@pikaa-ai/pikaa 0.3.1 → 0.3.4

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 (1870) hide show
  1. package/dist/cli.js +1169 -601
  2. package/dist/index.js +525 -204
  3. package/package.json +5 -3
  4. package/skills/adaptyv/references/api-endpoints.md +0 -690
  5. package/skills/aeon/references/anomaly_detection.md +0 -154
  6. package/skills/aeon/references/classification.md +0 -144
  7. package/skills/aeon/references/clustering.md +0 -123
  8. package/skills/aeon/references/datasets_benchmarking.md +0 -392
  9. package/skills/aeon/references/distances.md +0 -256
  10. package/skills/aeon/references/forecasting.md +0 -109
  11. package/skills/aeon/references/networks.md +0 -289
  12. package/skills/aeon/references/regression.md +0 -118
  13. package/skills/aeon/references/segmentation.md +0 -163
  14. package/skills/aeon/references/similarity_search.md +0 -187
  15. package/skills/aeon/references/transformations.md +0 -246
  16. package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
  17. package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
  18. package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
  19. package/skills/analytical-method-validation/references/framework-selection.md +0 -87
  20. package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
  21. package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
  22. package/skills/analytical-method-validation/references/source-ledger.md +0 -125
  23. package/skills/analytical-method-validation/references/statistics.md +0 -209
  24. package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
  25. package/skills/analytical-method-validation/scripts/_common.py +0 -955
  26. package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
  27. package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
  28. package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
  29. package/skills/analytical-method-validation/scripts/check_response.py +0 -243
  30. package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
  31. package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
  32. package/skills/anndata/references/best_practices.md +0 -532
  33. package/skills/anndata/references/concatenation.md +0 -399
  34. package/skills/anndata/references/data_structure.md +0 -314
  35. package/skills/anndata/references/io_operations.md +0 -466
  36. package/skills/anndata/references/manipulation.md +0 -516
  37. package/skills/arbor/references/arbor-upstream.md +0 -91
  38. package/skills/arbor/references/executor-brief.md +0 -68
  39. package/skills/arbor/references/htr-methodology.md +0 -177
  40. package/skills/arbor/references/report-template.md +0 -39
  41. package/skills/arbor/scripts/tree.py +0 -564
  42. package/skills/arboreto/references/algorithms.md +0 -152
  43. package/skills/arboreto/references/basic_inference.md +0 -181
  44. package/skills/arboreto/references/distributed_computing.md +0 -242
  45. package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
  46. package/skills/astropy/references/coordinates.md +0 -280
  47. package/skills/astropy/references/cosmology.md +0 -309
  48. package/skills/astropy/references/fits.md +0 -398
  49. package/skills/astropy/references/tables.md +0 -495
  50. package/skills/astropy/references/time.md +0 -412
  51. package/skills/astropy/references/units.md +0 -178
  52. package/skills/astropy/references/wcs_and_other_modules.md +0 -377
  53. package/skills/autoskill/config.yaml +0 -53
  54. package/skills/autoskill/references/https-proxy.md +0 -62
  55. package/skills/autoskill/references/screenpipe-config.yaml +0 -61
  56. package/skills/autoskill/scripts/autoskill.py +0 -35
  57. package/skills/autoskill/scripts/backends.py +0 -116
  58. package/skills/autoskill/scripts/cluster.py +0 -54
  59. package/skills/autoskill/scripts/doctor.py +0 -108
  60. package/skills/autoskill/scripts/fetch_window.py +0 -33
  61. package/skills/autoskill/scripts/match_skills.py +0 -46
  62. package/skills/autoskill/scripts/promote.py +0 -58
  63. package/skills/autoskill/scripts/redact.py +0 -40
  64. package/skills/autoskill/scripts/run.py +0 -194
  65. package/skills/autoskill/scripts/synthesize.py +0 -72
  66. package/skills/benchling-integration/references/api_endpoints.md +0 -883
  67. package/skills/benchling-integration/references/authentication.md +0 -390
  68. package/skills/benchling-integration/references/core_capabilities.md +0 -355
  69. package/skills/benchling-integration/references/eventbridge.md +0 -255
  70. package/skills/benchling-integration/references/sdk_reference.md +0 -772
  71. package/skills/bids/references/beps.yml +0 -637
  72. package/skills/bids/references/bids_schema.json +0 -21015
  73. package/skills/bids/references/bids_specification.md +0 -165
  74. package/skills/bids/references/conversion_tools.md +0 -475
  75. package/skills/bids/references/core_workflows.md +0 -552
  76. package/skills/bids/references/metadata_fields.md +0 -365
  77. package/skills/bids/scripts/update_schema.py +0 -89
  78. package/skills/biopython/references/advanced.md +0 -580
  79. package/skills/biopython/references/alignment.md +0 -377
  80. package/skills/biopython/references/blast.md +0 -463
  81. package/skills/biopython/references/databases.md +0 -492
  82. package/skills/biopython/references/phylogenetics.md +0 -566
  83. package/skills/biopython/references/sequence_io.md +0 -289
  84. package/skills/biopython/references/structure.md +0 -564
  85. package/skills/bioservices/references/identifier_mapping.md +0 -685
  86. package/skills/bioservices/references/services_reference.md +0 -638
  87. package/skills/bioservices/references/workflow_patterns.md +0 -813
  88. package/skills/bioservices/scripts/batch_id_converter.py +0 -347
  89. package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
  90. package/skills/bioservices/scripts/pathway_analysis.py +0 -309
  91. package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
  92. package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
  93. package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
  94. package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
  95. package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
  96. package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
  97. package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
  98. package/skills/cellxgene-census/references/census_schema.md +0 -218
  99. package/skills/cellxgene-census/references/common_patterns.md +0 -368
  100. package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
  101. package/skills/cirq/references/building.md +0 -307
  102. package/skills/cirq/references/experiments.md +0 -572
  103. package/skills/cirq/references/hardware.md +0 -527
  104. package/skills/cirq/references/noise.md +0 -514
  105. package/skills/cirq/references/simulation.md +0 -353
  106. package/skills/cirq/references/transformation.md +0 -416
  107. package/skills/citation-management/assets/bibtex_template.bib +0 -264
  108. package/skills/citation-management/assets/citation_checklist.md +0 -386
  109. package/skills/citation-management/references/best_practices.md +0 -91
  110. package/skills/citation-management/references/bibtex_formatting.md +0 -908
  111. package/skills/citation-management/references/citation_validation.md +0 -835
  112. package/skills/citation-management/references/core_workflow.md +0 -569
  113. package/skills/citation-management/references/example_workflows.md +0 -126
  114. package/skills/citation-management/references/google_scholar_search.md +0 -732
  115. package/skills/citation-management/references/metadata_extraction.md +0 -870
  116. package/skills/citation-management/references/pubmed_search.md +0 -839
  117. package/skills/citation-management/references/script_reference.md +0 -250
  118. package/skills/citation-management/references/search_strategies.md +0 -110
  119. package/skills/citation-management/scripts/_common.py +0 -331
  120. package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
  121. package/skills/citation-management/scripts/extract_metadata.py +0 -690
  122. package/skills/citation-management/scripts/format_bibtex.py +0 -356
  123. package/skills/citation-management/scripts/search_google_scholar.py +0 -268
  124. package/skills/citation-management/scripts/search_openalex.py +0 -297
  125. package/skills/citation-management/scripts/search_pubmed.py +0 -419
  126. package/skills/citation-management/scripts/validate_citations.py +0 -688
  127. package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
  128. package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
  129. package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
  130. package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
  131. package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
  132. package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
  133. package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
  134. package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
  135. package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
  136. package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
  137. package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
  138. package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
  139. package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
  140. package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
  141. package/skills/clinical-decision-support/references/security_validation.md +0 -60
  142. package/skills/clinical-decision-support/references/sources.md +0 -119
  143. package/skills/clinical-decision-support/references/study_reporting.md +0 -134
  144. package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
  145. package/skills/clinical-decision-support/scripts/_common.py +0 -223
  146. package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
  147. package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
  148. package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
  149. package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
  150. package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
  151. package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
  152. package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
  153. package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
  154. package/skills/clinical-reports/assets/case_report_template.json +0 -43
  155. package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
  156. package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
  157. package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
  158. package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
  159. package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
  160. package/skills/clinical-reports/assets/lab_report_template.json +0 -36
  161. package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
  162. package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
  163. package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
  164. package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
  165. package/skills/clinical-reports/assets/research_summary_template.json +0 -36
  166. package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
  167. package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
  168. package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
  169. package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
  170. package/skills/clinical-reports/references/data_presentation.md +0 -92
  171. package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
  172. package/skills/clinical-reports/references/medical_terminology.md +0 -84
  173. package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
  174. package/skills/clinical-reports/references/professional_review.md +0 -78
  175. package/skills/clinical-reports/references/report_type_routing.md +0 -57
  176. package/skills/clinical-reports/references/safety_reporting.md +0 -109
  177. package/skills/clinical-reports/references/sources.md +0 -75
  178. package/skills/clinical-reports/scripts/_common.py +0 -263
  179. package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
  180. package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
  181. package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
  182. package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
  183. package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
  184. package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
  185. package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
  186. package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
  187. package/skills/cobrapy/references/api_quick_reference.md +0 -665
  188. package/skills/cobrapy/references/workflows.md +0 -600
  189. package/skills/consciousness-council/references/advanced-configurations.md +0 -96
  190. package/skills/dask/references/arrays.md +0 -495
  191. package/skills/dask/references/bags.md +0 -468
  192. package/skills/dask/references/best-practices.md +0 -277
  193. package/skills/dask/references/dataframes.md +0 -370
  194. package/skills/dask/references/futures.md +0 -541
  195. package/skills/dask/references/schedulers.md +0 -517
  196. package/skills/database-lookup/references/addgene.md +0 -38
  197. package/skills/database-lookup/references/alphafold.md +0 -52
  198. package/skills/database-lookup/references/alphavantage.md +0 -261
  199. package/skills/database-lookup/references/bea.md +0 -409
  200. package/skills/database-lookup/references/bindingdb.md +0 -85
  201. package/skills/database-lookup/references/biogrid.md +0 -110
  202. package/skills/database-lookup/references/bls.md +0 -235
  203. package/skills/database-lookup/references/brenda.md +0 -71
  204. package/skills/database-lookup/references/cbioportal.md +0 -206
  205. package/skills/database-lookup/references/census.md +0 -251
  206. package/skills/database-lookup/references/chebi.md +0 -103
  207. package/skills/database-lookup/references/chembl.md +0 -80
  208. package/skills/database-lookup/references/clinicaltrials.md +0 -86
  209. package/skills/database-lookup/references/clinpgx.md +0 -64
  210. package/skills/database-lookup/references/clinvar.md +0 -91
  211. package/skills/database-lookup/references/cod.md +0 -121
  212. package/skills/database-lookup/references/cosmic.md +0 -59
  213. package/skills/database-lookup/references/dailymed.md +0 -65
  214. package/skills/database-lookup/references/database_selection_guide.md +0 -166
  215. package/skills/database-lookup/references/datacommons.md +0 -237
  216. package/skills/database-lookup/references/dbsnp.md +0 -143
  217. package/skills/database-lookup/references/disgenet.md +0 -52
  218. package/skills/database-lookup/references/drugbank.md +0 -54
  219. package/skills/database-lookup/references/ecb.md +0 -191
  220. package/skills/database-lookup/references/emdb.md +0 -37
  221. package/skills/database-lookup/references/ena.md +0 -372
  222. package/skills/database-lookup/references/encode.md +0 -47
  223. package/skills/database-lookup/references/ensembl.md +0 -539
  224. package/skills/database-lookup/references/epa.md +0 -232
  225. package/skills/database-lookup/references/eurostat.md +0 -237
  226. package/skills/database-lookup/references/fda.md +0 -64
  227. package/skills/database-lookup/references/federal-reserve.md +0 -216
  228. package/skills/database-lookup/references/fred.md +0 -297
  229. package/skills/database-lookup/references/gene-ontology.md +0 -147
  230. package/skills/database-lookup/references/geo.md +0 -130
  231. package/skills/database-lookup/references/gnomad.md +0 -93
  232. package/skills/database-lookup/references/gtex.md +0 -136
  233. package/skills/database-lookup/references/gwas-catalog.md +0 -46
  234. package/skills/database-lookup/references/hca.md +0 -35
  235. package/skills/database-lookup/references/hpo.md +0 -48
  236. package/skills/database-lookup/references/human-protein-atlas.md +0 -57
  237. package/skills/database-lookup/references/interpro.md +0 -120
  238. package/skills/database-lookup/references/jaspar.md +0 -50
  239. package/skills/database-lookup/references/kegg.md +0 -78
  240. package/skills/database-lookup/references/lincs-l1000.md +0 -68
  241. package/skills/database-lookup/references/materials-project.md +0 -123
  242. package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
  243. package/skills/database-lookup/references/monarch.md +0 -46
  244. package/skills/database-lookup/references/mousemine.md +0 -40
  245. package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
  246. package/skills/database-lookup/references/nasa.md +0 -121
  247. package/skills/database-lookup/references/ncbi-gene.md +0 -64
  248. package/skills/database-lookup/references/ncbi-protein.md +0 -104
  249. package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
  250. package/skills/database-lookup/references/nist.md +0 -105
  251. package/skills/database-lookup/references/noaa.md +0 -199
  252. package/skills/database-lookup/references/omim.md +0 -114
  253. package/skills/database-lookup/references/opentargets.md +0 -459
  254. package/skills/database-lookup/references/openweathermap.md +0 -255
  255. package/skills/database-lookup/references/pdb.md +0 -121
  256. package/skills/database-lookup/references/pride.md +0 -74
  257. package/skills/database-lookup/references/pubchem.md +0 -145
  258. package/skills/database-lookup/references/quickgo.md +0 -45
  259. package/skills/database-lookup/references/reactome.md +0 -140
  260. package/skills/database-lookup/references/retrieval-contract.md +0 -123
  261. package/skills/database-lookup/references/rummageo.md +0 -32
  262. package/skills/database-lookup/references/sdss.md +0 -130
  263. package/skills/database-lookup/references/sec-edgar.md +0 -315
  264. package/skills/database-lookup/references/simbad.md +0 -405
  265. package/skills/database-lookup/references/sra.md +0 -149
  266. package/skills/database-lookup/references/string.md +0 -283
  267. package/skills/database-lookup/references/tcga-gdc.md +0 -58
  268. package/skills/database-lookup/references/treasury.md +0 -215
  269. package/skills/database-lookup/references/ucsc-genome.md +0 -135
  270. package/skills/database-lookup/references/uniprot.md +0 -283
  271. package/skills/database-lookup/references/usgs.md +0 -260
  272. package/skills/database-lookup/references/uspto.md +0 -130
  273. package/skills/database-lookup/references/who.md +0 -283
  274. package/skills/database-lookup/references/worldbank.md +0 -239
  275. package/skills/database-lookup/references/zinc.md +0 -202
  276. package/skills/datamol/references/conformers_module.md +0 -131
  277. package/skills/datamol/references/core_api.md +0 -136
  278. package/skills/datamol/references/core_workflows.md +0 -451
  279. package/skills/datamol/references/descriptors_viz.md +0 -195
  280. package/skills/datamol/references/fragments_scaffolds.md +0 -174
  281. package/skills/datamol/references/io_module.md +0 -112
  282. package/skills/datamol/references/reactions_data.md +0 -218
  283. package/skills/datamol/references/workflow_patterns.md +0 -104
  284. package/skills/deepchem/references/api_reference.md +0 -305
  285. package/skills/deepchem/references/core_capabilities.md +0 -276
  286. package/skills/deepchem/references/typical_workflows.md +0 -109
  287. package/skills/deepchem/references/workflows.md +0 -491
  288. package/skills/deepchem/scripts/graph_neural_network.py +0 -350
  289. package/skills/deepchem/scripts/predict_solubility.py +0 -223
  290. package/skills/deepchem/scripts/transfer_learning.py +0 -443
  291. package/skills/deepspot-m/references/api.md +0 -186
  292. package/skills/deepspot-m/references/whole_slide.md +0 -174
  293. package/skills/deeptools/assets/quick_reference.md +0 -65
  294. package/skills/deeptools/references/core_workflows.md +0 -134
  295. package/skills/deeptools/references/effective_genome_sizes.md +0 -118
  296. package/skills/deeptools/references/normalization_methods.md +0 -424
  297. package/skills/deeptools/references/tools_reference.md +0 -569
  298. package/skills/deeptools/references/workflows.md +0 -476
  299. package/skills/deeptools/scripts/validate_files.py +0 -195
  300. package/skills/deeptools/scripts/workflow_generator.py +0 -520
  301. package/skills/depmap/references/dependency_analysis.md +0 -178
  302. package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
  303. package/skills/diffdock/assets/batch_template.csv +0 -4
  304. package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
  305. package/skills/diffdock/references/confidence_and_limitations.md +0 -182
  306. package/skills/diffdock/references/parameters_reference.md +0 -173
  307. package/skills/diffdock/references/workflows_examples.md +0 -401
