@pikaa-ai/pikaa 0.3.1 → 0.3.5
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.
- package/dist/cli.js +1181 -600
- package/dist/index.js +525 -204
- package/package.json +5 -3
- package/skills/adaptyv/references/api-endpoints.md +0 -690
- package/skills/aeon/references/anomaly_detection.md +0 -154
- package/skills/aeon/references/classification.md +0 -144
- package/skills/aeon/references/clustering.md +0 -123
- package/skills/aeon/references/datasets_benchmarking.md +0 -392
- package/skills/aeon/references/distances.md +0 -256
- package/skills/aeon/references/forecasting.md +0 -109
- package/skills/aeon/references/networks.md +0 -289
- package/skills/aeon/references/regression.md +0 -118
- package/skills/aeon/references/segmentation.md +0 -163
- package/skills/aeon/references/similarity_search.md +0 -187
- package/skills/aeon/references/transformations.md +0 -246
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
- package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
- package/skills/analytical-method-validation/references/framework-selection.md +0 -87
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
- package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
- package/skills/analytical-method-validation/references/source-ledger.md +0 -125
- package/skills/analytical-method-validation/references/statistics.md +0 -209
- package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
- package/skills/analytical-method-validation/scripts/_common.py +0 -955
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
- package/skills/analytical-method-validation/scripts/check_response.py +0 -243
- package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
- package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
- package/skills/anndata/references/best_practices.md +0 -532
- package/skills/anndata/references/concatenation.md +0 -399
- package/skills/anndata/references/data_structure.md +0 -314
- package/skills/anndata/references/io_operations.md +0 -466
- package/skills/anndata/references/manipulation.md +0 -516
- package/skills/arbor/references/arbor-upstream.md +0 -91
- package/skills/arbor/references/executor-brief.md +0 -68
- package/skills/arbor/references/htr-methodology.md +0 -177
- package/skills/arbor/references/report-template.md +0 -39
- package/skills/arbor/scripts/tree.py +0 -564
- package/skills/arboreto/references/algorithms.md +0 -152
- package/skills/arboreto/references/basic_inference.md +0 -181
- package/skills/arboreto/references/distributed_computing.md +0 -242
- package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
- package/skills/astropy/references/coordinates.md +0 -280
- package/skills/astropy/references/cosmology.md +0 -309
- package/skills/astropy/references/fits.md +0 -398
- package/skills/astropy/references/tables.md +0 -495
- package/skills/astropy/references/time.md +0 -412
- package/skills/astropy/references/units.md +0 -178
- package/skills/astropy/references/wcs_and_other_modules.md +0 -377
- package/skills/autoskill/config.yaml +0 -53
- package/skills/autoskill/references/https-proxy.md +0 -62
- package/skills/autoskill/references/screenpipe-config.yaml +0 -61
- package/skills/autoskill/scripts/autoskill.py +0 -35
- package/skills/autoskill/scripts/backends.py +0 -116
- package/skills/autoskill/scripts/cluster.py +0 -54
- package/skills/autoskill/scripts/doctor.py +0 -108
- package/skills/autoskill/scripts/fetch_window.py +0 -33
- package/skills/autoskill/scripts/match_skills.py +0 -46
- package/skills/autoskill/scripts/promote.py +0 -58
- package/skills/autoskill/scripts/redact.py +0 -40
- package/skills/autoskill/scripts/run.py +0 -194
- package/skills/autoskill/scripts/synthesize.py +0 -72
- package/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/skills/benchling-integration/references/authentication.md +0 -390
- package/skills/benchling-integration/references/core_capabilities.md +0 -355
- package/skills/benchling-integration/references/eventbridge.md +0 -255
- package/skills/benchling-integration/references/sdk_reference.md +0 -772
- package/skills/bids/references/beps.yml +0 -637
- package/skills/bids/references/bids_schema.json +0 -21015
- package/skills/bids/references/bids_specification.md +0 -165
- package/skills/bids/references/conversion_tools.md +0 -475
- package/skills/bids/references/core_workflows.md +0 -552
- package/skills/bids/references/metadata_fields.md +0 -365
- package/skills/bids/scripts/update_schema.py +0 -89
- package/skills/biopython/references/advanced.md +0 -580
- package/skills/biopython/references/alignment.md +0 -377
- package/skills/biopython/references/blast.md +0 -463
- package/skills/biopython/references/databases.md +0 -492
- package/skills/biopython/references/phylogenetics.md +0 -566
- package/skills/biopython/references/sequence_io.md +0 -289
- package/skills/biopython/references/structure.md +0 -564
- package/skills/bioservices/references/identifier_mapping.md +0 -685
- package/skills/bioservices/references/services_reference.md +0 -638
- package/skills/bioservices/references/workflow_patterns.md +0 -813
- package/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
- package/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
- package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
- package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
- package/skills/cellxgene-census/references/census_schema.md +0 -218
- package/skills/cellxgene-census/references/common_patterns.md +0 -368
- package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
- package/skills/cirq/references/building.md +0 -307
- package/skills/cirq/references/experiments.md +0 -572
- package/skills/cirq/references/hardware.md +0 -527
- package/skills/cirq/references/noise.md +0 -514
- package/skills/cirq/references/simulation.md +0 -353
- package/skills/cirq/references/transformation.md +0 -416
- package/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/skills/citation-management/assets/citation_checklist.md +0 -386
- package/skills/citation-management/references/best_practices.md +0 -91
- package/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/skills/citation-management/references/citation_validation.md +0 -835
- package/skills/citation-management/references/core_workflow.md +0 -569
- package/skills/citation-management/references/example_workflows.md +0 -126
- package/skills/citation-management/references/google_scholar_search.md +0 -732
- package/skills/citation-management/references/metadata_extraction.md +0 -870
- package/skills/citation-management/references/pubmed_search.md +0 -839
- package/skills/citation-management/references/script_reference.md +0 -250
- package/skills/citation-management/references/search_strategies.md +0 -110
- package/skills/citation-management/scripts/_common.py +0 -331
- package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
- package/skills/citation-management/scripts/extract_metadata.py +0 -690
- package/skills/citation-management/scripts/format_bibtex.py +0 -356
- package/skills/citation-management/scripts/search_google_scholar.py +0 -268
- package/skills/citation-management/scripts/search_openalex.py +0 -297
- package/skills/citation-management/scripts/search_pubmed.py +0 -419
- package/skills/citation-management/scripts/validate_citations.py +0 -688
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
- package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
- package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
- package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
- package/skills/clinical-decision-support/references/security_validation.md +0 -60
- package/skills/clinical-decision-support/references/sources.md +0 -119
- package/skills/clinical-decision-support/references/study_reporting.md +0 -134
- package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
- package/skills/clinical-decision-support/scripts/_common.py +0 -223
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
- package/skills/clinical-reports/assets/case_report_template.json +0 -43
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
- package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
- package/skills/clinical-reports/assets/lab_report_template.json +0 -36
- package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
- package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
- package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
- package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
- package/skills/clinical-reports/assets/research_summary_template.json +0 -36
- package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
- package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
- package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
- package/skills/clinical-reports/references/data_presentation.md +0 -92
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
- package/skills/clinical-reports/references/medical_terminology.md +0 -84
- package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
- package/skills/clinical-reports/references/professional_review.md +0 -78
- package/skills/clinical-reports/references/report_type_routing.md +0 -57
- package/skills/clinical-reports/references/safety_reporting.md +0 -109
- package/skills/clinical-reports/references/sources.md +0 -75
- package/skills/clinical-reports/scripts/_common.py +0 -263
- package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
- package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
- package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
- package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
- package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
