@saibolla/ada 0.1.2

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 (1432) hide show
  1. package/.ada/SYSTEM.md +81 -0
  2. package/.ada/agents/researcher.md +69 -0
  3. package/.ada/agents/reviewer.md +92 -0
  4. package/.ada/agents/verifier.md +45 -0
  5. package/.ada/agents/writer.md +54 -0
  6. package/.ada/settings.json +32 -0
  7. package/.ada/themes/ada.json +85 -0
  8. package/.env.example +31 -0
  9. package/AGENTS.md +79 -0
  10. package/LICENSE +191 -0
  11. package/README.md +188 -0
  12. package/bin/ada.js +26 -0
  13. package/dist/bootstrap/sync.js +143 -0
  14. package/dist/cli.js +404 -0
  15. package/dist/config/paths.js +32 -0
  16. package/dist/index.js +10 -0
  17. package/dist/model/catalog.js +255 -0
  18. package/dist/model/commands.js +180 -0
  19. package/dist/pi/launch.js +33 -0
  20. package/dist/pi/package-presets.js +55 -0
  21. package/dist/pi/runtime.js +81 -0
  22. package/dist/pi/settings.js +108 -0
  23. package/dist/pi/web-access.js +74 -0
  24. package/dist/search/commands.js +12 -0
  25. package/dist/setup/doctor.js +126 -0
  26. package/dist/setup/preview.js +117 -0
  27. package/dist/setup/prompts.js +34 -0
  28. package/dist/setup/setup.js +98 -0
  29. package/dist/setup/update.js +133 -0
  30. package/dist/system/executables.js +38 -0
  31. package/dist/system/node-version.js +31 -0
  32. package/dist/system/open-url.js +35 -0
  33. package/dist/system/promise-polyfill.js +12 -0
  34. package/dist/ui/terminal.js +64 -0
  35. package/dist/web/launch.js +48 -0
  36. package/dist/web-search.js +1 -0
  37. package/extensions/docparser/constants.ts +62 -0
  38. package/extensions/docparser/deps.ts +584 -0
  39. package/extensions/docparser/doctor.ts +353 -0
  40. package/extensions/docparser/index.ts +9 -0
  41. package/extensions/docparser/input.ts +230 -0
  42. package/extensions/docparser/request.ts +67 -0
  43. package/extensions/docparser/schema.ts +82 -0
  44. package/extensions/docparser/tool.ts +305 -0
  45. package/extensions/docparser/types.ts +99 -0
  46. package/extensions/research-tools/alpha.ts +107 -0
  47. package/extensions/research-tools/header.ts +284 -0
  48. package/extensions/research-tools/help.ts +93 -0
  49. package/extensions/research-tools/project-scaffold.ts +64 -0
  50. package/extensions/research-tools/project.ts +123 -0
  51. package/extensions/research-tools/shared.ts +16 -0
  52. package/extensions/research-tools.ts +42 -0
  53. package/logo.d.mts +3 -0
  54. package/logo.mjs +14 -0
  55. package/metadata/commands.d.mts +46 -0
  56. package/metadata/commands.mjs +133 -0
  57. package/package.json +80 -0
  58. package/prompts/audit.md +17 -0
  59. package/prompts/autoresearch.md +66 -0
  60. package/prompts/compare.md +18 -0
  61. package/prompts/deepresearch.md +189 -0
  62. package/prompts/draft.md +19 -0
  63. package/prompts/jobs.md +16 -0
  64. package/prompts/litreview.md +18 -0
  65. package/prompts/log.md +14 -0
  66. package/prompts/replicate.md +24 -0
  67. package/prompts/review.md +18 -0
  68. package/prompts/watch.md +16 -0
  69. package/scripts/build-native-bundle.mjs +349 -0
  70. package/scripts/check-node-version.mjs +35 -0
  71. package/scripts/patch-embedded-pi.mjs +588 -0
  72. package/scripts/prepare-runtime-workspace.mjs +162 -0
  73. package/scripts/prune-runtime-deps.mjs +131 -0
  74. package/scripts/release.sh +152 -0
  75. package/skills/adaptyv/SKILL.md +112 -0
  76. package/skills/adaptyv/reference/api_reference.md +308 -0
  77. package/skills/adaptyv/reference/examples.md +913 -0
  78. package/skills/adaptyv/reference/experiments.md +360 -0
  79. package/skills/adaptyv/reference/protein_optimization.md +637 -0
  80. package/skills/aeon/SKILL.md +372 -0
  81. package/skills/aeon/references/anomaly_detection.md +154 -0
  82. package/skills/aeon/references/classification.md +144 -0
  83. package/skills/aeon/references/clustering.md +123 -0
  84. package/skills/aeon/references/datasets_benchmarking.md +387 -0
  85. package/skills/aeon/references/distances.md +256 -0
  86. package/skills/aeon/references/forecasting.md +140 -0
  87. package/skills/aeon/references/networks.md +289 -0
  88. package/skills/aeon/references/regression.md +118 -0
  89. package/skills/aeon/references/segmentation.md +163 -0
  90. package/skills/aeon/references/similarity_search.md +187 -0
  91. package/skills/aeon/references/transformations.md +246 -0
  92. package/skills/alpha-research/SKILL.md +42 -0
  93. package/skills/alpha-vantage/SKILL.md +142 -0
  94. package/skills/alpha-vantage/references/commodities.md +153 -0
  95. package/skills/alpha-vantage/references/economic-indicators.md +158 -0
  96. package/skills/alpha-vantage/references/forex-crypto.md +154 -0
  97. package/skills/alpha-vantage/references/fundamentals.md +223 -0
  98. package/skills/alpha-vantage/references/intelligence.md +138 -0
  99. package/skills/alpha-vantage/references/options.md +93 -0
  100. package/skills/alpha-vantage/references/technical-indicators.md +374 -0
  101. package/skills/alpha-vantage/references/time-series.md +157 -0
  102. package/skills/alphafold-database/SKILL.md +511 -0
  103. package/skills/alphafold-database/references/api_reference.md +423 -0
  104. package/skills/anndata/SKILL.md +398 -0
  105. package/skills/anndata/references/best_practices.md +525 -0
  106. package/skills/anndata/references/concatenation.md +396 -0
  107. package/skills/anndata/references/data_structure.md +314 -0
  108. package/skills/anndata/references/io_operations.md +404 -0
  109. package/skills/anndata/references/manipulation.md +516 -0
  110. package/skills/arboreto/SKILL.md +241 -0
  111. package/skills/arboreto/references/algorithms.md +138 -0
  112. package/skills/arboreto/references/basic_inference.md +151 -0
  113. package/skills/arboreto/references/distributed_computing.md +242 -0
  114. package/skills/arboreto/scripts/basic_grn_inference.py +97 -0
  115. package/skills/arxiv-database/SKILL.md +362 -0
  116. package/skills/arxiv-database/references/api_reference.md +430 -0
  117. package/skills/arxiv-database/scripts/arxiv_search.py +414 -0
  118. package/skills/astropy/SKILL.md +329 -0
  119. package/skills/astropy/references/coordinates.md +273 -0
  120. package/skills/astropy/references/cosmology.md +307 -0
  121. package/skills/astropy/references/fits.md +396 -0
  122. package/skills/astropy/references/tables.md +489 -0
  123. package/skills/astropy/references/time.md +404 -0
  124. package/skills/astropy/references/units.md +178 -0
  125. package/skills/astropy/references/wcs_and_other_modules.md +373 -0
  126. package/skills/autoresearch/SKILL.md +12 -0
  127. package/skills/benchling-integration/SKILL.md +478 -0
  128. package/skills/benchling-integration/references/api_endpoints.md +883 -0
  129. package/skills/benchling-integration/references/authentication.md +379 -0
  130. package/skills/benchling-integration/references/sdk_reference.md +774 -0
  131. package/skills/bgpt-paper-search/SKILL.md +81 -0
  132. package/skills/bindingdb-database/SKILL.md +332 -0
  133. package/skills/bindingdb-database/references/affinity_queries.md +178 -0
  134. package/skills/biopython/SKILL.md +441 -0
  135. package/skills/biopython/references/advanced.md +577 -0
  136. package/skills/biopython/references/alignment.md +362 -0
  137. package/skills/biopython/references/blast.md +455 -0
  138. package/skills/biopython/references/databases.md +484 -0
  139. package/skills/biopython/references/phylogenetics.md +566 -0
  140. package/skills/biopython/references/sequence_io.md +285 -0
  141. package/skills/biopython/references/structure.md +564 -0
  142. package/skills/biorxiv-database/SKILL.md +481 -0
  143. package/skills/biorxiv-database/references/api_reference.md +280 -0
  144. package/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
  145. package/skills/bioservices/SKILL.md +359 -0
  146. package/skills/bioservices/references/identifier_mapping.md +685 -0
  147. package/skills/bioservices/references/services_reference.md +636 -0
  148. package/skills/bioservices/references/workflow_patterns.md +811 -0
  149. package/skills/bioservices/scripts/batch_id_converter.py +347 -0
  150. package/skills/bioservices/scripts/compound_cross_reference.py +378 -0
  151. package/skills/bioservices/scripts/pathway_analysis.py +309 -0
  152. package/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
  153. package/skills/brenda-database/SKILL.md +717 -0
  154. package/skills/brenda-database/references/api_reference.md +537 -0
  155. package/skills/brenda-database/scripts/brenda_queries.py +844 -0
  156. package/skills/brenda-database/scripts/brenda_visualization.py +772 -0
  157. package/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
  158. package/skills/cbioportal-database/SKILL.md +367 -0
  159. package/skills/cbioportal-database/references/study_exploration.md +128 -0
  160. package/skills/cellxgene-census/SKILL.md +509 -0
  161. package/skills/cellxgene-census/references/census_schema.md +182 -0
  162. package/skills/cellxgene-census/references/common_patterns.md +351 -0
  163. package/skills/chembl-database/SKILL.md +387 -0
  164. package/skills/chembl-database/references/api_reference.md +272 -0
  165. package/skills/chembl-database/scripts/example_queries.py +278 -0
  166. package/skills/cirq/SKILL.md +344 -0
  167. package/skills/cirq/references/building.md +307 -0
  168. package/skills/cirq/references/experiments.md +572 -0
  169. package/skills/cirq/references/hardware.md +515 -0
  170. package/skills/cirq/references/noise.md +515 -0
  171. package/skills/cirq/references/simulation.md +350 -0
  172. package/skills/cirq/references/transformation.md +416 -0
  173. package/skills/citation-management/SKILL.md +1113 -0
  174. package/skills/citation-management/assets/bibtex_template.bib +264 -0
  175. package/skills/citation-management/assets/citation_checklist.md +386 -0
  176. package/skills/citation-management/references/bibtex_formatting.md +908 -0
  177. package/skills/citation-management/references/citation_validation.md +794 -0
  178. package/skills/citation-management/references/google_scholar_search.md +725 -0
  179. package/skills/citation-management/references/metadata_extraction.md +870 -0
  180. package/skills/citation-management/references/pubmed_search.md +839 -0
  181. package/skills/citation-management/scripts/doi_to_bibtex.py +204 -0
  182. package/skills/citation-management/scripts/extract_metadata.py +569 -0
  183. package/skills/citation-management/scripts/format_bibtex.py +349 -0
  184. package/skills/citation-management/scripts/search_google_scholar.py +282 -0
  185. package/skills/citation-management/scripts/search_pubmed.py +398 -0
  186. package/skills/citation-management/scripts/validate_citations.py +497 -0
  187. package/skills/clinical-decision-support/SKILL.md +510 -0
  188. package/skills/clinical-decision-support/assets/biomarker_report_template.tex +380 -0
  189. package/skills/clinical-decision-support/assets/clinical_pathway_template.tex +222 -0
  190. package/skills/clinical-decision-support/assets/cohort_analysis_template.tex +359 -0
  191. package/skills/clinical-decision-support/assets/color_schemes.tex +149 -0
  192. package/skills/clinical-decision-support/assets/example_gbm_cohort.md +208 -0
  193. package/skills/clinical-decision-support/assets/recommendation_strength_guide.md +328 -0
  194. package/skills/clinical-decision-support/assets/treatment_recommendation_template.tex +529 -0
  195. package/skills/clinical-decision-support/references/README.md +129 -0
  196. package/skills/clinical-decision-support/references/biomarker_classification.md +719 -0
  197. package/skills/clinical-decision-support/references/clinical_decision_algorithms.md +604 -0
  198. package/skills/clinical-decision-support/references/evidence_synthesis.md +840 -0
  199. package/skills/clinical-decision-support/references/outcome_analysis.md +640 -0
  200. package/skills/clinical-decision-support/references/patient_cohort_analysis.md +427 -0
  201. package/skills/clinical-decision-support/references/treatment_recommendations.md +521 -0
  202. package/skills/clinical-decision-support/scripts/biomarker_classifier.py +384 -0
  203. package/skills/clinical-decision-support/scripts/build_decision_tree.py +447 -0
  204. package/skills/clinical-decision-support/scripts/create_cohort_tables.py +524 -0
  205. package/skills/clinical-decision-support/scripts/generate_survival_analysis.py +422 -0
  206. package/skills/clinical-decision-support/scripts/validate_cds_document.py +335 -0
  207. package/skills/clinical-reports/SKILL.md +1131 -0
  208. package/skills/clinical-reports/assets/case_report_template.md +352 -0
  209. package/skills/clinical-reports/assets/clinical_trial_csr_template.md +353 -0
  210. package/skills/clinical-reports/assets/clinical_trial_sae_template.md +359 -0
  211. package/skills/clinical-reports/assets/consult_note_template.md +305 -0
  212. package/skills/clinical-reports/assets/discharge_summary_template.md +453 -0
  213. package/skills/clinical-reports/assets/hipaa_compliance_checklist.md +395 -0
  214. package/skills/clinical-reports/assets/history_physical_template.md +305 -0
  215. package/skills/clinical-reports/assets/lab_report_template.md +309 -0
  216. package/skills/clinical-reports/assets/pathology_report_template.md +249 -0
  217. package/skills/clinical-reports/assets/quality_checklist.md +338 -0
  218. package/skills/clinical-reports/assets/radiology_report_template.md +318 -0
  219. package/skills/clinical-reports/assets/soap_note_template.md +253 -0
  220. package/skills/clinical-reports/references/README.md +236 -0
  221. package/skills/clinical-reports/references/case_report_guidelines.md +570 -0
  222. package/skills/clinical-reports/references/clinical_trial_reporting.md +693 -0
  223. package/skills/clinical-reports/references/data_presentation.md +530 -0
  224. package/skills/clinical-reports/references/diagnostic_reports_standards.md +629 -0
  225. package/skills/clinical-reports/references/medical_terminology.md +588 -0
  226. package/skills/clinical-reports/references/patient_documentation.md +744 -0
  227. package/skills/clinical-reports/references/peer_review_standards.md +585 -0
  228. package/skills/clinical-reports/references/regulatory_compliance.md +577 -0
  229. package/skills/clinical-reports/scripts/check_deidentification.py +346 -0
  230. package/skills/clinical-reports/scripts/compliance_checker.py +78 -0
  231. package/skills/clinical-reports/scripts/extract_clinical_data.py +102 -0
  232. package/skills/clinical-reports/scripts/format_adverse_events.py +103 -0
  233. package/skills/clinical-reports/scripts/generate_report_template.py +163 -0
  234. package/skills/clinical-reports/scripts/terminology_validator.py +133 -0
  235. package/skills/clinical-reports/scripts/validate_case_report.py +334 -0
  236. package/skills/clinical-reports/scripts/validate_trial_report.py +89 -0
  237. package/skills/clinicaltrials-database/SKILL.md +505 -0
  238. package/skills/clinicaltrials-database/references/api_reference.md +358 -0
  239. package/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
  240. package/skills/clinpgx-database/SKILL.md +636 -0
  241. package/skills/clinpgx-database/references/api_reference.md +757 -0
  242. package/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
  243. package/skills/clinvar-database/SKILL.md +360 -0
  244. package/skills/clinvar-database/references/api_reference.md +227 -0
  245. package/skills/clinvar-database/references/clinical_significance.md +218 -0
  246. package/skills/clinvar-database/references/data_formats.md +358 -0
  247. package/skills/cobrapy/SKILL.md +461 -0
  248. package/skills/cobrapy/references/api_quick_reference.md +655 -0
  249. package/skills/cobrapy/references/workflows.md +593 -0
  250. package/skills/consciousness-council/SKILL.md +150 -0
  251. package/skills/consciousness-council/references/advanced-configurations.md +96 -0
  252. package/skills/cosmic-database/SKILL.md +334 -0
  253. package/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