  308. package/skills/diffdock/scripts/analyze_results.py +0 -346
  309. package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
  310. package/skills/diffdock/scripts/setup_check.py +0 -283
  311. package/skills/dnanexus-integration/references/app-development.md +0 -371
  312. package/skills/dnanexus-integration/references/authentication.md +0 -226
  313. package/skills/dnanexus-integration/references/configuration.md +0 -444
  314. package/skills/dnanexus-integration/references/data-operations.md +0 -474
  315. package/skills/dnanexus-integration/references/job-execution.md +0 -482
  316. package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
  317. package/skills/dnanexus-integration/references/python-sdk.md +0 -548
  318. package/skills/dnanexus-integration/references/sources.md +0 -168
  319. package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
  320. package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
  321. package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
  322. package/skills/docx/LICENSE.txt +0 -30
  323. package/skills/docx/scripts/__init__.py +0 -1
  324. package/skills/docx/scripts/accept_changes.py +0 -135
  325. package/skills/docx/scripts/comment.py +0 -368
  326. package/skills/docx/scripts/merge_runs.py +0 -310
  327. package/skills/docx/scripts/office/helpers/__init__.py +0 -111
  328. package/skills/docx/scripts/office/helpers/pptx_chart.py +0 -170
  329. package/skills/docx/scripts/office/helpers/pptx_slide.py +0 -60
  330. package/skills/docx/scripts/office/helpers/pptx_theme.py +0 -114
  331. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
  332. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
  333. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
  334. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
  335. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
  336. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
  337. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
  338. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
  339. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
  340. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
  341. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
  342. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
  343. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
  344. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
  345. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
  346. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
  347. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
  348. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
  349. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
  350. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
  351. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
  352. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
  353. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
  354. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
  355. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
  356. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
  357. package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
  358. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
  359. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
  360. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
  361. package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
  362. package/skills/docx/scripts/office/schemas/mce/mc.xsd +0 -75
  363. package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
  364. package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
  365. package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
  366. package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
  367. package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
  368. package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
  369. package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
  370. package/skills/docx/scripts/office/soffice.py +0 -232
  371. package/skills/docx/scripts/office/validate.py +0 -173
  372. package/skills/docx/scripts/office/validators/__init__.py +0 -15
  373. package/skills/docx/scripts/office/validators/base.py +0 -875
  374. package/skills/docx/scripts/office/validators/docx.py +0 -466
  375. package/skills/docx/scripts/office/validators/pptx.py +0 -441
  376. package/skills/docx/scripts/office/validators/redlining.py +0 -299
  377. package/skills/docx/scripts/templates/comments.xml +0 -3
  378. package/skills/docx/scripts/templates/commentsExtended.xml +0 -3
  379. package/skills/docx/scripts/templates/commentsExtensible.xml +0 -3
  380. package/skills/docx/scripts/templates/commentsIds.xml +0 -3
  381. package/skills/docx/scripts/templates/people.xml +0 -3
  382. package/skills/esm/references/biohub-platform.md +0 -111
  383. package/skills/esm/references/esm-c-api.md +0 -609
  384. package/skills/esm/references/esm3-api.md +0 -462
  385. package/skills/esm/references/forge-api.md +0 -675
  386. package/skills/esm/references/workflows.md +0 -685
  387. package/skills/etetoolkit/references/api_reference.md +0 -546
  388. package/skills/etetoolkit/references/migration-ete3-to-ete4.md +0 -579
  389. package/skills/etetoolkit/references/taxonomy.md +0 -362
  390. package/skills/etetoolkit/references/visualization.md +0 -516
  391. package/skills/etetoolkit/references/workflows.md +0 -537
  392. package/skills/etetoolkit/scripts/quick_visualize.py +0 -455
  393. package/skills/etetoolkit/scripts/tree_operations.py +0 -446
  394. package/skills/exa-search/references/web-extract.md +0 -53
  395. package/skills/exa-search/references/web-search.md +0 -119
  396. package/skills/exa-search/scripts/exa_extract.py +0 -117
  397. package/skills/exa-search/scripts/exa_search.py +0 -179
  398. package/skills/experimental-design/references/design_types.md +0 -129
  399. package/skills/experimental-design/references/factorial_and_doe.md +0 -130
  400. package/skills/experimental-design/references/randomization_and_blocking.md +0 -116
  401. package/skills/experimental-design/references/sequential_and_adaptive.md +0 -97
  402. package/skills/experimental-design/scripts/doe_designs.py +0 -183
  403. package/skills/experimental-design/scripts/randomization.py +0 -171
  404. package/skills/exploratory-data-analysis/assets/report_template.md +0 -202
  405. package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +0 -192
  406. package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +0 -183
  407. package/skills/exploratory-data-analysis/references/general_scientific_formats.md +0 -259
  408. package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +0 -189
  409. package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -217
  410. package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -191
  411. package/skills/exploratory-data-analysis/scripts/__init__.py +0 -1
  412. package/skills/exploratory-data-analysis/scripts/_capabilities.py +0 -576
  413. package/skills/exploratory-data-analysis/scripts/_common.py +0 -460
  414. package/skills/exploratory-data-analysis/scripts/_structured.py +0 -391
  415. package/skills/exploratory-data-analysis/scripts/_tabular.py +0 -905
  416. package/skills/exploratory-data-analysis/scripts/capability_manifest.py +0 -184
  417. package/skills/exploratory-data-analysis/scripts/distribution_sensitivity.py +0 -117
  418. package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -345
  419. package/skills/exploratory-data-analysis/scripts/image_inspector.py +0 -214
  420. package/skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py +0 -130
  421. package/skills/exploratory-data-analysis/scripts/report_scaffold.py +0 -143
  422. package/skills/exploratory-data-analysis/scripts/sequence_inspector.py +0 -255
  423. package/skills/exploratory-data-analysis/scripts/tabular_profile.py +0 -109
  424. package/skills/flowio/references/api_reference.md +0 -355
  425. package/skills/flowio/references/fcs_semantics.md +0 -315
  426. package/skills/flowio/references/sources.md +0 -89
  427. package/skills/flowio/references/troubleshooting.md +0 -399
  428. package/skills/flowio/references/workflows.md +0 -368
  429. package/skills/flowio/scripts/inspect_fcs.py +0 -439
  430. package/skills/fluidsim/references/advanced_features.md +0 -347
  431. package/skills/fluidsim/references/installation.md +0 -263
  432. package/skills/fluidsim/references/output_analysis.md +0 -314
  433. package/skills/fluidsim/references/parameters.md +0 -322
  434. package/skills/fluidsim/references/simulation_workflow.md +0 -329
  435. package/skills/fluidsim/references/solvers.md +0 -191
  436. package/skills/fluidsim/scripts/__init__.py +0 -1
  437. package/skills/fluidsim/scripts/_common.py +0 -491
  438. package/skills/fluidsim/scripts/_schema.py +0 -872
  439. package/skills/fluidsim/scripts/budget_summary.py +0 -396
  440. package/skills/fluidsim/scripts/grid_resource_estimator.py +0 -286
  441. package/skills/fluidsim/scripts/output_inventory.py +0 -353
  442. package/skills/fluidsim/scripts/restart_compatibility.py +0 -424
  443. package/skills/fluidsim/scripts/simulation_dry_run.py +0 -246
  444. package/skills/fluidsim/scripts/solver_config_validator.py +0 -70
  445. package/skills/generate-image/references/models.md +0 -173
  446. package/skills/generate-image/scripts/generate_image.py +0 -752
  447. package/skills/geniml/references/bedspace.md +0 -267
  448. package/skills/geniml/references/consensus_peaks.md +0 -334
  449. package/skills/geniml/references/region2vec.md +0 -289
  450. package/skills/geniml/references/scembed.md +0 -307
  451. package/skills/geniml/references/utilities.md +0 -385
  452. package/skills/geniml/scripts/__init__.py +0 -1
  453. package/skills/geniml/scripts/_common.py +0 -399
  454. package/skills/geniml/scripts/bed_validator.py +0 -363
  455. package/skills/geniml/scripts/consensus_plan.py +0 -416
  456. package/skills/geniml/scripts/corpus_auditor.py +0 -304
  457. package/skills/geniml/scripts/embedding_plan.py +0 -476
  458. package/skills/geniml/scripts/model_artifact_inspector.py +0 -358
  459. package/skills/geniml/scripts/tokenizer_compatibility.py +0 -321
  460. package/skills/genomic-coordinates/references/format-conventions.md +0 -205
  461. package/skills/genomic-coordinates/references/reference-builds.md +0 -154
  462. package/skills/genomic-coordinates/references/transcript-coordinates.md +0 -141
  463. package/skills/genomic-coordinates/references/variant-representation.md +0 -155
  464. package/skills/genomic-coordinates/scripts/_common.py +0 -335
  465. package/skills/genomic-coordinates/scripts/audit_intervals.py +0 -511
  466. package/skills/genomic-coordinates/scripts/check_contigs.py +0 -382
  467. package/skills/genomic-coordinates/scripts/convert_coords.py +0 -180
  468. package/skills/genomic-coordinates/scripts/normalize_variant.py +0 -290
  469. package/skills/genomic-intelligence/references/api-and-auth.md +0 -45
  470. package/skills/genomic-intelligence/references/mcp.md +0 -94
  471. package/skills/genomic-intelligence/references/sequence-acquisition.md +0 -52
  472. package/skills/genomic-intelligence/references/tasks.md +0 -75
  473. package/skills/geomaster/references/advanced-gis.md +0 -376
  474. package/skills/geomaster/references/big-data.md +0 -363
  475. package/skills/geomaster/references/code-examples.md +0 -531
  476. package/skills/geomaster/references/coordinate-systems.md +0 -364
  477. package/skills/geomaster/references/core-libraries.md +0 -273
  478. package/skills/geomaster/references/data-sources.md +0 -330
  479. package/skills/geomaster/references/gis-software.md +0 -369
  480. package/skills/geomaster/references/industry-applications.md +0 -420
  481. package/skills/geomaster/references/machine-learning.md +0 -462
  482. package/skills/geomaster/references/programming-languages.md +0 -456
  483. package/skills/geomaster/references/remote-sensing.md +0 -370
  484. package/skills/geomaster/references/scientific-domains.md +0 -416
  485. package/skills/geomaster/references/specialized-topics.md +0 -428
  486. package/skills/geomaster/references/troubleshooting.md +0 -439
  487. package/skills/geopandas/references/crs-management.md +0 -231
  488. package/skills/geopandas/references/data-io.md +0 -323
  489. package/skills/geopandas/references/data-structures.md +0 -207
  490. package/skills/geopandas/references/geometric-operations.md +0 -262
  491. package/skills/geopandas/references/spatial-analysis.md +0 -294
  492. package/skills/geopandas/references/visualization.md +0 -230
  493. package/skills/geopandas/scripts/_common.py +0 -605
  494. package/skills/geopandas/scripts/crs_reprojection_plan.py +0 -210
  495. package/skills/geopandas/scripts/export_plan.py +0 -305
  496. package/skills/geopandas/scripts/geometry_validity_report.py +0 -227
  497. package/skills/geopandas/scripts/sensitive_coordinates_checklist.py +0 -230
  498. package/skills/geopandas/scripts/spatial_join_audit.py +0 -368
  499. package/skills/geopandas/scripts/vector_inventory.py +0 -140
  500. package/skills/get-available-resources/references/resource_semantics.md +0 -206
  501. package/skills/get-available-resources/references/snapshot_schema.md +0 -172
  502. package/skills/get-available-resources/references/sources.md +0 -124
  503. package/skills/get-available-resources/scripts/_common.py +0 -190
  504. package/skills/get-available-resources/scripts/accelerator_diagnostics.py +0 -151
  505. package/skills/get-available-resources/scripts/detect_resources.py +0 -1767
  506. package/skills/get-available-resources/scripts/plan_workload.py +0 -311
  507. package/skills/get-available-resources/scripts/snapshot_tools.py +0 -486
  508. package/skills/gget/references/common_workflows.md +0 -120
  509. package/skills/gget/references/database_info.md +0 -336
  510. package/skills/gget/references/module_catalog.md +0 -733
  511. package/skills/gget/references/module_reference.md +0 -526
  512. package/skills/gget/references/workflows.md +0 -815
  513. package/skills/gget/scripts/batch_sequence_analysis.py +0 -192
  514. package/skills/gget/scripts/enrichment_pipeline.py +0 -235
  515. package/skills/gget/scripts/gene_analysis.py +0 -175
  516. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md +0 -53
  517. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +0 -85
  518. package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +0 -71
  519. package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md +0 -60
  520. package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md +0 -63
  521. package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md +0 -55
  522. package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md +0 -49
  523. package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md +0 -56
  524. package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md +0 -49
  525. package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md +0 -62
  526. package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md +0 -44
  527. package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md +0 -47
  528. package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +0 -73
  529. package/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md +0 -67
  530. package/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md +0 -58
  531. package/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md +0 -43
  532. package/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md +0 -58
  533. package/skills/glycoengineering/references/glycan_databases.md +0 -165
  534. package/skills/gtars/references/cli.md +0 -334
  535. package/skills/gtars/references/coverage.md +0 -224
  536. package/skills/gtars/references/overlap.md +0 -220
  537. package/skills/gtars/references/python-api.md +0 -280
  538. package/skills/gtars/references/refget.md +0 -318
  539. package/skills/gtars/references/tokenizers.md +0 -256
  540. package/skills/gtars/scripts/__init__.py +0 -1
  541. package/skills/gtars/scripts/_common.py +0 -461
  542. package/skills/gtars/scripts/artifact_inspector.py +0 -328
  543. package/skills/gtars/scripts/bed_validator.py +0 -183
  544. package/skills/gtars/scripts/coverage_preflight.py +0 -256
  545. package/skills/gtars/scripts/execution_plan.py +0 -365
  546. package/skills/gtars/scripts/refget_digest_plan.py +0 -311
  547. package/skills/gtars/scripts/tokenizer_manifest.py +0 -238
  548. package/skills/histolab/references/core_capabilities.md +0 -305
  549. package/skills/histolab/references/filters_preprocessing.md +0 -537
  550. package/skills/histolab/references/slide_management.md +0 -184
  551. package/skills/histolab/references/tile_extraction.md +0 -421
  552. package/skills/histolab/references/tissue_masks.md +0 -251
  553. package/skills/histolab/references/typical_workflows.md +0 -196
  554. package/skills/histolab/references/visualization.md +0 -548
  555. package/skills/hugging-science/references/flagship-resources.md +0 -81
  556. package/skills/hugging-science/references/topics-and-slugs.md +0 -82
  557. package/skills/hugging-science/references/using-datasets.md +0 -107
  558. package/skills/hugging-science/references/using-models.md +0 -122
  559. package/skills/hugging-science/references/using-spaces.md +0 -119
  560. package/skills/hugging-science/scripts/fetch_catalog.py +0 -358
  561. package/skills/hypogenic/assets/dataset_manifest.example.json +0 -30
  562. package/skills/hypogenic/assets/result.example.json +0 -18
  563. package/skills/hypogenic/assets/run_config.example.json +0 -46
  564. package/skills/hypogenic/assets/task_config.example.yaml +0 -38
  565. package/skills/hypogenic/references/configuration.md +0 -136
  566. package/skills/hypogenic/references/datasets.md +0 -146
  567. package/skills/hypogenic/references/evaluation.md +0 -155
  568. package/skills/hypogenic/references/security.md +0 -167
  569. package/skills/hypogenic/references/sources.md +0 -113
  570. package/skills/hypogenic/references/upstream.md +0 -188
  571. package/skills/hypogenic/scripts/__init__.py +0 -1
  572. package/skills/hypogenic/scripts/_common.py +0 -1312
  573. package/skills/hypogenic/scripts/audit_dataset.py +0 -410
  574. package/skills/hypogenic/scripts/evaluate_local.py +0 -250
  575. package/skills/hypogenic/scripts/inspect_outputs.py +0 -166
  576. package/skills/hypogenic/scripts/plan_run.py +0 -247
  577. package/skills/hypogenic/scripts/validate_config.py +0 -192
  578. package/skills/hypothesis-generation/assets/evidence_ledger_template.csv +0 -2
  579. package/skills/hypothesis-generation/assets/falsification_controls_template.json +0 -116
  580. package/skills/hypothesis-generation/assets/hypothesis_record_template.json +0 -331
  581. package/skills/hypothesis-generation/assets/operationalization_template.json +0 -56
  582. package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv +0 -3
  583. package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md +0 -137
  584. package/skills/hypothesis-generation/assets/search_boundary_template.json +0 -23
  585. package/skills/hypothesis-generation/assets/source_ledger.csv +0 -37
  586. package/skills/hypothesis-generation/references/causal_inference_and_claims.md +0 -190
  587. package/skills/hypothesis-generation/references/concepts_and_workflow.md +0 -173
  588. package/skills/hypothesis-generation/references/ethics_safety_and_ai.md +0 -216
  589. package/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -301
  590. package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -203
  591. package/skills/hypothesis-generation/references/literature_search_strategies.md +0 -208
  592. package/skills/hypothesis-generation/references/preregistration_and_open_science.md +0 -205
  593. package/skills/hypothesis-generation/references/security_validation.md +0 -74
  594. package/skills/hypothesis-generation/references/source_ledger.md +0 -116
  595. package/skills/hypothesis-generation/references/tool_reference.md +0 -246
  596. package/skills/hypothesis-generation/scripts/_common.py +0 -412
  597. package/skills/hypothesis-generation/scripts/audit_evidence_ledger.py +0 -337
  598. package/skills/hypothesis-generation/scripts/check_falsification_controls.py +0 -455
  599. package/skills/hypothesis-generation/scripts/check_operationalization.py +0 -237
  600. package/skills/hypothesis-generation/scripts/generate_preregistration_scaffold.py +0 -384
  601. package/skills/hypothesis-generation/scripts/lint_causal_claims.py +0 -189
  602. package/skills/hypothesis-generation/scripts/validate_hypothesis_schema.py +0 -1078
  603. package/skills/hypothesis-generation/scripts/validate_prediction_matrix.py +0 -286
  604. package/skills/imaging-data-commons/references/bigquery_guide.md +0 -858
  605. package/skills/imaging-data-commons/references/cli_guide.md +0 -287