- package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
- package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
- package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
- package/skills/cobrapy/references/api_quick_reference.md +0 -665
- package/skills/cobrapy/references/workflows.md +0 -600
- package/skills/consciousness-council/references/advanced-configurations.md +0 -96
- package/skills/dask/references/arrays.md +0 -495
- package/skills/dask/references/bags.md +0 -468
- package/skills/dask/references/best-practices.md +0 -277
- package/skills/dask/references/dataframes.md +0 -370
- package/skills/dask/references/futures.md +0 -541
- package/skills/dask/references/schedulers.md +0 -517
- package/skills/database-lookup/references/addgene.md +0 -38
- package/skills/database-lookup/references/alphafold.md +0 -52
- package/skills/database-lookup/references/alphavantage.md +0 -261
- package/skills/database-lookup/references/bea.md +0 -409
- package/skills/database-lookup/references/bindingdb.md +0 -85
- package/skills/database-lookup/references/biogrid.md +0 -110
- package/skills/database-lookup/references/bls.md +0 -235
- package/skills/database-lookup/references/brenda.md +0 -71
- package/skills/database-lookup/references/cbioportal.md +0 -206
- package/skills/database-lookup/references/census.md +0 -251
- package/skills/database-lookup/references/chebi.md +0 -103
- package/skills/database-lookup/references/chembl.md +0 -80
- package/skills/database-lookup/references/clinicaltrials.md +0 -86
- package/skills/database-lookup/references/clinpgx.md +0 -64
- package/skills/database-lookup/references/clinvar.md +0 -91
- package/skills/database-lookup/references/cod.md +0 -121
- package/skills/database-lookup/references/cosmic.md +0 -59
- package/skills/database-lookup/references/dailymed.md +0 -65
- package/skills/database-lookup/references/database_selection_guide.md +0 -166
- package/skills/database-lookup/references/datacommons.md +0 -237
- package/skills/database-lookup/references/dbsnp.md +0 -143
- package/skills/database-lookup/references/disgenet.md +0 -52
- package/skills/database-lookup/references/drugbank.md +0 -54
- package/skills/database-lookup/references/ecb.md +0 -191
- package/skills/database-lookup/references/emdb.md +0 -37
- package/skills/database-lookup/references/ena.md +0 -372
- package/skills/database-lookup/references/encode.md +0 -47
- package/skills/database-lookup/references/ensembl.md +0 -539
- package/skills/database-lookup/references/epa.md +0 -232
- package/skills/database-lookup/references/eurostat.md +0 -237
- package/skills/database-lookup/references/fda.md +0 -64
- package/skills/database-lookup/references/federal-reserve.md +0 -216
- package/skills/database-lookup/references/fred.md +0 -297
- package/skills/database-lookup/references/gene-ontology.md +0 -147
- package/skills/database-lookup/references/geo.md +0 -130
- package/skills/database-lookup/references/gnomad.md +0 -93
- package/skills/database-lookup/references/gtex.md +0 -136
- package/skills/database-lookup/references/gwas-catalog.md +0 -46
- package/skills/database-lookup/references/hca.md +0 -35
- package/skills/database-lookup/references/hpo.md +0 -48
- package/skills/database-lookup/references/human-protein-atlas.md +0 -57
- package/skills/database-lookup/references/interpro.md +0 -120
- package/skills/database-lookup/references/jaspar.md +0 -50
- package/skills/database-lookup/references/kegg.md +0 -78
- package/skills/database-lookup/references/lincs-l1000.md +0 -68
- package/skills/database-lookup/references/materials-project.md +0 -123
- package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
- package/skills/database-lookup/references/monarch.md +0 -46
- package/skills/database-lookup/references/mousemine.md +0 -40
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
- package/skills/database-lookup/references/nasa.md +0 -121
- package/skills/database-lookup/references/ncbi-gene.md +0 -64
- package/skills/database-lookup/references/ncbi-protein.md +0 -104
- package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
- package/skills/database-lookup/references/nist.md +0 -105
- package/skills/database-lookup/references/noaa.md +0 -199
- package/skills/database-lookup/references/omim.md +0 -114
- package/skills/database-lookup/references/opentargets.md +0 -459
- package/skills/database-lookup/references/openweathermap.md +0 -255
- package/skills/database-lookup/references/pdb.md +0 -121
- package/skills/database-lookup/references/pride.md +0 -74
- package/skills/database-lookup/references/pubchem.md +0 -145
- package/skills/database-lookup/references/quickgo.md +0 -45
- package/skills/database-lookup/references/reactome.md +0 -140
- package/skills/database-lookup/references/retrieval-contract.md +0 -123
- package/skills/database-lookup/references/rummageo.md +0 -32
- package/skills/database-lookup/references/sdss.md +0 -130
- package/skills/database-lookup/references/sec-edgar.md +0 -315
- package/skills/database-lookup/references/simbad.md +0 -405
- package/skills/database-lookup/references/sra.md +0 -149
- package/skills/database-lookup/references/string.md +0 -283
- package/skills/database-lookup/references/tcga-gdc.md +0 -58
- package/skills/database-lookup/references/treasury.md +0 -215
- package/skills/database-lookup/references/ucsc-genome.md +0 -135
- package/skills/database-lookup/references/uniprot.md +0 -283
- package/skills/database-lookup/references/usgs.md +0 -260
- package/skills/database-lookup/references/uspto.md +0 -130
- package/skills/database-lookup/references/who.md +0 -283
- package/skills/database-lookup/references/worldbank.md +0 -239
- package/skills/database-lookup/references/zinc.md +0 -202
- package/skills/datamol/references/conformers_module.md +0 -131
- package/skills/datamol/references/core_api.md +0 -136
- package/skills/datamol/references/core_workflows.md +0 -451
- package/skills/datamol/references/descriptors_viz.md +0 -195
- package/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/skills/datamol/references/io_module.md +0 -112
- package/skills/datamol/references/reactions_data.md +0 -218
- package/skills/datamol/references/workflow_patterns.md +0 -104
- package/skills/deepchem/references/api_reference.md +0 -305
- package/skills/deepchem/references/core_capabilities.md +0 -276
- package/skills/deepchem/references/typical_workflows.md +0 -109
- package/skills/deepchem/references/workflows.md +0 -491
- package/skills/deepchem/scripts/graph_neural_network.py +0 -350
- package/skills/deepchem/scripts/predict_solubility.py +0 -223
- package/skills/deepchem/scripts/transfer_learning.py +0 -443
- package/skills/deepspot-m/references/api.md +0 -186
- package/skills/deepspot-m/references/whole_slide.md +0 -174
- package/skills/deeptools/assets/quick_reference.md +0 -65
- package/skills/deeptools/references/core_workflows.md +0 -134
- package/skills/deeptools/references/effective_genome_sizes.md +0 -118
- package/skills/deeptools/references/normalization_methods.md +0 -424
- package/skills/deeptools/references/tools_reference.md +0 -569
- package/skills/deeptools/references/workflows.md +0 -476
- package/skills/deeptools/scripts/validate_files.py +0 -195
- package/skills/deeptools/scripts/workflow_generator.py +0 -520
- package/skills/depmap/references/dependency_analysis.md +0 -178
- package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
- package/skills/diffdock/assets/batch_template.csv +0 -4
- package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
- package/skills/diffdock/references/confidence_and_limitations.md +0 -182
- package/skills/diffdock/references/parameters_reference.md +0 -173
- package/skills/diffdock/references/workflows_examples.md +0 -401
- package/skills/diffdock/scripts/analyze_results.py +0 -346
- package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
- package/skills/diffdock/scripts/setup_check.py +0 -283
- package/skills/dnanexus-integration/references/app-development.md +0 -371
- package/skills/dnanexus-integration/references/authentication.md +0 -226
- package/skills/dnanexus-integration/references/configuration.md +0 -444
- package/skills/dnanexus-integration/references/data-operations.md +0 -474
- package/skills/dnanexus-integration/references/job-execution.md +0 -482
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
- package/skills/dnanexus-integration/references/python-sdk.md +0 -548
- package/skills/dnanexus-integration/references/sources.md +0 -168
- package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
- package/skills/docx/LICENSE.txt +0 -30
- package/skills/docx/scripts/__init__.py +0 -1
- package/skills/docx/scripts/accept_changes.py +0 -135
- package/skills/docx/scripts/comment.py +0 -368
- package/skills/docx/scripts/merge_runs.py +0 -310
- package/skills/docx/scripts/office/helpers/__init__.py +0 -111
- package/skills/docx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/docx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/docx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/docx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/docx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/docx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/docx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/docx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/docx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/docx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/docx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/docx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/docx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/docx/scripts/office/soffice.py +0 -232
- package/skills/docx/scripts/office/validate.py +0 -173