  254. package/skills/cosmic-database/scripts/download_cosmic.py +231 -0
  255. package/skills/crawl4ai/SKILL.md +172 -0
  256. package/skills/dask/SKILL.md +454 -0
  257. package/skills/dask/references/arrays.md +497 -0
  258. package/skills/dask/references/bags.md +468 -0
  259. package/skills/dask/references/best-practices.md +277 -0
  260. package/skills/dask/references/dataframes.md +368 -0
  261. package/skills/dask/references/futures.md +541 -0
  262. package/skills/dask/references/schedulers.md +504 -0
  263. package/skills/datacommons-client/SKILL.md +253 -0
  264. package/skills/datacommons-client/references/getting_started.md +417 -0
  265. package/skills/datacommons-client/references/node.md +250 -0
  266. package/skills/datacommons-client/references/observation.md +185 -0
  267. package/skills/datacommons-client/references/resolve.md +246 -0
  268. package/skills/datamol/SKILL.md +704 -0
  269. package/skills/datamol/references/conformers_module.md +131 -0
  270. package/skills/datamol/references/core_api.md +130 -0
  271. package/skills/datamol/references/descriptors_viz.md +195 -0
  272. package/skills/datamol/references/fragments_scaffolds.md +174 -0
  273. package/skills/datamol/references/io_module.md +109 -0
  274. package/skills/datamol/references/reactions_data.md +218 -0
  275. package/skills/deep-research/SKILL.md +12 -0
  276. package/skills/deepchem/SKILL.md +595 -0
  277. package/skills/deepchem/references/api_reference.md +303 -0
  278. package/skills/deepchem/references/workflows.md +491 -0
  279. package/skills/deepchem/scripts/graph_neural_network.py +338 -0
  280. package/skills/deepchem/scripts/predict_solubility.py +224 -0
  281. package/skills/deepchem/scripts/transfer_learning.py +375 -0
  282. package/skills/deeptools/SKILL.md +529 -0
  283. package/skills/deeptools/assets/quick_reference.md +58 -0
  284. package/skills/deeptools/references/effective_genome_sizes.md +116 -0
  285. package/skills/deeptools/references/normalization_methods.md +410 -0
  286. package/skills/deeptools/references/tools_reference.md +533 -0
  287. package/skills/deeptools/references/workflows.md +474 -0
  288. package/skills/deeptools/scripts/validate_files.py +195 -0
  289. package/skills/deeptools/scripts/workflow_generator.py +454 -0
  290. package/skills/denario/SKILL.md +213 -0
  291. package/skills/denario/references/examples.md +494 -0
  292. package/skills/denario/references/installation.md +213 -0
  293. package/skills/denario/references/llm_configuration.md +265 -0
  294. package/skills/denario/references/research_pipeline.md +471 -0
  295. package/skills/depmap/SKILL.md +300 -0
  296. package/skills/depmap/references/dependency_analysis.md +178 -0
  297. package/skills/dhdna-profiler/SKILL.md +162 -0
  298. package/skills/dhdna-profiler/references/advanced-profiling.md +72 -0
  299. package/skills/diffdock/SKILL.md +481 -0
  300. package/skills/diffdock/assets/batch_template.csv +4 -0
  301. package/skills/diffdock/assets/custom_inference_config.yaml +90 -0
  302. package/skills/diffdock/references/confidence_and_limitations.md +182 -0
  303. package/skills/diffdock/references/parameters_reference.md +163 -0
  304. package/skills/diffdock/references/workflows_examples.md +392 -0
  305. package/skills/diffdock/scripts/analyze_results.py +334 -0
  306. package/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
  307. package/skills/diffdock/scripts/setup_check.py +278 -0
  308. package/skills/dnanexus-integration/SKILL.md +381 -0
  309. package/skills/dnanexus-integration/references/app-development.md +247 -0
  310. package/skills/dnanexus-integration/references/configuration.md +646 -0
  311. package/skills/dnanexus-integration/references/data-operations.md +400 -0
  312. package/skills/dnanexus-integration/references/job-execution.md +412 -0
  313. package/skills/dnanexus-integration/references/python-sdk.md +523 -0
  314. package/skills/docker/SKILL.md +84 -0
  315. package/skills/docx/LICENSE.txt +30 -0
  316. package/skills/docx/SKILL.md +590 -0
  317. package/skills/docx/scripts/__init__.py +1 -0
  318. package/skills/docx/scripts/accept_changes.py +135 -0
  319. package/skills/docx/scripts/comment.py +318 -0
  320. package/skills/docx/scripts/office/helpers/__init__.py +0 -0
  321. package/skills/docx/scripts/office/helpers/merge_runs.py +199 -0
  322. package/skills/docx/scripts/office/helpers/simplify_redlines.py +197 -0
  323. package/skills/docx/scripts/office/pack.py +159 -0
  324. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  325. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  326. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  327. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  328. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  329. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  330. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  331. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  332. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  333. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  334. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  335. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  336. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  337. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  338. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  339. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  340. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  341. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  342. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  343. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  344. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  345. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  346. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  347. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  348. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  349. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  350. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  351. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  352. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  353. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  354. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  355. package/skills/docx/scripts/office/schemas/mce/mc.xsd +75 -0
  356. package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  357. package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  358. package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  359. package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  360. package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  361. package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  362. package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  363. package/skills/docx/scripts/office/soffice.py +183 -0
  364. package/skills/docx/scripts/office/unpack.py +132 -0
  365. package/skills/docx/scripts/office/validate.py +111 -0
  366. package/skills/docx/scripts/office/validators/__init__.py +15 -0
  367. package/skills/docx/scripts/office/validators/base.py +847 -0
  368. package/skills/docx/scripts/office/validators/docx.py +446 -0
  369. package/skills/docx/scripts/office/validators/pptx.py +275 -0
  370. package/skills/docx/scripts/office/validators/redlining.py +247 -0
  371. package/skills/docx/scripts/templates/comments.xml +3 -0
  372. package/skills/docx/scripts/templates/commentsExtended.xml +3 -0
  373. package/skills/docx/scripts/templates/commentsExtensible.xml +3 -0
  374. package/skills/docx/scripts/templates/commentsIds.xml +3 -0
  375. package/skills/docx/scripts/templates/people.xml +3 -0
  376. package/skills/drugbank-database/SKILL.md +188 -0
  377. package/skills/drugbank-database/references/chemical-analysis.md +590 -0
  378. package/skills/drugbank-database/references/data-access.md +242 -0
  379. package/skills/drugbank-database/references/drug-queries.md +386 -0
  380. package/skills/drugbank-database/references/interactions.md +425 -0
  381. package/skills/drugbank-database/references/targets-pathways.md +518 -0
  382. package/skills/drugbank-database/scripts/drugbank_helper.py +350 -0
  383. package/skills/edgartools/SKILL.md +136 -0
  384. package/skills/edgartools/references/ai-integration.md +274 -0
  385. package/skills/edgartools/references/companies.md +268 -0
  386. package/skills/edgartools/references/data-objects.md +237 -0
  387. package/skills/edgartools/references/entity-facts.md +372 -0
  388. package/skills/edgartools/references/filings.md +387 -0
  389. package/skills/edgartools/references/financial-data.md +274 -0
  390. package/skills/edgartools/references/xbrl.md +373 -0
  391. package/skills/eli5/SKILL.md +25 -0
  392. package/skills/ena-database/SKILL.md +202 -0
  393. package/skills/ena-database/references/api_reference.md +490 -0
  394. package/skills/ensembl-database/SKILL.md +309 -0
  395. package/skills/ensembl-database/references/api_endpoints.md +346 -0
  396. package/skills/ensembl-database/scripts/ensembl_query.py +427 -0
  397. package/skills/esm/SKILL.md +304 -0
  398. package/skills/esm/references/esm-c-api.md +583 -0
  399. package/skills/esm/references/esm3-api.md +452 -0
  400. package/skills/esm/references/forge-api.md +657 -0
  401. package/skills/esm/references/workflows.md +685 -0
  402. package/skills/etetoolkit/SKILL.md +621 -0
  403. package/skills/etetoolkit/references/api_reference.md +583 -0
  404. package/skills/etetoolkit/references/visualization.md +783 -0
  405. package/skills/etetoolkit/references/workflows.md +774 -0
  406. package/skills/etetoolkit/scripts/quick_visualize.py +214 -0
  407. package/skills/etetoolkit/scripts/tree_operations.py +229 -0
  408. package/skills/exploratory-data-analysis/SKILL.md +444 -0
  409. package/skills/exploratory-data-analysis/assets/report_template.md +196 -0
  410. package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
  411. package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
  412. package/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
  413. package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
  414. package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
  415. package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
  416. package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
  417. package/skills/fda-database/SKILL.md +516 -0
  418. package/skills/fda-database/references/animal_veterinary.md +377 -0
  419. package/skills/fda-database/references/api_basics.md +687 -0
  420. package/skills/fda-database/references/devices.md +632 -0
  421. package/skills/fda-database/references/drugs.md +468 -0
  422. package/skills/fda-database/references/foods.md +374 -0
  423. package/skills/fda-database/references/other.md +472 -0
  424. package/skills/fda-database/scripts/fda_examples.py +335 -0
  425. package/skills/fda-database/scripts/fda_query.py +440 -0
  426. package/skills/flowio/SKILL.md +606 -0
  427. package/skills/flowio/references/api_reference.md +372 -0
  428. package/skills/fluidsim/SKILL.md +347 -0
  429. package/skills/fluidsim/references/advanced_features.md +398 -0
  430. package/skills/fluidsim/references/installation.md +68 -0
  431. package/skills/fluidsim/references/output_analysis.md +283 -0
  432. package/skills/fluidsim/references/parameters.md +198 -0
  433. package/skills/fluidsim/references/simulation_workflow.md +172 -0
  434. package/skills/fluidsim/references/solvers.md +94 -0
  435. package/skills/fred-economic-data/SKILL.md +433 -0
  436. package/skills/fred-economic-data/references/api_basics.md +212 -0
  437. package/skills/fred-economic-data/references/categories.md +442 -0
  438. package/skills/fred-economic-data/references/geofred.md +588 -0
  439. package/skills/fred-economic-data/references/releases.md +642 -0
  440. package/skills/fred-economic-data/references/series.md +584 -0
  441. package/skills/fred-economic-data/references/sources.md +423 -0
  442. package/skills/fred-economic-data/references/tags.md +485 -0
  443. package/skills/fred-economic-data/scripts/fred_examples.py +354 -0
  444. package/skills/fred-economic-data/scripts/fred_query.py +590 -0
  445. package/skills/gene-database/SKILL.md +177 -0
  446. package/skills/gene-database/references/api_reference.md +404 -0
  447. package/skills/gene-database/references/common_workflows.md +428 -0
  448. package/skills/gene-database/scripts/batch_gene_lookup.py +298 -0
  449. package/skills/gene-database/scripts/fetch_gene_data.py +277 -0
  450. package/skills/gene-database/scripts/query_gene.py +251 -0
  451. package/skills/generate-image/SKILL.md +183 -0
  452. package/skills/generate-image/scripts/generate_image.py +281 -0
  453. package/skills/geniml/SKILL.md +316 -0
  454. package/skills/geniml/references/bedspace.md +127 -0
  455. package/skills/geniml/references/consensus_peaks.md +238 -0
  456. package/skills/geniml/references/region2vec.md +90 -0
  457. package/skills/geniml/references/scembed.md +197 -0
  458. package/skills/geniml/references/utilities.md +385 -0
  459. package/skills/geo-database/SKILL.md +813 -0
  460. package/skills/geo-database/references/geo_reference.md +829 -0
  461. package/skills/geomaster/README.md +105 -0
  462. package/skills/geomaster/SKILL.md +365 -0
  463. package/skills/geomaster/references/advanced-gis.md +376 -0
  464. package/skills/geomaster/references/big-data.md +363 -0
  465. package/skills/geomaster/references/code-examples.md +531 -0
  466. package/skills/geomaster/references/coordinate-systems.md +364 -0
  467. package/skills/geomaster/references/core-libraries.md +273 -0
  468. package/skills/geomaster/references/data-sources.md +330 -0
  469. package/skills/geomaster/references/gis-software.md +369 -0
  470. package/skills/geomaster/references/industry-applications.md +420 -0
  471. package/skills/geomaster/references/machine-learning.md +462 -0
  472. package/skills/geomaster/references/programming-languages.md +456 -0
  473. package/skills/geomaster/references/remote-sensing.md +370 -0
  474. package/skills/geomaster/references/scientific-domains.md +416 -0
  475. package/skills/geomaster/references/specialized-topics.md +428 -0
  476. package/skills/geomaster/references/troubleshooting.md +439 -0
  477. package/skills/geopandas/SKILL.md +249 -0
  478. package/skills/geopandas/references/crs-management.md +243 -0
  479. package/skills/geopandas/references/data-io.md +165 -0
  480. package/skills/geopandas/references/data-structures.md +70 -0
  481. package/skills/geopandas/references/geometric-operations.md +221 -0
  482. package/skills/geopandas/references/spatial-analysis.md +184 -0
  483. package/skills/geopandas/references/visualization.md +243 -0
  484. package/skills/get-available-resources/SKILL.md +275 -0
  485. package/skills/get-available-resources/scripts/detect_resources.py +401 -0
  486. package/skills/gget/SKILL.md +869 -0
  487. package/skills/gget/references/database_info.md +300 -0
  488. package/skills/gget/references/module_reference.md +467 -0
  489. package/skills/gget/references/workflows.md +814 -0
  490. package/skills/gget/scripts/batch_sequence_analysis.py +191 -0
  491. package/skills/gget/scripts/enrichment_pipeline.py +235 -0
  492. package/skills/gget/scripts/gene_analysis.py +161 -0
  493. package/skills/ginkgo-cloud-lab/SKILL.md +56 -0
  494. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +85 -0
  495. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +71 -0
  496. package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +87 -0
  497. package/skills/glycoengineering/SKILL.md +338 -0
  498. package/skills/glycoengineering/references/glycan_databases.md +165 -0
  499. package/skills/gnomad-database/SKILL.md +395 -0
  500. package/skills/gnomad-database/references/graphql_queries.md +219 -0
  501. package/skills/gnomad-database/references/variant_interpretation.md +85 -0
  502. package/skills/gtars/SKILL.md +283 -0
  503. package/skills/gtars/references/cli.md +222 -0