  606. package/skills/imaging-data-commons/references/clinical_data_guide.md +0 -328
  607. package/skills/imaging-data-commons/references/cloud_storage_guide.md +0 -333
  608. package/skills/imaging-data-commons/references/dicomweb_guide.md +0 -399
  609. package/skills/imaging-data-commons/references/digital_pathology_guide.md +0 -403
  610. package/skills/imaging-data-commons/references/index_tables_guide.md +0 -203
  611. package/skills/imaging-data-commons/references/licensing_and_citation.md +0 -230
  612. package/skills/imaging-data-commons/references/mcp_guide.md +0 -181
  613. package/skills/imaging-data-commons/references/parquet_access_guide.md +0 -200
  614. package/skills/imaging-data-commons/references/rest_api_guide.md +0 -612
  615. package/skills/imaging-data-commons/references/sql_patterns.md +0 -462
  616. package/skills/imaging-data-commons/references/use_cases.md +0 -277
  617. package/skills/imaging-data-commons/scripts/check_version.py +0 -132
  618. package/skills/infographics/references/color_palettes.md +0 -496
  619. package/skills/infographics/references/design_principles.md +0 -636
  620. package/skills/infographics/references/infographic_type_catalog.md +0 -158
  621. package/skills/infographics/references/infographic_types.md +0 -907
  622. package/skills/infographics/references/iterative_refinement.md +0 -119
  623. package/skills/infographics/scripts/generate_infographic.py +0 -291
  624. package/skills/infographics/scripts/generate_infographic_ai.py +0 -1446
  625. package/skills/iso-standards-readiness/assets/templates/capa-record-template.json +0 -99
  626. package/skills/iso-standards-readiness/assets/templates/document-register-template.json +0 -75
  627. package/skills/iso-standards-readiness/assets/templates/evidence-manifest-template.json +0 -65
  628. package/skills/iso-standards-readiness/assets/templates/laboratory-scope-intake-template.json +0 -111
  629. package/skills/iso-standards-readiness/assets/templates/medical-laboratory-scope-intake-template.json +0 -111
  630. package/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md +0 -148
  631. package/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md +0 -132
  632. package/skills/iso-standards-readiness/assets/templates/qmsr-transition-template.json +0 -181
  633. package/skills/iso-standards-readiness/assets/templates/quality-manual-template.md +0 -182
  634. package/skills/iso-standards-readiness/assets/templates/scope-intake-template.json +0 -109
  635. package/skills/iso-standards-readiness/assets/templates/supplier-controls-template.json +0 -119
  636. package/skills/iso-standards-readiness/assets/templates/traceability-matrix-template.json +0 -154
  637. package/skills/iso-standards-readiness/references/assurance-lanes.md +0 -116
  638. package/skills/iso-standards-readiness/references/evidence-architecture.md +0 -282
  639. package/skills/iso-standards-readiness/references/gap-analysis-checklist.md +0 -346
  640. package/skills/iso-standards-readiness/references/iso-13485.md +0 -236
  641. package/skills/iso-standards-readiness/references/iso-14971.md +0 -172
  642. package/skills/iso-standards-readiness/references/iso-15189.md +0 -219
  643. package/skills/iso-standards-readiness/references/iso-17025.md +0 -208
  644. package/skills/iso-standards-readiness/references/quality-manual-guide.md +0 -282
  645. package/skills/iso-standards-readiness/references/source-ledger.md +0 -357
  646. package/skills/iso-standards-readiness/scripts/_catalog.py +0 -248
  647. package/skills/iso-standards-readiness/scripts/_common.py +0 -558
  648. package/skills/iso-standards-readiness/scripts/audit_document_records.py +0 -148
  649. package/skills/iso-standards-readiness/scripts/check_capa.py +0 -240
  650. package/skills/iso-standards-readiness/scripts/check_qmsr_transition.py +0 -164
  651. package/skills/iso-standards-readiness/scripts/check_supplier_controls.py +0 -166
  652. package/skills/iso-standards-readiness/scripts/check_traceability.py +0 -171
  653. package/skills/iso-standards-readiness/scripts/gap_analyzer.py +0 -167
  654. package/skills/iso-standards-readiness/scripts/validate_evidence_manifest.py +0 -246
  655. package/skills/iso-standards-readiness/scripts/validate_scope_intake.py +0 -209
  656. package/skills/lab-hardware-cad/assets/standards.json +0 -198
  657. package/skills/lab-hardware-cad/references/behavior-rigs.md +0 -136
  658. package/skills/lab-hardware-cad/references/build123d-patterns.md +0 -363
  659. package/skills/lab-hardware-cad/references/fabrication-limits.md +0 -156
  660. package/skills/lab-hardware-cad/references/labware-adapters.md +0 -190
  661. package/skills/lab-hardware-cad/references/microfluidics.md +0 -157
  662. package/skills/lab-hardware-cad/references/optomechanics.md +0 -148
  663. package/skills/lab-hardware-cad/references/validation.md +0 -132
  664. package/skills/lab-hardware-cad/scripts/_common.py +0 -650
  665. package/skills/lab-hardware-cad/scripts/check.py +0 -645
  666. package/skills/lab-hardware-cad/scripts/gen.py +0 -264
  667. package/skills/lab-hardware-cad/scripts/snapshot.py +0 -278
  668. package/skills/labarchive-integration/references/api_reference.md +0 -250
  669. package/skills/labarchive-integration/references/authentication_guide.md +0 -191
  670. package/skills/labarchive-integration/references/integrations.md +0 -162
  671. package/skills/labarchive-integration/references/sources.md +0 -213
  672. package/skills/labarchive-integration/scripts/entry_operations.py +0 -381
  673. package/skills/labarchive-integration/scripts/notebook_operations.py +0 -451
  674. package/skills/labarchive-integration/scripts/setup_config.py +0 -258
  675. package/skills/lamindb/references/annotation-validation.md +0 -510
  676. package/skills/lamindb/references/core-concepts.md +0 -383
  677. package/skills/lamindb/references/data-management.md +0 -432
  678. package/skills/lamindb/references/integrations.md +0 -663
  679. package/skills/lamindb/references/ontologies.md +0 -498
  680. package/skills/lamindb/references/setup-deployment.md +0 -755
  681. package/skills/latchbio-integration/references/data-management.md +0 -257
  682. package/skills/latchbio-integration/references/latch-mcp.md +0 -158
  683. package/skills/latchbio-integration/references/nextflow-snakemake.md +0 -258
  684. package/skills/latchbio-integration/references/operations-and-debugging.md +0 -320
  685. package/skills/latchbio-integration/references/registry.md +0 -275
  686. package/skills/latchbio-integration/references/resource-configuration.md +0 -274
  687. package/skills/latchbio-integration/references/ui-and-automation.md +0 -355
  688. package/skills/latchbio-integration/references/verified-workflows.md +0 -226
  689. package/skills/latchbio-integration/references/workflow-creation.md +0 -275
  690. package/skills/latchbio-integration/scripts/inspect_latch_sdk.py +0 -290
  691. package/skills/latex-posters/assets/baposter_template.tex +0 -257
  692. package/skills/latex-posters/assets/beamerposter_template.tex +0 -244
  693. package/skills/latex-posters/assets/poster_quality_checklist.md +0 -358
  694. package/skills/latex-posters/assets/tikzposter_template.tex +0 -251
  695. package/skills/latex-posters/references/ai_graphics_for_posters.md +0 -524
  696. package/skills/latex-posters/references/compilation_and_quality_control.md +0 -467
  697. package/skills/latex-posters/references/latex_poster_packages.md +0 -745
  698. package/skills/latex-posters/references/latex_poster_reference.md +0 -241
  699. package/skills/latex-posters/references/poster_content_guide.md +0 -748
  700. package/skills/latex-posters/references/poster_design_principles.md +0 -806
  701. package/skills/latex-posters/references/poster_layout_design.md +0 -900
  702. package/skills/latex-posters/references/poster_patterns_and_presentation.md +0 -81
  703. package/skills/latex-posters/scripts/generate_schematic.py +0 -198
  704. package/skills/latex-posters/scripts/generate_schematic_ai.py +0 -950
  705. package/skills/latex-posters/scripts/review_poster.sh +0 -214
  706. package/skills/liteparse/references/api_reference.md +0 -169
  707. package/skills/liteparse/references/choosing_a_parser.md +0 -70
  708. package/skills/liteparse/references/cli_reference.md +0 -118
  709. package/skills/liteparse/references/ocr_and_formats.md +0 -143
  710. package/skills/liteparse/references/output_formats.md +0 -146
  711. package/skills/liteparse/scripts/batch_parse_dir.py +0 -163
  712. package/skills/literature-review/assets/review_template.md +0 -412
  713. package/skills/literature-review/references/citation_styles.md +0 -166
  714. package/skills/literature-review/references/core_workflow.md +0 -260
  715. package/skills/literature-review/references/database_strategies.md +0 -455
  716. package/skills/literature-review/references/example_workflow.md +0 -68
  717. package/skills/literature-review/references/search_and_citation.md +0 -157
  718. package/skills/literature-review/scripts/generate_pdf.py +0 -176
  719. package/skills/literature-review/scripts/generate_schematic.py +0 -198
  720. package/skills/literature-review/scripts/generate_schematic_ai.py +0 -950
  721. package/skills/literature-review/scripts/search_databases.py +0 -303
  722. package/skills/literature-review/scripts/verify_citations.py +0 -222
  723. package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +0 -221
  724. package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +0 -108
  725. package/skills/markdown-mermaid-writing/references/diagrams/block.md +0 -177
  726. package/skills/markdown-mermaid-writing/references/diagrams/c4.md +0 -136
  727. package/skills/markdown-mermaid-writing/references/diagrams/class.md +0 -246
  728. package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +0 -384
  729. package/skills/markdown-mermaid-writing/references/diagrams/er.md +0 -222
  730. package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +0 -177
  731. package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +0 -138
  732. package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +0 -74
  733. package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +0 -107
  734. package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +0 -74
  735. package/skills/markdown-mermaid-writing/references/diagrams/packet.md +0 -55
  736. package/skills/markdown-mermaid-writing/references/diagrams/pie.md +0 -52
  737. package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +0 -66
  738. package/skills/markdown-mermaid-writing/references/diagrams/radar.md +0 -59
  739. package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +0 -88
  740. package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +0 -71
  741. package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +0 -174
  742. package/skills/markdown-mermaid-writing/references/diagrams/state.md +0 -150
  743. package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +0 -96
  744. package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +0 -66
  745. package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +0 -108
  746. package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +0 -53
  747. package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +0 -71
  748. package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +0 -733
  749. package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +0 -458
  750. package/skills/markdown-mermaid-writing/templates/decision_record.md +0 -211
  751. package/skills/markdown-mermaid-writing/templates/how_to_guide.md +0 -275
  752. package/skills/markdown-mermaid-writing/templates/issue.md +0 -303
  753. package/skills/markdown-mermaid-writing/templates/kanban.md +0 -223
  754. package/skills/markdown-mermaid-writing/templates/presentation.md +0 -312
  755. package/skills/markdown-mermaid-writing/templates/project_documentation.md +0 -412
  756. package/skills/markdown-mermaid-writing/templates/pull_request.md +0 -319
  757. package/skills/markdown-mermaid-writing/templates/research_paper.md +0 -304
  758. package/skills/markdown-mermaid-writing/templates/status_report.md +0 -185
  759. package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +0 -149
  760. package/skills/market-research-reports/assets/claims_ledger_template.csv +0 -4
  761. package/skills/market-research-reports/assets/competitor_feature_matrix_template.csv +0 -5
  762. package/skills/market-research-reports/assets/consistency_check_template.csv +0 -3
  763. package/skills/market-research-reports/assets/forecast_sensitivity_template.json +0 -90
  764. package/skills/market-research-reports/assets/market_report_template.tex +0 -279
  765. package/skills/market-research-reports/assets/market_research.sty +0 -241
  766. package/skills/market-research-reports/assets/market_sizing_scenarios_template.json +0 -129
  767. package/skills/market-research-reports/assets/report_manifest_template.json +0 -27
  768. package/skills/market-research-reports/assets/source_ledger_template.csv +0 -4
  769. package/skills/market-research-reports/references/data_analysis_patterns.md +0 -290
  770. package/skills/market-research-reports/references/evidence_model.md +0 -148
  771. package/skills/market-research-reports/references/methods_and_ethics.md +0 -162
  772. package/skills/market-research-reports/references/official_data_sources.md +0 -196
  773. package/skills/market-research-reports/references/report_structure_guide.md +0 -283
  774. package/skills/market-research-reports/references/sources.md +0 -73
  775. package/skills/market-research-reports/references/visual_generation_guide.md +0 -158
  776. package/skills/market-research-reports/scripts/_common.py +0 -312
  777. package/skills/market-research-reports/scripts/audit_claim_citations.py +0 -326
  778. package/skills/market-research-reports/scripts/calculate_market_sizing.py +0 -389
  779. package/skills/market-research-reports/scripts/check_unit_consistency.py +0 -217
  780. package/skills/market-research-reports/scripts/forecast_sensitivity.py +0 -326
  781. package/skills/market-research-reports/scripts/generate_report_scaffold.py +0 -444
  782. package/skills/market-research-reports/scripts/validate_competitor_matrix.py +0 -223
  783. package/skills/market-research-reports/scripts/validate_evidence_ledger.py +0 -291
  784. package/skills/markitdown/references/api_reference.md +0 -418
  785. package/skills/markitdown/references/cloud_and_ocr.md +0 -320
  786. package/skills/markitdown/references/file_formats.md +0 -281
  787. package/skills/markitdown/references/mcp_and_plugins.md +0 -243
  788. package/skills/markitdown/references/migration.md +0 -356
  789. package/skills/markitdown/references/security.md +0 -246
  790. package/skills/markitdown/references/workflows.md +0 -309
  791. package/skills/markitdown/scripts/batch_convert.py +0 -354
  792. package/skills/markitdown/scripts/convert_literature.py +0 -405
  793. package/skills/markitdown/scripts/inspect_installation.py +0 -162
  794. package/skills/matchms/references/filtering.md +0 -299
  795. package/skills/matchms/references/importing_exporting.md +0 -323
  796. package/skills/matchms/references/migration.md +0 -387
  797. package/skills/matchms/references/similarity.md +0 -413
  798. package/skills/matchms/references/sources.md +0 -113
  799. package/skills/matchms/references/workflows.md +0 -451
  800. package/skills/matchms/scripts/library_search.py +0 -593
  801. package/skills/matlab/assets/project_manifest_template.json +0 -33
  802. package/skills/matlab/assets/python_compatibility_r2026a.json +0 -27
  803. package/skills/matlab/assets/reproducibility_manifest_template.json +0 -32
  804. package/skills/matlab/references/data-import-export.md +0 -221
  805. package/skills/matlab/references/executing-scripts.md +0 -213
  806. package/skills/matlab/references/graphics-visualization.md +0 -181
  807. package/skills/matlab/references/mathematics.md +0 -208
  808. package/skills/matlab/references/matrices-arrays.md +0 -228
  809. package/skills/matlab/references/octave-compatibility.md +0 -212
  810. package/skills/matlab/references/programming.md +0 -225
  811. package/skills/matlab/references/python-integration.md +0 -248
  812. package/skills/matlab/scripts/_common.py +0 -263
  813. package/skills/matlab/scripts/generate_function_scaffold.py +0 -165
  814. package/skills/matlab/scripts/inventory_mat_file.py +0 -351
  815. package/skills/matlab/scripts/plan_batch_command.py +0 -257
  816. package/skills/matlab/scripts/plan_python_compatibility.py +0 -176
  817. package/skills/matlab/scripts/reproducibility_report.py +0 -233
  818. package/skills/matlab/scripts/scan_m_code.py +0 -433
  819. package/skills/matlab/scripts/validate_project_manifest.py +0 -348
  820. package/skills/matplotlib/references/api_reference.md +0 -409
  821. package/skills/matplotlib/references/common_issues.md +0 -562
  822. package/skills/matplotlib/references/plot_types.md +0 -469
  823. package/skills/matplotlib/references/styling_guide.md +0 -600
  824. package/skills/matplotlib/scripts/plot_template.py +0 -406
  825. package/skills/matplotlib/scripts/style_configurator.py +0 -412
  826. package/skills/medchem/references/api_guide.md +0 -331
  827. package/skills/medchem/references/rules_catalog.md +0 -328
  828. package/skills/medchem/scripts/filter_molecules.py +0 -302
  829. package/skills/modal/references/api_reference.md +0 -225
  830. package/skills/modal/references/examples.md +0 -276
  831. package/skills/modal/references/functions.md +0 -260
  832. package/skills/modal/references/getting-started.md +0 -171
  833. package/skills/modal/references/gpu.md +0 -177
  834. package/skills/modal/references/images.md +0 -266
  835. package/skills/modal/references/resources.md +0 -117
  836. package/skills/modal/references/scaling.md +0 -173
  837. package/skills/modal/references/scheduled-jobs.md +0 -147
  838. package/skills/modal/references/secrets.md +0 -119
  839. package/skills/modal/references/volumes.md +0 -247
  840. package/skills/modal/references/web-endpoints.md +0 -259
  841. package/skills/molecular-dynamics/references/mdanalysis_analysis.md +0 -208
  842. package/skills/molfeat/references/api_reference.md +0 -429
  843. package/skills/molfeat/references/available_featurizers.md +0 -335
  844. package/skills/molfeat/references/choosing_a_featurizer.md +0 -192
  845. package/skills/molfeat/references/examples.md +0 -720
  846. package/skills/ncats-arax/references/output-schema.md +0 -186
  847. package/skills/ncats-arax/references/query-contract.md +0 -140
  848. package/skills/ncats-arax/scripts/arax_client.py +0 -2087
  849. package/skills/networkx/references/algorithms.md +0 -384
  850. package/skills/networkx/references/generators.md +0 -385
  851. package/skills/networkx/references/graph-basics.md +0 -284
  852. package/skills/networkx/references/io.md +0 -457
  853. package/skills/networkx/references/visualization.md +0 -531
  854. package/skills/neurokit2/references/bio_module.md +0 -244
  855. package/skills/neurokit2/references/complexity.md +0 -212
  856. package/skills/neurokit2/references/ecg_cardiac.md +0 -193
  857. package/skills/neurokit2/references/eda.md +0 -185
  858. package/skills/neurokit2/references/eeg.md +0 -204
  859. package/skills/neurokit2/references/emg.md +0 -157
  860. package/skills/neurokit2/references/eog.md +0 -154
  861. package/skills/neurokit2/references/epochs_events.md +0 -199
  862. package/skills/neurokit2/references/hrv.md +0 -205
  863. package/skills/neurokit2/references/ppg.md +0 -191
  864. package/skills/neurokit2/references/rsp.md +0 -212
  865. package/skills/neurokit2/references/signal_processing.md +0 -160
  866. package/skills/neurokit2/scripts/_common.py +0 -567
  867. package/skills/neurokit2/scripts/ecg_hrv_pipeline.py +0 -303
  868. package/skills/neurokit2/scripts/eda_pipeline.py +0 -288
  869. package/skills/neurokit2/scripts/generate_synthetic.py +0 -221
  870. package/skills/neurokit2/scripts/inspect_signal.py +0 -362
  871. package/skills/neurokit2/scripts/plan_epochs.py +0 -281
  872. package/skills/neurokit2/scripts/validate_multimodal.py +0 -350
  873. package/skills/neuropixels-analysis/assets/analysis_template.py +0 -271
  874. package/skills/neuropixels-analysis/references/AI_CURATION.md +0 -164
  875. package/skills/neuropixels-analysis/references/ANALYSIS.md +0 -392
  876. package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +0 -435
  877. package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +0 -323
  878. package/skills/neuropixels-analysis/references/PREPROCESSING.md +0 -273
  879. package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +0 -359
  880. package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +0 -339
  881. package/skills/neuropixels-analysis/references/api_reference.md +0 -229
  882. package/skills/neuropixels-analysis/references/plotting_guide.md +0 -454