- package/skills/docx/scripts/office/validators/__init__.py +0 -15
- package/skills/docx/scripts/office/validators/base.py +0 -875
- package/skills/docx/scripts/office/validators/docx.py +0 -466
- package/skills/docx/scripts/office/validators/pptx.py +0 -441
- package/skills/docx/scripts/office/validators/redlining.py +0 -299
- package/skills/docx/scripts/templates/comments.xml +0 -3
- package/skills/docx/scripts/templates/commentsExtended.xml +0 -3
- package/skills/docx/scripts/templates/commentsExtensible.xml +0 -3
- package/skills/docx/scripts/templates/commentsIds.xml +0 -3
- package/skills/docx/scripts/templates/people.xml +0 -3
- package/skills/esm/references/biohub-platform.md +0 -111
- package/skills/esm/references/esm-c-api.md +0 -609
- package/skills/esm/references/esm3-api.md +0 -462
- package/skills/esm/references/forge-api.md +0 -675
- package/skills/esm/references/workflows.md +0 -685
- package/skills/etetoolkit/references/api_reference.md +0 -546
- package/skills/etetoolkit/references/migration-ete3-to-ete4.md +0 -579
- package/skills/etetoolkit/references/taxonomy.md +0 -362
- package/skills/etetoolkit/references/visualization.md +0 -516
- package/skills/etetoolkit/references/workflows.md +0 -537
- package/skills/etetoolkit/scripts/quick_visualize.py +0 -455
- package/skills/etetoolkit/scripts/tree_operations.py +0 -446
- package/skills/exa-search/references/web-extract.md +0 -53
- package/skills/exa-search/references/web-search.md +0 -119
- package/skills/exa-search/scripts/exa_extract.py +0 -117
- package/skills/exa-search/scripts/exa_search.py +0 -179
- package/skills/experimental-design/references/design_types.md +0 -129
- package/skills/experimental-design/references/factorial_and_doe.md +0 -130
- package/skills/experimental-design/references/randomization_and_blocking.md +0 -116
- package/skills/experimental-design/references/sequential_and_adaptive.md +0 -97
- package/skills/experimental-design/scripts/doe_designs.py +0 -183
- package/skills/experimental-design/scripts/randomization.py +0 -171
- package/skills/exploratory-data-analysis/assets/report_template.md +0 -202
- package/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +0 -192
- package/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +0 -183
- package/skills/exploratory-data-analysis/references/general_scientific_formats.md +0 -259
- package/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +0 -189
- package/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +0 -217
- package/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +0 -191
- package/skills/exploratory-data-analysis/scripts/__init__.py +0 -1
- package/skills/exploratory-data-analysis/scripts/_capabilities.py +0 -576
- package/skills/exploratory-data-analysis/scripts/_common.py +0 -460
- package/skills/exploratory-data-analysis/scripts/_structured.py +0 -391
- package/skills/exploratory-data-analysis/scripts/_tabular.py +0 -905
- package/skills/exploratory-data-analysis/scripts/capability_manifest.py +0 -184
- package/skills/exploratory-data-analysis/scripts/distribution_sensitivity.py +0 -117
- package/skills/exploratory-data-analysis/scripts/eda_analyzer.py +0 -345
- package/skills/exploratory-data-analysis/scripts/image_inspector.py +0 -214
- package/skills/exploratory-data-analysis/scripts/missingness_leakage_audit.py +0 -130
- package/skills/exploratory-data-analysis/scripts/report_scaffold.py +0 -143
- package/skills/exploratory-data-analysis/scripts/sequence_inspector.py +0 -255
- package/skills/exploratory-data-analysis/scripts/tabular_profile.py +0 -109
- package/skills/flowio/references/api_reference.md +0 -355
- package/skills/flowio/references/fcs_semantics.md +0 -315
- package/skills/flowio/references/sources.md +0 -89
- package/skills/flowio/references/troubleshooting.md +0 -399
- package/skills/flowio/references/workflows.md +0 -368
- package/skills/flowio/scripts/inspect_fcs.py +0 -439
- package/skills/fluidsim/references/advanced_features.md +0 -347
- package/skills/fluidsim/references/installation.md +0 -263
- package/skills/fluidsim/references/output_analysis.md +0 -314
- package/skills/fluidsim/references/parameters.md +0 -322
- package/skills/fluidsim/references/simulation_workflow.md +0 -329
- package/skills/fluidsim/references/solvers.md +0 -191
- package/skills/fluidsim/scripts/__init__.py +0 -1
- package/skills/fluidsim/scripts/_common.py +0 -491
- package/skills/fluidsim/scripts/_schema.py +0 -872
- package/skills/fluidsim/scripts/budget_summary.py +0 -396
- package/skills/fluidsim/scripts/grid_resource_estimator.py +0 -286
- package/skills/fluidsim/scripts/output_inventory.py +0 -353
- package/skills/fluidsim/scripts/restart_compatibility.py +0 -424
- package/skills/fluidsim/scripts/simulation_dry_run.py +0 -246
- package/skills/fluidsim/scripts/solver_config_validator.py +0 -70
- package/skills/generate-image/references/models.md +0 -173
- package/skills/generate-image/scripts/generate_image.py +0 -752
- package/skills/geniml/references/bedspace.md +0 -267
- package/skills/geniml/references/consensus_peaks.md +0 -334
- package/skills/geniml/references/region2vec.md +0 -289
- package/skills/geniml/references/scembed.md +0 -307
- package/skills/geniml/references/utilities.md +0 -385
- package/skills/geniml/scripts/__init__.py +0 -1
- package/skills/geniml/scripts/_common.py +0 -399
- package/skills/geniml/scripts/bed_validator.py +0 -363
- package/skills/geniml/scripts/consensus_plan.py +0 -416
- package/skills/geniml/scripts/corpus_auditor.py +0 -304
- package/skills/geniml/scripts/embedding_plan.py +0 -476
- package/skills/geniml/scripts/model_artifact_inspector.py +0 -358
- package/skills/geniml/scripts/tokenizer_compatibility.py +0 -321
- package/skills/genomic-coordinates/references/format-conventions.md +0 -205
- package/skills/genomic-coordinates/references/reference-builds.md +0 -154
- package/skills/genomic-coordinates/references/transcript-coordinates.md +0 -141
- package/skills/genomic-coordinates/references/variant-representation.md +0 -155
- package/skills/genomic-coordinates/scripts/_common.py +0 -335
- package/skills/genomic-coordinates/scripts/audit_intervals.py +0 -511
- package/skills/genomic-coordinates/scripts/check_contigs.py +0 -382
- package/skills/genomic-coordinates/scripts/convert_coords.py +0 -180
- package/skills/genomic-coordinates/scripts/normalize_variant.py +0 -290
- package/skills/genomic-intelligence/references/api-and-auth.md +0 -45
- package/skills/genomic-intelligence/references/mcp.md +0 -94
- package/skills/genomic-intelligence/references/sequence-acquisition.md +0 -52
- package/skills/genomic-intelligence/references/tasks.md +0 -75
- package/skills/geomaster/references/advanced-gis.md +0 -376
- package/skills/geomaster/references/big-data.md +0 -363
- package/skills/geomaster/references/code-examples.md +0 -531
- package/skills/geomaster/references/coordinate-systems.md +0 -364
- package/skills/geomaster/references/core-libraries.md +0 -273
- package/skills/geomaster/references/data-sources.md +0 -330
- package/skills/geomaster/references/gis-software.md +0 -369
- package/skills/geomaster/references/industry-applications.md +0 -420
- package/skills/geomaster/references/machine-learning.md +0 -462
- package/skills/geomaster/references/programming-languages.md +0 -456
- package/skills/geomaster/references/remote-sensing.md +0 -370
- package/skills/geomaster/references/scientific-domains.md +0 -416
- package/skills/geomaster/references/specialized-topics.md +0 -428
- package/skills/geomaster/references/troubleshooting.md +0 -439
- package/skills/geopandas/references/crs-management.md +0 -231
- package/skills/geopandas/references/data-io.md +0 -323
- package/skills/geopandas/references/data-structures.md +0 -207
- package/skills/geopandas/references/geometric-operations.md +0 -262
- package/skills/geopandas/references/spatial-analysis.md +0 -294
- package/skills/geopandas/references/visualization.md +0 -230
- package/skills/geopandas/scripts/_common.py +0 -605
- package/skills/geopandas/scripts/crs_reprojection_plan.py +0 -210
- package/skills/geopandas/scripts/export_plan.py +0 -305
- package/skills/geopandas/scripts/geometry_validity_report.py +0 -227
- package/skills/geopandas/scripts/sensitive_coordinates_checklist.py +0 -230
- package/skills/geopandas/scripts/spatial_join_audit.py +0 -368
- package/skills/geopandas/scripts/vector_inventory.py +0 -140
- package/skills/get-available-resources/references/resource_semantics.md +0 -206
- package/skills/get-available-resources/references/snapshot_schema.md +0 -172
- package/skills/get-available-resources/references/sources.md +0 -124
- package/skills/get-available-resources/scripts/_common.py +0 -190
- package/skills/get-available-resources/scripts/accelerator_diagnostics.py +0 -151
- package/skills/get-available-resources/scripts/detect_resources.py +0 -1767
- package/skills/get-available-resources/scripts/plan_workload.py +0 -311
- package/skills/get-available-resources/scripts/snapshot_tools.py +0 -486
- package/skills/gget/references/common_workflows.md +0 -120
- package/skills/gget/references/database_info.md +0 -336
- package/skills/gget/references/module_catalog.md +0 -733
- package/skills/gget/references/module_reference.md +0 -526
- package/skills/gget/references/workflows.md +0 -815
- package/skills/gget/scripts/batch_sequence_analysis.py +0 -192
- package/skills/gget/scripts/enrichment_pipeline.py +0 -235
- package/skills/gget/scripts/gene_analysis.py +0 -175
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-hibit.md +0 -53
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-optimization.md +0 -85