  504. package/skills/gtars/references/coverage.md +172 -0
  505. package/skills/gtars/references/overlap.md +156 -0
  506. package/skills/gtars/references/python-api.md +211 -0
  507. package/skills/gtars/references/refget.md +147 -0
  508. package/skills/gtars/references/tokenizers.md +103 -0
  509. package/skills/gtex-database/SKILL.md +315 -0
  510. package/skills/gtex-database/references/api_reference.md +191 -0
  511. package/skills/gwas-database/SKILL.md +606 -0
  512. package/skills/gwas-database/references/api_reference.md +793 -0
  513. package/skills/hedgefundmonitor/SKILL.md +128 -0
  514. package/skills/hedgefundmonitor/references/api-overview.md +93 -0
  515. package/skills/hedgefundmonitor/references/datasets.md +150 -0
  516. package/skills/hedgefundmonitor/references/endpoints-combined.md +196 -0
  517. package/skills/hedgefundmonitor/references/endpoints-metadata.md +136 -0
  518. package/skills/hedgefundmonitor/references/endpoints-series-data.md +126 -0
  519. package/skills/hedgefundmonitor/references/examples.md +287 -0
  520. package/skills/hedgefundmonitor/references/parameters.md +104 -0
  521. package/skills/histolab/SKILL.md +676 -0
  522. package/skills/histolab/references/filters_preprocessing.md +514 -0
  523. package/skills/histolab/references/slide_management.md +172 -0
  524. package/skills/histolab/references/tile_extraction.md +421 -0
  525. package/skills/histolab/references/tissue_masks.md +251 -0
  526. package/skills/histolab/references/visualization.md +547 -0
  527. package/skills/hmdb-database/SKILL.md +194 -0
  528. package/skills/hmdb-database/references/hmdb_data_fields.md +267 -0
  529. package/skills/hypogenic/SKILL.md +653 -0
  530. package/skills/hypogenic/references/config_template.yaml +150 -0
  531. package/skills/hypothesis-generation/SKILL.md +297 -0
  532. package/skills/hypothesis-generation/assets/FORMATTING_GUIDE.md +672 -0
  533. package/skills/hypothesis-generation/assets/hypothesis_generation.sty +307 -0
  534. package/skills/hypothesis-generation/assets/hypothesis_report_template.tex +572 -0
  535. package/skills/hypothesis-generation/references/experimental_design_patterns.md +329 -0
  536. package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +198 -0
  537. package/skills/hypothesis-generation/references/literature_search_strategies.md +622 -0
  538. package/skills/imaging-data-commons/SKILL.md +843 -0
  539. package/skills/imaging-data-commons/references/bigquery_guide.md +556 -0
  540. package/skills/imaging-data-commons/references/cli_guide.md +272 -0
  541. package/skills/imaging-data-commons/references/clinical_data_guide.md +324 -0
  542. package/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
  543. package/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
  544. package/skills/imaging-data-commons/references/digital_pathology_guide.md +403 -0
  545. package/skills/imaging-data-commons/references/index_tables_guide.md +146 -0
  546. package/skills/imaging-data-commons/references/sql_patterns.md +207 -0
  547. package/skills/imaging-data-commons/references/use_cases.md +186 -0
  548. package/skills/infographics/SKILL.md +563 -0
  549. package/skills/infographics/references/color_palettes.md +496 -0
  550. package/skills/infographics/references/design_principles.md +636 -0
  551. package/skills/infographics/references/infographic_types.md +907 -0
  552. package/skills/infographics/scripts/generate_infographic.py +234 -0
  553. package/skills/infographics/scripts/generate_infographic_ai.py +1290 -0
  554. package/skills/interpro-database/SKILL.md +305 -0
  555. package/skills/interpro-database/references/domain_analysis.md +159 -0
  556. package/skills/iso-13485-certification/SKILL.md +678 -0
  557. package/skills/iso-13485-certification/assets/templates/procedures/CAPA-procedure-template.md +453 -0
  558. package/skills/iso-13485-certification/assets/templates/procedures/document-control-procedure-template.md +567 -0
  559. package/skills/iso-13485-certification/assets/templates/quality-manual-template.md +521 -0
  560. package/skills/iso-13485-certification/references/gap-analysis-checklist.md +568 -0
  561. package/skills/iso-13485-certification/references/iso-13485-requirements.md +610 -0
  562. package/skills/iso-13485-certification/references/mandatory-documents.md +606 -0
  563. package/skills/iso-13485-certification/references/quality-manual-guide.md +688 -0
  564. package/skills/iso-13485-certification/scripts/gap_analyzer.py +440 -0
  565. package/skills/jaspar-database/SKILL.md +351 -0
  566. package/skills/jaspar-database/references/api_reference.md +182 -0
  567. package/skills/jobs/SKILL.md +10 -0
  568. package/skills/kegg-database/SKILL.md +375 -0
  569. package/skills/kegg-database/references/kegg_reference.md +326 -0
  570. package/skills/kegg-database/scripts/kegg_api.py +251 -0
  571. package/skills/labarchive-integration/SKILL.md +266 -0
  572. package/skills/labarchive-integration/references/api_reference.md +342 -0
  573. package/skills/labarchive-integration/references/authentication_guide.md +357 -0
  574. package/skills/labarchive-integration/references/integrations.md +425 -0
  575. package/skills/labarchive-integration/scripts/entry_operations.py +334 -0
  576. package/skills/labarchive-integration/scripts/notebook_operations.py +269 -0
  577. package/skills/labarchive-integration/scripts/setup_config.py +205 -0
  578. package/skills/lamindb/SKILL.md +388 -0
  579. package/skills/lamindb/references/annotation-validation.md +513 -0
  580. package/skills/lamindb/references/core-concepts.md +380 -0
  581. package/skills/lamindb/references/data-management.md +433 -0
  582. package/skills/lamindb/references/integrations.md +642 -0
  583. package/skills/lamindb/references/ontologies.md +497 -0
  584. package/skills/lamindb/references/setup-deployment.md +733 -0
  585. package/skills/latchbio-integration/SKILL.md +351 -0
  586. package/skills/latchbio-integration/references/data-management.md +427 -0
  587. package/skills/latchbio-integration/references/resource-configuration.md +429 -0
  588. package/skills/latchbio-integration/references/verified-workflows.md +487 -0
  589. package/skills/latchbio-integration/references/workflow-creation.md +254 -0
  590. package/skills/latex-posters/SKILL.md +1602 -0
  591. package/skills/latex-posters/assets/baposter_template.tex +257 -0
  592. package/skills/latex-posters/assets/beamerposter_template.tex +244 -0
  593. package/skills/latex-posters/assets/poster_quality_checklist.md +358 -0
  594. package/skills/latex-posters/assets/tikzposter_template.tex +251 -0
  595. package/skills/latex-posters/references/README.md +417 -0
  596. package/skills/latex-posters/references/latex_poster_packages.md +745 -0
  597. package/skills/latex-posters/references/poster_content_guide.md +748 -0
  598. package/skills/latex-posters/references/poster_design_principles.md +806 -0
  599. package/skills/latex-posters/references/poster_layout_design.md +900 -0
  600. package/skills/latex-posters/scripts/review_poster.sh +214 -0
  601. package/skills/literature-review/SKILL.md +637 -0
  602. package/skills/literature-review/assets/review_template.md +412 -0
  603. package/skills/literature-review/references/citation_styles.md +166 -0
  604. package/skills/literature-review/references/database_strategies.md +455 -0
  605. package/skills/literature-review/scripts/generate_pdf.py +176 -0
  606. package/skills/literature-review/scripts/search_databases.py +303 -0
  607. package/skills/literature-review/scripts/verify_citations.py +222 -0
  608. package/skills/markdown-mermaid-writing/SKILL.md +327 -0
  609. package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +221 -0
  610. package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +108 -0
  611. package/skills/markdown-mermaid-writing/references/diagrams/block.md +177 -0
  612. package/skills/markdown-mermaid-writing/references/diagrams/c4.md +136 -0
  613. package/skills/markdown-mermaid-writing/references/diagrams/class.md +246 -0
  614. package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +384 -0
  615. package/skills/markdown-mermaid-writing/references/diagrams/er.md +222 -0
  616. package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +177 -0
  617. package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +138 -0
  618. package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +74 -0
  619. package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +107 -0
  620. package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +74 -0
  621. package/skills/markdown-mermaid-writing/references/diagrams/packet.md +55 -0
  622. package/skills/markdown-mermaid-writing/references/diagrams/pie.md +52 -0
  623. package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +66 -0
  624. package/skills/markdown-mermaid-writing/references/diagrams/radar.md +59 -0
  625. package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +88 -0
  626. package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +71 -0
  627. package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +174 -0
  628. package/skills/markdown-mermaid-writing/references/diagrams/state.md +150 -0
  629. package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +96 -0
  630. package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +66 -0
  631. package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +108 -0
  632. package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +53 -0
  633. package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +71 -0
  634. package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +733 -0
  635. package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +458 -0
  636. package/skills/markdown-mermaid-writing/templates/decision_record.md +211 -0
  637. package/skills/markdown-mermaid-writing/templates/how_to_guide.md +275 -0
  638. package/skills/markdown-mermaid-writing/templates/issue.md +303 -0
  639. package/skills/markdown-mermaid-writing/templates/kanban.md +223 -0
  640. package/skills/markdown-mermaid-writing/templates/presentation.md +312 -0
  641. package/skills/markdown-mermaid-writing/templates/project_documentation.md +412 -0
  642. package/skills/markdown-mermaid-writing/templates/pull_request.md +319 -0
  643. package/skills/markdown-mermaid-writing/templates/research_paper.md +304 -0
  644. package/skills/markdown-mermaid-writing/templates/status_report.md +185 -0
  645. package/skills/market-research-reports/SKILL.md +905 -0
  646. package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +428 -0
  647. package/skills/market-research-reports/assets/market_report_template.tex +1380 -0
  648. package/skills/market-research-reports/assets/market_research.sty +564 -0
  649. package/skills/market-research-reports/references/data_analysis_patterns.md +548 -0
  650. package/skills/market-research-reports/references/report_structure_guide.md +999 -0
  651. package/skills/market-research-reports/references/visual_generation_guide.md +1077 -0
  652. package/skills/market-research-reports/scripts/generate_market_visuals.py +529 -0
  653. package/skills/markitdown/SKILL.md +488 -0
  654. package/skills/markitdown/assets/example_usage.md +463 -0
  655. package/skills/markitdown/references/api_reference.md +396 -0
  656. package/skills/markitdown/references/file_formats.md +542 -0
  657. package/skills/markitdown/scripts/batch_convert.py +228 -0
  658. package/skills/markitdown/scripts/convert_literature.py +283 -0
  659. package/skills/markitdown/scripts/convert_with_ai.py +240 -0
  660. package/skills/matchms/SKILL.md +201 -0
  661. package/skills/matchms/references/filtering.md +288 -0
  662. package/skills/matchms/references/importing_exporting.md +416 -0
  663. package/skills/matchms/references/similarity.md +380 -0
  664. package/skills/matchms/references/workflows.md +647 -0
  665. package/skills/matlab/SKILL.md +376 -0
  666. package/skills/matlab/references/data-import-export.md +479 -0
  667. package/skills/matlab/references/executing-scripts.md +444 -0
  668. package/skills/matlab/references/graphics-visualization.md +579 -0
  669. package/skills/matlab/references/mathematics.md +553 -0
  670. package/skills/matlab/references/matrices-arrays.md +349 -0
  671. package/skills/matlab/references/octave-compatibility.md +544 -0
  672. package/skills/matlab/references/programming.md +672 -0
  673. package/skills/matlab/references/python-integration.md +433 -0
  674. package/skills/matplotlib/SKILL.md +359 -0
  675. package/skills/matplotlib/references/api_reference.md +412 -0
  676. package/skills/matplotlib/references/common_issues.md +563 -0
  677. package/skills/matplotlib/references/plot_types.md +476 -0
  678. package/skills/matplotlib/references/styling_guide.md +589 -0
  679. package/skills/matplotlib/scripts/plot_template.py +401 -0
  680. package/skills/matplotlib/scripts/style_configurator.py +409 -0
  681. package/skills/medchem/SKILL.md +404 -0
  682. package/skills/medchem/references/api_guide.md +600 -0
  683. package/skills/medchem/references/rules_catalog.md +604 -0
  684. package/skills/medchem/scripts/filter_molecules.py +418 -0
  685. package/skills/metabolomics-workbench-database/SKILL.md +257 -0
  686. package/skills/metabolomics-workbench-database/references/api_reference.md +494 -0
  687. package/skills/modal/SKILL.md +406 -0
  688. package/skills/modal/references/api_reference.md +187 -0
  689. package/skills/modal/references/examples.md +266 -0
  690. package/skills/modal/references/functions.md +260 -0
  691. package/skills/modal/references/getting-started.md +175 -0
  692. package/skills/modal/references/gpu.md +174 -0
  693. package/skills/modal/references/images.md +259 -0
  694. package/skills/modal/references/resources.md +117 -0
  695. package/skills/modal/references/scaling.md +173 -0
  696. package/skills/modal/references/scheduled-jobs.md +143 -0
  697. package/skills/modal/references/secrets.md +119 -0
  698. package/skills/modal/references/volumes.md +247 -0
  699. package/skills/modal/references/web-endpoints.md +254 -0
  700. package/skills/modal-compute/SKILL.md +56 -0
  701. package/skills/molecular-dynamics/SKILL.md +457 -0
  702. package/skills/molecular-dynamics/references/mdanalysis_analysis.md +208 -0
  703. package/skills/molfeat/SKILL.md +509 -0
  704. package/skills/molfeat/references/api_reference.md +428 -0
  705. package/skills/molfeat/references/available_featurizers.md +333 -0
  706. package/skills/molfeat/references/examples.md +723 -0
  707. package/skills/monarch-database/SKILL.md +372 -0
  708. package/skills/monarch-database/references/phenotype_ontology.md +160 -0
  709. package/skills/networkx/SKILL.md +435 -0
  710. package/skills/networkx/references/algorithms.md +383 -0
  711. package/skills/networkx/references/generators.md +378 -0
  712. package/skills/networkx/references/graph-basics.md +283 -0
  713. package/skills/networkx/references/io.md +441 -0
  714. package/skills/networkx/references/visualization.md +529 -0
  715. package/skills/neurokit2/SKILL.md +354 -0
  716. package/skills/neurokit2/references/bio_module.md +417 -0
  717. package/skills/neurokit2/references/complexity.md +715 -0
  718. package/skills/neurokit2/references/ecg_cardiac.md +355 -0
  719. package/skills/neurokit2/references/eda.md +497 -0
  720. package/skills/neurokit2/references/eeg.md +506 -0
  721. package/skills/neurokit2/references/emg.md +408 -0
  722. package/skills/neurokit2/references/eog.md +407 -0
  723. package/skills/neurokit2/references/epochs_events.md +471 -0
  724. package/skills/neurokit2/references/hrv.md +480 -0
  725. package/skills/neurokit2/references/ppg.md +413 -0
  726. package/skills/neurokit2/references/rsp.md +510 -0
  727. package/skills/neurokit2/references/signal_processing.md +648 -0
  728. package/skills/neuropixels-analysis/SKILL.md +348 -0
  729. package/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
  730. package/skills/neuropixels-analysis/references/AI_CURATION.md +345 -0
  731. package/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