  883. package/skills/neuropixels-analysis/references/standard_workflow.md +0 -305
  884. package/skills/neuropixels-analysis/scripts/compute_metrics.py +0 -182
  885. package/skills/neuropixels-analysis/scripts/explore_recording.py +0 -168
  886. package/skills/neuropixels-analysis/scripts/export_to_phy.py +0 -79
  887. package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +0 -442
  888. package/skills/neuropixels-analysis/scripts/preprocess_recording.py +0 -122
  889. package/skills/neuropixels-analysis/scripts/run_sorting.py +0 -98
  890. package/skills/nextflow/references/configuration.md +0 -276
  891. package/skills/nextflow/references/containers.md +0 -92
  892. package/skills/nextflow/references/developing.md +0 -301
  893. package/skills/nextflow/references/language.md +0 -327
  894. package/skills/nextflow/references/nf-core-tools.md +0 -130
  895. package/skills/nextflow/references/running-pipelines.md +0 -131
  896. package/skills/nextflow/references/testing.md +0 -189
  897. package/skills/omero-integration/references/advanced.md +0 -273
  898. package/skills/omero-integration/references/connection.md +0 -293
  899. package/skills/omero-integration/references/data_access.md +0 -359
  900. package/skills/omero-integration/references/image_processing.md +0 -286
  901. package/skills/omero-integration/references/metadata.md +0 -313
  902. package/skills/omero-integration/references/rois.md +0 -291
  903. package/skills/omero-integration/references/scripts.md +0 -304
  904. package/skills/omero-integration/references/sources.md +0 -194
  905. package/skills/omero-integration/references/tables.md +0 -269
  906. package/skills/omero-integration/scripts/export_image_metadata.py +0 -560
  907. package/skills/omero-integration/scripts/inventory.py +0 -302
  908. package/skills/omero-integration/scripts/omero_common.py +0 -490
  909. package/skills/omero-integration/scripts/plan_transfer.py +0 -393
  910. package/skills/omero-integration/scripts/validate_config.py +0 -140
  911. package/skills/onekgpd/assets/kgpe.json +0 -48032
  912. package/skills/onekgpd/references/annotation_vocabularies.md +0 -187
  913. package/skills/onekgpd/references/onekgpd_commands.md +0 -296
  914. package/skills/onekgpd/scripts/onekgpd_api.py +0 -794
  915. package/skills/onekgpd/scripts/onekgpd_meta.py +0 -485
  916. package/skills/ontology-term-resolution/references/curation-rules.md +0 -110
  917. package/skills/ontology-term-resolution/references/ols4-api.md +0 -135
  918. package/skills/ontology-term-resolution/references/ontology-registry.md +0 -110
  919. package/skills/ontology-term-resolution/scripts/ols_client.py +0 -341
  920. package/skills/ontology-term-resolution/scripts/resolve_terms.py +0 -255
  921. package/skills/ontology-term-resolution/scripts/validate_terms.py +0 -297
  922. package/skills/open-notebook/references/api_reference.md +0 -715
  923. package/skills/open-notebook/references/architecture.md +0 -163
  924. package/skills/open-notebook/references/configuration.md +0 -226
  925. package/skills/open-notebook/references/examples.md +0 -290
  926. package/skills/open-notebook/scripts/chat_interaction.py +0 -190
  927. package/skills/open-notebook/scripts/notebook_management.py +0 -142
  928. package/skills/open-notebook/scripts/source_ingestion.py +0 -160
  929. package/skills/openpiv/references/advanced_algorithms.md +0 -233
  930. package/skills/openpiv/scripts/__init__.py +0 -1
  931. package/skills/openpiv/scripts/analyze.py +0 -143
  932. package/skills/openpiv/scripts/run_example.py +0 -78
  933. package/skills/openpiv/scripts/runner.py +0 -214
  934. package/skills/opentrons-integration/references/api_reference.md +0 -382
  935. package/skills/opentrons-integration/references/liquid_handling.md +0 -387
  936. package/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md +0 -328
  937. package/skills/opentrons-integration/references/modules_and_deck.md +0 -409
  938. package/skills/opentrons-integration/references/protocol_authoring.md +0 -352
  939. package/skills/opentrons-integration/references/sources.md +0 -151
  940. package/skills/opentrons-integration/references/validation_and_operations.md +0 -314
  941. package/skills/opentrons-integration/requirements-flex.txt +0 -1
  942. package/skills/opentrons-integration/requirements-ot2.txt +0 -1
  943. package/skills/opentrons-integration/scripts/absorbance_reader_template.py +0 -82
  944. package/skills/opentrons-integration/scripts/basic_protocol_template.py +0 -68
  945. package/skills/opentrons-integration/scripts/ot2_basic_protocol_template.py +0 -63
  946. package/skills/opentrons-integration/scripts/pcr_setup_template.py +0 -146
  947. package/skills/opentrons-integration/scripts/runtime_parameters_template.py +0 -110
  948. package/skills/opentrons-integration/scripts/serial_dilution_template.py +0 -113
  949. package/skills/optimize-for-gpu/references/code_transformation_patterns.md +0 -301
  950. package/skills/optimize-for-gpu/references/cucim.md +0 -679
  951. package/skills/optimize-for-gpu/references/cudf.md +0 -762
  952. package/skills/optimize-for-gpu/references/cugraph.md +0 -733
  953. package/skills/optimize-for-gpu/references/cuml.md +0 -710
  954. package/skills/optimize-for-gpu/references/cupy.md +0 -668
  955. package/skills/optimize-for-gpu/references/cuspatial.md +0 -420
  956. package/skills/optimize-for-gpu/references/cuvs.md +0 -671
  957. package/skills/optimize-for-gpu/references/cuxfilter.md +0 -600
  958. package/skills/optimize-for-gpu/references/decision_framework.md +0 -234
  959. package/skills/optimize-for-gpu/references/installation.md +0 -121
  960. package/skills/optimize-for-gpu/references/kvikio.md +0 -612
  961. package/skills/optimize-for-gpu/references/numba.md +0 -808
  962. package/skills/optimize-for-gpu/references/raft.md +0 -312
  963. package/skills/optimize-for-gpu/references/warp.md +0 -623
  964. package/skills/pacsomatic/config.yaml +0 -42
  965. package/skills/pacsomatic/references/agent-playbook.md +0 -73
  966. package/skills/pacsomatic/references/config-and-output.md +0 -100
  967. package/skills/pacsomatic/references/pacsomatic_guide.md +0 -254
  968. package/skills/pacsomatic/scripts/run_pacsomatic.py +0 -794
  969. package/skills/paper-lookup/references/arxiv.md +0 -275
  970. package/skills/paper-lookup/references/biorxiv.md +0 -163
  971. package/skills/paper-lookup/references/core.md +0 -150
  972. package/skills/paper-lookup/references/crossref.md +0 -181
  973. package/skills/paper-lookup/references/europepmc.md +0 -226
  974. package/skills/paper-lookup/references/medrxiv.md +0 -126
  975. package/skills/paper-lookup/references/openalex.md +0 -174
  976. package/skills/paper-lookup/references/pmc.md +0 -228
  977. package/skills/paper-lookup/references/pubmed.md +0 -124
  978. package/skills/paper-lookup/references/semantic-scholar.md +0 -203
  979. package/skills/paper-lookup/references/unpaywall.md +0 -127
  980. package/skills/paper-lookup/scripts/_common.py +0 -227
  981. package/skills/paper-lookup/scripts/arxiv_atom.py +0 -200
  982. package/skills/paper-lookup/scripts/jats_to_text.py +0 -324
  983. package/skills/paper-lookup/scripts/openalex_abstract.py +0 -163
  984. package/skills/paper-lookup/scripts/paginate.py +0 -490
  985. package/skills/paperclip/references/cli-reference.md +0 -389
  986. package/skills/paperclip/references/installation.md +0 -341
  987. package/skills/paperclip/references/map-reduce.md +0 -252
  988. package/skills/paperclip/references/python-sdk.md +0 -323
  989. package/skills/paperclip/references/repos-and-workspace.md +0 -271
  990. package/skills/paperclip/references/search-and-retrieval.md +0 -281
  991. package/skills/parallel-web/references/data-enrichment.md +0 -104
  992. package/skills/parallel-web/references/deep-research.md +0 -91
  993. package/skills/parallel-web/references/findall.md +0 -81
  994. package/skills/parallel-web/references/monitor.md +0 -83
  995. package/skills/parallel-web/references/web-extract.md +0 -59
  996. package/skills/parallel-web/references/web-search.md +0 -100
  997. package/skills/pathml/references/data_management.md +0 -357
  998. package/skills/pathml/references/graphs.md +0 -335
  999. package/skills/pathml/references/image_loading.md +0 -301
  1000. package/skills/pathml/references/machine_learning.md +0 -408
  1001. package/skills/pathml/references/multiparametric.md +0 -352
  1002. package/skills/pathml/references/preprocessing.md +0 -371
  1003. package/skills/pathml/scripts/_common.py +0 -385
  1004. package/skills/pathml/scripts/image_qc.py +0 -325
  1005. package/skills/pathml/scripts/plan_inference.py +0 -282
  1006. package/skills/pathml/scripts/plan_pipeline.py +0 -239
  1007. package/skills/pathml/scripts/slide_manifest.py +0 -405
  1008. package/skills/pathml/scripts/validate_spatial_schema.py +0 -420
  1009. package/skills/pathogen-variant-surveillance/references/lapis-api.md +0 -209
  1010. package/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md +0 -126
  1011. package/skills/pathogen-variant-surveillance/references/surveillance-caveats.md +0 -149
  1012. package/skills/pathogen-variant-surveillance/scripts/lapis_client.py +0 -776
  1013. package/skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py +0 -310
  1014. package/skills/pathogen-variant-surveillance/scripts/mutation_profile.py +0 -215
  1015. package/skills/pathogen-variant-surveillance/scripts/reporting_lag.py +0 -217
  1016. package/skills/pathogen-variant-surveillance/scripts/resolve_lineage.py +0 -198
  1017. package/skills/pathway-enrichment/references/databases-and-gene-sets.md +0 -140
  1018. package/skills/pathway-enrichment/references/gseapy.md +0 -189
  1019. package/skills/pathway-enrichment/references/interpretation.md +0 -118
  1020. package/skills/pathway-enrichment/scripts/run_enrichment.py +0 -231
  1021. package/skills/pdf/LICENSE.txt +0 -30
  1022. package/skills/pdf/forms.md +0 -294
  1023. package/skills/pdf/reference.md +0 -612
  1024. package/skills/pdf/scripts/check_bounding_boxes.py +0 -65
  1025. package/skills/pdf/scripts/check_fillable_fields.py +0 -11
  1026. package/skills/pdf/scripts/convert_pdf_to_images.py +0 -33
  1027. package/skills/pdf/scripts/create_validation_image.py +0 -37
  1028. package/skills/pdf/scripts/extract_form_field_info.py +0 -122
  1029. package/skills/pdf/scripts/extract_form_structure.py +0 -115
  1030. package/skills/pdf/scripts/fill_fillable_fields.py +0 -98
  1031. package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +0 -107
  1032. package/skills/peer-review/assets/citation_references_template.csv +0 -2
  1033. package/skills/peer-review/assets/claim_evidence_matrix_template.csv +0 -4
  1034. package/skills/peer-review/assets/reporting_checklist_template.csv +0 -31
  1035. package/skills/peer-review/assets/reporting_guidelines.json +0 -466
  1036. package/skills/peer-review/assets/review_intake_template.json +0 -52
  1037. package/skills/peer-review/assets/review_scaffold_template.md +0 -68
  1038. package/skills/peer-review/assets/source_ledger.csv +0 -32
  1039. package/skills/peer-review/assets/statistical_reproducibility_template.json +0 -210
  1040. package/skills/peer-review/assets/study_profile_template.json +0 -12
  1041. package/skills/peer-review/references/common_issues.md +0 -257
  1042. package/skills/peer-review/references/ethical_review_practice.md +0 -233
  1043. package/skills/peer-review/references/reporting_standards.md +0 -249
  1044. package/skills/peer-review/references/security_validation.md +0 -75
  1045. package/skills/peer-review/references/statistical_reproducibility.md +0 -329
  1046. package/skills/peer-review/references/tool_reference.md +0 -253
  1047. package/skills/peer-review/scripts/_common.py +0 -398
  1048. package/skills/peer-review/scripts/audit_citations.py +0 -207
  1049. package/skills/peer-review/scripts/audit_statistics_reproducibility.py +0 -305
  1050. package/skills/peer-review/scripts/generate_review_scaffold.py +0 -81
  1051. package/skills/peer-review/scripts/lint_review.py +0 -254
  1052. package/skills/peer-review/scripts/select_reporting_guidelines.py +0 -383
  1053. package/skills/peer-review/scripts/validate_claim_evidence.py +0 -221
  1054. package/skills/peer-review/scripts/validate_review_intake.py +0 -452
  1055. package/skills/pennylane/references/advanced_features.md +0 -667
  1056. package/skills/pennylane/references/devices_backends.md +0 -562
  1057. package/skills/pennylane/references/getting_started.md +0 -232
  1058. package/skills/pennylane/references/optimization.md +0 -670
  1059. package/skills/pennylane/references/quantum_chemistry.md +0 -576
  1060. package/skills/pennylane/references/quantum_circuits.md +0 -443
  1061. package/skills/pennylane/references/quantum_ml.md +0 -555
  1062. package/skills/phylogenetics/references/iqtree_inference.md +0 -181
  1063. package/skills/phylogenetics/scripts/phylogenetic_analysis.py +0 -272
  1064. package/skills/pi-agent/references/compaction.md +0 -76
  1065. package/skills/pi-agent/references/containerization.md +0 -80
  1066. package/skills/pi-agent/references/custom-provider.md +0 -131
  1067. package/skills/pi-agent/references/development.md +0 -61
  1068. package/skills/pi-agent/references/environment-variables.md +0 -57
  1069. package/skills/pi-agent/references/extensions.md +0 -185
  1070. package/skills/pi-agent/references/json.md +0 -69
  1071. package/skills/pi-agent/references/keybindings.md +0 -58
  1072. package/skills/pi-agent/references/llama-cpp.md +0 -69
  1073. package/skills/pi-agent/references/models.md +0 -114
  1074. package/skills/pi-agent/references/overview.md +0 -37
  1075. package/skills/pi-agent/references/packages.md +0 -103
  1076. package/skills/pi-agent/references/pi-interview.md +0 -123
  1077. package/skills/pi-agent/references/pi-mcp-adapter.md +0 -191
  1078. package/skills/pi-agent/references/pi-subagents.md +0 -371
  1079. package/skills/pi-agent/references/pi-web-access.md +0 -243
  1080. package/skills/pi-agent/references/prompt-templates.md +0 -48
  1081. package/skills/pi-agent/references/providers.md +0 -122
  1082. package/skills/pi-agent/references/quickstart.md +0 -73
  1083. package/skills/pi-agent/references/rpc.md +0 -95
  1084. package/skills/pi-agent/references/sdk.md +0 -151
  1085. package/skills/pi-agent/references/security.md +0 -52
  1086. package/skills/pi-agent/references/session-format.md +0 -90
  1087. package/skills/pi-agent/references/sessions.md +0 -56
  1088. package/skills/pi-agent/references/settings.md +0 -102
  1089. package/skills/pi-agent/references/shell-aliases.md +0 -15
  1090. package/skills/pi-agent/references/skills.md +0 -83
  1091. package/skills/pi-agent/references/terminal-setup.md +0 -87
  1092. package/skills/pi-agent/references/termux.md +0 -31
  1093. package/skills/pi-agent/references/themes.md +0 -69
  1094. package/skills/pi-agent/references/tmux.md +0 -44
  1095. package/skills/pi-agent/references/tui.md +0 -97
  1096. package/skills/pi-agent/references/usage.md +0 -129
  1097. package/skills/pi-agent/references/windows.md +0 -23
  1098. package/skills/pkpd-modeling/assets/nca-reporting-checklist.md +0 -72
  1099. package/skills/pkpd-modeling/assets/popk-analysis-plan.md +0 -136
  1100. package/skills/pkpd-modeling/references/antimicrobial-and-tdm.md +0 -110
  1101. package/skills/pkpd-modeling/references/bioequivalence.md +0 -132
  1102. package/skills/pkpd-modeling/references/dataset-standards.md +0 -103
  1103. package/skills/pkpd-modeling/references/ddi-and-qt.md +0 -132
  1104. package/skills/pkpd-modeling/references/nca-conventions.md +0 -128
  1105. package/skills/pkpd-modeling/references/pbpk.md +0 -103
  1106. package/skills/pkpd-modeling/references/pd-and-exposure-response.md +0 -149
  1107. package/skills/pkpd-modeling/references/population-pk.md +0 -133
  1108. package/skills/pkpd-modeling/references/regulatory-guidance.md +0 -82
  1109. package/skills/pkpd-modeling/references/software-ecosystem.md +0 -123
  1110. package/skills/pkpd-modeling/references/source-ledger.md +0 -89
  1111. package/skills/pkpd-modeling/references/special-populations.md +0 -126
  1112. package/skills/pkpd-modeling/references/structural-models.md +0 -140
  1113. package/skills/pkpd-modeling/references/tmdd-and-biologics.md +0 -115
  1114. package/skills/pkpd-modeling/scripts/_common.py +0 -327
  1115. package/skills/pkpd-modeling/scripts/_models.py +0 -673
  1116. package/skills/pkpd-modeling/scripts/allometry_and_fih.py +0 -346
  1117. package/skills/pkpd-modeling/scripts/bioequivalence.py +0 -480
  1118. package/skills/pkpd-modeling/scripts/check_popk_dataset.py +0 -400
  1119. package/skills/pkpd-modeling/scripts/ddi_static.py +0 -346
  1120. package/skills/pkpd-modeling/scripts/exposure_response.py +0 -328
  1121. package/skills/pkpd-modeling/scripts/fit_compartmental.py +0 -558
  1122. package/skills/pkpd-modeling/scripts/nca.py +0 -587
  1123. package/skills/pkpd-modeling/scripts/simulate_regimen.py +0 -323
  1124. package/skills/pkpd-modeling/scripts/tdm_bayes.py +0 -312
  1125. package/skills/polars/references/best_practices.md +0 -651
  1126. package/skills/polars/references/core_concepts.md +0 -380
  1127. package/skills/polars/references/io_guide.md +0 -564
  1128. package/skills/polars/references/operations.md +0 -602
  1129. package/skills/polars/references/pandas_migration.md +0 -417
  1130. package/skills/polars/references/transformations.md +0 -549
  1131. package/skills/polars-bio/references/bioframe_migration.md +0 -250
  1132. package/skills/polars-bio/references/configuration.md +0 -187
  1133. package/skills/polars-bio/references/file_io.md +0 -469
  1134. package/skills/polars-bio/references/interval_operations.md +0 -370
  1135. package/skills/polars-bio/references/pileup_operations.md +0 -176
  1136. package/skills/polars-bio/references/sql_processing.md +0 -224
  1137. package/skills/pptx/LICENSE.txt +0 -30
  1138. package/skills/pptx/scripts/__init__.py +0 -0
  1139. package/skills/pptx/scripts/add_slide.py +0 -367
  1140. package/skills/pptx/scripts/clean.py +0 -309
  1141. package/skills/pptx/scripts/office/helpers/__init__.py +0 -111
  1142. package/skills/pptx/scripts/office/helpers/pptx_chart.py +0 -170
  1143. package/skills/pptx/scripts/office/helpers/pptx_slide.py +0 -60
  1144. package/skills/pptx/scripts/office/helpers/pptx_theme.py +0 -114
  1145. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
  1146. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
  1147. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
  1148. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
  1149. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
  1150. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
  1151. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
  1152. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
  1153. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
  1154. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
  1155. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
  1156. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
  1157. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
  1158. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
  1159. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
  1160. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
  1161. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
  1162. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
  1163. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
  1164. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
  1165. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
  1166. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
  1167. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
  1168. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
  1169. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
  1170. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
  1171. package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
  1172. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
  1173. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
  1174. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
  1175. package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
  1176. package/skills/pptx/scripts/office/schemas/mce/mc.xsd +0 -75
  1177. package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
  1178. package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
  1179. package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
  1180. package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
  1181. package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
  1182. package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
  1183. package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