- package/skills/ginkgo-cloud-lab/references/cell-free-protein-expression-validation.md +0 -71
- package/skills/ginkgo-cloud-lab/references/cfps-expression-purification-quantification.md +0 -60
- package/skills/ginkgo-cloud-lab/references/cfps-strep-purification-thermal-shift.md +0 -63
- package/skills/ginkgo-cloud-lab/references/cfps-strep-tag-purification-a280.md +0 -55
- package/skills/ginkgo-cloud-lab/references/echo-ms-cfps-detection.md +0 -49
- package/skills/ginkgo-cloud-lab/references/echo-ms-method-onboarding.md +0 -56
- package/skills/ginkgo-cloud-lab/references/ecoli-expression-purification-quantification.md +0 -49
- package/skills/ginkgo-cloud-lab/references/ecoli-minibinder-expression-histag-a280.md +0 -62
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-hibit.md +0 -44
- package/skills/ginkgo-cloud-lab/references/ecoli-protein-expression-histag-a280.md +0 -47
- package/skills/ginkgo-cloud-lab/references/fluorescent-pixel-art-generation.md +0 -73
- package/skills/ginkgo-cloud-lab/references/ivt-rna-synthesis-qpcr.md +0 -67
- package/skills/ginkgo-cloud-lab/references/minibinder-strep-tag-a280.md +0 -58
- package/skills/ginkgo-cloud-lab/references/pichia-protein-expression-labchip.md +0 -43
- package/skills/ginkgo-cloud-lab/references/spr-target-onboarding.md +0 -58
- package/skills/glycoengineering/references/glycan_databases.md +0 -165
- package/skills/gtars/references/cli.md +0 -334
- package/skills/gtars/references/coverage.md +0 -224
- package/skills/gtars/references/overlap.md +0 -220
- package/skills/gtars/references/python-api.md +0 -280
- package/skills/gtars/references/refget.md +0 -318
- package/skills/gtars/references/tokenizers.md +0 -256
- package/skills/gtars/scripts/__init__.py +0 -1
- package/skills/gtars/scripts/_common.py +0 -461
- package/skills/gtars/scripts/artifact_inspector.py +0 -328
- package/skills/gtars/scripts/bed_validator.py +0 -183
- package/skills/gtars/scripts/coverage_preflight.py +0 -256
- package/skills/gtars/scripts/execution_plan.py +0 -365
- package/skills/gtars/scripts/refget_digest_plan.py +0 -311
- package/skills/gtars/scripts/tokenizer_manifest.py +0 -238
- package/skills/histolab/references/core_capabilities.md +0 -305
- package/skills/histolab/references/filters_preprocessing.md +0 -537
- package/skills/histolab/references/slide_management.md +0 -184
- package/skills/histolab/references/tile_extraction.md +0 -421
- package/skills/histolab/references/tissue_masks.md +0 -251
- package/skills/histolab/references/typical_workflows.md +0 -196
- package/skills/histolab/references/visualization.md +0 -548
- package/skills/hugging-science/references/flagship-resources.md +0 -81
- package/skills/hugging-science/references/topics-and-slugs.md +0 -82
- package/skills/hugging-science/references/using-datasets.md +0 -107
- package/skills/hugging-science/references/using-models.md +0 -122
- package/skills/hugging-science/references/using-spaces.md +0 -119
- package/skills/hugging-science/scripts/fetch_catalog.py +0 -358
- package/skills/hypogenic/assets/dataset_manifest.example.json +0 -30
- package/skills/hypogenic/assets/result.example.json +0 -18
- package/skills/hypogenic/assets/run_config.example.json +0 -46
- package/skills/hypogenic/assets/task_config.example.yaml +0 -38
- package/skills/hypogenic/references/configuration.md +0 -136
- package/skills/hypogenic/references/datasets.md +0 -146
- package/skills/hypogenic/references/evaluation.md +0 -155
- package/skills/hypogenic/references/security.md +0 -167
- package/skills/hypogenic/references/sources.md +0 -113
- package/skills/hypogenic/references/upstream.md +0 -188
- package/skills/hypogenic/scripts/__init__.py +0 -1
- package/skills/hypogenic/scripts/_common.py +0 -1312
- package/skills/hypogenic/scripts/audit_dataset.py +0 -410
- package/skills/hypogenic/scripts/evaluate_local.py +0 -250
- package/skills/hypogenic/scripts/inspect_outputs.py +0 -166
- package/skills/hypogenic/scripts/plan_run.py +0 -247
- package/skills/hypogenic/scripts/validate_config.py +0 -192
- package/skills/hypothesis-generation/assets/evidence_ledger_template.csv +0 -2
- package/skills/hypothesis-generation/assets/falsification_controls_template.json +0 -116
- package/skills/hypothesis-generation/assets/hypothesis_record_template.json +0 -331
- package/skills/hypothesis-generation/assets/operationalization_template.json +0 -56
- package/skills/hypothesis-generation/assets/prediction_rival_matrix_template.csv +0 -3
- package/skills/hypothesis-generation/assets/preregistration_scaffold_template.md +0 -137
- package/skills/hypothesis-generation/assets/search_boundary_template.json +0 -23
- package/skills/hypothesis-generation/assets/source_ledger.csv +0 -37
- package/skills/hypothesis-generation/references/causal_inference_and_claims.md +0 -190
- package/skills/hypothesis-generation/references/concepts_and_workflow.md +0 -173
- package/skills/hypothesis-generation/references/ethics_safety_and_ai.md +0 -216
- package/skills/hypothesis-generation/references/experimental_design_patterns.md +0 -301
- package/skills/hypothesis-generation/references/hypothesis_quality_criteria.md +0 -203
- package/skills/hypothesis-generation/references/literature_search_strategies.md +0 -208
- package/skills/hypothesis-generation/references/preregistration_and_open_science.md +0 -205
- package/skills/hypothesis-generation/references/security_validation.md +0 -74
- package/skills/hypothesis-generation/references/source_ledger.md +0 -116
- package/skills/hypothesis-generation/references/tool_reference.md +0 -246
- package/skills/hypothesis-generation/scripts/_common.py +0 -412
- package/skills/hypothesis-generation/scripts/audit_evidence_ledger.py +0 -337
- package/skills/hypothesis-generation/scripts/check_falsification_controls.py +0 -455
- package/skills/hypothesis-generation/scripts/check_operationalization.py +0 -237
- package/skills/hypothesis-generation/scripts/generate_preregistration_scaffold.py +0 -384
- package/skills/hypothesis-generation/scripts/lint_causal_claims.py +0 -189
- package/skills/hypothesis-generation/scripts/validate_hypothesis_schema.py +0 -1078
- package/skills/hypothesis-generation/scripts/validate_prediction_matrix.py +0 -286
- package/skills/imaging-data-commons/references/bigquery_guide.md +0 -858
- package/skills/imaging-data-commons/references/cli_guide.md +0 -287
- package/skills/imaging-data-commons/references/clinical_data_guide.md +0 -328
- package/skills/imaging-data-commons/references/cloud_storage_guide.md +0 -333
- package/skills/imaging-data-commons/references/dicomweb_guide.md +0 -399
- package/skills/imaging-data-commons/references/digital_pathology_guide.md +0 -403
- package/skills/imaging-data-commons/references/index_tables_guide.md +0 -203
- package/skills/imaging-data-commons/references/licensing_and_citation.md +0 -230
- package/skills/imaging-data-commons/references/mcp_guide.md +0 -181
- package/skills/imaging-data-commons/references/parquet_access_guide.md +0 -200
- package/skills/imaging-data-commons/references/rest_api_guide.md +0 -612
- package/skills/imaging-data-commons/references/sql_patterns.md +0 -462
- package/skills/imaging-data-commons/references/use_cases.md +0 -277
- package/skills/imaging-data-commons/scripts/check_version.py +0 -132
- package/skills/infographics/references/color_palettes.md +0 -496
- package/skills/infographics/references/design_principles.md +0 -636
- package/skills/infographics/references/infographic_type_catalog.md +0 -158
- package/skills/infographics/references/infographic_types.md +0 -907
- package/skills/infographics/references/iterative_refinement.md +0 -119
- package/skills/infographics/scripts/generate_infographic.py +0 -291
- package/skills/infographics/scripts/generate_infographic_ai.py +0 -1446
- package/skills/iso-standards-readiness/assets/templates/capa-record-template.json +0 -99
- package/skills/iso-standards-readiness/assets/templates/document-register-template.json +0 -75
- package/skills/iso-standards-readiness/assets/templates/evidence-manifest-template.json +0 -65
- package/skills/iso-standards-readiness/assets/templates/laboratory-scope-intake-template.json +0 -111
- package/skills/iso-standards-readiness/assets/templates/medical-laboratory-scope-intake-template.json +0 -111
- package/skills/iso-standards-readiness/assets/templates/procedures/CAPA-procedure-template.md +0 -148
- package/skills/iso-standards-readiness/assets/templates/procedures/document-control-procedure-template.md +0 -132
- package/skills/iso-standards-readiness/assets/templates/qmsr-transition-template.json +0 -181
- package/skills/iso-standards-readiness/assets/templates/quality-manual-template.md +0 -182
- package/skills/iso-standards-readiness/assets/templates/scope-intake-template.json +0 -109
- package/skills/iso-standards-readiness/assets/templates/supplier-controls-template.json +0 -119
- package/skills/iso-standards-readiness/assets/templates/traceability-matrix-template.json +0 -154
- package/skills/iso-standards-readiness/references/assurance-lanes.md +0 -116
- package/skills/iso-standards-readiness/references/evidence-architecture.md +0 -282
- package/skills/iso-standards-readiness/references/gap-analysis-checklist.md +0 -346
- package/skills/iso-standards-readiness/references/iso-13485.md +0 -236
- package/skills/iso-standards-readiness/references/iso-14971.md +0 -172
- package/skills/iso-standards-readiness/references/iso-15189.md +0 -219
- package/skills/iso-standards-readiness/references/iso-17025.md +0 -208
- package/skills/iso-standards-readiness/references/quality-manual-guide.md +0 -282
- package/skills/iso-standards-readiness/references/source-ledger.md +0 -357
- package/skills/iso-standards-readiness/scripts/_catalog.py +0 -248