  732. package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +358 -0
  733. package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
  734. package/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
  735. package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
  736. package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
  737. package/skills/neuropixels-analysis/references/api_reference.md +415 -0
  738. package/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
  739. package/skills/neuropixels-analysis/references/standard_workflow.md +385 -0
  740. package/skills/neuropixels-analysis/scripts/compute_metrics.py +178 -0
  741. package/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
  742. package/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
  743. package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +432 -0
  744. package/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
  745. package/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
  746. package/skills/offer-k-dense-web/SKILL.md +21 -0
  747. package/skills/omero-integration/SKILL.md +249 -0
  748. package/skills/omero-integration/references/advanced.md +631 -0
  749. package/skills/omero-integration/references/connection.md +369 -0
  750. package/skills/omero-integration/references/data_access.md +544 -0
  751. package/skills/omero-integration/references/image_processing.md +665 -0
  752. package/skills/omero-integration/references/metadata.md +688 -0
  753. package/skills/omero-integration/references/rois.md +648 -0
  754. package/skills/omero-integration/references/scripts.md +637 -0
  755. package/skills/omero-integration/references/tables.md +532 -0
  756. package/skills/open-notebook/SKILL.md +289 -0
  757. package/skills/open-notebook/references/api_reference.md +715 -0
  758. package/skills/open-notebook/references/architecture.md +163 -0
  759. package/skills/open-notebook/references/configuration.md +226 -0
  760. package/skills/open-notebook/references/examples.md +290 -0
  761. package/skills/open-notebook/scripts/chat_interaction.py +190 -0
  762. package/skills/open-notebook/scripts/notebook_management.py +142 -0
  763. package/skills/open-notebook/scripts/source_ingestion.py +160 -0
  764. package/skills/open-notebook/scripts/test_open_notebook_skill.py +423 -0
  765. package/skills/openalex-database/SKILL.md +496 -0
  766. package/skills/openalex-database/references/api_guide.md +371 -0
  767. package/skills/openalex-database/references/common_queries.md +381 -0
  768. package/skills/openalex-database/scripts/openalex_client.py +337 -0
  769. package/skills/openalex-database/scripts/query_helpers.py +306 -0
  770. package/skills/opentargets-database/SKILL.md +371 -0
  771. package/skills/opentargets-database/references/api_reference.md +249 -0
  772. package/skills/opentargets-database/references/evidence_types.md +306 -0
  773. package/skills/opentargets-database/references/target_annotations.md +401 -0
  774. package/skills/opentargets-database/scripts/query_opentargets.py +403 -0
  775. package/skills/opentrons-integration/SKILL.md +571 -0
  776. package/skills/opentrons-integration/references/api_reference.md +366 -0
  777. package/skills/opentrons-integration/scripts/basic_protocol_template.py +67 -0
  778. package/skills/opentrons-integration/scripts/pcr_setup_template.py +154 -0
  779. package/skills/opentrons-integration/scripts/serial_dilution_template.py +96 -0
  780. package/skills/paper-2-web/SKILL.md +495 -0
  781. package/skills/paper-2-web/references/installation.md +141 -0
  782. package/skills/paper-2-web/references/paper2poster.md +346 -0
  783. package/skills/paper-2-web/references/paper2video.md +305 -0
  784. package/skills/paper-2-web/references/paper2web.md +187 -0
  785. package/skills/paper-2-web/references/usage_examples.md +436 -0
  786. package/skills/paper-code-audit/SKILL.md +12 -0
  787. package/skills/paper-writing/SKILL.md +12 -0
  788. package/skills/parallel-web/SKILL.md +314 -0
  789. package/skills/parallel-web/references/api_reference.md +244 -0
  790. package/skills/parallel-web/references/deep_research_guide.md +362 -0
  791. package/skills/parallel-web/references/extraction_patterns.md +338 -0
  792. package/skills/parallel-web/references/search_best_practices.md +297 -0
  793. package/skills/parallel-web/references/workflow_recipes.md +456 -0
  794. package/skills/parallel-web/scripts/parallel_web.py +568 -0
  795. package/skills/parse-document/SKILL.md +139 -0
  796. package/skills/pathml/SKILL.md +164 -0
  797. package/skills/pathml/references/data_management.md +742 -0
  798. package/skills/pathml/references/graphs.md +653 -0
  799. package/skills/pathml/references/image_loading.md +448 -0
  800. package/skills/pathml/references/machine_learning.md +725 -0
  801. package/skills/pathml/references/multiparametric.md +686 -0
  802. package/skills/pathml/references/preprocessing.md +722 -0
  803. package/skills/pdb-database/SKILL.md +307 -0
  804. package/skills/pdb-database/references/api_reference.md +617 -0
  805. package/skills/pdf/LICENSE.txt +30 -0
  806. package/skills/pdf/SKILL.md +314 -0
  807. package/skills/pdf/forms.md +294 -0
  808. package/skills/pdf/reference.md +612 -0
  809. package/skills/pdf/scripts/check_bounding_boxes.py +65 -0
  810. package/skills/pdf/scripts/check_fillable_fields.py +11 -0
  811. package/skills/pdf/scripts/convert_pdf_to_images.py +33 -0
  812. package/skills/pdf/scripts/create_validation_image.py +37 -0
  813. package/skills/pdf/scripts/extract_form_field_info.py +122 -0
  814. package/skills/pdf/scripts/extract_form_structure.py +115 -0
  815. package/skills/pdf/scripts/fill_fillable_fields.py +98 -0
  816. package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +107 -0
  817. package/skills/peer-review/SKILL.md +569 -0
  818. package/skills/peer-review/references/common_issues.md +552 -0
  819. package/skills/peer-review/references/reporting_standards.md +290 -0
  820. package/skills/pennylane/SKILL.md +224 -0
  821. package/skills/pennylane/references/advanced_features.md +667 -0
  822. package/skills/pennylane/references/devices_backends.md +596 -0
  823. package/skills/pennylane/references/getting_started.md +227 -0
  824. package/skills/pennylane/references/optimization.md +671 -0
  825. package/skills/pennylane/references/quantum_chemistry.md +567 -0
  826. package/skills/pennylane/references/quantum_circuits.md +437 -0
  827. package/skills/pennylane/references/quantum_ml.md +571 -0
  828. package/skills/perplexity-search/SKILL.md +446 -0
  829. package/skills/perplexity-search/assets/.env.example +16 -0
  830. package/skills/perplexity-search/references/model_comparison.md +386 -0
  831. package/skills/perplexity-search/references/openrouter_setup.md +454 -0
  832. package/skills/perplexity-search/references/search_strategies.md +258 -0
  833. package/skills/perplexity-search/scripts/perplexity_search.py +277 -0
  834. package/skills/perplexity-search/scripts/setup_env.py +171 -0
  835. package/skills/phylogenetics/SKILL.md +404 -0
  836. package/skills/phylogenetics/references/iqtree_inference.md +181 -0
  837. package/skills/phylogenetics/scripts/phylogenetic_analysis.py +270 -0
  838. package/skills/plotly/SKILL.md +265 -0
  839. package/skills/plotly/references/chart-types.md +488 -0
  840. package/skills/plotly/references/export-interactivity.md +453 -0
  841. package/skills/plotly/references/graph-objects.md +302 -0
  842. package/skills/plotly/references/layouts-styling.md +457 -0
  843. package/skills/plotly/references/plotly-express.md +213 -0
  844. package/skills/polars/SKILL.md +385 -0
  845. package/skills/polars/references/best_practices.md +649 -0
  846. package/skills/polars/references/core_concepts.md +378 -0
  847. package/skills/polars/references/io_guide.md +557 -0
  848. package/skills/polars/references/operations.md +602 -0
  849. package/skills/polars/references/pandas_migration.md +417 -0
  850. package/skills/polars/references/transformations.md +549 -0
  851. package/skills/polars-bio/SKILL.md +374 -0
  852. package/skills/polars-bio/references/bioframe_migration.md +250 -0
  853. package/skills/polars-bio/references/configuration.md +175 -0
  854. package/skills/polars-bio/references/file_io.md +414 -0
  855. package/skills/polars-bio/references/interval_operations.md +362 -0
  856. package/skills/polars-bio/references/pileup_operations.md +176 -0
  857. package/skills/polars-bio/references/sql_processing.md +224 -0
  858. package/skills/pptx/LICENSE.txt +30 -0
  859. package/skills/pptx/SKILL.md +232 -0
  860. package/skills/pptx/editing.md +205 -0
  861. package/skills/pptx/pptxgenjs.md +420 -0
  862. package/skills/pptx/scripts/__init__.py +0 -0
  863. package/skills/pptx/scripts/add_slide.py +195 -0
  864. package/skills/pptx/scripts/clean.py +286 -0
  865. package/skills/pptx/scripts/office/helpers/__init__.py +0 -0
  866. package/skills/pptx/scripts/office/helpers/merge_runs.py +199 -0
  867. package/skills/pptx/scripts/office/helpers/simplify_redlines.py +197 -0
  868. package/skills/pptx/scripts/office/pack.py +159 -0
  869. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  870. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  871. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  872. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  873. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  874. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  875. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  876. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  877. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  878. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  879. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  880. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  881. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  882. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  883. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  884. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  885. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  886. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  887. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  888. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  889. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  890. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  891. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  892. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  893. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  894. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  895. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  896. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  897. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  898. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  899. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  900. package/skills/pptx/scripts/office/schemas/mce/mc.xsd +75 -0
  901. package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  902. package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  903. package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  904. package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  905. package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  906. package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  907. package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  908. package/skills/pptx/scripts/office/soffice.py +183 -0
  909. package/skills/pptx/scripts/office/unpack.py +132 -0
  910. package/skills/pptx/scripts/office/validate.py +111 -0
  911. package/skills/pptx/scripts/office/validators/__init__.py +15 -0
  912. package/skills/pptx/scripts/office/validators/base.py +847 -0
  913. package/skills/pptx/scripts/office/validators/docx.py +446 -0
  914. package/skills/pptx/scripts/office/validators/pptx.py +275 -0
  915. package/skills/pptx/scripts/office/validators/redlining.py +247 -0
  916. package/skills/pptx/scripts/thumbnail.py +289 -0
  917. package/skills/pptx-posters/SKILL.md +414 -0
  918. package/skills/pptx-posters/assets/poster_html_template.html +257 -0
  919. package/skills/pptx-posters/assets/poster_quality_checklist.md +358 -0
  920. package/skills/pptx-posters/references/poster_content_guide.md +748 -0
  921. package/skills/pptx-posters/references/poster_design_principles.md +806 -0
  922. package/skills/pptx-posters/references/poster_layout_design.md +900 -0
  923. package/skills/preview/SKILL.md +27 -0
  924. package/skills/primekg/SKILL.md +97 -0
  925. package/skills/primekg/scripts/query_primekg.py +123 -0
  926. package/skills/protocolsio-integration/SKILL.md +419 -0
  927. package/skills/protocolsio-integration/references/additional_features.md +387 -0
  928. package/skills/protocolsio-integration/references/authentication.md +100 -0
  929. package/skills/protocolsio-integration/references/discussions.md +225 -0
  930. package/skills/protocolsio-integration/references/file_manager.md +412 -0
  931. package/skills/protocolsio-integration/references/protocols_api.md +294 -0
  932. package/skills/protocolsio-integration/references/workspaces.md +293 -0
  933. package/skills/pubchem-database/SKILL.md +572 -0
  934. package/skills/pubchem-database/references/api_reference.md +440 -0
  935. package/skills/pubchem-database/scripts/bioactivity_query.py +367 -0
  936. package/skills/pubchem-database/scripts/compound_search.py +297 -0
  937. package/skills/pubmed-database/SKILL.md +458 -0
  938. package/skills/pubmed-database/references/api_reference.md +298 -0
  939. package/skills/pubmed-database/references/common_queries.md +453 -0
  940. package/skills/pubmed-database/references/search_syntax.md +436 -0
  941. package/skills/pufferlib/SKILL.md +434 -0
  942. package/skills/pufferlib/references/environments.md +508 -0
  943. package/skills/pufferlib/references/integration.md +621 -0
  944. package/skills/pufferlib/references/policies.md +653 -0
  945. package/skills/pufferlib/references/training.md +360 -0
  946. package/skills/pufferlib/references/vectorization.md +557 -0
  947. package/skills/pufferlib/scripts/env_template.py +340 -0
  948. package/skills/pufferlib/scripts/train_template.py +239 -0
  949. package/skills/pydeseq2/SKILL.md +557 -0
  950. package/skills/pydeseq2/references/api_reference.md +228 -0
  951. package/skills/pydeseq2/references/workflow_guide.md +582 -0
  952. package/skills/pydeseq2/scripts/run_deseq2_analysis.py +353 -0
  953. package/skills/pydicom/SKILL.md +432 -0
  954. package/skills/pydicom/references/common_tags.md +228 -0
  955. package/skills/pydicom/references/transfer_syntaxes.md +352 -0
  956. package/skills/pydicom/scripts/anonymize_dicom.py +137 -0
  957. package/skills/pydicom/scripts/dicom_to_image.py +172 -0
  958. package/skills/pydicom/scripts/extract_metadata.py +173 -0
  959. package/skills/pyhealth/SKILL.md +489 -0
  960. package/skills/pyhealth/references/datasets.md +178 -0
  961. package/skills/pyhealth/references/medical_coding.md +284 -0
  962. package/skills/pyhealth/references/models.md +594 -0
  963. package/skills/pyhealth/references/preprocessing.md +638 -0
  964. package/skills/pyhealth/references/tasks.md +379 -0
  965. package/skills/pyhealth/references/training_evaluation.md +648 -0
  966. package/skills/pylabrobot/SKILL.md +183 -0
  967. package/skills/pylabrobot/references/analytical-equipment.md +464 -0
  968. package/skills/pylabrobot/references/hardware-backends.md +480 -0
  969. package/skills/pylabrobot/references/liquid-handling.md +403 -0
  970. package/skills/pylabrobot/references/material-handling.md +620 -0
  971. package/skills/pylabrobot/references/resources.md +489 -0
  972. package/skills/pylabrobot/references/visualization.md +532 -0
  973. package/skills/pymatgen/SKILL.md +689 -0
  974. package/skills/pymatgen/references/analysis_modules.md +530 -0
  975. package/skills/pymatgen/references/core_classes.md +318 -0
  976. package/skills/pymatgen/references/io_formats.md +469 -0