  1184. package/skills/pptx/scripts/office/soffice.py +0 -232
  1185. package/skills/pptx/scripts/office/validate.py +0 -173
  1186. package/skills/pptx/scripts/office/validators/__init__.py +0 -15
  1187. package/skills/pptx/scripts/office/validators/base.py +0 -875
  1188. package/skills/pptx/scripts/office/validators/docx.py +0 -466
  1189. package/skills/pptx/scripts/office/validators/pptx.py +0 -441
  1190. package/skills/pptx/scripts/office/validators/redlining.py +0 -299
  1191. package/skills/pptx/scripts/thumbnail.py +0 -311
  1192. package/skills/pptx-posters/assets/generation_dependencies.json +0 -5
  1193. package/skills/pptx-posters/assets/poster_manifest_template.json +0 -154
  1194. package/skills/pptx-posters/assets/poster_quality_checklist.md +0 -192
  1195. package/skills/pptx-posters/references/manifest_spec.md +0 -297
  1196. package/skills/pptx-posters/references/poster_content_guide.md +0 -176
  1197. package/skills/pptx-posters/references/poster_design_principles.md +0 -226
  1198. package/skills/pptx-posters/references/poster_layout_design.md +0 -189
  1199. package/skills/pptx-posters/references/pptx_security.md +0 -202
  1200. package/skills/pptx-posters/references/security_validation.md +0 -90
  1201. package/skills/pptx-posters/references/source_ledger.md +0 -256
  1202. package/skills/pptx-posters/scripts/_common.py +0 -396
  1203. package/skills/pptx-posters/scripts/_manifest.py +0 -1318
  1204. package/skills/pptx-posters/scripts/_pptx.py +0 -1484
  1205. package/skills/pptx-posters/scripts/check_layout.py +0 -179
  1206. package/skills/pptx-posters/scripts/check_palette.py +0 -142
  1207. package/skills/pptx-posters/scripts/generate_poster.py +0 -427
  1208. package/skills/pptx-posters/scripts/inspect_pptx.py +0 -40
  1209. package/skills/pptx-posters/scripts/inventory_images.py +0 -252
  1210. package/skills/pptx-posters/scripts/plan_export.py +0 -201
  1211. package/skills/pptx-posters/scripts/validate_manifest.py +0 -55
  1212. package/skills/primekg/scripts/query_primekg.py +0 -128
  1213. package/skills/protocolsio-integration/assets/protocol-snapshot.schema.json +0 -179
  1214. package/skills/protocolsio-integration/references/additional_features.md +0 -202
  1215. package/skills/protocolsio-integration/references/authentication.md +0 -135
  1216. package/skills/protocolsio-integration/references/discussions.md +0 -192
  1217. package/skills/protocolsio-integration/references/file_manager.md +0 -256
  1218. package/skills/protocolsio-integration/references/protocols_api.md +0 -256
  1219. package/skills/protocolsio-integration/references/workspaces.md +0 -192
  1220. package/skills/protocolsio-integration/scripts/__init__.py +0 -1
  1221. package/skills/protocolsio-integration/scripts/_common.py +0 -613
  1222. package/skills/protocolsio-integration/scripts/pagination_helper.py +0 -248
  1223. package/skills/protocolsio-integration/scripts/plan_write_request.py +0 -657
  1224. package/skills/protocolsio-integration/scripts/protocols_read.py +0 -493
  1225. package/skills/protocolsio-integration/scripts/validate_auth_config.py +0 -128
  1226. package/skills/protocolsio-integration/scripts/validate_protocol_json.py +0 -358
  1227. package/skills/pufferlib/references/environments.md +0 -260
  1228. package/skills/pufferlib/references/integration.md +0 -192
  1229. package/skills/pufferlib/references/policies.md +0 -181
  1230. package/skills/pufferlib/references/training.md +0 -287
  1231. package/skills/pufferlib/references/vectorization.md +0 -210
  1232. package/skills/pufferlib/scripts/__init__.py +0 -1
  1233. package/skills/pufferlib/scripts/_common.py +0 -199
  1234. package/skills/pufferlib/scripts/benchmark_vectorization.py +0 -244
  1235. package/skills/pufferlib/scripts/env_contract_validator.py +0 -198
  1236. package/skills/pufferlib/scripts/env_template.py +0 -210
  1237. package/skills/pufferlib/scripts/inspect_checkpoint.py +0 -225
  1238. package/skills/pufferlib/scripts/repro_plan.py +0 -177
  1239. package/skills/pufferlib/scripts/train_template.py +0 -282
  1240. package/skills/pufferlib/scripts/validate_plan.py +0 -570
  1241. package/skills/pydeseq2/references/analysis_patterns.md +0 -70
  1242. package/skills/pydeseq2/references/api_reference.md +0 -256
  1243. package/skills/pydeseq2/references/core_workflow_steps.md +0 -162
  1244. package/skills/pydeseq2/references/workflow_guide.md +0 -603
  1245. package/skills/pydeseq2/scripts/run_deseq2_analysis.py +0 -388
  1246. package/skills/pydicom/references/common_tags.md +0 -277
  1247. package/skills/pydicom/references/transfer_syntaxes.md +0 -348
  1248. package/skills/pydicom/scripts/__init__.py +0 -1
  1249. package/skills/pydicom/scripts/_common.py +0 -916
  1250. package/skills/pydicom/scripts/anonymize_dicom.py +0 -713
  1251. package/skills/pydicom/scripts/deidentification_audit.py +0 -380
  1252. package/skills/pydicom/scripts/dicom_inventory.py +0 -402
  1253. package/skills/pydicom/scripts/dicom_to_image.py +0 -459
  1254. package/skills/pydicom/scripts/extract_metadata.py +0 -330
  1255. package/skills/pydicom/scripts/pixel_frame_planner.py +0 -303
  1256. package/skills/pydicom/scripts/transfer_syntax_inspector.py +0 -245
  1257. package/skills/pydicom/scripts/uid_mapping_validator.py +0 -240
  1258. package/skills/pyhealth/assets/starter_pipeline.py +0 -58
  1259. package/skills/pyhealth/references/datasets.md +0 -126
  1260. package/skills/pyhealth/references/examples.md +0 -237
  1261. package/skills/pyhealth/references/installation.md +0 -112
  1262. package/skills/pyhealth/references/medcode.md +0 -94
  1263. package/skills/pyhealth/references/models.md +0 -114
  1264. package/skills/pyhealth/references/tasks.md +0 -143
  1265. package/skills/pylabrobot/assets/protocol-manifest.schema.json +0 -367
  1266. package/skills/pylabrobot/references/analytical-equipment.md +0 -200
  1267. package/skills/pylabrobot/references/hardware-backends.md +0 -215
  1268. package/skills/pylabrobot/references/liquid-handling.md +0 -223
  1269. package/skills/pylabrobot/references/material-handling.md +0 -229
  1270. package/skills/pylabrobot/references/resources.md +0 -238
  1271. package/skills/pylabrobot/references/visualization.md +0 -187
  1272. package/skills/pylabrobot/scripts/__init__.py +0 -1
  1273. package/skills/pylabrobot/scripts/_common.py +0 -718
  1274. package/skills/pylabrobot/scripts/check_deck_geometry.py +0 -52
  1275. package/skills/pylabrobot/scripts/generate_simulation_plan.py +0 -140
  1276. package/skills/pylabrobot/scripts/inspect_backends.py +0 -216
  1277. package/skills/pylabrobot/scripts/plan_transfers.py +0 -59
  1278. package/skills/pylabrobot/scripts/validate_manifest.py +0 -47
  1279. package/skills/pymatgen/references/analysis_modules.md +0 -352
  1280. package/skills/pymatgen/references/core_classes.md +0 -290
  1281. package/skills/pymatgen/references/io_formats.md +0 -323
  1282. package/skills/pymatgen/references/materials_project_api.md +0 -406
  1283. package/skills/pymatgen/references/transformations_workflows.md +0 -385
  1284. package/skills/pymatgen/scripts/_common.py +0 -316
  1285. package/skills/pymatgen/scripts/artifact_manifest.py +0 -172
  1286. package/skills/pymatgen/scripts/composition_structure_validator.py +0 -300
  1287. package/skills/pymatgen/scripts/io_conversion_plan.py +0 -204
  1288. package/skills/pymatgen/scripts/mp_query.py +0 -416
  1289. package/skills/pymatgen/scripts/phase_diagram_generator.py +0 -415
  1290. package/skills/pymatgen/scripts/structure_analyzer.py +0 -293
  1291. package/skills/pymatgen/scripts/structure_converter.py +0 -219
  1292. package/skills/pymatgen/scripts/symmetry_sensitivity_report.py +0 -212
  1293. package/skills/pymc/assets/hierarchical_model_template.py +0 -332
  1294. package/skills/pymc/assets/linear_regression_template.py +0 -244
  1295. package/skills/pymc/references/distributions.md +0 -345
  1296. package/skills/pymc/references/model_patterns.md +0 -130
  1297. package/skills/pymc/references/sampling_inference.md +0 -432
  1298. package/skills/pymc/references/standard_workflow.md +0 -176
  1299. package/skills/pymc/references/workflows.md +0 -530
  1300. package/skills/pymc/scripts/model_comparison.py +0 -409
  1301. package/skills/pymc/scripts/model_diagnostics.py +0 -328
  1302. package/skills/pymoo/references/algorithms.md +0 -232
  1303. package/skills/pymoo/references/constraints_mcdm.md +0 -417
  1304. package/skills/pymoo/references/operators.md +0 -345
  1305. package/skills/pymoo/references/parallelization.md +0 -80
  1306. package/skills/pymoo/references/problems.md +0 -265
  1307. package/skills/pymoo/references/quick_start_workflows.md +0 -404
  1308. package/skills/pymoo/references/visualization.md +0 -353
  1309. package/skills/pymoo/scripts/custom_problem_example.py +0 -181
  1310. package/skills/pymoo/scripts/decision_making_example.py +0 -161
  1311. package/skills/pymoo/scripts/many_objective_example.py +0 -74
  1312. package/skills/pymoo/scripts/multi_objective_example.py +0 -63
  1313. package/skills/pymoo/scripts/single_objective_example.py +0 -59
  1314. package/skills/pyopenms/references/data_structures.md +0 -498
  1315. package/skills/pyopenms/references/feature_detection.md +0 -495
  1316. package/skills/pyopenms/references/file_io.md +0 -359
  1317. package/skills/pyopenms/references/identification.md +0 -431
  1318. package/skills/pyopenms/references/metabolomics.md +0 -548
  1319. package/skills/pyopenms/references/signal_processing.md +0 -444
  1320. package/skills/pyopenms/scripts/accurate_mass_search.py +0 -111
  1321. package/skills/pyopenms/scripts/align_link_quantify.py +0 -140
  1322. package/skills/pyopenms/scripts/consensus_to_matrix.py +0 -70
  1323. package/skills/pyopenms/scripts/convert_format.py +0 -95
  1324. package/skills/pyopenms/scripts/detect_adducts.py +0 -90
  1325. package/skills/pyopenms/scripts/detect_features_centroided.py +0 -80
  1326. package/skills/pyopenms/scripts/detect_features_metabo.py +0 -110
  1327. package/skills/pyopenms/scripts/digest_protein.py +0 -102
  1328. package/skills/pyopenms/scripts/export_gnps_sirius.py +0 -90
  1329. package/skills/pyopenms/scripts/extract_chromatograms.py +0 -105
  1330. package/skills/pyopenms/scripts/inspect_ms_data.py +0 -167
  1331. package/skills/pyopenms/scripts/mass_calculator.py +0 -92
  1332. package/skills/pyopenms/scripts/plot_ms_data.py +0 -129
  1333. package/skills/pyopenms/scripts/process_identifications.py +0 -111
  1334. package/skills/pyopenms/scripts/process_spectra.py +0 -124
  1335. package/skills/pyopenms/scripts/theoretical_spectrum.py +0 -75
  1336. package/skills/pysam/references/alignment_files.md +0 -374
  1337. package/skills/pysam/references/api_reference.md +0 -421
  1338. package/skills/pysam/references/common_workflows.md +0 -442
  1339. package/skills/pysam/references/coordinates_and_indexing.md +0 -318
  1340. package/skills/pysam/references/cram_and_performance.md +0 -314
  1341. package/skills/pysam/references/migration_to_0_24.md +0 -177
  1342. package/skills/pysam/references/sequence_files.md +0 -316
  1343. package/skills/pysam/references/sources.md +0 -132
  1344. package/skills/pysam/references/variant_files.md +0 -396
  1345. package/skills/pysam/scripts/alignment_qc.py +0 -326
  1346. package/skills/pysam/scripts/filter_alignments.py +0 -359
  1347. package/skills/pysam/scripts/inspect_hts.py +0 -485
  1348. package/skills/pysam/scripts/variant_summary.py +0 -362
  1349. package/skills/pytdc/references/datasets.md +0 -242
  1350. package/skills/pytdc/references/oracles.md +0 -273
  1351. package/skills/pytdc/references/sources.md +0 -165
  1352. package/skills/pytdc/references/utilities.md +0 -364
  1353. package/skills/pytdc/scripts/_common.py +0 -205
  1354. package/skills/pytdc/scripts/benchmark_evaluation.py +0 -367
  1355. package/skills/pytdc/scripts/cache_audit.py +0 -146
  1356. package/skills/pytdc/scripts/discover_metadata.py +0 -174
  1357. package/skills/pytdc/scripts/load_and_split_data.py +0 -374
  1358. package/skills/pytdc/scripts/molecular_generation.py +0 -417
  1359. package/skills/pytorch-lightning/references/best_practices.md +0 -724
  1360. package/skills/pytorch-lightning/references/callbacks.md +0 -564
  1361. package/skills/pytorch-lightning/references/data_module.md +0 -565
  1362. package/skills/pytorch-lightning/references/distributed_training.md +0 -644
  1363. package/skills/pytorch-lightning/references/lightning_module.md +0 -487
  1364. package/skills/pytorch-lightning/references/logging.md +0 -636
  1365. package/skills/pytorch-lightning/references/trainer.md +0 -641
  1366. package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +0 -473
  1367. package/skills/pytorch-lightning/scripts/template_datamodule.py +0 -328
  1368. package/skills/pytorch-lightning/scripts/template_lightning_module.py +0 -220
  1369. package/skills/pyzotero/references/authentication.md +0 -105
  1370. package/skills/pyzotero/references/cli.md +0 -102
  1371. package/skills/pyzotero/references/collections.md +0 -113
  1372. package/skills/pyzotero/references/error-handling.md +0 -108
  1373. package/skills/pyzotero/references/exports.md +0 -102
  1374. package/skills/pyzotero/references/files-attachments.md +0 -97
  1375. package/skills/pyzotero/references/full-text.md +0 -68
  1376. package/skills/pyzotero/references/mcp.md +0 -90
  1377. package/skills/pyzotero/references/pagination.md +0 -79
  1378. package/skills/pyzotero/references/read-api.md +0 -137
  1379. package/skills/pyzotero/references/saved-searches.md +0 -77
  1380. package/skills/pyzotero/references/search-params.md +0 -90
  1381. package/skills/pyzotero/references/tags.md +0 -87
  1382. package/skills/pyzotero/references/write-api.md +0 -123
  1383. package/skills/qiskit/references/algorithms.md +0 -311
  1384. package/skills/qiskit/references/backends.md +0 -382
  1385. package/skills/qiskit/references/circuits.md +0 -319
  1386. package/skills/qiskit/references/migration.md +0 -338
  1387. package/skills/qiskit/references/patterns.md +0 -386
  1388. package/skills/qiskit/references/primitives.md +0 -400
  1389. package/skills/qiskit/references/setup.md +0 -253
  1390. package/skills/qiskit/references/sources.md +0 -156
  1391. package/skills/qiskit/references/testing.md +0 -428
  1392. package/skills/qiskit/references/transpilation.md +0 -333
  1393. package/skills/qiskit/references/visualization.md +0 -361
  1394. package/skills/qiskit/scripts/check_environment.py +0 -260
  1395. package/skills/qiskit/scripts/inspect_runtime.py +0 -224
  1396. package/skills/qiskit/scripts/run_local_primitives.py +0 -200
  1397. package/skills/qutip/references/advanced.md +0 -413
  1398. package/skills/qutip/references/analysis.md +0 -319
  1399. package/skills/qutip/references/core_concepts.md +0 -300
  1400. package/skills/qutip/references/time_evolution.md +0 -373
  1401. package/skills/qutip/references/visualization.md +0 -334
  1402. package/skills/qutip/scripts/_common.py +0 -370
  1403. package/skills/qutip/scripts/convergence_sweep.py +0 -358
  1404. package/skills/qutip/scripts/qobj_model_validator.py +0 -327
  1405. package/skills/qutip/scripts/result_audit.py +0 -395
  1406. package/skills/qutip/scripts/solver_config_planner.py +0 -297
  1407. package/skills/qutip/scripts/steady_state_spectrum_planner.py +0 -245
  1408. package/skills/qutip/scripts/two_level_simulation.py +0 -394
  1409. package/skills/rdkit/references/api_reference.md +0 -443
  1410. package/skills/rdkit/references/core_capabilities.md +0 -604
  1411. package/skills/rdkit/references/descriptors_reference.md +0 -595
  1412. package/skills/rdkit/references/smarts_patterns.md +0 -668
  1413. package/skills/rdkit/references/workflows_and_best_practices.md +0 -169
  1414. package/skills/rdkit/scripts/molecular_properties.py +0 -243
  1415. package/skills/rdkit/scripts/similarity_search.py +0 -297
  1416. package/skills/rdkit/scripts/substructure_filter.py +0 -386
  1417. package/skills/relsa-severity-assessment/assets/example_cohort.csv +0 -55
  1418. package/skills/relsa-severity-assessment/references/forecasting.md +0 -155
  1419. package/skills/relsa-severity-assessment/references/relsa-method.md +0 -175
  1420. package/skills/relsa-severity-assessment/references/thresholds-and-zones.md +0 -154
  1421. package/skills/relsa-severity-assessment/scripts/_common.py +0 -287
  1422. package/skills/relsa-severity-assessment/scripts/forecast_relsa.py +0 -757
  1423. package/skills/relsa-severity-assessment/scripts/kde_thresholds.py +0 -369
  1424. package/skills/relsa-severity-assessment/scripts/relsa_score.py +0 -488
  1425. package/skills/research-grants/assets/budget_justification_template.md +0 -453
  1426. package/skills/research-grants/assets/nih_specific_aims_template.md +0 -166
  1427. package/skills/research-grants/assets/nsf_project_summary_template.md +0 -92
  1428. package/skills/research-grants/references/broader_impacts.md +0 -392
  1429. package/skills/research-grants/references/core_components.md +0 -397
  1430. package/skills/research-grants/references/darpa_guidelines.md +0 -636
  1431. package/skills/research-grants/references/doe_guidelines.md +0 -586
  1432. package/skills/research-grants/references/nih_guidelines.md +0 -853
  1433. package/skills/research-grants/references/nsf_guidelines.md +0 -570
  1434. package/skills/research-grants/references/nstc_guidelines.md +0 -733
  1435. package/skills/research-grants/references/proposal_types_and_resubmission.md +0 -81
  1436. package/skills/research-grants/references/review_criteria.md +0 -93
  1437. package/skills/research-grants/references/specific_aims_guide.md +0 -458
  1438. package/skills/research-grants/references/writing_principles.md +0 -94
  1439. package/skills/research-lookup/scripts/manuscript_packet.py +0 -754
  1440. package/skills/research-lookup/scripts/research_lookup.py +0 -1204
  1441. package/skills/rowan/references/access_and_pricing.md +0 -37
  1442. package/skills/rowan/references/batch_and_webhooks.md +0 -255
  1443. package/skills/rowan/references/end_to_end_example.md +0 -119
  1444. package/skills/rowan/references/troubleshooting.md +0 -106
  1445. package/skills/rowan/references/workflow_catalog.md +0 -308
  1446. package/skills/scanpy/assets/analysis_template.py +0 -301
  1447. package/skills/scanpy/assets/celltype_mapping.json +0 -10
  1448. package/skills/scanpy/assets/gene_signatures.json +0 -9
  1449. package/skills/scanpy/assets/pipeline_config.json +0 -19
  1450. package/skills/scanpy/references/analysis_workflow.md +0 -236
  1451. package/skills/scanpy/references/api_reference.md +0 -267
  1452. package/skills/scanpy/references/plotting_guide.md +0 -365
  1453. package/skills/scanpy/references/r_interop.md +0 -292
  1454. package/skills/scanpy/references/standard_workflow.md +0 -223
  1455. package/skills/scanpy/scripts/_common.py +0 -127
  1456. package/skills/scanpy/scripts/annotate.py +0 -84
  1457. package/skills/scanpy/scripts/batch_correct.py +0 -65
  1458. package/skills/scanpy/scripts/cluster.py +0 -63
  1459. package/skills/scanpy/scripts/convert.py +0 -43
  1460. package/skills/scanpy/scripts/find_markers.py +0 -75
  1461. package/skills/scanpy/scripts/inspect_data.py +0 -81
  1462. package/skills/scanpy/scripts/plot.py +0 -78
  1463. package/skills/scanpy/scripts/preprocess.py +0 -88
  1464. package/skills/scanpy/scripts/pseudobulk.py +0 -74
  1465. package/skills/scanpy/scripts/qc_analysis.py +0 -104
  1466. package/skills/scanpy/scripts/reduce_dimensions.py +0 -64
  1467. package/skills/scanpy/scripts/run_pipeline.py +0 -182
  1468. package/skills/scanpy/scripts/score_genes.py +0 -82
  1469. package/skills/scanpy/scripts/subset.py +0 -64
  1470. package/skills/scholar-evaluation/assets/evaluation_template.json +0 -50
  1471. package/skills/scholar-evaluation/assets/evidence_manifest_template.json +0 -63
  1472. package/skills/scholar-evaluation/assets/process_checklist_template.json +0 -70
  1473. package/skills/scholar-evaluation/assets/ratings_template.csv +0 -21
  1474. package/skills/scholar-evaluation/assets/rubric_template.json +0 -301
  1475. package/skills/scholar-evaluation/references/evaluation_framework.md +0 -264
  1476. package/skills/scholar-evaluation/references/local_tooling.md +0 -232
  1477. package/skills/scholar-evaluation/references/responsible_assessment.md +0 -196
  1478. package/skills/scholar-evaluation/references/security_validation.md +0 -95
  1479. package/skills/scholar-evaluation/references/source_ledger.md +0 -222
  1480. package/skills/scholar-evaluation/scripts/_common.py +0 -986
  1481. package/skills/scholar-evaluation/scripts/calculate_scores.py +0 -57
  1482. package/skills/scholar-evaluation/scripts/check_process.py +0 -231
  1483. package/skills/scholar-evaluation/scripts/check_traceability.py +0 -233
  1484. package/skills/scholar-evaluation/scripts/generate_report_scaffold.py +0 -231