- package/skills/iso-standards-readiness/scripts/_common.py +0 -558
- package/skills/iso-standards-readiness/scripts/audit_document_records.py +0 -148
- package/skills/iso-standards-readiness/scripts/check_capa.py +0 -240
- package/skills/iso-standards-readiness/scripts/check_qmsr_transition.py +0 -164
- package/skills/iso-standards-readiness/scripts/check_supplier_controls.py +0 -166
- package/skills/iso-standards-readiness/scripts/check_traceability.py +0 -171
- package/skills/iso-standards-readiness/scripts/gap_analyzer.py +0 -167
- package/skills/iso-standards-readiness/scripts/validate_evidence_manifest.py +0 -246
- package/skills/iso-standards-readiness/scripts/validate_scope_intake.py +0 -209
- package/skills/lab-hardware-cad/assets/standards.json +0 -198
- package/skills/lab-hardware-cad/references/behavior-rigs.md +0 -136
- package/skills/lab-hardware-cad/references/build123d-patterns.md +0 -363
- package/skills/lab-hardware-cad/references/fabrication-limits.md +0 -156
- package/skills/lab-hardware-cad/references/labware-adapters.md +0 -190
- package/skills/lab-hardware-cad/references/microfluidics.md +0 -157
- package/skills/lab-hardware-cad/references/optomechanics.md +0 -148
- package/skills/lab-hardware-cad/references/validation.md +0 -132
- package/skills/lab-hardware-cad/scripts/_common.py +0 -650
- package/skills/lab-hardware-cad/scripts/check.py +0 -645
- package/skills/lab-hardware-cad/scripts/gen.py +0 -264
- package/skills/lab-hardware-cad/scripts/snapshot.py +0 -278
- package/skills/labarchive-integration/references/api_reference.md +0 -250
- package/skills/labarchive-integration/references/authentication_guide.md +0 -191
- package/skills/labarchive-integration/references/integrations.md +0 -162
- package/skills/labarchive-integration/references/sources.md +0 -213
- package/skills/labarchive-integration/scripts/entry_operations.py +0 -381
- package/skills/labarchive-integration/scripts/notebook_operations.py +0 -451
- package/skills/labarchive-integration/scripts/setup_config.py +0 -258
- package/skills/lamindb/references/annotation-validation.md +0 -510
- package/skills/lamindb/references/core-concepts.md +0 -383
- package/skills/lamindb/references/data-management.md +0 -432
- package/skills/lamindb/references/integrations.md +0 -663
- package/skills/lamindb/references/ontologies.md +0 -498
- package/skills/lamindb/references/setup-deployment.md +0 -755
- package/skills/latchbio-integration/references/data-management.md +0 -257
- package/skills/latchbio-integration/references/latch-mcp.md +0 -158
- package/skills/latchbio-integration/references/nextflow-snakemake.md +0 -258
- package/skills/latchbio-integration/references/operations-and-debugging.md +0 -320
- package/skills/latchbio-integration/references/registry.md +0 -275
- package/skills/latchbio-integration/references/resource-configuration.md +0 -274
- package/skills/latchbio-integration/references/ui-and-automation.md +0 -355
- package/skills/latchbio-integration/references/verified-workflows.md +0 -226
- package/skills/latchbio-integration/references/workflow-creation.md +0 -275
- package/skills/latchbio-integration/scripts/inspect_latch_sdk.py +0 -290
- package/skills/latex-posters/assets/baposter_template.tex +0 -257
- package/skills/latex-posters/assets/beamerposter_template.tex +0 -244
- package/skills/latex-posters/assets/poster_quality_checklist.md +0 -358
- package/skills/latex-posters/assets/tikzposter_template.tex +0 -251
- package/skills/latex-posters/references/ai_graphics_for_posters.md +0 -524
- package/skills/latex-posters/references/compilation_and_quality_control.md +0 -467
- package/skills/latex-posters/references/latex_poster_packages.md +0 -745
- package/skills/latex-posters/references/latex_poster_reference.md +0 -241
- package/skills/latex-posters/references/poster_content_guide.md +0 -748
- package/skills/latex-posters/references/poster_design_principles.md +0 -806
- package/skills/latex-posters/references/poster_layout_design.md +0 -900
- package/skills/latex-posters/references/poster_patterns_and_presentation.md +0 -81
- package/skills/latex-posters/scripts/generate_schematic.py +0 -198
- package/skills/latex-posters/scripts/generate_schematic_ai.py +0 -950
- package/skills/latex-posters/scripts/review_poster.sh +0 -214
- package/skills/liteparse/references/api_reference.md +0 -169
- package/skills/liteparse/references/choosing_a_parser.md +0 -70
- package/skills/liteparse/references/cli_reference.md +0 -118
- package/skills/liteparse/references/ocr_and_formats.md +0 -143
- package/skills/liteparse/references/output_formats.md +0 -146
- package/skills/liteparse/scripts/batch_parse_dir.py +0 -163
- package/skills/literature-review/assets/review_template.md +0 -412
- package/skills/literature-review/references/citation_styles.md +0 -166
- package/skills/literature-review/references/core_workflow.md +0 -260
- package/skills/literature-review/references/database_strategies.md +0 -455
- package/skills/literature-review/references/example_workflow.md +0 -68
- package/skills/literature-review/references/search_and_citation.md +0 -157
- package/skills/literature-review/scripts/generate_pdf.py +0 -176
- package/skills/literature-review/scripts/generate_schematic.py +0 -198
- package/skills/literature-review/scripts/generate_schematic_ai.py +0 -950
- package/skills/literature-review/scripts/search_databases.py +0 -303
- package/skills/literature-review/scripts/verify_citations.py +0 -222
- package/skills/markdown-mermaid-writing/assets/examples/example-research-report.md +0 -221
- package/skills/markdown-mermaid-writing/references/diagrams/architecture.md +0 -108
- package/skills/markdown-mermaid-writing/references/diagrams/block.md +0 -177
- package/skills/markdown-mermaid-writing/references/diagrams/c4.md +0 -136
- package/skills/markdown-mermaid-writing/references/diagrams/class.md +0 -246
- package/skills/markdown-mermaid-writing/references/diagrams/complex_examples.md +0 -384
- package/skills/markdown-mermaid-writing/references/diagrams/er.md +0 -222
- package/skills/markdown-mermaid-writing/references/diagrams/flowchart.md +0 -177
- package/skills/markdown-mermaid-writing/references/diagrams/gantt.md +0 -138
- package/skills/markdown-mermaid-writing/references/diagrams/git_graph.md +0 -74
- package/skills/markdown-mermaid-writing/references/diagrams/kanban.md +0 -107
- package/skills/markdown-mermaid-writing/references/diagrams/mindmap.md +0 -74
- package/skills/markdown-mermaid-writing/references/diagrams/packet.md +0 -55
- package/skills/markdown-mermaid-writing/references/diagrams/pie.md +0 -52
- package/skills/markdown-mermaid-writing/references/diagrams/quadrant.md +0 -66
- package/skills/markdown-mermaid-writing/references/diagrams/radar.md +0 -59
- package/skills/markdown-mermaid-writing/references/diagrams/requirement.md +0 -88
- package/skills/markdown-mermaid-writing/references/diagrams/sankey.md +0 -71
- package/skills/markdown-mermaid-writing/references/diagrams/sequence.md +0 -174
- package/skills/markdown-mermaid-writing/references/diagrams/state.md +0 -150
- package/skills/markdown-mermaid-writing/references/diagrams/timeline.md +0 -96
- package/skills/markdown-mermaid-writing/references/diagrams/treemap.md +0 -66
- package/skills/markdown-mermaid-writing/references/diagrams/user_journey.md +0 -108
- package/skills/markdown-mermaid-writing/references/diagrams/xy_chart.md +0 -53
- package/skills/markdown-mermaid-writing/references/diagrams/zenuml.md +0 -71
- package/skills/markdown-mermaid-writing/references/markdown_style_guide.md +0 -733
- package/skills/markdown-mermaid-writing/references/mermaid_style_guide.md +0 -458
- package/skills/markdown-mermaid-writing/templates/decision_record.md +0 -211
- package/skills/markdown-mermaid-writing/templates/how_to_guide.md +0 -275
- package/skills/markdown-mermaid-writing/templates/issue.md +0 -303
- package/skills/markdown-mermaid-writing/templates/kanban.md +0 -223
- package/skills/markdown-mermaid-writing/templates/presentation.md +0 -312
- package/skills/markdown-mermaid-writing/templates/project_documentation.md +0 -412
- package/skills/markdown-mermaid-writing/templates/pull_request.md +0 -319
- package/skills/markdown-mermaid-writing/templates/research_paper.md +0 -304
- package/skills/markdown-mermaid-writing/templates/status_report.md +0 -185
- package/skills/market-research-reports/assets/FORMATTING_GUIDE.md +0 -149
- package/skills/market-research-reports/assets/claims_ledger_template.csv +0 -4
- package/skills/market-research-reports/assets/competitor_feature_matrix_template.csv +0 -5
- package/skills/market-research-reports/assets/consistency_check_template.csv +0 -3
- package/skills/market-research-reports/assets/forecast_sensitivity_template.json +0 -90
- package/skills/market-research-reports/assets/market_report_template.tex +0 -279
- package/skills/market-research-reports/assets/market_research.sty +0 -241
- package/skills/market-research-reports/assets/market_sizing_scenarios_template.json +0 -129
- package/skills/market-research-reports/assets/report_manifest_template.json +0 -27
- package/skills/market-research-reports/assets/source_ledger_template.csv +0 -4
- package/skills/market-research-reports/references/data_analysis_patterns.md +0 -290
- package/skills/market-research-reports/references/evidence_model.md +0 -148
- package/skills/market-research-reports/references/methods_and_ethics.md +0 -162
- package/skills/market-research-reports/references/official_data_sources.md +0 -196
- package/skills/market-research-reports/references/report_structure_guide.md +0 -283
- package/skills/market-research-reports/references/sources.md +0 -73
