+
199
+
200
+ if __name__ == "__main__":
201
+ # Example 1: Evaluate a trained model
202
+ model_path = "./models/best_model/best_model.zip"
203
+ evaluate_agent(
204
+ model_path=model_path,
205
+ env_id="CartPole-v1",
206
+ n_eval_episodes=10,
207
+ deterministic=True,
208
+ )
209
+
210
+ # Example 2: Record videos of agent behavior
211
+ # evaluate_agent(
212
+ # model_path=model_path,
213
+ # env_id="CartPole-v1",
214
+ # n_eval_episodes=5,
215
+ # deterministic=True,
216
+ # record_video=True,
217
+ # video_folder="./videos/",
218
+ # )
219
+
220
+ # Example 3: Watch agent play with rendering
221
+ # watch_agent(
222
+ # model_path=model_path,
223
+ # env_id="CartPole-v1",
224
+ # n_episodes=3,
225
+ # deterministic=True,
226
+ # )
227
+
228
+ # Example 4: Compare multiple models
229
+ # compare_models(
230
+ # model_paths=[
231
+ # "./models/model_100k.zip",
232
+ # "./models/model_200k.zip",
233
+ # "./models/best_model/best_model.zip",
234
+ # ],
235
+ # env_id="CartPole-v1",
236
+ # n_eval_episodes=10,
237
+ # )
238
+
239
+ # Example 5: Evaluate with VecNormalize statistics
240
+ # evaluate_agent(
241
+ # model_path="./models/best_model/best_model.zip",
242
+ # env_id="Pendulum-v1",
243
+ # n_eval_episodes=10,
244
+ # vec_normalize_path="./models/vec_normalize.pkl",
245
+ # )