  977. package/skills/pymatgen/references/materials_project_api.md +517 -0
  978. package/skills/pymatgen/references/transformations_workflows.md +591 -0
  979. package/skills/pymatgen/scripts/phase_diagram_generator.py +233 -0
  980. package/skills/pymatgen/scripts/structure_analyzer.py +266 -0
  981. package/skills/pymatgen/scripts/structure_converter.py +169 -0
  982. package/skills/pymc/SKILL.md +570 -0
  983. package/skills/pymc/assets/hierarchical_model_template.py +333 -0
  984. package/skills/pymc/assets/linear_regression_template.py +241 -0
  985. package/skills/pymc/references/distributions.md +320 -0
  986. package/skills/pymc/references/sampling_inference.md +424 -0
  987. package/skills/pymc/references/workflows.md +526 -0
  988. package/skills/pymc/scripts/model_comparison.py +387 -0
  989. package/skills/pymc/scripts/model_diagnostics.py +350 -0
  990. package/skills/pymoo/SKILL.md +569 -0
  991. package/skills/pymoo/references/algorithms.md +180 -0
  992. package/skills/pymoo/references/constraints_mcdm.md +417 -0
  993. package/skills/pymoo/references/operators.md +345 -0
  994. package/skills/pymoo/references/problems.md +265 -0
  995. package/skills/pymoo/references/visualization.md +353 -0
  996. package/skills/pymoo/scripts/custom_problem_example.py +181 -0
  997. package/skills/pymoo/scripts/decision_making_example.py +161 -0
  998. package/skills/pymoo/scripts/many_objective_example.py +72 -0
  999. package/skills/pymoo/scripts/multi_objective_example.py +63 -0
  1000. package/skills/pymoo/scripts/single_objective_example.py +59 -0
  1001. package/skills/pyopenms/SKILL.md +215 -0
  1002. package/skills/pyopenms/references/data_structures.md +497 -0
  1003. package/skills/pyopenms/references/feature_detection.md +410 -0
  1004. package/skills/pyopenms/references/file_io.md +349 -0
  1005. package/skills/pyopenms/references/identification.md +422 -0
  1006. package/skills/pyopenms/references/metabolomics.md +482 -0
  1007. package/skills/pyopenms/references/signal_processing.md +433 -0
  1008. package/skills/pysam/SKILL.md +263 -0
  1009. package/skills/pysam/references/alignment_files.md +280 -0
  1010. package/skills/pysam/references/common_workflows.md +520 -0
  1011. package/skills/pysam/references/sequence_files.md +407 -0
  1012. package/skills/pysam/references/variant_files.md +365 -0
  1013. package/skills/pytdc/SKILL.md +458 -0
  1014. package/skills/pytdc/references/datasets.md +246 -0
  1015. package/skills/pytdc/references/oracles.md +400 -0
  1016. package/skills/pytdc/references/utilities.md +684 -0
  1017. package/skills/pytdc/scripts/benchmark_evaluation.py +327 -0
  1018. package/skills/pytdc/scripts/load_and_split_data.py +214 -0
  1019. package/skills/pytdc/scripts/molecular_generation.py +404 -0
  1020. package/skills/pytorch-lightning/SKILL.md +172 -0
  1021. package/skills/pytorch-lightning/references/best_practices.md +724 -0
  1022. package/skills/pytorch-lightning/references/callbacks.md +564 -0
  1023. package/skills/pytorch-lightning/references/data_module.md +565 -0
  1024. package/skills/pytorch-lightning/references/distributed_training.md +643 -0
  1025. package/skills/pytorch-lightning/references/lightning_module.md +487 -0
  1026. package/skills/pytorch-lightning/references/logging.md +654 -0
  1027. package/skills/pytorch-lightning/references/trainer.md +641 -0
  1028. package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +454 -0
  1029. package/skills/pytorch-lightning/scripts/template_datamodule.py +328 -0
  1030. package/skills/pytorch-lightning/scripts/template_lightning_module.py +219 -0
  1031. package/skills/pyzotero/SKILL.md +111 -0
  1032. package/skills/pyzotero/references/authentication.md +90 -0
  1033. package/skills/pyzotero/references/cli.md +100 -0
  1034. package/skills/pyzotero/references/collections.md +113 -0
  1035. package/skills/pyzotero/references/error-handling.md +103 -0
  1036. package/skills/pyzotero/references/exports.md +102 -0
  1037. package/skills/pyzotero/references/files-attachments.md +97 -0
  1038. package/skills/pyzotero/references/full-text.md +68 -0
  1039. package/skills/pyzotero/references/pagination.md +79 -0
  1040. package/skills/pyzotero/references/read-api.md +137 -0
  1041. package/skills/pyzotero/references/saved-searches.md +77 -0
  1042. package/skills/pyzotero/references/search-params.md +90 -0
  1043. package/skills/pyzotero/references/tags.md +87 -0
  1044. package/skills/pyzotero/references/write-api.md +123 -0
  1045. package/skills/qiskit/SKILL.md +273 -0
  1046. package/skills/qiskit/references/algorithms.md +607 -0
  1047. package/skills/qiskit/references/backends.md +433 -0
  1048. package/skills/qiskit/references/circuits.md +197 -0
  1049. package/skills/qiskit/references/patterns.md +533 -0
  1050. package/skills/qiskit/references/primitives.md +277 -0
  1051. package/skills/qiskit/references/setup.md +99 -0
  1052. package/skills/qiskit/references/transpilation.md +286 -0
  1053. package/skills/qiskit/references/visualization.md +415 -0
  1054. package/skills/qutip/SKILL.md +316 -0
  1055. package/skills/qutip/references/advanced.md +555 -0
  1056. package/skills/qutip/references/analysis.md +523 -0
  1057. package/skills/qutip/references/core_concepts.md +293 -0
  1058. package/skills/qutip/references/time_evolution.md +348 -0
  1059. package/skills/qutip/references/visualization.md +431 -0
  1060. package/skills/rdkit/SKILL.md +778 -0
  1061. package/skills/rdkit/references/api_reference.md +432 -0
  1062. package/skills/rdkit/references/descriptors_reference.md +595 -0
  1063. package/skills/rdkit/references/smarts_patterns.md +668 -0
  1064. package/skills/rdkit/scripts/molecular_properties.py +243 -0
  1065. package/skills/rdkit/scripts/similarity_search.py +297 -0
  1066. package/skills/rdkit/scripts/substructure_filter.py +386 -0
  1067. package/skills/reactome-database/SKILL.md +276 -0
  1068. package/skills/reactome-database/references/api_reference.md +465 -0
  1069. package/skills/reactome-database/scripts/reactome_query.py +286 -0
  1070. package/skills/replication/SKILL.md +14 -0
  1071. package/skills/research-grants/SKILL.md +955 -0
  1072. package/skills/research-grants/assets/budget_justification_template.md +453 -0
  1073. package/skills/research-grants/assets/nih_specific_aims_template.md +166 -0
  1074. package/skills/research-grants/assets/nsf_project_summary_template.md +92 -0
  1075. package/skills/research-grants/references/README.md +285 -0
  1076. package/skills/research-grants/references/broader_impacts.md +392 -0
  1077. package/skills/research-grants/references/darpa_guidelines.md +636 -0
  1078. package/skills/research-grants/references/doe_guidelines.md +586 -0
  1079. package/skills/research-grants/references/nih_guidelines.md +851 -0
  1080. package/skills/research-grants/references/nsf_guidelines.md +570 -0
  1081. package/skills/research-grants/references/nstc_guidelines.md +733 -0
  1082. package/skills/research-grants/references/specific_aims_guide.md +458 -0
  1083. package/skills/research-lookup/README.md +156 -0
  1084. package/skills/research-lookup/SKILL.md +413 -0
  1085. package/skills/research-lookup/examples.py +174 -0
  1086. package/skills/research-lookup/lookup.py +187 -0
  1087. package/skills/research-lookup/research_lookup.py +566 -0
  1088. package/skills/research-lookup/scripts/research_lookup.py +566 -0
  1089. package/skills/rowan/SKILL.md +427 -0
  1090. package/skills/rowan/references/api_reference.md +413 -0
  1091. package/skills/rowan/references/molecule_handling.md +429 -0
  1092. package/skills/rowan/references/proteins_and_organization.md +499 -0
  1093. package/skills/rowan/references/rdkit_native.md +438 -0
  1094. package/skills/rowan/references/results_interpretation.md +481 -0
  1095. package/skills/rowan/references/workflow_types.md +591 -0
  1096. package/skills/runpod-compute/SKILL.md +48 -0
  1097. package/skills/scanpy/SKILL.md +384 -0
  1098. package/skills/scanpy/assets/analysis_template.py +295 -0
  1099. package/skills/scanpy/references/api_reference.md +251 -0
  1100. package/skills/scanpy/references/plotting_guide.md +352 -0
  1101. package/skills/scanpy/references/standard_workflow.md +206 -0
  1102. package/skills/scanpy/scripts/qc_analysis.py +200 -0
  1103. package/skills/scholar-evaluation/SKILL.md +298 -0
  1104. package/skills/scholar-evaluation/references/evaluation_framework.md +663 -0
  1105. package/skills/scholar-evaluation/scripts/calculate_scores.py +378 -0
  1106. package/skills/scientific-brainstorming/SKILL.md +189 -0
  1107. package/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
  1108. package/skills/scientific-critical-thinking/SKILL.md +570 -0
  1109. package/skills/scientific-critical-thinking/references/common_biases.md +364 -0
  1110. package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +484 -0
  1111. package/skills/scientific-critical-thinking/references/experimental_design.md +496 -0
  1112. package/skills/scientific-critical-thinking/references/logical_fallacies.md +478 -0
  1113. package/skills/scientific-critical-thinking/references/scientific_method.md +169 -0
  1114. package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +506 -0
  1115. package/skills/scientific-schematics/SKILL.md +619 -0
  1116. package/skills/scientific-schematics/references/QUICK_REFERENCE.md +207 -0
  1117. package/skills/scientific-schematics/references/README.md +327 -0
  1118. package/skills/scientific-schematics/references/best_practices.md +560 -0
  1119. package/skills/scientific-schematics/scripts/example_usage.sh +89 -0
  1120. package/skills/scientific-schematics/scripts/generate_schematic.py +139 -0
  1121. package/skills/scientific-schematics/scripts/generate_schematic_ai.py +844 -0
  1122. package/skills/scientific-slides/SKILL.md +1154 -0
  1123. package/skills/scientific-slides/assets/beamer_template_conference.tex +407 -0
  1124. package/skills/scientific-slides/assets/beamer_template_defense.tex +906 -0
  1125. package/skills/scientific-slides/assets/beamer_template_seminar.tex +870 -0
  1126. package/skills/scientific-slides/assets/powerpoint_design_guide.md +662 -0
  1127. package/skills/scientific-slides/assets/timing_guidelines.md +597 -0
  1128. package/skills/scientific-slides/references/beamer_guide.md +1019 -0
  1129. package/skills/scientific-slides/references/data_visualization_slides.md +708 -0
  1130. package/skills/scientific-slides/references/presentation_structure.md +642 -0
  1131. package/skills/scientific-slides/references/slide_design_principles.md +849 -0
  1132. package/skills/scientific-slides/references/talk_types_guide.md +687 -0
  1133. package/skills/scientific-slides/references/visual_review_workflow.md +775 -0
  1134. package/skills/scientific-slides/scripts/generate_slide_image.py +140 -0
  1135. package/skills/scientific-slides/scripts/generate_slide_image_ai.py +763 -0
  1136. package/skills/scientific-slides/scripts/pdf_to_images.py +221 -0
  1137. package/skills/scientific-slides/scripts/slides_to_pdf.py +235 -0
  1138. package/skills/scientific-slides/scripts/validate_presentation.py +403 -0
  1139. package/skills/scientific-visualization/SKILL.md +777 -0
  1140. package/skills/scientific-visualization/assets/color_palettes.py +197 -0
  1141. package/skills/scientific-visualization/assets/nature.mplstyle +63 -0
  1142. package/skills/scientific-visualization/assets/presentation.mplstyle +61 -0
  1143. package/skills/scientific-visualization/assets/publication.mplstyle +68 -0
  1144. package/skills/scientific-visualization/references/color_palettes.md +348 -0
  1145. package/skills/scientific-visualization/references/journal_requirements.md +320 -0
  1146. package/skills/scientific-visualization/references/matplotlib_examples.md +620 -0
  1147. package/skills/scientific-visualization/references/publication_guidelines.md +205 -0
  1148. package/skills/scientific-visualization/scripts/figure_export.py +343 -0
  1149. package/skills/scientific-visualization/scripts/style_presets.py +416 -0
  1150. package/skills/scientific-workflows/SKILL.md +1684 -0
  1151. package/skills/scientific-writing/SKILL.md +718 -0
  1152. package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +574 -0
  1153. package/skills/scientific-writing/assets/scientific_report.sty +606 -0
  1154. package/skills/scientific-writing/assets/scientific_report_template.tex +449 -0
  1155. package/skills/scientific-writing/references/citation_styles.md +720 -0
  1156. package/skills/scientific-writing/references/figures_tables.md +806 -0
  1157. package/skills/scientific-writing/references/imrad_structure.md +686 -0
  1158. package/skills/scientific-writing/references/professional_report_formatting.md +664 -0
  1159. package/skills/scientific-writing/references/reporting_guidelines.md +748 -0
  1160. package/skills/scientific-writing/references/writing_principles.md +824 -0
  1161. package/skills/scikit-bio/SKILL.md +435 -0
  1162. package/skills/scikit-bio/references/api_reference.md +749 -0
  1163. package/skills/scikit-learn/SKILL.md +519 -0
  1164. package/skills/scikit-learn/references/model_evaluation.md +592 -0
  1165. package/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
  1166. package/skills/scikit-learn/references/preprocessing.md +606 -0
  1167. package/skills/scikit-learn/references/quick_reference.md +433 -0
  1168. package/skills/scikit-learn/references/supervised_learning.md +378 -0
  1169. package/skills/scikit-learn/references/unsupervised_learning.md +505 -0
  1170. package/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
  1171. package/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
  1172. package/skills/scikit-survival/SKILL.md +397 -0
  1173. package/skills/scikit-survival/references/competing-risks.md +397 -0
  1174. package/skills/scikit-survival/references/cox-models.md +182 -0
  1175. package/skills/scikit-survival/references/data-handling.md +494 -0
  1176. package/skills/scikit-survival/references/ensemble-models.md +327 -0
  1177. package/skills/scikit-survival/references/evaluation-metrics.md +378 -0
  1178. package/skills/scikit-survival/references/svm-models.md +411 -0
  1179. package/skills/scvelo/SKILL.md +321 -0
  1180. package/skills/scvelo/references/velocity_models.md +168 -0
  1181. package/skills/scvelo/scripts/rna_velocity_workflow.py +232 -0
  1182. package/skills/scvi-tools/SKILL.md +188 -0
  1183. package/skills/scvi-tools/references/differential-expression.md +581 -0
  1184. package/skills/scvi-tools/references/models-atac-seq.md +321 -0
  1185. package/skills/scvi-tools/references/models-multimodal.md +367 -0
  1186. package/skills/scvi-tools/references/models-scrna-seq.md +330 -0
  1187. package/skills/scvi-tools/references/models-spatial.md +438 -0
  1188. package/skills/scvi-tools/references/models-specialized.md +408 -0
  1189. package/skills/scvi-tools/references/theoretical-foundations.md +438 -0
  1190. package/skills/scvi-tools/references/workflows.md +546 -0
  1191. package/skills/seaborn/SKILL.md +671 -0
  1192. package/skills/seaborn/references/examples.md +822 -0
  1193. package/skills/seaborn/references/function_reference.md +770 -0
  1194. package/skills/seaborn/references/objects_interface.md +964 -0
  1195. package/skills/semantic-scholar/SKILL.md +123 -0
  1196. package/skills/session-log/SKILL.md +10 -0
  1197. package/skills/session-search/SKILL.md +26 -0
  1198. package/skills/setup/SKILL.md +216 -0
  1199. package/skills/shap/SKILL.md +564 -0
  1200. package/skills/shap/references/explainers.md +339 -0
  1201. package/skills/shap/references/plots.md +507 -0
  1202. package/skills/shap/references/theory.md +449 -0
  1203. package/skills/shap/references/workflows.md +605 -0
  1204. package/skills/simpy/SKILL.md +427 -0
  1205. package/skills/simpy/references/events.md +374 -0
  1206. package/skills/simpy/references/monitoring.md +475 -0
  1207. package/skills/simpy/references/process-interaction.md +424 -0
  1208. package/skills/simpy/references/real-time.md +395 -0