  1485. package/skills/scholar-evaluation/scripts/summarize_agreement.py +0 -235
  1486. package/skills/scholar-evaluation/scripts/validate_rubric.py +0 -54
  1487. package/skills/scholar-evaluation/scripts/weight_sensitivity.py +0 -251
  1488. package/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -292
  1489. package/skills/scientific-brainstorming/references/facilitation_workflows.md +0 -284
  1490. package/skills/scientific-brainstorming/references/idea_evaluation.md +0 -268
  1491. package/skills/scientific-brainstorming/references/responsible_ai.md +0 -220
  1492. package/skills/scientific-brainstorming/references/sources.md +0 -364
  1493. package/skills/scientific-brainstorming/scripts/_common.py +0 -307
  1494. package/skills/scientific-brainstorming/scripts/evaluate_matrix.py +0 -518
  1495. package/skills/scientific-brainstorming/scripts/session_scaffold.py +0 -248
  1496. package/skills/scientific-brainstorming/scripts/validate_register.py +0 -654
  1497. package/skills/scientific-critical-thinking/references/common_biases.md +0 -364
  1498. package/skills/scientific-critical-thinking/references/core_capabilities.md +0 -407
  1499. package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -485
  1500. package/skills/scientific-critical-thinking/references/experimental_design.md +0 -496
  1501. package/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -478
  1502. package/skills/scientific-critical-thinking/references/scientific_method.md +0 -169
  1503. package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -506
  1504. package/skills/scientific-schematics/references/best_practices.md +0 -574
  1505. package/skills/scientific-schematics/references/iterative_refinement.md +0 -315
  1506. package/skills/scientific-schematics/scripts/example_usage.sh +0 -92
  1507. package/skills/scientific-schematics/scripts/generate_schematic.py +0 -198
  1508. package/skills/scientific-schematics/scripts/generate_schematic_ai.py +0 -950
  1509. package/skills/scientific-slides/assets/beamer_template_conference.tex +0 -407
  1510. package/skills/scientific-slides/assets/beamer_template_defense.tex +0 -906
  1511. package/skills/scientific-slides/assets/beamer_template_seminar.tex +0 -870
  1512. package/skills/scientific-slides/assets/powerpoint_design_guide.md +0 -662
  1513. package/skills/scientific-slides/assets/timing_guidelines.md +0 -597
  1514. package/skills/scientific-slides/references/beamer_guide.md +0 -1019
  1515. package/skills/scientific-slides/references/common_pitfalls.md +0 -85
  1516. package/skills/scientific-slides/references/data_visualization_slides.md +0 -708
  1517. package/skills/scientific-slides/references/presentation_structure.md +0 -642
  1518. package/skills/scientific-slides/references/presentation_workflow.md +0 -196
  1519. package/skills/scientific-slides/references/prompt_writing.md +0 -42
  1520. package/skills/scientific-slides/references/script_reference.md +0 -143
  1521. package/skills/scientific-slides/references/slide_capabilities.md +0 -360
  1522. package/skills/scientific-slides/references/slide_design_principles.md +0 -849
  1523. package/skills/scientific-slides/references/talk_types_guide.md +0 -687
  1524. package/skills/scientific-slides/references/visual_review_workflow.md +0 -775
  1525. package/skills/scientific-slides/scripts/generate_schematic.py +0 -198
  1526. package/skills/scientific-slides/scripts/generate_schematic_ai.py +0 -950
  1527. package/skills/scientific-slides/scripts/generate_slide_image.py +0 -197
  1528. package/skills/scientific-slides/scripts/generate_slide_image_ai.py +0 -877
  1529. package/skills/scientific-slides/scripts/pdf_to_images.py +0 -221
  1530. package/skills/scientific-slides/scripts/slides_to_pdf.py +0 -235
  1531. package/skills/scientific-slides/scripts/validate_presentation.py +0 -408
  1532. package/skills/scientific-visualization/assets/color_palettes.py +0 -263
  1533. package/skills/scientific-visualization/assets/nature.mplstyle +0 -68
  1534. package/skills/scientific-visualization/assets/presentation.mplstyle +0 -68
  1535. package/skills/scientific-visualization/assets/publication.mplstyle +0 -77
  1536. package/skills/scientific-visualization/assets/publisher_profiles.json +0 -269
  1537. package/skills/scientific-visualization/references/color_palettes.md +0 -227
  1538. package/skills/scientific-visualization/references/journal_requirements.md +0 -169
  1539. package/skills/scientific-visualization/references/matplotlib_examples.md +0 -336
  1540. package/skills/scientific-visualization/references/publication_guidelines.md +0 -196
  1541. package/skills/scientific-visualization/references/sources.md +0 -76
  1542. package/skills/scientific-visualization/scripts/_common.py +0 -136
  1543. package/skills/scientific-visualization/scripts/export_plan.py +0 -493
  1544. package/skills/scientific-visualization/scripts/figure_export.py +0 -642
  1545. package/skills/scientific-visualization/scripts/image_metadata.py +0 -731
  1546. package/skills/scientific-visualization/scripts/palette_audit.py +0 -327
  1547. package/skills/scientific-visualization/scripts/style_presets.py +0 -501
  1548. package/skills/scientific-visualization/scripts/style_preview.py +0 -232
  1549. package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +0 -60
  1550. package/skills/scientific-writing/assets/authorship_template.json +0 -56
  1551. package/skills/scientific-writing/assets/claim_evidence_template.csv +0 -2
  1552. package/skills/scientific-writing/assets/consistency_manifest_template.json +0 -43
  1553. package/skills/scientific-writing/assets/manuscript_manifest_template.json +0 -37
  1554. package/skills/scientific-writing/assets/manuscript_scaffold.md +0 -65
  1555. package/skills/scientific-writing/assets/reporting_coverage_template.json +0 -6
  1556. package/skills/scientific-writing/assets/reporting_guidelines.json +0 -529
  1557. package/skills/scientific-writing/assets/source_manifest_template.json +0 -27
  1558. package/skills/scientific-writing/references/authorship_ai_confidentiality.md +0 -111
  1559. package/skills/scientific-writing/references/citation_styles.md +0 -92
  1560. package/skills/scientific-writing/references/cli_reference.md +0 -113
  1561. package/skills/scientific-writing/references/evidence_workflow.md +0 -94
  1562. package/skills/scientific-writing/references/figures_tables.md +0 -94
  1563. package/skills/scientific-writing/references/imrad_structure.md +0 -114
  1564. package/skills/scientific-writing/references/journal_policies.md +0 -56
  1565. package/skills/scientific-writing/references/professional_report_formatting.md +0 -82
  1566. package/skills/scientific-writing/references/reporting_guidelines.md +0 -107
  1567. package/skills/scientific-writing/references/research_integrity_open_science.md +0 -97
  1568. package/skills/scientific-writing/references/source_ledger.md +0 -268
  1569. package/skills/scientific-writing/references/writing_principles.md +0 -97
  1570. package/skills/scientific-writing/scripts/_common.py +0 -240
  1571. package/skills/scientific-writing/scripts/audit_claims.py +0 -241
  1572. package/skills/scientific-writing/scripts/check_consistency.py +0 -408
  1573. package/skills/scientific-writing/scripts/check_references.py +0 -219
  1574. package/skills/scientific-writing/scripts/lint_manuscript.py +0 -171
  1575. package/skills/scientific-writing/scripts/scaffold_manuscript.py +0 -143
  1576. package/skills/scientific-writing/scripts/select_reporting_guidelines.py +0 -214
  1577. package/skills/scientific-writing/scripts/validate_authorship.py +0 -322
  1578. package/skills/scientific-writing/scripts/validate_manifest.py +0 -460
  1579. package/skills/scikit-bio/references/api_reference.md +0 -766
  1580. package/skills/scikit-learn/references/common_workflows.md +0 -107
  1581. package/skills/scikit-learn/references/core_capabilities.md +0 -133
  1582. package/skills/scikit-learn/references/model_evaluation.md +0 -592
  1583. package/skills/scikit-learn/references/pipelines_and_composition.md +0 -612
  1584. package/skills/scikit-learn/references/preprocessing.md +0 -606
  1585. package/skills/scikit-learn/references/quick_reference.md +0 -436
  1586. package/skills/scikit-learn/references/supervised_learning.md +0 -379
  1587. package/skills/scikit-learn/references/unsupervised_learning.md +0 -517
  1588. package/skills/scikit-learn/scripts/classification_pipeline.py +0 -257
  1589. package/skills/scikit-learn/scripts/clustering_analysis.py +0 -386
  1590. package/skills/scikit-survival/references/competing-risks.md +0 -302
  1591. package/skills/scikit-survival/references/cox-models.md +0 -252
  1592. package/skills/scikit-survival/references/data-handling.md +0 -278
  1593. package/skills/scikit-survival/references/ensemble-models.md +0 -287
  1594. package/skills/scikit-survival/references/evaluation-metrics.md +0 -391
  1595. package/skills/scikit-survival/references/svm-models.md +0 -277
  1596. package/skills/scikit-survival/scripts/_common.py +0 -456
  1597. package/skills/scikit-survival/scripts/competing_risk_cif.py +0 -286
  1598. package/skills/scikit-survival/scripts/evaluate_survival_metrics.py +0 -296
  1599. package/skills/scikit-survival/scripts/model_report.py +0 -297
  1600. package/skills/scikit-survival/scripts/train_survival_model.py +0 -583
  1601. package/skills/scikit-survival/scripts/validate_survival_csv.py +0 -172
  1602. package/skills/scvelo/references/velocity_models.md +0 -168
  1603. package/skills/scvelo/scripts/rna_velocity_workflow.py +0 -240
  1604. package/skills/scvi-tools/references/differential-expression.md +0 -597
  1605. package/skills/scvi-tools/references/models-atac-seq.md +0 -329
  1606. package/skills/scvi-tools/references/models-multimodal.md +0 -400
  1607. package/skills/scvi-tools/references/models-scrna-seq.md +0 -333
  1608. package/skills/scvi-tools/references/models-spatial.md +0 -432
  1609. package/skills/scvi-tools/references/models-specialized.md +0 -376
  1610. package/skills/scvi-tools/references/theoretical-foundations.md +0 -438
  1611. package/skills/scvi-tools/references/workflows.md +0 -559
  1612. package/skills/seaborn/references/examples.md +0 -824
  1613. package/skills/seaborn/references/function_reference.md +0 -772
  1614. package/skills/seaborn/references/grids_and_levels.md +0 -85
  1615. package/skills/seaborn/references/objects_interface.md +0 -963
  1616. package/skills/seaborn/references/palettes_and_theming.md +0 -110
  1617. package/skills/seaborn/references/patterns_and_troubleshooting.md +0 -114
  1618. package/skills/seaborn/references/plotting_functions.md +0 -178
  1619. package/skills/shap/references/data-maskers.md +0 -287
  1620. package/skills/shap/references/explainers.md +0 -376
  1621. package/skills/shap/references/migration.md +0 -415
  1622. package/skills/shap/references/modalities.md +0 -353
  1623. package/skills/shap/references/plots.md +0 -406
  1624. package/skills/shap/references/theory.md +0 -352
  1625. package/skills/shap/references/troubleshooting.md +0 -442
  1626. package/skills/shap/references/workflows.md +0 -565
  1627. package/skills/shap/scripts/tabular_report.py +0 -326
  1628. package/skills/simpy/references/cli-guide.md +0 -266
  1629. package/skills/simpy/references/events.md +0 -225
  1630. package/skills/simpy/references/monitoring.md +0 -260
  1631. package/skills/simpy/references/process-interaction.md +0 -269
  1632. package/skills/simpy/references/real-time.md +0 -174
  1633. package/skills/simpy/references/resources.md +0 -274
  1634. package/skills/simpy/references/simulation-methodology.md +0 -293
  1635. package/skills/simpy/references/sources.md +0 -167
  1636. package/skills/simpy/scripts/_common.py +0 -473
  1637. package/skills/simpy/scripts/basic_simulation_template.py +0 -415
  1638. package/skills/simpy/scripts/bounded_queue_scenario.py +0 -126
  1639. package/skills/simpy/scripts/event_trace_summary.py +0 -296
  1640. package/skills/simpy/scripts/replication_runner.py +0 -194
  1641. package/skills/simpy/scripts/resource_monitor.py +0 -474
  1642. package/skills/simpy/scripts/validate_simulation_config.py +0 -111
  1643. package/skills/stable-baselines3/references/algorithms.md +0 -348
  1644. package/skills/stable-baselines3/references/callbacks.md +0 -571
  1645. package/skills/stable-baselines3/references/custom_environments.md +0 -528
  1646. package/skills/stable-baselines3/references/vectorized_envs.md +0 -580
  1647. package/skills/stable-baselines3/scripts/custom_env_template.py +0 -314
  1648. package/skills/stable-baselines3/scripts/evaluate_agent.py +0 -245
  1649. package/skills/stable-baselines3/scripts/train_rl_agent.py +0 -165
  1650. package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +0 -379
  1651. package/skills/statistical-analysis/references/bayesian_statistics.md +0 -686
  1652. package/skills/statistical-analysis/references/effect_sizes_and_power.md +0 -649
  1653. package/skills/statistical-analysis/references/reporting_standards.md +0 -482
  1654. package/skills/statistical-analysis/references/test_selection_guide.md +0 -129
  1655. package/skills/statistical-analysis/scripts/assumption_checks.py +0 -652
  1656. package/skills/statistical-power/references/closed_form_recipes.md +0 -174
  1657. package/skills/statistical-power/references/effect_sizes.md +0 -121
  1658. package/skills/statistical-power/references/simulation_based_power.md +0 -101
  1659. package/skills/statistical-power/scripts/power.py +0 -320
  1660. package/skills/statistical-power/scripts/simulate_power.py +0 -217
  1661. package/skills/statsmodels/references/discrete_choice.md +0 -669
  1662. package/skills/statsmodels/references/glm.md +0 -619
  1663. package/skills/statsmodels/references/linear_models.md +0 -447
  1664. package/skills/statsmodels/references/model_selection.md +0 -99
  1665. package/skills/statsmodels/references/modeling_capabilities.md +0 -168
  1666. package/skills/statsmodels/references/quick_start_guide.md +0 -154
  1667. package/skills/statsmodels/references/stats_diagnostics.md +0 -859
  1668. package/skills/statsmodels/references/time_series.md +0 -723
  1669. package/skills/sympy/references/advanced-topics.md +0 -635
  1670. package/skills/sympy/references/code-generation-printing.md +0 -628
  1671. package/skills/sympy/references/core-capabilities.md +0 -348
  1672. package/skills/sympy/references/core_capabilities.md +0 -190
  1673. package/skills/sympy/references/matrices-linear-algebra.md +0 -526
  1674. package/skills/sympy/references/physics-mechanics.md +0 -592
  1675. package/skills/tamarind/references/api_reference.md +0 -165
  1676. package/skills/tamarind/references/examples.md +0 -132
  1677. package/skills/tamarind/references/tool_catalog.md +0 -66
  1678. package/skills/tamarind/references/workflows.md +0 -263
  1679. package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +0 -524
  1680. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +0 -448
  1681. package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
  1682. package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +0 -568
  1683. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
  1684. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +0 -59
  1685. package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +0 -109
  1686. package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +0 -147
  1687. package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +0 -248
  1688. package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +0 -544
  1689. package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +0 -5441
  1690. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
  1691. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +0 -13
  1692. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +0 -188
  1693. package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
  1694. package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +0 -5939
  1695. package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +0 -53
  1696. package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +0 -167
  1697. package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +0 -37
  1698. package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +0 -123
  1699. package/skills/timesfm-forecasting/references/api_reference.md +0 -231
  1700. package/skills/timesfm-forecasting/references/data_preparation.md +0 -272
  1701. package/skills/timesfm-forecasting/references/examples_and_validation.md +0 -103
  1702. package/skills/timesfm-forecasting/references/output_and_config.md +0 -93
  1703. package/skills/timesfm-forecasting/references/performance_tuning.md +0 -80
  1704. package/skills/timesfm-forecasting/references/system_requirements.md +0 -201
  1705. package/skills/timesfm-forecasting/references/workflows.md +0 -126
  1706. package/skills/timesfm-forecasting/scripts/check_system.py +0 -521
  1707. package/skills/timesfm-forecasting/scripts/forecast_csv.py +0 -269
  1708. package/skills/torch-geometric/references/custom_datasets.md +0 -239
  1709. package/skills/torch-geometric/references/explainability.md +0 -208
  1710. package/skills/torch-geometric/references/heterogeneous.md +0 -241
  1711. package/skills/torch-geometric/references/link_prediction.md +0 -226
  1712. package/skills/torch-geometric/references/message_passing.md +0 -121
  1713. package/skills/torch-geometric/references/scaling.md +0 -269
  1714. package/skills/torchdrug/references/core_concepts.md +0 -241
  1715. package/skills/torchdrug/references/datasets.md +0 -179
  1716. package/skills/torchdrug/references/knowledge_graphs.md +0 -226
  1717. package/skills/torchdrug/references/models_architectures.md +0 -223
  1718. package/skills/torchdrug/references/molecular_generation.md +0 -246
  1719. package/skills/torchdrug/references/molecular_property_prediction.md +0 -239
  1720. package/skills/torchdrug/references/protein_modeling.md +0 -221
  1721. package/skills/torchdrug/references/retrosynthesis.md +0 -247
  1722. package/skills/transformers/references/generation.md +0 -473
  1723. package/skills/transformers/references/models.md +0 -371
  1724. package/skills/transformers/references/pipelines.md +0 -334
  1725. package/skills/transformers/references/tokenizers.md +0 -449
  1726. package/skills/transformers/references/training.md +0 -504
  1727. package/skills/treatment-plans/assets/clinician_authored_intervention_template.json +0 -11
  1728. package/skills/treatment-plans/assets/goals_monitoring_checkpoint_template.json +0 -13
  1729. package/skills/treatment-plans/assets/informed_preference_shared_decision_template.json +0 -11
  1730. package/skills/treatment-plans/assets/intended_use_handoff_template.json +0 -83
  1731. package/skills/treatment-plans/assets/source_fact_manifest_template.json +0 -11
  1732. package/skills/treatment-plans/assets/transition_reconciliation_template.json +0 -27
  1733. package/skills/treatment-plans/references/documentation_workflow.md +0 -165
  1734. package/skills/treatment-plans/references/privacy_governance.md +0 -119
  1735. package/skills/treatment-plans/references/safety_scope.md +0 -101
  1736. package/skills/treatment-plans/references/security_validation.md +0 -68
  1737. package/skills/treatment-plans/references/shared_decision_handoff.md +0 -138
  1738. package/skills/treatment-plans/references/source_boundaries.md +0 -127
  1739. package/skills/treatment-plans/references/source_ledger.md +0 -131
  1740. package/skills/treatment-plans/scripts/_common.py +0 -1160
  1741. package/skills/treatment-plans/scripts/check_completeness.py +0 -572
  1742. package/skills/treatment-plans/scripts/check_consistency.py +0 -386
  1743. package/skills/treatment-plans/scripts/generate_template.py +0 -133
  1744. package/skills/treatment-plans/scripts/privacy_process_check.py +0 -213
  1745. package/skills/treatment-plans/scripts/timeline_generator.py +0 -260
  1746. package/skills/treatment-plans/scripts/validate_traceability.py +0 -147
  1747. package/skills/treatment-plans/scripts/validate_treatment_plan.py +0 -95
  1748. package/skills/umap-learn/references/api_reference.md +0 -574
  1749. package/skills/uncertainty-and-units/references/domain-conversions.md +0 -188
  1750. package/skills/uncertainty-and-units/references/gum-methodology.md +0 -219
  1751. package/skills/uncertainty-and-units/references/pint-recipes.md +0 -228
  1752. package/skills/uncertainty-and-units/references/plausibility-scales.md +0 -168
  1753. package/skills/uncertainty-and-units/references/reporting-rules.md +0 -133
  1754. package/skills/uncertainty-and-units/references/uncertainties-recipes.md +0 -167
  1755. package/skills/uncertainty-and-units/scripts/_common.py +0 -666
  1756. package/skills/uncertainty-and-units/scripts/audit_units.py +0 -575