- package/skills/market-research-reports/references/visual_generation_guide.md +0 -158
- package/skills/market-research-reports/scripts/_common.py +0 -312
- package/skills/market-research-reports/scripts/audit_claim_citations.py +0 -326
- package/skills/market-research-reports/scripts/calculate_market_sizing.py +0 -389
- package/skills/market-research-reports/scripts/check_unit_consistency.py +0 -217
- package/skills/market-research-reports/scripts/forecast_sensitivity.py +0 -326
- package/skills/market-research-reports/scripts/generate_report_scaffold.py +0 -444
- package/skills/market-research-reports/scripts/validate_competitor_matrix.py +0 -223
- package/skills/market-research-reports/scripts/validate_evidence_ledger.py +0 -291
- package/skills/markitdown/references/api_reference.md +0 -418
- package/skills/markitdown/references/cloud_and_ocr.md +0 -320
- package/skills/markitdown/references/file_formats.md +0 -281
- package/skills/markitdown/references/mcp_and_plugins.md +0 -243
- package/skills/markitdown/references/migration.md +0 -356
- package/skills/markitdown/references/security.md +0 -246
- package/skills/markitdown/references/workflows.md +0 -309
- package/skills/markitdown/scripts/batch_convert.py +0 -354
- package/skills/markitdown/scripts/convert_literature.py +0 -405
- package/skills/markitdown/scripts/inspect_installation.py +0 -162
- package/skills/matchms/references/filtering.md +0 -299
- package/skills/matchms/references/importing_exporting.md +0 -323
- package/skills/matchms/references/migration.md +0 -387
- package/skills/matchms/references/similarity.md +0 -413
- package/skills/matchms/references/sources.md +0 -113
- package/skills/matchms/references/workflows.md +0 -451
- package/skills/matchms/scripts/library_search.py +0 -593
- package/skills/matlab/assets/project_manifest_template.json +0 -33
- package/skills/matlab/assets/python_compatibility_r2026a.json +0 -27
- package/skills/matlab/assets/reproducibility_manifest_template.json +0 -32
- package/skills/matlab/references/data-import-export.md +0 -221
- package/skills/matlab/references/executing-scripts.md +0 -213
- package/skills/matlab/references/graphics-visualization.md +0 -181
- package/skills/matlab/references/mathematics.md +0 -208
- package/skills/matlab/references/matrices-arrays.md +0 -228
- package/skills/matlab/references/octave-compatibility.md +0 -212
- package/skills/matlab/references/programming.md +0 -225
- package/skills/matlab/references/python-integration.md +0 -248
- package/skills/matlab/scripts/_common.py +0 -263
- package/skills/matlab/scripts/generate_function_scaffold.py +0 -165
- package/skills/matlab/scripts/inventory_mat_file.py +0 -351
- package/skills/matlab/scripts/plan_batch_command.py +0 -257
- package/skills/matlab/scripts/plan_python_compatibility.py +0 -176
- package/skills/matlab/scripts/reproducibility_report.py +0 -233
- package/skills/matlab/scripts/scan_m_code.py +0 -433
- package/skills/matlab/scripts/validate_project_manifest.py +0 -348
- package/skills/matplotlib/references/api_reference.md +0 -409
- package/skills/matplotlib/references/common_issues.md +0 -562
- package/skills/matplotlib/references/plot_types.md +0 -469
- package/skills/matplotlib/references/styling_guide.md +0 -600
- package/skills/matplotlib/scripts/plot_template.py +0 -406
- package/skills/matplotlib/scripts/style_configurator.py +0 -412
- package/skills/medchem/references/api_guide.md +0 -331
- package/skills/medchem/references/rules_catalog.md +0 -328
- package/skills/medchem/scripts/filter_molecules.py +0 -302
- package/skills/modal/references/api_reference.md +0 -225
- package/skills/modal/references/examples.md +0 -276
- package/skills/modal/references/functions.md +0 -260
- package/skills/modal/references/getting-started.md +0 -171
- package/skills/modal/references/gpu.md +0 -177
- package/skills/modal/references/images.md +0 -266
- package/skills/modal/references/resources.md +0 -117
- package/skills/modal/references/scaling.md +0 -173
- package/skills/modal/references/scheduled-jobs.md +0 -147
- package/skills/modal/references/secrets.md +0 -119
- package/skills/modal/references/volumes.md +0 -247
- package/skills/modal/references/web-endpoints.md +0 -259
- package/skills/molecular-dynamics/references/mdanalysis_analysis.md +0 -208
- package/skills/molfeat/references/api_reference.md +0 -429
- package/skills/molfeat/references/available_featurizers.md +0 -335
- package/skills/molfeat/references/choosing_a_featurizer.md +0 -192
- package/skills/molfeat/references/examples.md +0 -720
- package/skills/ncats-arax/references/output-schema.md +0 -186
- package/skills/ncats-arax/references/query-contract.md +0 -140
- package/skills/ncats-arax/scripts/arax_client.py +0 -2087
- package/skills/networkx/references/algorithms.md +0 -384
- package/skills/networkx/references/generators.md +0 -385
- package/skills/networkx/references/graph-basics.md +0 -284
- package/skills/networkx/references/io.md +0 -457
- package/skills/networkx/references/visualization.md +0 -531
- package/skills/neurokit2/references/bio_module.md +0 -244
- package/skills/neurokit2/references/complexity.md +0 -212
- package/skills/neurokit2/references/ecg_cardiac.md +0 -193
- package/skills/neurokit2/references/eda.md +0 -185
- package/skills/neurokit2/references/eeg.md +0 -204
- package/skills/neurokit2/references/emg.md +0 -157
- package/skills/neurokit2/references/eog.md +0 -154
- package/skills/neurokit2/references/epochs_events.md +0 -199
- package/skills/neurokit2/references/hrv.md +0 -205
- package/skills/neurokit2/references/ppg.md +0 -191
- package/skills/neurokit2/references/rsp.md +0 -212
- package/skills/neurokit2/references/signal_processing.md +0 -160
- package/skills/neurokit2/scripts/_common.py +0 -567
- package/skills/neurokit2/scripts/ecg_hrv_pipeline.py +0 -303
- package/skills/neurokit2/scripts/eda_pipeline.py +0 -288
- package/skills/neurokit2/scripts/generate_synthetic.py +0 -221
- package/skills/neurokit2/scripts/inspect_signal.py +0 -362
- package/skills/neurokit2/scripts/plan_epochs.py +0 -281
- package/skills/neurokit2/scripts/validate_multimodal.py +0 -350
- package/skills/neuropixels-analysis/assets/analysis_template.py +0 -271
- package/skills/neuropixels-analysis/references/AI_CURATION.md +0 -164
- package/skills/neuropixels-analysis/references/ANALYSIS.md +0 -392
- package/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +0 -435
- package/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +0 -323
- package/skills/neuropixels-analysis/references/PREPROCESSING.md +0 -273
- package/skills/neuropixels-analysis/references/QUALITY_METRICS.md +0 -359
- package/skills/neuropixels-analysis/references/SPIKE_SORTING.md +0 -339
- package/skills/neuropixels-analysis/references/api_reference.md +0 -229
- package/skills/neuropixels-analysis/references/plotting_guide.md +0 -454
- package/skills/neuropixels-analysis/references/standard_workflow.md +0 -305
- package/skills/neuropixels-analysis/scripts/compute_metrics.py +0 -182
- package/skills/neuropixels-analysis/scripts/explore_recording.py +0 -168
- package/skills/neuropixels-analysis/scripts/export_to_phy.py +0 -79
- package/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +0 -442
- package/skills/neuropixels-analysis/scripts/preprocess_recording.py +0 -122
- package/skills/neuropixels-analysis/scripts/run_sorting.py +0 -98
- package/skills/nextflow/references/configuration.md +0 -276
- package/skills/nextflow/references/containers.md +0 -92
- package/skills/nextflow/references/developing.md +0 -301
- package/skills/nextflow/references/language.md +0 -327
- package/skills/nextflow/references/nf-core-tools.md +0 -130
- package/skills/nextflow/references/running-pipelines.md +0 -131
- package/skills/nextflow/references/testing.md +0 -189
- package/skills/omero-integration/references/advanced.md +0 -273
- package/skills/omero-integration/references/connection.md +0 -293
- package/skills/omero-integration/references/data_access.md +0 -359
- package/skills/omero-integration/references/image_processing.md +0 -286
- package/skills/omero-integration/references/metadata.md +0 -313
- package/skills/omero-integration/references/rois.md +0 -291
- package/skills/omero-integration/references/scripts.md +0 -304
- package/skills/omero-integration/references/sources.md +0 -194
- package/skills/omero-integration/references/tables.md +0 -269
- package/skills/omero-integration/scripts/export_image_metadata.py +0 -560
- package/skills/omero-integration/scripts/inventory.py +0 -302
- package/skills/omero-integration/scripts/omero_common.py +0 -490
- package/skills/omero-integration/scripts/plan_transfer.py +0 -393
- package/skills/omero-integration/scripts/validate_config.py +0 -140
- package/skills/onekgpd/assets/kgpe.json +0 -48032
- package/skills/onekgpd/references/annotation_vocabularies.md +0 -187
- package/skills/onekgpd/references/onekgpd_commands.md +0 -296
- package/skills/onekgpd/scripts/onekgpd_api.py +0 -794
- package/skills/onekgpd/scripts/onekgpd_meta.py +0 -485
- package/skills/ontology-term-resolution/references/curation-rules.md +0 -110
- package/skills/ontology-term-resolution/references/ols4-api.md +0 -135
- package/skills/ontology-term-resolution/references/ontology-registry.md +0 -110
- package/skills/ontology-term-resolution/scripts/ols_client.py +0 -341
- package/skills/ontology-term-resolution/scripts/resolve_terms.py +0 -255
- package/skills/ontology-term-resolution/scripts/validate_terms.py +0 -297
- package/skills/open-notebook/references/api_reference.md +0 -715
- package/skills/open-notebook/references/architecture.md +0 -163
- package/skills/open-notebook/references/configuration.md +0 -226