  1209. package/skills/simpy/references/resources.md +275 -0
  1210. package/skills/simpy/scripts/basic_simulation_template.py +193 -0
  1211. package/skills/simpy/scripts/resource_monitor.py +345 -0
  1212. package/skills/source-comparison/SKILL.md +12 -0
  1213. package/skills/stable-baselines3/SKILL.md +297 -0
  1214. package/skills/stable-baselines3/references/algorithms.md +333 -0
  1215. package/skills/stable-baselines3/references/callbacks.md +556 -0
  1216. package/skills/stable-baselines3/references/custom_environments.md +526 -0
  1217. package/skills/stable-baselines3/references/vectorized_envs.md +568 -0
  1218. package/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
  1219. package/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
  1220. package/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
  1221. package/skills/statistical-analysis/SKILL.md +630 -0
  1222. package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
  1223. package/skills/statistical-analysis/references/bayesian_statistics.md +661 -0
  1224. package/skills/statistical-analysis/references/effect_sizes_and_power.md +581 -0
  1225. package/skills/statistical-analysis/references/reporting_standards.md +469 -0
  1226. package/skills/statistical-analysis/references/test_selection_guide.md +129 -0
  1227. package/skills/statistical-analysis/scripts/assumption_checks.py +539 -0
  1228. package/skills/statsmodels/SKILL.md +612 -0
  1229. package/skills/statsmodels/references/discrete_choice.md +669 -0
  1230. package/skills/statsmodels/references/glm.md +619 -0
  1231. package/skills/statsmodels/references/linear_models.md +447 -0
  1232. package/skills/statsmodels/references/stats_diagnostics.md +859 -0
  1233. package/skills/statsmodels/references/time_series.md +716 -0
  1234. package/skills/string-database/SKILL.md +532 -0
  1235. package/skills/string-database/references/string_reference.md +455 -0
  1236. package/skills/string-database/scripts/string_api.py +369 -0
  1237. package/skills/sympy/SKILL.md +498 -0
  1238. package/skills/sympy/references/advanced-topics.md +635 -0
  1239. package/skills/sympy/references/code-generation-printing.md +599 -0
  1240. package/skills/sympy/references/core-capabilities.md +348 -0
  1241. package/skills/sympy/references/matrices-linear-algebra.md +526 -0
  1242. package/skills/sympy/references/physics-mechanics.md +592 -0
  1243. package/skills/tiledbvcf/SKILL.md +459 -0
  1244. package/skills/timesfm-forecasting/SKILL.md +785 -0
  1245. package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +524 -0
  1246. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +448 -0
  1247. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
  1248. package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +568 -0
  1249. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
  1250. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +59 -0
  1251. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +109 -0
  1252. package/skills/timesfm-forecasting/examples/global-temperature/README.md +178 -0
  1253. package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +147 -0
  1254. package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +248 -0
  1255. package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +544 -0
  1256. package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +5441 -0
  1257. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
  1258. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +13 -0
  1259. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +188 -0
  1260. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
  1261. package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +5939 -0
  1262. package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +53 -0
  1263. package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +167 -0
  1264. package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +37 -0
  1265. package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +123 -0
  1266. package/skills/timesfm-forecasting/references/api_reference.md +231 -0
  1267. package/skills/timesfm-forecasting/references/data_preparation.md +272 -0
  1268. package/skills/timesfm-forecasting/references/system_requirements.md +201 -0
  1269. package/skills/timesfm-forecasting/scripts/check_system.py +520 -0
  1270. package/skills/timesfm-forecasting/scripts/forecast_csv.py +269 -0
  1271. package/skills/torch-geometric/SKILL.md +674 -0
  1272. package/skills/torch-geometric/references/datasets_reference.md +574 -0
  1273. package/skills/torch-geometric/references/layers_reference.md +485 -0
  1274. package/skills/torch-geometric/references/transforms_reference.md +679 -0
  1275. package/skills/torch-geometric/scripts/benchmark_model.py +309 -0
  1276. package/skills/torch-geometric/scripts/create_gnn_template.py +529 -0
  1277. package/skills/torch-geometric/scripts/visualize_graph.py +313 -0
  1278. package/skills/torchdrug/SKILL.md +448 -0
  1279. package/skills/torchdrug/references/core_concepts.md +565 -0
  1280. package/skills/torchdrug/references/datasets.md +380 -0
  1281. package/skills/torchdrug/references/knowledge_graphs.md +320 -0
  1282. package/skills/torchdrug/references/models_architectures.md +541 -0
  1283. package/skills/torchdrug/references/molecular_generation.md +352 -0
  1284. package/skills/torchdrug/references/molecular_property_prediction.md +169 -0
  1285. package/skills/torchdrug/references/protein_modeling.md +272 -0
  1286. package/skills/torchdrug/references/retrosynthesis.md +436 -0
  1287. package/skills/transformers/SKILL.md +162 -0
  1288. package/skills/transformers/references/generation.md +467 -0
  1289. package/skills/transformers/references/models.md +361 -0
  1290. package/skills/transformers/references/pipelines.md +335 -0
  1291. package/skills/transformers/references/tokenizers.md +447 -0
  1292. package/skills/transformers/references/training.md +500 -0
  1293. package/skills/treatment-plans/SKILL.md +1580 -0
  1294. package/skills/treatment-plans/assets/STYLING_QUICK_REFERENCE.md +185 -0
  1295. package/skills/treatment-plans/assets/chronic_disease_management_plan.tex +665 -0
  1296. package/skills/treatment-plans/assets/general_medical_treatment_plan.tex +547 -0
  1297. package/skills/treatment-plans/assets/medical_treatment_plan.sty +222 -0
  1298. package/skills/treatment-plans/assets/mental_health_treatment_plan.tex +774 -0
  1299. package/skills/treatment-plans/assets/one_page_treatment_plan.tex +193 -0
  1300. package/skills/treatment-plans/assets/pain_management_plan.tex +799 -0
  1301. package/skills/treatment-plans/assets/perioperative_care_plan.tex +753 -0
  1302. package/skills/treatment-plans/assets/quality_checklist.md +471 -0
  1303. package/skills/treatment-plans/assets/rehabilitation_treatment_plan.tex +756 -0
  1304. package/skills/treatment-plans/references/README.md +488 -0
  1305. package/skills/treatment-plans/references/goal_setting_frameworks.md +411 -0
  1306. package/skills/treatment-plans/references/intervention_guidelines.md +507 -0
  1307. package/skills/treatment-plans/references/regulatory_compliance.md +476 -0
  1308. package/skills/treatment-plans/references/specialty_specific_guidelines.md +655 -0
  1309. package/skills/treatment-plans/references/treatment_plan_standards.md +485 -0
  1310. package/skills/treatment-plans/scripts/check_completeness.py +318 -0
  1311. package/skills/treatment-plans/scripts/generate_template.py +244 -0
  1312. package/skills/treatment-plans/scripts/timeline_generator.py +369 -0
  1313. package/skills/treatment-plans/scripts/validate_treatment_plan.py +367 -0
  1314. package/skills/umap-learn/SKILL.md +477 -0
  1315. package/skills/umap-learn/references/api_reference.md +532 -0
  1316. package/skills/uniprot-database/SKILL.md +193 -0
  1317. package/skills/uniprot-database/references/api_examples.md +413 -0
  1318. package/skills/uniprot-database/references/api_fields.md +275 -0
  1319. package/skills/uniprot-database/references/id_mapping_databases.md +285 -0
  1320. package/skills/uniprot-database/references/query_syntax.md +256 -0
  1321. package/skills/uniprot-database/scripts/uniprot_client.py +341 -0
  1322. package/skills/usfiscaldata/SKILL.md +163 -0
  1323. package/skills/usfiscaldata/references/api-basics.md +86 -0
  1324. package/skills/usfiscaldata/references/datasets-debt.md +163 -0
  1325. package/skills/usfiscaldata/references/datasets-fiscal.md +196 -0
  1326. package/skills/usfiscaldata/references/datasets-interest-rates.md +182 -0
  1327. package/skills/usfiscaldata/references/datasets-securities.md +216 -0
  1328. package/skills/usfiscaldata/references/examples.md +258 -0
  1329. package/skills/usfiscaldata/references/parameters.md +155 -0
  1330. package/skills/usfiscaldata/references/response-format.md +176 -0
  1331. package/skills/uspto-database/SKILL.md +605 -0
  1332. package/skills/uspto-database/references/additional_apis.md +394 -0
  1333. package/skills/uspto-database/references/patentsearch_api.md +266 -0
  1334. package/skills/uspto-database/references/peds_api.md +212 -0
  1335. package/skills/uspto-database/references/trademark_api.md +358 -0
  1336. package/skills/uspto-database/scripts/patent_search.py +290 -0
  1337. package/skills/uspto-database/scripts/peds_client.py +285 -0
  1338. package/skills/uspto-database/scripts/trademark_client.py +311 -0
  1339. package/skills/vaex/SKILL.md +180 -0
  1340. package/skills/vaex/references/core_dataframes.md +367 -0
  1341. package/skills/vaex/references/data_processing.md +555 -0
  1342. package/skills/vaex/references/io_operations.md +703 -0
  1343. package/skills/vaex/references/machine_learning.md +728 -0
  1344. package/skills/vaex/references/performance.md +571 -0
  1345. package/skills/vaex/references/visualization.md +613 -0
  1346. package/skills/venue-templates/SKILL.md +688 -0
  1347. package/skills/venue-templates/assets/examples/cell_summary_example.md +247 -0
  1348. package/skills/venue-templates/assets/examples/medical_structured_abstract.md +313 -0
  1349. package/skills/venue-templates/assets/examples/nature_abstract_examples.md +213 -0
  1350. package/skills/venue-templates/assets/examples/neurips_introduction_example.md +245 -0
  1351. package/skills/venue-templates/assets/grants/nih_specific_aims.tex +235 -0
  1352. package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +375 -0
  1353. package/skills/venue-templates/assets/journals/nature_article.tex +171 -0
  1354. package/skills/venue-templates/assets/journals/neurips_article.tex +283 -0
  1355. package/skills/venue-templates/assets/journals/plos_one.tex +317 -0
  1356. package/skills/venue-templates/assets/posters/beamerposter_academic.tex +311 -0
  1357. package/skills/venue-templates/references/cell_press_style.md +483 -0
  1358. package/skills/venue-templates/references/conferences_formatting.md +564 -0
  1359. package/skills/venue-templates/references/cs_conference_style.md +463 -0
  1360. package/skills/venue-templates/references/grants_requirements.md +787 -0
  1361. package/skills/venue-templates/references/journals_formatting.md +486 -0
  1362. package/skills/venue-templates/references/medical_journal_styles.md +535 -0
  1363. package/skills/venue-templates/references/ml_conference_style.md +556 -0
  1364. package/skills/venue-templates/references/nature_science_style.md +405 -0
  1365. package/skills/venue-templates/references/posters_guidelines.md +628 -0
  1366. package/skills/venue-templates/references/reviewer_expectations.md +417 -0
  1367. package/skills/venue-templates/references/venue_writing_styles.md +321 -0
  1368. package/skills/venue-templates/scripts/customize_template.py +206 -0
  1369. package/skills/venue-templates/scripts/query_template.py +260 -0
  1370. package/skills/venue-templates/scripts/validate_format.py +255 -0
  1371. package/skills/watch/SKILL.md +12 -0
  1372. package/skills/what-if-oracle/SKILL.md +168 -0
  1373. package/skills/what-if-oracle/references/scenario-templates.md +137 -0
  1374. package/skills/writing/SKILL.md +414 -0
  1375. package/skills/xlsx/LICENSE.txt +30 -0
  1376. package/skills/xlsx/SKILL.md +292 -0
  1377. package/skills/xlsx/scripts/office/helpers/__init__.py +0 -0
  1378. package/skills/xlsx/scripts/office/helpers/merge_runs.py +199 -0
  1379. package/skills/xlsx/scripts/office/helpers/simplify_redlines.py +197 -0
  1380. package/skills/xlsx/scripts/office/pack.py +159 -0
  1381. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
  1382. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
  1383. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
  1384. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
  1385. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
  1386. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
  1387. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
  1388. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
  1389. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
  1390. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
  1391. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
  1392. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
  1393. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
  1394. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
  1395. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
  1396. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
  1397. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
  1398. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
  1399. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
  1400. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
  1401. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
  1402. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
  1403. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
  1404. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
  1405. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
  1406. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
  1407. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
  1408. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
  1409. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
  1410. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
  1411. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
  1412. package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +75 -0
  1413. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +560 -0
  1414. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +67 -0
  1415. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +14 -0
  1416. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +20 -0
  1417. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +13 -0
  1418. package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
  1419. package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +8 -0
  1420. package/skills/xlsx/scripts/office/soffice.py +183 -0
  1421. package/skills/xlsx/scripts/office/unpack.py +132 -0
  1422. package/skills/xlsx/scripts/office/validate.py +111 -0
  1423. package/skills/xlsx/scripts/office/validators/__init__.py +15 -0
  1424. package/skills/xlsx/scripts/office/validators/base.py +847 -0
  1425. package/skills/xlsx/scripts/office/validators/docx.py +446 -0
  1426. package/skills/xlsx/scripts/office/validators/pptx.py +275 -0
  1427. package/skills/xlsx/scripts/office/validators/redlining.py +247 -0
  1428. package/skills/xlsx/scripts/recalc.py +184 -0
  1429. package/skills/zarr-python/SKILL.md +777 -0
  1430. package/skills/zarr-python/references/api_reference.md +515 -0
  1431. package/skills/zinc-database/SKILL.md +402 -0
  1432. package/skills/zinc-database/references/api_reference.md +692 -0
@@ -0,0 +1,346 @@
1
+ # Paper2Poster: Academic Poster Generation
2
+
3
+ ## Overview
4
+
5
+ Paper2Poster automatically generates professional academic posters from research papers. The system extracts key content, designs visually appealing layouts, and creates print-ready posters suitable for conferences, symposiums, and academic presentations.