  1757. package/skills/uncertainty-and-units/scripts/check_plausibility.py +0 -894
  1758. package/skills/uncertainty-and-units/scripts/convert_units.py +0 -280
  1759. package/skills/uncertainty-and-units/scripts/format_result.py +0 -326
  1760. package/skills/uncertainty-and-units/scripts/propagate_uncertainty.py +0 -662
  1761. package/skills/uncertainty-and-units/scripts/uncertainty_budget.py +0 -363
  1762. package/skills/usfiscaldata/references/api-basics.md +0 -105
  1763. package/skills/usfiscaldata/references/datasets-debt.md +0 -166
  1764. package/skills/usfiscaldata/references/datasets-fiscal.md +0 -212
  1765. package/skills/usfiscaldata/references/datasets-interest-rates.md +0 -188
  1766. package/skills/usfiscaldata/references/datasets-securities.md +0 -238
  1767. package/skills/usfiscaldata/references/examples.md +0 -258
  1768. package/skills/usfiscaldata/references/parameters.md +0 -182
  1769. package/skills/usfiscaldata/references/response-format.md +0 -178
  1770. package/skills/vaex/references/core_dataframes.md +0 -373
  1771. package/skills/vaex/references/data_processing.md +0 -555
  1772. package/skills/vaex/references/io_operations.md +0 -718
  1773. package/skills/vaex/references/machine_learning.md +0 -728
  1774. package/skills/vaex/references/performance.md +0 -571
  1775. package/skills/vaex/references/visualization.md +0 -644
  1776. package/skills/venue-templates/assets/examples/cell_summary_example.md +0 -247
  1777. package/skills/venue-templates/assets/examples/medical_structured_abstract.md +0 -313
  1778. package/skills/venue-templates/assets/examples/nature_abstract_examples.md +0 -213
  1779. package/skills/venue-templates/assets/examples/neurips_introduction_example.md +0 -245
  1780. package/skills/venue-templates/assets/grants/nih_specific_aims.tex +0 -237
  1781. package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +0 -384
  1782. package/skills/venue-templates/assets/journals/elsarticle-harv.bst +0 -1598
  1783. package/skills/venue-templates/assets/journals/elsarticle-num-names.bst +0 -1535
  1784. package/skills/venue-templates/assets/journals/elsarticle-num.bst +0 -1509
  1785. package/skills/venue-templates/assets/journals/elsarticle-template-harv.tex +0 -286
  1786. package/skills/venue-templates/assets/journals/elsarticle-template-num-names.tex +0 -284
  1787. package/skills/venue-templates/assets/journals/elsarticle-template-num.tex +0 -286
  1788. package/skills/venue-templates/assets/journals/nature_article.tex +0 -174
  1789. package/skills/venue-templates/assets/journals/neurips_article.tex +0 -292
  1790. package/skills/venue-templates/assets/journals/plos_one.tex +0 -320
  1791. package/skills/venue-templates/assets/posters/beamerposter_academic.tex +0 -312
  1792. package/skills/venue-templates/references/cell_press_style.md +0 -486
  1793. package/skills/venue-templates/references/conferences_formatting.md +0 -175
  1794. package/skills/venue-templates/references/cs_conference_style.md +0 -465
  1795. package/skills/venue-templates/references/grants_requirements.md +0 -267
  1796. package/skills/venue-templates/references/journals_formatting.md +0 -200
  1797. package/skills/venue-templates/references/medical_journal_styles.md +0 -536
  1798. package/skills/venue-templates/references/ml_conference_style.md +0 -562
  1799. package/skills/venue-templates/references/nature_science_style.md +0 -407
  1800. package/skills/venue-templates/references/posters_guidelines.md +0 -630
  1801. package/skills/venue-templates/references/reviewer_expectations.md +0 -422
  1802. package/skills/venue-templates/references/venue_writing_styles.md +0 -323
  1803. package/skills/venue-templates/scripts/customize_template.py +0 -206
  1804. package/skills/venue-templates/scripts/query_template.py +0 -202
  1805. package/skills/venue-templates/scripts/validate_format.py +0 -321
  1806. package/skills/waypoint-bio/references/cli-reference.md +0 -210
  1807. package/skills/waypoint-bio/references/compass-benchmark.md +0 -124
  1808. package/skills/waypoint-bio/references/data-preparation.md +0 -200
  1809. package/skills/waypoint-bio/references/python-api.md +0 -219
  1810. package/skills/waypoint-bio/scripts/profiler_to_waypoint.py +0 -481
  1811. package/skills/waypoint-bio/scripts/vocab_coverage.py +0 -235
  1812. package/skills/what-if-oracle/references/scenario-templates.md +0 -137
  1813. package/skills/xlsx/LICENSE.txt +0 -30
  1814. package/skills/xlsx/scripts/office/helpers/__init__.py +0 -111
  1815. package/skills/xlsx/scripts/office/helpers/pptx_chart.py +0 -170
  1816. package/skills/xlsx/scripts/office/helpers/pptx_slide.py +0 -60
  1817. package/skills/xlsx/scripts/office/helpers/pptx_theme.py +0 -114
  1818. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
  1819. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
  1820. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
  1821. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
  1822. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
  1823. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
  1824. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
  1825. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
  1826. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
  1827. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
  1828. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
  1829. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
  1830. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
  1831. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
  1832. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
  1833. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
  1834. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
  1835. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
  1836. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
  1837. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
  1838. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
  1839. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
  1840. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
  1841. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
  1842. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
  1843. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
  1844. package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
  1845. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
  1846. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
  1847. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
  1848. package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
  1849. package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +0 -75
  1850. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
  1851. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
  1852. package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
  1853. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
  1854. package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
  1855. package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
  1856. package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
  1857. package/skills/xlsx/scripts/office/soffice.py +0 -232
  1858. package/skills/xlsx/scripts/office/validate.py +0 -173
  1859. package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
  1860. package/skills/xlsx/scripts/office/validators/base.py +0 -875
  1861. package/skills/xlsx/scripts/office/validators/docx.py +0 -466
  1862. package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
  1863. package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
  1864. package/skills/xlsx/scripts/recalc.py +0 -308
  1865. package/skills/zarr-python/references/api_reference.md +0 -162
  1866. package/skills/zarr-python/references/chunking_and_compression.md +0 -138
  1867. package/skills/zarr-python/references/integration.md +0 -147
  1868. package/skills/zarr-python/references/performance_and_patterns.md +0 -198
  1869. package/skills/zarr-python/references/storage_backends.md +0 -91
  1870. package/skills/zarr-python/references/v3_migration.md +0 -127
@@ -1,206 +0,0 @@
1
- # Resource Semantics
2
-
3
- Research and behavior cut-off: **2026-07-23**. See
4
- [`sources.md`](sources.md) for the official documentation used.
5
-
6
- ## Core rule: inventory is not entitlement
7
-
8
- Never treat a host-wide count as a promise that the current process can use it.
9
- Interpret usable resources as the intersection of independently observed
10
- constraints:
11
-
12
- 1. host inventory;
13
- 2. process affinity or processor-group scope;
14
- 3. cgroup/container constraints;
15
- 4. scheduler allocation;
16
- 5. accelerator visibility and device permissions; and
17
- 6. application runtime compatibility.
18
-
19
- Missing evidence means **unknown**, not unlimited. Scheduler variables can
20
- describe an allocation without proving that affinity or cgroup enforcement is
21
- enabled. Conversely, a cgroup or affinity mask can be stricter than the
22
- scheduler request.
23
-
24
- ## CPU
25
-
26
- ### Physical and logical CPUs
27
-
28
- - A logical CPU is an operating-system scheduling unit. Simultaneous
29
- multithreading can expose multiple logical CPUs on one physical core.
30
- - A physical-core count describes topology, not the number of independent
31
- workers the process may start.
32
- - `os.cpu_count()` and `psutil.cpu_count(logical=True)` are host/system
33
- inventory. They can exceed the CPUs usable by the process.
34
- - `os.process_cpu_count()` (Python 3.13+) is process-aware. On supported
35
- platforms, affinity APIs provide a more explicit process constraint.
36
- - On Windows systems with multiple processor groups, a system-wide logical
37
- count and one process/thread group's usable count can differ.
38
-
39
- The detector reports host logical and physical counts separately. It never
40
- derives physical cores from a logical count.
41
-
42
- ### Affinity, cpusets, and quotas
43
-
44
- - Process affinity limits the logical CPUs on which a process may execute.
45
- - Linux `cpuset.cpus.effective` reports CPUs actually granted after parent
46
- constraints. The requested `cpuset.cpus` can differ.
47
- - `/proc/self/status` exposes `Cpus_allowed_list`, but the detector prefers
48
- affinity APIs and cgroup effective cpusets.
49
- - cgroup v2 `cpu.max` is `$MAX $PERIOD`. `max` means no local bandwidth limit.
50
- A finite ratio is CPU-time capacity, possibly fractional; it is not a core
51
- topology count.
52
- - Parent cgroups also constrain children, so the detector takes the most
53
- restrictive finite ancestor quota.
54
-
55
- For a `cpu.max` ratio of 1.5, the snapshot reports
56
- `capacity_cores: 1.5` and a conservative CPU-bound worker ceiling of 1. A
57
- workload may choose more threads for latency hiding, but it should expect
58
- throttling and must not describe those threads as 1.5 physical cores.
59
-
60
- ### Python worker pools
61
-
62
- - Current Python `multiprocessing.Pool` and `ProcessPoolExecutor` defaults use
63
- `os.process_cpu_count()` when available.
64
- - Python 3.14 no longer uses `fork` as the default start method on any platform.
65
- Code that depends on a particular start method must request it deliberately.
66
- - Process workers do not make each worker's native-library threads disappear.
67
- BLAS/OpenMP threads multiplied by process workers commonly oversubscribe an
68
- allocation.
69
- - Windows `ProcessPoolExecutor` has a documented maximum of 61 workers.
70
-
71
- Use the workload planner's worker and threads-per-worker values as conservative
72
- ceilings, then benchmark a real representative workload. Do not run a synthetic
73
- stress test merely to discover capacity.
74
-
75
- ## Memory
76
-
77
- ### Host and effective memory
78
-
79
- - `psutil.virtual_memory().total` and `.available` describe system-visible
80
- memory, not necessarily the process limit.
81
- - Linux `/proc/meminfo` `MemAvailable` is the standard-library fallback for a
82
- host-availability estimate.
83
- - cgroup v2 `memory.current` is current cgroup usage.
84
- - `memory.high` is a throttle/reclaim pressure boundary. Exceeding it does not
85
- itself invoke the cgroup OOM killer, and the value can be breached.
86
- - `memory.max` is the hard cgroup limit. If usage cannot be reduced at that
87
- boundary, the cgroup OOM killer can run.
88
- - Parent memory limits are hierarchical. Shared ancestor usage can reduce what
89
- remains for a child, so effective remaining memory is the minimum finite
90
- `limit - current` observed through the ancestor chain.
91
- - Slurm memory variables describe requested/allocated memory, but strict
92
- enforcement depends on site configuration.
93
-
94
- The detector keeps host total/available values, cgroup values, scheduler values,
95
- and the conservative effective values distinct. A point-in-time "available"
96
- value can change immediately and is not a reservation.
97
-
98
- ### macOS unified memory
99
-
100
- On Apple silicon, CPU and integrated GPU share unified memory. Do not add a
101
- fictional GPU VRAM amount to system RAM. The snapshot marks the memory model as
102
- `unified_cpu_gpu` and leaves dedicated GPU memory null. Metal framework support
103
- and model/operator support still require application-specific checks.
104
-
105
- ## Accelerators
106
-
107
- Accelerator usability has separate layers:
108
-
109
- 1. **Hardware or management visibility** — a management query returns a device.
110
- 2. **Allocation visibility** — scheduler and named visibility variables permit
111
- a device or a subset.
112
- 3. **Device permission** — the process/container can open the required device
113
- interfaces.
114
- 4. **Driver/runtime compatibility** — driver, CUDA/ROCm/Metal runtime, and
115
- framework versions are compatible.
116
- 5. **Workload compatibility** — the requested operation and data type are
117
- implemented on that backend.
118
-
119
- `nvidia-smi` success confirms NVIDIA management visibility only. It does not
120
- prove that CUDA libraries exist or are compatible. NVIDIA documents driver and
121
- runtime compatibility as a separate requirement.
122
-
123
- AMD SMI or ROCm SMI success likewise does not prove HIP/ROCm runtime usability.
124
- New deployments should prefer `amd-smi`; `rocm-smi` is retained as a read-only
125
- fallback. On Linux, AMD recommends `ROCR_VISIBLE_DEVICES`; on Windows it
126
- recommends `HIP_VISIBLE_DEVICES`.
127
-
128
- An Apple integrated GPU is a Metal candidate, not a CUDA GPU. AMD GPUs are ROCm
129
- candidates, not CUDA GPUs. Neural engines, TPUs, FPGAs, and other accelerators
130
- must also remain distinct from CUDA devices if another inventory source adds
131
- them.
132
-
133
- The detector reads only these accelerator variable names and redacts their
134
- values:
135
-
136
- - `NVIDIA_VISIBLE_DEVICES`
137
- - `CUDA_VISIBLE_DEVICES`
138
- - `ROCR_VISIBLE_DEVICES`
139
- - `HIP_VISIBLE_DEVICES`
140
-
141
- Counts derived from those values are only upper bounds. Environment variables
142
- are not a security boundary and can be reset by an application; device
143
- namespace/cgroup controls are stronger isolation.
144
-
145
- ## Slurm and other schedulers
146
-
147
- The detector allowlists named Slurm variables and never dumps the environment.
148
- It records field names, parsed bounded counts, and memory quantities, but not
149
- job IDs, GPU UUIDs, node names, submit hosts, or paths.
150
-
151
- Important scopes:
152
-
153
- - `SLURM_CPUS_PER_TASK`: requested CPUs per task; suitable as a per-process
154
- upper bound for one task process.
155
- - `SLURM_CPUS_ON_NODE`: CPUs allocated to the current batch step on the node;
156
- it can be shared among tasks.
157
- - `SLURM_JOB_CPUS_PER_NODE`: a per-node allocation list, not a process count.
158
- - `SLURM_MEM_PER_CPU`: memory per allocated CPU. It becomes a per-task bound
159
- only when CPUs per task is known.
160
- - `SLURM_MEM_PER_NODE`: shared per-node memory upper bound.
161
- - `SLURM_GPUS_PER_TASK`: requested GPUs per task.
162
- - `SLURM_GPUS_ON_NODE`: GPUs allocated to the batch step on the node.
163
-
164
- Slurm CPU confinement requires site configuration such as task affinity or
165
- `task/cgroup` with core constraints. Memory requests are not strictly enforced
166
- unless the site enables an enforcement mechanism. Use affinity and cgroup
167
- observations as enforcement evidence; do not trust visible node inventory.
168
-
169
- For other schedulers, use their documented allocation API or variables and the
170
- same rule: allocation metadata and kernel enforcement are different facts.
171
- Do not guess from generic environment names.
172
-
173
- ## Containers and OCI
174
-
175
- Docker containers have no CPU or memory limit by default. When configured,
176
- Docker maps CPU and memory flags to cgroup controls. OCI runtime configuration
177
- also defines CPU, memory, and device constraints.
178
-
179
- Inside a container:
180
-
181
- - host inventory may remain visible;
182
- - a CPU quota can be smaller than the visible CPU set;
183
- - a cpuset can be smaller than the quota's apparent capacity;
184
- - cgroup memory can be smaller than host RAM;
185
- - GPU management tools can see a different set from the application runtime;
186
- and
187
- - mounted-volume capacity can differ from writable quota.
188
-
189
- Always report observed cgroup controls and uncertainty. A container marker
190
- without a finite cgroup value does not imply a finite limit.
191
-
192
- ## Disk
193
-
194
- Capacity, free blocks, user-writable blocks, path permission, filesystem quota,
195
- and actual ability to complete a write are different:
196
-
197
- - capacity is the filesystem's total size;
198
- - free blocks can include blocks reserved from an unprivileged user;
199
- - POSIX `f_bavail` estimates blocks available to the current user;
200
- - `os.access(..., os.W_OK)` is a non-writing permission check, not proof that a
201
- future write will succeed;
202
- - project/user quotas and remote storage policies can be stricter than block
203
- counts.
204
-
205
- The detector does not create a probe file. It redacts the absolute working path
206
- and labels the scope as the working filesystem.
@@ -1,172 +0,0 @@
1
- # Snapshot Schema 1.1
2
-
3
- The detector emits one JSON object with sorted keys. Values vary by observation,
4
- but field names and meanings are stable for schema `1.1`.
5
-
6
- ## Top-level contract
7
-
8
- - `schema_version`: `"1.1"`.
9
- - `snapshot_kind`: `"effective_resource_snapshot"`.
10
- - `observed_at`: UTC observation time.
11
- - `completeness`: `complete`, `complete_with_informational_notes`, or
12
- `partial`.
13
- - `platform`: OS family, architecture, and Python version. Hostname is omitted.
14
- - `privacy`: explicit redaction flags.
15
- - `cpu`, `memory`, `disk`, `accelerators`: resource observations.
16
- - `cgroup_v2`, `container`, `scheduler`: execution-context observations.
17
- - `warnings`: bounded sorted warning records.
18
- - `provenance`: bounded sorted source/status records.
19
-
20
- Null means unavailable, not zero and not unlimited. Zero is used only when a
21
- source explicitly establishes zero (for example, a named accelerator visibility
22
- variable that hides all devices).
23
-
24
- ## CPU
25
-
26
- `cpu.host`:
27
-
28
- - `logical`: system-visible logical CPUs.
29
- - `physical`: system-visible physical cores, or null. This value is not
30
- converted into an effective process count.
31
-
32
- `cpu.process`:
33
-
34
- - `affinity_logical`: size of the current affinity set when supported.
35
- - `python_available_logical`: `os.process_cpu_count()` when supported.
36
-
37
- `cpu.cgroup_v2`:
38
-
39
- - `cpuset_logical`: count from `cpuset.cpus.effective`.
40
- - `quota_cores`: most restrictive finite ancestor `cpu.max` ratio. This may be
41
- fractional.
42
-
43
- `cpu.effective`:
44
-
45
- - `capacity_cores`: minimum positive host/process/cgroup/scheduler capacity.
46
- - `worker_ceiling`: conservative bounded floor for CPU process workers.
47
- - `limiting_sources`: sources tied at that minimum.
48
-
49
- The effective value is intentionally not called a physical-core count.
50
-
51
- ## Memory
52
-
53
- `memory.host` preserves system-visible `total_bytes` and `available_bytes`.
54
-
55
- `memory.cgroup_v2` preserves current-cgroup usage and hierarchical effective
56
- limits:
57
-
58
- - `current_bytes`
59
- - `available_bytes`
60
- - `high_bytes`
61
- - `max_bytes`
62
-
63
- `memory.effective`:
64
-
65
- - `hard_limit_bytes`: minimum of finite host total, cgroup hard limit, and
66
- interpretable scheduler allocation.
67
- - `available_bytes`: minimum of host available, hierarchical cgroup remaining,
68
- and scheduler upper bound.
69
- - `pressure_threshold_bytes`: cgroup `memory.high`; it is not relabeled as a
70
- hard limit.