- package/skills/open-notebook/references/examples.md +0 -290
- package/skills/open-notebook/scripts/chat_interaction.py +0 -190
- package/skills/open-notebook/scripts/notebook_management.py +0 -142
- package/skills/open-notebook/scripts/source_ingestion.py +0 -160
- package/skills/openpiv/references/advanced_algorithms.md +0 -233
- package/skills/openpiv/scripts/__init__.py +0 -1
- package/skills/openpiv/scripts/analyze.py +0 -143
- package/skills/openpiv/scripts/run_example.py +0 -78
- package/skills/openpiv/scripts/runner.py +0 -214
- package/skills/opentrons-integration/references/api_reference.md +0 -382
- package/skills/opentrons-integration/references/liquid_handling.md +0 -387
- package/skills/opentrons-integration/references/migration-api-2-19-to-2-29.md +0 -328
- package/skills/opentrons-integration/references/modules_and_deck.md +0 -409
- package/skills/opentrons-integration/references/protocol_authoring.md +0 -352
- package/skills/opentrons-integration/references/sources.md +0 -151
- package/skills/opentrons-integration/references/validation_and_operations.md +0 -314
- package/skills/opentrons-integration/requirements-flex.txt +0 -1
- package/skills/opentrons-integration/requirements-ot2.txt +0 -1
- package/skills/opentrons-integration/scripts/absorbance_reader_template.py +0 -82
- package/skills/opentrons-integration/scripts/basic_protocol_template.py +0 -68
- package/skills/opentrons-integration/scripts/ot2_basic_protocol_template.py +0 -63
- package/skills/opentrons-integration/scripts/pcr_setup_template.py +0 -146
- package/skills/opentrons-integration/scripts/runtime_parameters_template.py +0 -110
- package/skills/opentrons-integration/scripts/serial_dilution_template.py +0 -113
- package/skills/optimize-for-gpu/references/code_transformation_patterns.md +0 -301
- package/skills/optimize-for-gpu/references/cucim.md +0 -679
- package/skills/optimize-for-gpu/references/cudf.md +0 -762
- package/skills/optimize-for-gpu/references/cugraph.md +0 -733
- package/skills/optimize-for-gpu/references/cuml.md +0 -710
- package/skills/optimize-for-gpu/references/cupy.md +0 -668
- package/skills/optimize-for-gpu/references/cuspatial.md +0 -420
- package/skills/optimize-for-gpu/references/cuvs.md +0 -671
- package/skills/optimize-for-gpu/references/cuxfilter.md +0 -600
- package/skills/optimize-for-gpu/references/decision_framework.md +0 -234
- package/skills/optimize-for-gpu/references/installation.md +0 -121
- package/skills/optimize-for-gpu/references/kvikio.md +0 -612
- package/skills/optimize-for-gpu/references/numba.md +0 -808
- package/skills/optimize-for-gpu/references/raft.md +0 -312
- package/skills/optimize-for-gpu/references/warp.md +0 -623
- package/skills/pacsomatic/config.yaml +0 -42
- package/skills/pacsomatic/references/agent-playbook.md +0 -73
- package/skills/pacsomatic/references/config-and-output.md +0 -100
- package/skills/pacsomatic/references/pacsomatic_guide.md +0 -254
- package/skills/pacsomatic/scripts/run_pacsomatic.py +0 -794
- package/skills/paper-lookup/references/arxiv.md +0 -275
- package/skills/paper-lookup/references/biorxiv.md +0 -163
- package/skills/paper-lookup/references/core.md +0 -150
- package/skills/paper-lookup/references/crossref.md +0 -181
- package/skills/paper-lookup/references/europepmc.md +0 -226
- package/skills/paper-lookup/references/medrxiv.md +0 -126
- package/skills/paper-lookup/references/openalex.md +0 -174
- package/skills/paper-lookup/references/pmc.md +0 -228
- package/skills/paper-lookup/references/pubmed.md +0 -124
- package/skills/paper-lookup/references/semantic-scholar.md +0 -203
- package/skills/paper-lookup/references/unpaywall.md +0 -127
- package/skills/paper-lookup/scripts/_common.py +0 -227
- package/skills/paper-lookup/scripts/arxiv_atom.py +0 -200
- package/skills/paper-lookup/scripts/jats_to_text.py +0 -324
- package/skills/paper-lookup/scripts/openalex_abstract.py +0 -163
- package/skills/paper-lookup/scripts/paginate.py +0 -490
- package/skills/paperclip/references/cli-reference.md +0 -389
- package/skills/paperclip/references/installation.md +0 -341
- package/skills/paperclip/references/map-reduce.md +0 -252
- package/skills/paperclip/references/python-sdk.md +0 -323
- package/skills/paperclip/references/repos-and-workspace.md +0 -271
- package/skills/paperclip/references/search-and-retrieval.md +0 -281
- package/skills/parallel-web/references/data-enrichment.md +0 -104
- package/skills/parallel-web/references/deep-research.md +0 -91
- package/skills/parallel-web/references/findall.md +0 -81
- package/skills/parallel-web/references/monitor.md +0 -83
- package/skills/parallel-web/references/web-extract.md +0 -59
- package/skills/parallel-web/references/web-search.md +0 -100
- package/skills/pathml/references/data_management.md +0 -357
- package/skills/pathml/references/graphs.md +0 -335
- package/skills/pathml/references/image_loading.md +0 -301
- package/skills/pathml/references/machine_learning.md +0 -408
- package/skills/pathml/references/multiparametric.md +0 -352
- package/skills/pathml/references/preprocessing.md +0 -371
- package/skills/pathml/scripts/_common.py +0 -385
- package/skills/pathml/scripts/image_qc.py +0 -325
- package/skills/pathml/scripts/plan_inference.py +0 -282
- package/skills/pathml/scripts/plan_pipeline.py +0 -239
- package/skills/pathml/scripts/slide_manifest.py +0 -405
- package/skills/pathml/scripts/validate_spatial_schema.py +0 -420
- package/skills/pathogen-variant-surveillance/references/lapis-api.md +0 -209
- package/skills/pathogen-variant-surveillance/references/lineage-nomenclature.md +0 -126
- package/skills/pathogen-variant-surveillance/references/surveillance-caveats.md +0 -149
- package/skills/pathogen-variant-surveillance/scripts/lapis_client.py +0 -776
- package/skills/pathogen-variant-surveillance/scripts/lineage_prevalence.py +0 -310
- package/skills/pathogen-variant-surveillance/scripts/mutation_profile.py +0 -215
- package/skills/pathogen-variant-surveillance/scripts/reporting_lag.py +0 -217
- package/skills/pathogen-variant-surveillance/scripts/resolve_lineage.py +0 -198
- package/skills/pathway-enrichment/references/databases-and-gene-sets.md +0 -140
- package/skills/pathway-enrichment/references/gseapy.md +0 -189
- package/skills/pathway-enrichment/references/interpretation.md +0 -118
- package/skills/pathway-enrichment/scripts/run_enrichment.py +0 -231
- package/skills/pdf/LICENSE.txt +0 -30
- package/skills/pdf/forms.md +0 -294
- package/skills/pdf/reference.md +0 -612
- package/skills/pdf/scripts/check_bounding_boxes.py +0 -65
- package/skills/pdf/scripts/check_fillable_fields.py +0 -11
- package/skills/pdf/scripts/convert_pdf_to_images.py +0 -33
- package/skills/pdf/scripts/create_validation_image.py +0 -37
- package/skills/pdf/scripts/extract_form_field_info.py +0 -122
- package/skills/pdf/scripts/extract_form_structure.py +0 -115
- package/skills/pdf/scripts/fill_fillable_fields.py +0 -98
- package/skills/pdf/scripts/fill_pdf_form_with_annotations.py +0 -107
- package/skills/peer-review/assets/citation_references_template.csv +0 -2
- package/skills/peer-review/assets/claim_evidence_matrix_template.csv +0 -4
- package/skills/peer-review/assets/reporting_checklist_template.csv +0 -31
- package/skills/peer-review/assets/reporting_guidelines.json +0 -466
- package/skills/peer-review/assets/review_intake_template.json +0 -52
- package/skills/peer-review/assets/review_scaffold_template.md +0 -68
- package/skills/peer-review/assets/source_ledger.csv +0 -32
- package/skills/peer-review/assets/statistical_reproducibility_template.json +0 -210
- package/skills/peer-review/assets/study_profile_template.json +0 -12
- package/skills/peer-review/references/common_issues.md +0 -257
- package/skills/peer-review/references/ethical_review_practice.md +0 -233
- package/skills/peer-review/references/reporting_standards.md +0 -249
- package/skills/peer-review/references/security_validation.md +0 -75
- package/skills/peer-review/references/statistical_reproducibility.md +0 -329
- package/skills/peer-review/references/tool_reference.md +0 -253
- package/skills/peer-review/scripts/_common.py +0 -398
- package/skills/peer-review/scripts/audit_citations.py +0 -207
- package/skills/peer-review/scripts/audit_statistics_reproducibility.py +0 -305
- package/skills/peer-review/scripts/generate_review_scaffold.py +0 -81
- package/skills/peer-review/scripts/lint_review.py +0 -254
- package/skills/peer-review/scripts/select_reporting_guidelines.py +0 -383
- package/skills/peer-review/scripts/validate_claim_evidence.py +0 -221
- package/skills/peer-review/scripts/validate_review_intake.py +0 -452
- package/skills/pennylane/references/advanced_features.md +0 -667
- package/skills/pennylane/references/devices_backends.md +0 -562
- package/skills/pennylane/references/getting_started.md +0 -232
- package/skills/pennylane/references/optimization.md +0 -670
- package/skills/pennylane/references/quantum_chemistry.md +0 -576
- package/skills/pennylane/references/quantum_circuits.md +0 -443
- package/skills/pennylane/references/quantum_ml.md +0 -555
- package/skills/phylogenetics/references/iqtree_inference.md +0 -181
- package/skills/phylogenetics/scripts/phylogenetic_analysis.py +0 -272
- package/skills/pi-agent/references/compaction.md +0 -76
- package/skills/pi-agent/references/containerization.md +0 -80
- package/skills/pi-agent/references/custom-provider.md +0 -131
- package/skills/pi-agent/references/development.md +0 -61
- package/skills/pi-agent/references/environment-variables.md +0 -57
- package/skills/pi-agent/references/extensions.md +0 -185
- package/skills/pi-agent/references/json.md +0 -69
- package/skills/pi-agent/references/keybindings.md +0 -58