6
+
7
+ ## Core Capabilities
8
+
9
+ ### 1. Content Extraction
10
+ - Identifies key findings and contributions
11
+ - Extracts important figures and tables
12
+ - Summarizes methodology
13
+ - Highlights results and conclusions
14
+ - Preserves citations and references
15
+
16
+ ### 2. Layout Design
17
+ - Creates balanced, professional layouts
18
+ - Optimizes content density and white space
19
+ - Establishes clear visual hierarchy
20
+ - Supports multiple poster sizes
21
+ - Adapts to different content types
22
+
23
+ ### 3. Visual Design
24
+ - Applies color schemes and branding
25
+ - Optimizes typography for readability
26
+ - Ensures figure quality and sizing
27
+ - Creates cohesive visual identity
28
+ - Maintains academic presentation standards
29
+
30
+ ## Usage
31
+
32
+ ### Basic Poster Generation
33
+
34
+ ```bash
35
+ python pipeline_all.py \
36
+ --input-dir "path/to/papers" \
37
+ --output-dir "path/to/output" \
38
+ --model-choice 1 \
39
+ --generate-poster
40
+ ```
41
+
42
+ ### Custom Poster Dimensions
43
+
44
+ ```bash
45
+ python pipeline_all.py \
46
+ --input-dir "path/to/papers" \
47
+ --output-dir "path/to/output" \
48
+ --model-choice 2 \
49
+ --generate-poster \
50
+ --poster-width-inches 60 \
51
+ --poster-height-inches 40
52
+ ```
53
+
54
+ ### Parameters
55
+
56
+ **Basic Configuration:**
57
+ - `--input-dir`: Directory containing paper files
58
+ - `--output-dir`: Directory for generated posters
59
+ - `--model-choice`: LLM model selection (1=GPT-4, 2=GPT-4.1)
60
+ - `--generate-poster`: Enable poster generation
61
+
62
+ **Poster Dimensions:**
63
+ - `--poster-width-inches`: Width in inches (default: 48)
64
+ - `--poster-height-inches`: Height in inches (default: 36)
65
+ - `--poster-orientation`: Portrait or landscape (default: landscape)
66
+ - `--poster-dpi`: Resolution in DPI (default: 300)
67
+
68
+ **Design Options:**
69
+ - `--poster-template`: Template style (default: modern)
70
+ - `--color-scheme`: Color palette selection
71
+ - `--institution-branding`: Include institution colors and logos
72
+ - `--font-family`: Typography selection
73
+
74
+ ## Standard Poster Sizes
75
+
76
+ ### Conference Standard Sizes
77
+ - **4' × 3'** (48" × 36"): Most common conference poster
78
+ - **5' × 4'** (60" × 48"): Large format for major conferences
79
+ - **3' × 4'** (36" × 48"): Portrait orientation for narrow spaces
80
+ - **A0** (841mm × 1189mm): International standard
81
+ - **A1** (594mm × 841mm): Compact conference poster
82
+
83
+ ### Custom Sizes
84
+ The system supports any custom dimensions. Specify using:
85
+ ```bash
86
+ --poster-width-inches [width] --poster-height-inches [height]
87
+ ```
88
+
89
+ ## Input Requirements
90
+
91
+ ### Supported Input Formats
92
+ 1. **LaTeX source** (preferred)
93
+ - Main `.tex` file with complete paper
94
+ - All figures and tables referenced
95
+ - Compiled successfully
96
+
97
+ 2. **PDF**
98
+ - High-quality PDF with embedded fonts
99
+ - Selectable text (not scanned)
100
+ - High-resolution figures
101
+
102
+ ### Required Content Elements
103
+ - Title and authors
104
+ - Abstract or summary
105
+ - Methodology description
106
+ - Key results
107
+ - Conclusions
108
+ - References (optional but recommended)
109
+
110
+ ### Recommended Assets
111
+ - High-resolution figures (300 DPI minimum)
112
+ - Vector graphics (PDF, SVG, EPS)
113
+ - Institution logo
114
+ - Author photos (optional)
115
+ - QR codes for website/repo links
116
+
117
+ ## Output Structure
118
+
119
+ ```
120
+ output/paper_name/poster/
121
+ ├── poster_final.pdf # Print-ready poster
122
+ ├── poster_final.png # High-res PNG version
123
+ ├── poster_preview.pdf # Low-res preview
124
+ ├── poster_source/ # Source files
125
+ │ ├── layout.pptx # Editable PowerPoint
126
+ │ ├── layout.svg # Vector graphics
127
+ │ └── layout.json # Layout specification
128
+ ├── assets/ # Extracted assets
129
+ │ ├── figures/ # Poster figures
130
+ │ ├── logos/ # Institution logos
131
+ │ └── qrcodes/ # Generated QR codes
132
+ └── metadata/
133
+ ├── design_spec.json # Design specifications
134
+ └── content_map.json # Content organization
135
+ ```
136
+
137
+ ## Poster Layout Sections
138
+
139
+ ### Standard Sections
140
+ 1. **Header**
141
+ - Title (large, prominent)
142
+ - Authors and affiliations
143
+ - Institution logos
144
+ - Conference information
145
+
146
+ 2. **Introduction/Background**
147
+ - Problem statement
148
+ - Research motivation
149
+ - Brief literature context
150
+
151
+ 3. **Methods**
152
+ - Experimental design
153
+ - Key procedures
154
+ - Important parameters
155
+ - Visual workflow diagram
156
+
157
+ 4. **Results**
158
+ - Key findings (largest section)
159
+ - Primary figures and tables
160
+ - Statistical summaries
161
+ - Visual data representations
162
+
163
+ 5. **Conclusions**
164
+ - Main takeaways
165
+ - Implications
166
+ - Future work
167
+
168
+ 6. **References & Contact**
169
+ - Selected key references
170
+ - Author contact information
171
+ - QR codes for paper/website
172
+ - Acknowledgments
173
+
174
+ ## Design Templates
175
+
176
+ ### Modern Template (Default)
177
+ - Clean, minimalist design
178
+ - Bold colors for headers
179
+ - Ample white space
180
+ - Modern typography
181
+ - Focus on visual hierarchy
182
+
183
+ ### Academic Template
184
+ - Traditional academic styling
185
+ - Conservative color palette
186
+ - Dense information layout
187
+ - Classic serif typography
188
+ - Standard section organization
189
+
190
+ ### Visual Template
191
+ - Image-focused layout
192
+ - Large figure displays
193
+ - Minimal text density
194
+ - Infographic elements
195
+ - Story-driven flow
196
+
197
+ ### Technical Template
198
+ - Equation-friendly layout
199
+ - Code snippet support
200
+ - Detailed methodology sections
201
+ - Technical figure emphasis
202
+ - Engineering/CS aesthetic
203
+
204
+ ## Color Schemes
205
+
206
+ ### Predefined Schemes
207
+ - **Institutional**: Uses institution branding colors
208
+ - **Professional**: Navy blue and gray palette
209
+ - **Vibrant**: Bold, eye-catching colors
210
+ - **Nature**: Green and earth tones
211
+ - **Tech**: Modern blue and cyan
212
+ - **Warm**: Orange and red accents
213
+ - **Cool**: Blue and purple tones
214
+
215
+ ### Custom Color Schemes
216
+ Specify custom colors in configuration:
217
+ ```json
218
+ {
219
+ "primary": "#1E3A8A",
220
+ "secondary": "#3B82F6",
221
+ "accent": "#F59E0B",
222
+ "background": "#FFFFFF",
223
+ "text": "#1F2937"
224
+ }
225
+ ```
226
+
227
+ ## Typography Options
228
+
229
+ ### Font Families
230
+ - **Sans-serif** (default): Clean, modern, highly readable
231
+ - **Serif**: Traditional academic appearance
232
+ - **Mixed**: Serif for body, sans-serif for headers
233
+ - **Monospace**: For code and technical content
234
+
235
+ ### Size Hierarchy
236
+ - **Title**: 72-96pt
237
+ - **Section headers**: 48-60pt
238
+ - **Subsection headers**: 36-48pt
239
+ - **Body text**: 24-32pt
240
+ - **Captions**: 18-24pt
241
+ - **References**: 16-20pt
242
+
243
+ ## Quality Assurance
244
+
245
+ ### Automated Checks
246
+ - **Text readability**: Minimum font size verification
247
+ - **Color contrast**: Accessibility compliance
248
+ - **Figure quality**: Resolution and clarity checks
249
+ - **Layout balance**: Content distribution analysis
250
+ - **Branding consistency**: Logo and color verification
251
+
252
+ ### Manual Review Checklist
253
+ 1. ☐ All figures are high resolution and clear
254
+ 2. ☐ Text is readable from 3-6 feet away
255
+ 3. ☐ Color scheme is professional and consistent
256
+ 4. ☐ No text overlaps or layout issues
257
+ 5. ☐ Institution logos are correct and high quality
258
+ 6. ☐ QR codes work and link to correct URLs
259
+ 7. ☐ Author information is accurate
260
+ 8. ☐ Key findings are prominently displayed
261
+ 9. ☐ References are properly formatted
262
+ 10. ☐ File is correct size and resolution for printing
263
+
264
+ ## Print Preparation
265
+
266
+ ### File Specifications
267
+ - **Format**: PDF/X-1a or PDF/X-4 for professional printing
268
+ - **Resolution**: 300 DPI minimum, 600 DPI for fine details
269
+ - **Color mode**: CMYK for print (system auto-converts from RGB)
270
+ - **Bleed**: 0.125" bleed on all sides (automatically added)
271
+ - **Fonts**: All fonts embedded in PDF
272
+
273
+ ### Printing Recommendations
274
+ 1. **Print shop**: Use professional poster printing service
275
+ 2. **Paper type**: Matte or satin finish for academic posters
276
+ 3. **Backing**: Foam core or rigid backing for stability
277
+ 4. **Protection**: Lamination optional but recommended
278
+ 5. **Test print**: Print A4/Letter size preview first
279
+
280
+ ### Budget Options
281
+ - **Standard**: $50-100 for 4'×3' poster at professional shop
282
+ - **Economy**: $20-40 for print-only (no mounting)
283
+ - **Premium**: $150-300 for high-end materials and mounting
284
+ - **DIY**: <$10 for multiple pages tiled and assembled
285
+
286
+ ## Advanced Features
287
+
288
+ ### QR Code Generation
289
+ Automatically generates QR codes for:
290
+ - Paper PDF or DOI
291
+ - Project website
292
+ - GitHub repository
293
+ - Data repository
294
+ - Author profiles (ORCID, Google Scholar)
295
+
296
+ ### Institution Branding
297
+ When enabled:
298
+ - Extracts institution from author affiliations
299
+ - Searches for official logos (requires Google Search API)
300
+ - Applies institution color schemes
301
+ - Matches brand guidelines
302
+
303
+ ### Interactive Elements (Digital Posters)
304
+ For digital display or virtual conferences:
305
+ - Clickable links and references
306
+ - Embedded videos in figures
307
+ - Interactive data visualizations
308
+ - Animated transitions
309
+
310
+ ## Best Practices
311
+
312
+ ### Content Optimization
313
+ 1. **Focus on key findings**: Poster should tell story at a glance
314
+ 2. **Limit text**: Use bullet points, avoid paragraphs
315
+ 3. **Prioritize visuals**: Figures should dominate the space
316
+ 4. **Clear flow**: Guide viewer through logical progression
317
+ 5. **Highlight contributions**: Make novelty obvious
318
+
319
+ ### Design Optimization
320
+ 1. **Use contrast**: Ensure text is easily readable
321
+ 2. **Maintain hierarchy**: Size indicates importance
322
+ 3. **Balance content**: Avoid crowding any section
323
+ 4. **Consistent styling**: Same fonts, colors throughout
324
+ 5. **White space**: Don't fill every inch
325
+
326
+ ### Figure Optimization
327
+ 1. **Large enough**: Minimum 6" width for main figures
328
+ 2. **High resolution**: 300 DPI minimum
329
+ 3. **Clear labels**: Axis labels, legends readable
330
+ 4. **Remove clutter**: Simplify for poster format
331
+ 5. **Use captions**: Brief, informative descriptions
332
+
333
+ ## Limitations
334
+
335
+ - Complex equations may need manual adjustment for readability
336
+ - Very long papers may require content prioritization
337
+ - Custom branding requires manual specification or API access
338
+ - Multi-language support limited to common languages
339
+ - 3D visualizations may lose quality in 2D poster format
340
+
341
+ ## Integration with Other Components
342
+
343
+ Combine Paper2Poster with:
344
+ - **Paper2Web**: Use matching visual design and color scheme
345
+ - **Paper2Video**: Create poster walk-through video
346
+ - **AutoPR**: Generate social media graphics from poster
@@ -0,0 +1,305 @@
1
+ # Paper2Video: Presentation Video Generation
2
+
3
+ ## Overview
4
+
5
+ Paper2Video generates presentation videos from LaTeX sources, transforming academic papers into engaging video presentations. The system processes papers through multiple specialized modules to create professional presentation videos complete with slides, narration, and optional talking-head video.