71
- - `hard_limit_sources` and `available_limiting_sources`: tied minimum sources.
72
-
73
- `memory.model` is `unified_cpu_gpu` on Apple silicon and `system_ram`
74
- otherwise. Unified GPU memory is not added again as dedicated VRAM.
75
-
76
- ## Disk
77
-
78
- - `capacity_bytes`: total working-filesystem capacity.
79
- - `free_bytes`: filesystem free blocks.
80
- - `user_available_bytes`: user-available blocks where the OS exposes them.
81
- - `writable`: result of a non-writing access check.
82
- - `writability_check`: makes clear that no write probe occurred.
83
- - `scope`: `working_filesystem_path_redacted`.
84
-
85
- None of these values proves that a filesystem or project quota permits a write
86
- of the same size.
87
-
88
- ## Accelerators
89
-
90
- `accelerators.devices` contains management-visible or explicitly
91
- platform-inferred candidates:
92
-
93
- - `vendor`: `nvidia`, `amd`, or `apple`.
94
- - `device_class`: keeps integrated and discrete GPU concepts distinct.
95
- - `backend_candidate`: `cuda`, `rocm`, or `metal`.
96
- - `management_query`: visibility evidence.
97
- - `device_permission`: `not_tested`; a query does not prove device-node access.
98
- - `runtime_compatibility`: `not_tested` in detector output.
99
- - `memory.model`: dedicated/HBM, unified, or unknown.
100
- - `local_index`: local query index; stable UUIDs and PCI addresses are omitted.
101
-
102
- `candidate_counts` is a query count, not a usable-device count.
103
- `candidate_upper_bounds` conservatively intersects query count with parsed
104
- visibility/allocation counts when available. `runtime_usable_devices` remains
105
- null because no framework runtime is loaded.
106
-
107
- `visibility_environment` includes only four allowlisted variable names. Raw
108
- values are never emitted.
109
-
110
- ## Scheduler and cgroup
111
-
112
- `scheduler.fields_read` lists allowlisted Slurm names that were present.
113
- `scheduler.allocation` contains parsed bounded values and scopes.
114
- `scheduler.enforcement` remains `unknown`; variables alone do not prove
115
- confinement.
116
-
117
- `cgroup_v2.scope` says only `root`, `non_root`, `unknown`, or `not_applicable`.
118
- The cgroup path is not emitted.
119
-
120
- `container.detected` requires a known marker. A `cgroup_limit` can appear as
121
- evidence without asserting that the process is in a container.
122
-
123
- ## Warnings and provenance
124
-
125
- Warnings use:
126
-
127
- ```json
128
- {
129
- "code": "STABLE_MACHINE_CODE",
130
- "component": "cpu",
131
- "message": "Human-readable, sanitized explanation.",
132
- "severity": "info"
133
- }
134
- ```
135
-
136
- Probe exception text, stderr, paths, hostnames, device UUIDs, and broad
137
- environment content are excluded.
138
-
139
- Provenance uses:
140
-
141
- ```json
142
- {
143
- "component": "cpu.process.affinity_logical",
144
- "source": "os.sched_getaffinity",
145
- "status": "ok"
146
- }
147
- ```
148
-
149
- Possible status values include `ok`, `unavailable`, `absent`, `skipped`,
150
- `not_found`, `timeout`, `truncated`, `error`, and `parse_error`.
151
-
152
- ## Validation and diff
153
-
154
- Validate:
155
-
156
- ```bash
157
- python scripts/snapshot_tools.py validate resource-snapshot.json
158
- ```
159
-
160
- Diff while ignoring `observed_at`:
161
-
162
- ```bash
163
- python scripts/snapshot_tools.py diff before.json after.json
164
- ```
165
-
166
- Use `--include-volatile` only when timestamp changes matter. Diff output is
167
- bounded to 512 changes.
168
-
169
- All helper inputs are regular, non-symlink JSON files no larger than 1 MiB.
170
- Output defaults to stdout. Explicit file output is restricted to a `.json`
171
- filename in the current directory, refuses overwrite unless `--force` is used,
172
- and is opened with private permissions.
@@ -1,124 +0,0 @@
1
- # Official Sources
2
-
3
- Research cut-off: **2026-07-23**. Every URL below was consulted on that
4
- date. Undated living documentation is labeled "living docs"; a date in
5
- parentheses is the page/release date visible in the source.
6
-
7
- ## psutil
8
-
9
- - [psutil 7.2.2 documentation](https://psutil.readthedocs.io/) — living docs.
10
- Used for logical versus physical CPU counts, the warning that system CPU
11
- count can differ from process-usable CPUs under affinity/cgroups/Windows
12
- processor groups, `Process.cpu_affinity()`, `virtual_memory()`,
13
- `swap_memory()`, and `disk_usage()`.
14
- - [psutil 7.2.2 on PyPI](https://pypi.org/project/psutil/7.2.2/) — current
15
- stable package pin verified 2026-07-23.
16
-
17
- ## Python
18
-
19
- - [Python `os` documentation](https://docs.python.org/3/library/os.html) —
20
- Python 3.14.6 living docs. Used for `os.cpu_count()`,
21
- `os.process_cpu_count()`, and `os.sched_getaffinity()`.
22
- - [Python multiprocessing](https://docs.python.org/3/library/multiprocessing.html)
23
- — Python 3.14.6 living docs. Used for process-aware pool defaults and the
24
- Python 3.14 start-method change.
25
- - [Python concurrent.futures](https://docs.python.org/3/library/concurrent.futures.html)
26
- — Python 3.14.6 living docs. Used for `ProcessPoolExecutor` defaults,
27
- Windows' 61-worker maximum, and `ThreadPoolExecutor` defaults.
28
-
29
- ## Linux procfs and cgroup v2
30
-
31
- - [Linux kernel `/proc` filesystem documentation](https://docs.kernel.org/filesystems/proc.html)
32
- — living kernel docs. Used for `Cpus_allowed` and
33
- `Cpus_allowed_list`.
34
- - [Linux kernel cgroup v2 documentation](https://docs.kernel.org/admin-guide/cgroup-v2.html)
35
- — living kernel docs; page history begins 2014-07-15. Used for
36
- `cpu.max`, `cpuset.cpus.effective`, `memory.current`, `memory.high`,
37
- `memory.max`, hierarchy, reclaim, and cgroup OOM behavior.
38
- - [Linux kernel cpuset documentation](https://www.kernel.org/doc/html/latest/admin-guide/cgroup-v1/cpusets.html)
39
- — living kernel docs. Used to cross-check the interaction between affinity
40
- masks and cpuset constraints.
41
-
42
- ## Containers and OCI
43
-
44
- - [Docker resource constraints](https://docs.docker.com/engine/containers/resource_constraints/)
45
- — living docs. Used for Docker's default lack of constraints, `--cpus`,
46
- quota/period, cpusets, and memory controls.
47
- - [OCI Runtime Specification: Linux resources](https://specs.opencontainers.org/runtime-spec/config-linux/?v=v1.3.0)
48
- — OCI Runtime Spec 1.3.0. Used for CPU, memory, cgroup, and device resource
49
- semantics.
50
-
51
- ## NVIDIA
52
-
53
- - [NVIDIA System Management Interface manual](https://docs.nvidia.com/deploy/nvidia-smi/index.html)
54
- — living docs. Used for fixed `--query-gpu` fields and
55
- `--format=csv,noheader,nounits`; NVIDIA notes that index ordering is not
56
- stable, which is why snapshots do not claim a persistent identity.
57
- - [NVIDIA Container Toolkit specialized configurations](https://docs.nvidia.com/datacenter/cloud-native/container-toolkit/latest/docker-specialized.html)
58
- — living docs. Used for `NVIDIA_VISIBLE_DEVICES`, driver capabilities, and
59
- runtime constraints.
60
- - [NVIDIA `CUDA_VISIBLE_DEVICES`](https://docs.nvidia.com/deploy/topics/topic_5_2_1.html)
61
- — official deployment documentation. Used for CUDA application visibility.
62
- - [NVIDIA CUDA compatibility](https://docs.nvidia.com/deploy/cuda-compatibility/latest/why-cuda-compatibility.html)
63
- — living docs. Used to distinguish management visibility from compatible
64
- GPU, driver, CUDA runtime, and dynamically linked libraries.
65
-
66
- ## AMD ROCm
67
-
68
- - [AMD SMI CLI tool](https://rocm.docs.amd.com/projects/amdsmi/en/docs-7.2.0/how-to/amdsmi-cli-tool.html)
69
- — AMD SMI 7.2.0 docs. Used for read-only `list`/`static` JSON output and the
70
- meaning of unavailable fields.
71
- - [ROCm SMI Python/CLI usage](https://rocm.docs.amd.com/projects/rocm_smi_lib/en/latest/how-to/use-python.html)
72
- — living docs. Used for the legacy `rocm-smi` read-only fallback.
73
- - [ROCm GPU isolation techniques](https://rocm.docs.amd.com/en/docs-7.2.4/conceptual/gpu-isolation.html)
74
- — ROCm 7.2.4 docs. Used for `ROCR_VISIBLE_DEVICES`,
75
- `HIP_VISIBLE_DEVICES`, `CUDA_VISIBLE_DEVICES`, Docker device isolation, and
76
- the warning that environment variables are not isolation for untrusted code.
77
- - [ROCm environment variables](https://rocm.docs.amd.com/en/latest/reference/environment-variables/index.html)
78
- — living docs. Used for AMD's Linux/Windows visibility-variable
79
- recommendations.
80
-
81
- ## Apple
82
-
83
- - [Apple: Determining system capabilities](https://developer.apple.com/documentation/kernel/1387446-sysctlbyname/determining_system_capabilities)
84
- — living Apple Developer docs. Used for `hw.logicalcpu`,
85
- `hw.physicalcpu`, `hw.memsize`, performance levels, and the distinction
86
- between logical and physical cores.
87
- - [Apple `sysctl(3)` manual](https://developer.apple.com/library/archive/documentation/System/Conceptual/ManPages_iPhoneOS/man3/sysctl.3.html)
88
- — archived official manual. Used to cross-check physical-memory fields.
89
- - [Apple Developer Technical Support: system_profiler and integrated/SoC memory](https://developer.apple.com/forums/thread/688443)
90
- — Apple DTS response dated 2021-08-24. Used for parseable
91
- `system_profiler` output and the warning that DIMM-style details do not map
92
- cleanly to integrated or Apple silicon memory.
93
- - The fixed `system_profiler SPDisplaysDataType -json` and named `sysctl -n`
94
- queries were smoke-checked locally on Darwin 25.5.0 on 2026-07-23. The
95
- script never requests the full system profile.
96
-
97
- ## Slurm
98
-
99
- - [Slurm `sbatch`](https://slurm.schedmd.com/sbatch.html) — living SchedMD
100
- docs. Used for exact output environment-variable scopes:
101
- `SLURM_CPUS_ON_NODE`, `SLURM_CPUS_PER_TASK`,
102
- `SLURM_JOB_CPUS_PER_NODE`, `SLURM_MEM_PER_CPU`,
103
- `SLURM_MEM_PER_NODE`, `SLURM_NTASKS`, and GPU variables. Also used for
104
- the explicit warning that memory requests require configured enforcement.
105
- - [Slurm CPU Management Guide](https://slurm.schedmd.com/cpu_management.html)
106
- — living SchedMD docs. Used for `task/affinity`, `task/cgroup`,
107
- `ConstrainCores`, binding, and logical CPU/core allocation examples.
108
- - [Slurm `srun`](https://slurm.schedmd.com/srun.html) — updated
109
- 2026-07-14. Used for task confinement and GPU binding behavior.
110
- - [Slurm `scontrol`](https://slurm.schedmd.com/scontrol.html) — living docs.
111
- Used for the read-only `scontrol show job` interpretation workflow.
112
- - [Slurm `sstat`](https://slurm.schedmd.com/sstat.html) — living docs. Used
113
- for post-launch job-step accounting semantics.
114
-
115
- ## Windows
116
-
117
- - [Microsoft: Processor Groups](https://learn.microsoft.com/en-us/windows/win32/procthread/processor-groups)
118
- — living Microsoft docs. Used for the distinction between system logical
119
- processors, physical cores, and processor-group scheduling.
120
- - [GetLogicalProcessorInformation](https://learn.microsoft.com/en-us/windows/win32/api/sysinfoapi/nf-sysinfoapi-getlogicalprocessorinformation)
121
- — living Microsoft docs. Used for logical/physical relationships and the
122
- current-group limitation on systems over 64 logical processors.
123
- - [GetLogicalProcessorInformationEx](https://learn.microsoft.com/en-us/windows/win32/api/sysinfoapi/nf-sysinfoapi-getlogicalprocessorinformationex)
124
- — page dated 2023-03-06. Used for system-wide processor-group topology.
@@ -1,190 +0,0 @@
1
- #!/usr/bin/env python3
2
- """Shared, dependency-free safety and JSON helpers."""
3
-
4
- from __future__ import annotations
5
-
6
- import argparse
7
- import json
8
- import math
9
- import os
10
- import stat
11
- import sys
12
- from pathlib import Path
13
- from typing import Any
14
-
15
- SCHEMA_VERSION = "1.1"
16
- MAX_SNAPSHOT_BYTES = 1_048_576
17
- MAX_WORKERS = 1_024
18
- MAX_TASKS = 1_000_000_000
19
- MAX_BYTES = 1 << 63
20
-
21
-
22
- class ResourceToolError(ValueError):
23
- """A concise, user-safe CLI error."""
24
-
25
-
26
- def json_text(value: Any) -> str:
27
- """Serialize deterministic, standards-compliant JSON."""
28
- try:
29
- return (
30
- json.dumps(
31
- value,
32
- allow_nan=False,
33
- ensure_ascii=False,
34
- indent=2,
35
- sort_keys=True,
36
- )
37
- + "\n"
38
- )
39
- except (RecursionError, TypeError, ValueError) as exc:
40
- raise ResourceToolError("result is not valid JSON data") from exc
41
-
42
-
43
- def _safe_output_path(raw: str) -> Path:
44
- """Restrict writes to one explicit JSON filename in the current directory."""
45
- if not raw or len(raw) > 255:
46
- raise ResourceToolError("output must be a short JSON filename")
47
- candidate = Path(raw)
48
- if candidate.is_absolute() or len(candidate.parts) != 1:
49
- raise ResourceToolError(
50
- "output must be a filename in the current directory, not a path"
51
- )
52
- if candidate.name in {".", ".."} or candidate.suffix.lower() != ".json":
53
- raise ResourceToolError("output filename must end in .json")
54
- return Path.cwd() / candidate.name
55
-
56
-
57
- def emit_json(value: Any, output: str | None = None, *, force: bool = False) -> None:
58
- """Write JSON to stdout or an explicit private local file."""
59
- payload = json_text(value)
60
- if output is None:
61
- sys.stdout.write(payload)
62
- return
63
-
64
- destination = _safe_output_path(output)
65
- try:
66
- if destination.is_symlink():
67
- raise ResourceToolError("refusing to write through a symbolic link")
68
- flags = os.O_WRONLY | os.O_CREAT
69
- flags |= os.O_TRUNC if force else os.O_EXCL
70
- if hasattr(os, "O_NOFOLLOW"):
71
- flags |= os.O_NOFOLLOW
72
- descriptor = os.open(destination, flags, 0o600)
73
- try:
74
- if hasattr(os, "fchmod"):
75
- os.fchmod(descriptor, 0o600)
76
- with os.fdopen(descriptor, "w", encoding="utf-8") as stream:
77
- descriptor = -1
78
- stream.write(payload)
79
- stream.flush()
80
- os.fsync(stream.fileno())
81
- finally:
82
- if descriptor >= 0:
83
- os.close(descriptor)
84
- except FileExistsError as exc:
85
- raise ResourceToolError(
86
- f"{destination.name} already exists; use --force to replace it"
87
- ) from exc
88
- except OSError as exc:
89
- raise ResourceToolError(
90
- f"could not write the requested output file ({exc.__class__.__name__})"
91
- ) from exc
92
-
93
-
94
- def read_json_file(raw: str) -> dict[str, Any]:
95
- """Read one bounded regular JSON file without following symlinks."""
96
- path = Path(raw)
97
- try:
98
- if path.is_symlink():
99
- raise ResourceToolError("refusing to read a symbolic link")
100
- info = path.stat()
101
- if not stat.S_ISREG(info.st_mode):
102
- raise ResourceToolError("snapshot input must be a regular file")
103
- if info.st_size > MAX_SNAPSHOT_BYTES:
104
- raise ResourceToolError(
105
- f"snapshot input exceeds {MAX_SNAPSHOT_BYTES} bytes"
106
- )
107
- with path.open("rb") as stream:
108
- payload = stream.read(MAX_SNAPSHOT_BYTES + 1)
109
- if len(payload) > MAX_SNAPSHOT_BYTES:
110
- raise ResourceToolError(
111
- f"snapshot input exceeds {MAX_SNAPSHOT_BYTES} bytes"
112
- )
113
- except ResourceToolError:
114
- raise
115
- except OSError as exc:
116
- raise ResourceToolError(
117
- f"could not read snapshot ({exc.__class__.__name__})"
118
- ) from exc
119
- try:
120
- parsed = json.loads(payload)
121
- except (RecursionError, UnicodeDecodeError, json.JSONDecodeError) as exc:
122
- raise ResourceToolError("snapshot is not valid UTF-8 JSON") from exc
123
- if not isinstance(parsed, dict):
124
- raise ResourceToolError("snapshot JSON root must be an object")
125
- return parsed
126
-
127
-
128
- def bounded_int(
129
- value: Any,
130
- *,
131
- minimum: int = 0,
132
- maximum: int = MAX_BYTES,
133
- ) -> int | None:
134
- """Return a bounded integer without accepting booleans or floats."""
135
- if isinstance(value, bool):
136
- return None
137
- if isinstance(value, int) and minimum <= value <= maximum:
138
- return value
139
- return None
140
-
141
-
142
- def bounded_number(
143
- value: Any,
144
- *,
145
- minimum: float = 0.0,
146
- maximum: float = float(MAX_BYTES),
147
- ) -> float | None:
148
- """Return a finite bounded number without accepting booleans."""
149
- if isinstance(value, bool) or not isinstance(value, (int, float)):
150
- return None
151
- number = float(value)
152
- if not math.isfinite(number) or not minimum <= number <= maximum:
153
- return None
154
- return number
155
-
156
-
157
- def argparse_positive_int(
158
- value: str,
159
- *,
160
- maximum: int = MAX_TASKS,
161
- ) -> int:
162
- """Argparse converter for bounded positive integers."""
163
- try:
164
- parsed = int(value, 10)
165
- except ValueError as exc:
166
- raise argparse.ArgumentTypeError("must be an integer") from exc
167
- if not 1 <= parsed <= maximum:
168
- raise argparse.ArgumentTypeError(f"must be between 1 and {maximum}")
169
- return parsed
170
-
171
-
172
- def argparse_nonnegative_int(
173
- value: str,
174
- *,
175
- maximum: int = MAX_BYTES,
176
- ) -> int:
177
- """Argparse converter for bounded nonnegative integers."""
178
- try:
179
- parsed = int(value, 10)
180
- except ValueError as exc:
181
- raise argparse.ArgumentTypeError("must be an integer") from exc
182
- if not 0 <= parsed <= maximum:
183
- raise argparse.ArgumentTypeError(f"must be between 0 and {maximum}")
184
- return parsed
185
-
186
-
187
- def cli_error(parser: argparse.ArgumentParser, exc: Exception) -> int:
188
- """Print one safe CLI error without a traceback."""
189
- parser.exit(2, f"{parser.prog}: error: {exc}\n")
190
- return 2