6
+
7
+ ## Core Components
8
+
9
+ ### 1. Slide Generation Module
10
+ - Extracts key content from paper structure
11
+ - Creates visually appealing presentation slides
12
+ - Organizes content in logical flow
13
+ - Includes figures, tables, and equations
14
+ - Optimizes text density for readability
15
+
16
+ ### 2. Subtitle Generation Module
17
+ - Generates natural presentation script
18
+ - Synchronizes text with slide transitions
19
+ - Creates speaker notes and timing
20
+ - Supports multiple languages
21
+ - Optimizes for speech synthesis
22
+
23
+ ### 3. Speech Synthesis Module
24
+ - Converts subtitles to natural-sounding speech
25
+ - Supports multiple voices and accents
26
+ - Controls pacing and emphasis
27
+ - Generates audio track for video
28
+ - Handles technical terminology
29
+
30
+ ### 4. Cursor Movement Module
31
+ - Simulates presenter cursor movements
32
+ - Highlights key points on slides
33
+ - Guides viewer attention
34
+ - Creates natural presentation flow
35
+ - Synchronizes with narration
36
+
37
+ ### 5. Talking-Head Video Generation (Optional)
38
+ - Uses Hallo2 for realistic presenter video
39
+ - Lip-syncs with generated audio
40
+ - Requires reference image or video
41
+ - GPU-intensive (NVIDIA A6000 48GB minimum)
42
+ - Creates engaging presenter presence
43
+
44
+ ## Usage
45
+
46
+ ### Basic Video Generation (Without Talking-Head)
47
+
48
+ ```bash
49
+ python pipeline_light.py \
50
+ --model_name_t gpt-4.1 \
51
+ --model_name_v gpt-4.1 \
52
+ --result_dir /path/to/output \
53
+ --paper_latex_root /path/to/paper
54
+ ```
55
+
56
+ ### Full Video Generation (With Talking-Head)
57
+
58
+ ```bash
59
+ python pipeline_all.py \
60
+ --input-dir "path/to/papers" \
61
+ --output-dir "path/to/output" \
62
+ --model-choice 1 \
63
+ --enable-talking-head
64
+ ```
65
+
66
+ ### Parameters
67
+
68
+ **Model Configuration:**
69
+ - `--model_name_t`: Model for text/subtitle generation (default: gpt-4.1)
70
+ - `--model_name_v`: Model for visual/slide generation (default: gpt-4.1)
71
+ - `--model-choice`: Preset model configuration (1=GPT-4, 2=GPT-4.1)
72
+
73
+ **Input/Output:**
74
+ - `--paper_latex_root`: Root directory of LaTeX paper source
75
+ - `--result_dir` or `--output-dir`: Output directory for generated videos
76
+ - `--input-dir`: Directory containing multiple papers to process
77
+
78
+ **Video Options:**
79
+ - `--enable-talking-head`: Enable talking-head video generation (requires GPU)
80
+ - `--video-duration`: Target video duration in seconds (default: auto-calculated)
81
+ - `--slides-per-minute`: Control presentation pacing (default: 2-3)
82
+ - `--voice`: Voice selection for speech synthesis
83
+
84
+ **Quality Settings:**
85
+ - `--video-resolution`: Output resolution (default: 1920x1080)
86
+ - `--video-fps`: Frame rate (default: 30)
87
+ - `--audio-quality`: Audio bitrate (default: 192kbps)
88
+
89
+ ## Input Requirements
90
+
91
+ ### LaTeX Source Structure
92
+ ```
93
+ paper_directory/
94
+ ├── main.tex # Main paper file
95
+ ├── sections/ # Section files (if split)
96
+ │ ├── introduction.tex
97
+ │ ├── methods.tex
98
+ │ └── results.tex
99
+ ├── figures/ # Figure files
100
+ │ ├── fig1.pdf
101
+ │ ├── fig2.png
102
+ │ └── ...
103
+ ├── tables/ # Table files
104
+ └── bibliography.bib # References
105
+ ```
106
+
107
+ ### Required Elements
108
+ - Valid LaTeX source that compiles
109
+ - Proper section structure (abstract, introduction, methods, results, conclusion)
110
+ - High-quality figures (vector formats preferred)
111
+ - Complete bibliography
112
+
113
+ ### Optional Elements
114
+ - Author photos for talking-head generation
115
+ - Custom slide templates
116
+ - Background music or sound effects
117
+ - Institution branding assets
118
+
119
+ ## Output Structure
120
+
121
+ ```
122
+ output/paper_name/video/
123
+ ├── final_video.mp4 # Complete presentation video
124
+ ├── slides/ # Generated slide images
125
+ │ ├── slide_001.png
126
+ │ ├── slide_002.png
127
+ │ └── ...
128
+ ├── audio/ # Audio components
129
+ │ ├── narration.mp3 # Speech synthesis output
130
+ │ └── background.mp3 # Optional background audio
131
+ ├── subtitles/ # Subtitle files
132
+ │ ├── subtitles.srt # Standard subtitle format
133
+ │ └── subtitles.vtt # WebVTT format
134
+ ├── script/ # Presentation script
135
+ │ ├── full_script.txt # Complete narration text
136
+ │ └── slide_notes.json # Slide-by-slide notes
137
+ └── metadata/ # Video metadata
138
+ ├── timings.json # Slide timing information
139
+ └── video_info.json # Video properties
140
+ ```
141
+
142
+ ## Video Generation Process
143
+
144
+ ### Phase 1: Content Analysis
145
+ 1. Parse LaTeX source structure
146
+ 2. Extract key concepts and findings
147
+ 3. Identify important figures and equations
148
+ 4. Determine logical presentation flow
149
+
150
+ ### Phase 2: Slide Creation
151
+ 1. Design slide layouts based on content
152
+ 2. Allocate content across appropriate number of slides
153
+ 3. Incorporate figures and visual elements
154
+ 4. Apply consistent styling and branding
155
+
156
+ ### Phase 3: Script Generation
157
+ 1. Write natural presentation narration
158
+ 2. Time script sections to slides
159
+ 3. Add transitions and emphasis
160
+ 4. Optimize for speech synthesis
161
+
162
+ ### Phase 4: Audio Production
163
+ 1. Generate speech from script
164
+ 2. Add emphasis and pacing
165
+ 3. Include pauses for slide transitions
166
+ 4. Mix with optional background audio
167
+
168
+ ### Phase 5: Video Assembly
169
+ 1. Combine slides with timing information
170
+ 2. Synchronize audio track
171
+ 3. Add cursor movements and highlights
172
+ 4. Generate talking-head video (if enabled)
173
+ 5. Render final video file
174
+
175
+ ## Customization Options
176
+
177
+ ### Presentation Style
178
+ - **Academic**: Formal, detailed, comprehensive
179
+ - **Conference**: Focused on key findings, faster pace
180
+ - **Public**: Simplified language, engaging storytelling
181
+ - **Tutorial**: Step-by-step explanation, educational focus
182
+
183
+ ### Voice Configuration
184
+ Available voice options (via speech synthesis):
185
+ - Multiple languages and accents
186
+ - Male/female voice selection
187
+ - Speaking rate adjustment
188
+ - Pitch and tone customization
189
+
190
+ ### Visual Themes
191
+ - Institution branding colors
192
+ - Conference template matching
193
+ - Custom backgrounds and fonts
194
+ - Dark mode presentations
195
+
196
+ ## Quality Assessment
197
+
198
+ ### Content Quality Metrics
199
+ - **Completeness**: Coverage of paper content
200
+ - **Clarity**: Explanation quality and coherence
201
+ - **Flow**: Logical progression of ideas
202
+ - **Engagement**: Visual appeal and pacing
203
+
204
+ ### Technical Quality Metrics
205
+ - **Audio quality**: Speech clarity and naturalness
206
+ - **Video quality**: Resolution and encoding
207
+ - **Synchronization**: Audio-visual alignment
208
+ - **Timing**: Appropriate slide duration
209
+
210
+ ## Advanced Features
211
+
212
+ ### Multi-Language Support
213
+ - Generate presentations in multiple languages
214
+ - Automatic translation of script
215
+ - Language-appropriate voice selection
216
+ - Cultural adaptation of presentation style
217
+
218
+ ### Talking-Head Generation with Hallo2
219
+ Requires:
220
+ - NVIDIA A6000 GPU (48GB minimum)
221
+ - Reference image or short video of presenter
222
+ - Additional processing time (2-3x longer)
223
+
224
+ Benefits:
225
+ - More engaging presentation
226
+ - Professional presenter appearance
227
+ - Natural gestures and expressions
228
+ - Lip-sync accuracy
229
+
230
+ ### Interactive Elements
231
+ - Embedded clickable links
232
+ - Navigation menu
233
+ - Chapter markers
234
+ - Supplementary material links
235
+
236
+ ## Best Practices
237
+
238
+ ### Input Preparation
239
+ 1. **Clean LaTeX source**: Remove unnecessary comments and artifacts
240
+ 2. **High-quality figures**: Use vector formats when possible
241
+ 3. **Clear structure**: Well-organized sections and subsections
242
+ 4. **Complete content**: Include all necessary files and references
243
+
244
+ ### Model Selection
245
+ - **Text generation (model_name_t)**: GPT-4.1 for best script quality
246
+ - **Visual generation (model_name_v)**: GPT-4.1 for optimal slide design
247
+ - For faster processing with acceptable quality: GPT-3.5-turbo
248
+
249
+ ### Video Optimization
250
+ 1. **Target duration**: 10-15 minutes for conference talks, 30-45 for detailed presentations
251
+ 2. **Pacing**: 2-3 slides per minute for technical content
252
+ 3. **Resolution**: 1920x1080 for standard, 3840x2160 for high-quality
253
+ 4. **Audio**: 192kbps minimum for clear speech
254
+
255
+ ### Quality Review
256
+ Before finalizing:
257
+ 1. Watch entire video for content accuracy
258
+ 2. Check audio synchronization with slides
259
+ 3. Verify figure quality and readability
260
+ 4. Test subtitle accuracy and timing
261
+ 5. Review cursor movements for natural flow
262
+
263
+ ## Performance Considerations
264
+
265
+ ### Processing Time
266
+ - **Without talking-head**: 10-30 minutes per paper (depending on length)
267
+ - **With talking-head**: 30-120 minutes per paper
268
+ - **Factors**: Paper length, figure count, model speed, GPU availability
269
+
270
+ ### Resource Requirements
271
+ - **CPU**: Multi-core recommended for parallel processing
272
+ - **RAM**: 16GB minimum, 32GB for large papers
273
+ - **GPU**: Optional for standard, required for talking-head (A6000 48GB)
274
+ - **Storage**: 1-5GB per video depending on length and quality
275
+
276
+ ## Troubleshooting
277
+
278
+ ### Common Issues
279
+
280
+ **1. LaTeX parsing errors**
281
+ - Ensure LaTeX source compiles successfully
282
+ - Check for special packages or custom commands
283
+ - Verify all referenced files are present
284
+
285
+ **2. Speech synthesis problems**
286
+ - Check audio quality settings
287
+ - Verify text is properly formatted
288
+ - Test with different voice options
289
+
290
+ **3. Video rendering failures**
291
+ - Check available disk space
292
+ - Verify all dependencies are installed
293
+ - Review error logs for specific issues
294
+
295
+ **4. Talking-head generation errors**
296
+ - Confirm GPU memory (48GB required)
297
+ - Check CUDA drivers are up to date
298
+ - Verify reference image quality and format
299
+
300
+ ## Integration with Other Components
301
+
302
+ Combine Paper2Video with:
303
+ - **Paper2Web**: Embed video in generated website
304
+ - **Paper2Poster**: Use matching visual style
305
+ - **AutoPR**: Create promotional clips from full video