- package/skills/pi-agent/references/llama-cpp.md +0 -69
- package/skills/pi-agent/references/models.md +0 -114
- package/skills/pi-agent/references/overview.md +0 -37
- package/skills/pi-agent/references/packages.md +0 -103
- package/skills/pi-agent/references/pi-interview.md +0 -123
- package/skills/pi-agent/references/pi-mcp-adapter.md +0 -191
- package/skills/pi-agent/references/pi-subagents.md +0 -371
- package/skills/pi-agent/references/pi-web-access.md +0 -243
- package/skills/pi-agent/references/prompt-templates.md +0 -48
- package/skills/pi-agent/references/providers.md +0 -122
- package/skills/pi-agent/references/quickstart.md +0 -73
- package/skills/pi-agent/references/rpc.md +0 -95
- package/skills/pi-agent/references/sdk.md +0 -151
- package/skills/pi-agent/references/security.md +0 -52
- package/skills/pi-agent/references/session-format.md +0 -90
- package/skills/pi-agent/references/sessions.md +0 -56
- package/skills/pi-agent/references/settings.md +0 -102
- package/skills/pi-agent/references/shell-aliases.md +0 -15
- package/skills/pi-agent/references/skills.md +0 -83
- package/skills/pi-agent/references/terminal-setup.md +0 -87
- package/skills/pi-agent/references/termux.md +0 -31
- package/skills/pi-agent/references/themes.md +0 -69
- package/skills/pi-agent/references/tmux.md +0 -44
- package/skills/pi-agent/references/tui.md +0 -97
- package/skills/pi-agent/references/usage.md +0 -129
- package/skills/pi-agent/references/windows.md +0 -23
- package/skills/pkpd-modeling/assets/nca-reporting-checklist.md +0 -72
- package/skills/pkpd-modeling/assets/popk-analysis-plan.md +0 -136
- package/skills/pkpd-modeling/references/antimicrobial-and-tdm.md +0 -110
- package/skills/pkpd-modeling/references/bioequivalence.md +0 -132
- package/skills/pkpd-modeling/references/dataset-standards.md +0 -103
- package/skills/pkpd-modeling/references/ddi-and-qt.md +0 -132
- package/skills/pkpd-modeling/references/nca-conventions.md +0 -128
- package/skills/pkpd-modeling/references/pbpk.md +0 -103
- package/skills/pkpd-modeling/references/pd-and-exposure-response.md +0 -149
- package/skills/pkpd-modeling/references/population-pk.md +0 -133
- package/skills/pkpd-modeling/references/regulatory-guidance.md +0 -82
- package/skills/pkpd-modeling/references/software-ecosystem.md +0 -123
- package/skills/pkpd-modeling/references/source-ledger.md +0 -89
- package/skills/pkpd-modeling/references/special-populations.md +0 -126
- package/skills/pkpd-modeling/references/structural-models.md +0 -140
- package/skills/pkpd-modeling/references/tmdd-and-biologics.md +0 -115
- package/skills/pkpd-modeling/scripts/_common.py +0 -327
- package/skills/pkpd-modeling/scripts/_models.py +0 -673
- package/skills/pkpd-modeling/scripts/allometry_and_fih.py +0 -346
- package/skills/pkpd-modeling/scripts/bioequivalence.py +0 -480
- package/skills/pkpd-modeling/scripts/check_popk_dataset.py +0 -400
- package/skills/pkpd-modeling/scripts/ddi_static.py +0 -346
- package/skills/pkpd-modeling/scripts/exposure_response.py +0 -328
- package/skills/pkpd-modeling/scripts/fit_compartmental.py +0 -558
- package/skills/pkpd-modeling/scripts/nca.py +0 -587
- package/skills/pkpd-modeling/scripts/simulate_regimen.py +0 -323
- package/skills/pkpd-modeling/scripts/tdm_bayes.py +0 -312
- package/skills/polars/references/best_practices.md +0 -651
- package/skills/polars/references/core_concepts.md +0 -380
- package/skills/polars/references/io_guide.md +0 -564
- package/skills/polars/references/operations.md +0 -602
- package/skills/polars/references/pandas_migration.md +0 -417
- package/skills/polars/references/transformations.md +0 -549
- package/skills/polars-bio/references/bioframe_migration.md +0 -250
- package/skills/polars-bio/references/configuration.md +0 -187
- package/skills/polars-bio/references/file_io.md +0 -469
- package/skills/polars-bio/references/interval_operations.md +0 -370
- package/skills/polars-bio/references/pileup_operations.md +0 -176
- package/skills/polars-bio/references/sql_processing.md +0 -224
- package/skills/pptx/LICENSE.txt +0 -30
- package/skills/pptx/scripts/__init__.py +0 -0
- package/skills/pptx/scripts/add_slide.py +0 -367
- package/skills/pptx/scripts/clean.py +0 -309
- package/skills/pptx/scripts/office/helpers/__init__.py +0 -111
- package/skills/pptx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/pptx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/pptx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/pptx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/pptx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/pptx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/pptx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/pptx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/pptx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/pptx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/pptx/scripts/office/soffice.py +0 -232
- package/skills/pptx/scripts/office/validate.py +0 -173
- package/skills/pptx/scripts/office/validators/__init__.py +0 -15
- package/skills/pptx/scripts/office/validators/base.py +0 -875
- package/skills/pptx/scripts/office/validators/docx.py +0 -466
- package/skills/pptx/scripts/office/validators/pptx.py +0 -441
- package/skills/pptx/scripts/office/validators/redlining.py +0 -299
- package/skills/pptx/scripts/thumbnail.py +0 -311
- package/skills/pptx-posters/assets/generation_dependencies.json +0 -5
- package/skills/pptx-posters/assets/poster_manifest_template.json +0 -154
- package/skills/pptx-posters/assets/poster_quality_checklist.md +0 -192
- package/skills/pptx-posters/references/manifest_spec.md +0 -297
- package/skills/pptx-posters/references/poster_content_guide.md +0 -176
- package/skills/pptx-posters/references/poster_design_principles.md +0 -226
- package/skills/pptx-posters/references/poster_layout_design.md +0 -189
- package/skills/pptx-posters/references/pptx_security.md +0 -202
- package/skills/pptx-posters/references/security_validation.md +0 -90
- package/skills/pptx-posters/references/source_ledger.md +0 -256
- package/skills/pptx-posters/scripts/_common.py +0 -396
- package/skills/pptx-posters/scripts/_manifest.py +0 -1318
- package/skills/pptx-posters/scripts/_pptx.py +0 -1484
- package/skills/pptx-posters/scripts/check_layout.py +0 -179
- package/skills/pptx-posters/scripts/check_palette.py +0 -142
- package/skills/pptx-posters/scripts/generate_poster.py +0 -427
- package/skills/pptx-posters/scripts/inspect_pptx.py +0 -40
- package/skills/pptx-posters/scripts/inventory_images.py +0 -252
- package/skills/pptx-posters/scripts/plan_export.py +0 -201
- package/skills/pptx-posters/scripts/validate_manifest.py +0 -55
- package/skills/primekg/scripts/query_primekg.py +0 -128
- package/skills/protocolsio-integration/assets/protocol-snapshot.schema.json +0 -179
- package/skills/protocolsio-integration/references/additional_features.md +0 -202
- package/skills/protocolsio-integration/references/authentication.md +0 -135
- package/skills/protocolsio-integration/references/discussions.md +0 -192
- package/skills/protocolsio-integration/references/file_manager.md +0 -256
- package/skills/protocolsio-integration/references/protocols_api.md +0 -256
- package/skills/protocolsio-integration/references/workspaces.md +0 -192
- package/skills/protocolsio-integration/scripts/__init__.py +0 -1
- package/skills/protocolsio-integration/scripts/_common.py +0 -613
- package/skills/protocolsio-integration/scripts/pagination_helper.py +0 -248
- package/skills/protocolsio-integration/scripts/plan_write_request.py +0 -657
- package/skills/protocolsio-integration/scripts/protocols_read.py +0 -493
- package/skills/protocolsio-integration/scripts/validate_auth_config.py +0 -128
- package/skills/protocolsio-integration/scripts/validate_protocol_json.py +0 -358
- package/skills/pufferlib/references/environments.md +0 -260
- package/skills/pufferlib/references/integration.md +0 -192
- package/skills/pufferlib/references/policies.md +0 -181
- package/skills/pufferlib/references/training.md +0 -287
- package/skills/pufferlib/references/vectorization.md +0 -210
- package/skills/pufferlib/scripts/__init__.py +0 -1
- package/skills/pufferlib/scripts/_common.py +0 -199
- package/skills/pufferlib/scripts/benchmark_vectorization.py +0 -244
- package/skills/pufferlib/scripts/env_contract_validator.py +0 -198
- package/skills/pufferlib/scripts/env_template.py +0 -210
- package/skills/pufferlib/scripts/inspect_checkpoint.py +0 -225
- package/skills/pufferlib/scripts/repro_plan.py +0 -177
- package/skills/pufferlib/scripts/train_template.py +0 -282
- package/skills/pufferlib/scripts/validate_plan.py +0 -570
- package/skills/pydeseq2/references/analysis_patterns.md +0 -70
- package/skills/pydeseq2/references/api_reference.md +0 -256
- package/skills/pydeseq2/references/core_workflow_steps.md +0 -162
- package/skills/pydeseq2/references/workflow_guide.md +0 -603
- package/skills/pydeseq2/scripts/run_deseq2_analysis.py +0 -388
- package/skills/pydicom/references/common_tags.md +0 -277
- package/skills/pydicom/references/transfer_syntaxes.md +0 -348
- package/skills/pydicom/scripts/__init__.py +0 -1
- package/skills/pydicom/scripts/_common.py +0 -916
- package/skills/pydicom/scripts/anonymize_dicom.py +0 -713
- package/skills/pydicom/scripts/deidentification_audit.py +0 -380
- package/skills/pydicom/scripts/dicom_inventory.py +0 -402
- package/skills/pydicom/scripts/dicom_to_image.py +0 -459
- package/skills/pydicom/scripts/extract_metadata.py +0 -330
- package/skills/pydicom/scripts/pixel_frame_planner.py +0 -303
- package/skills/pydicom/scripts/transfer_syntax_inspector.py +0 -245
- package/skills/pydicom/scripts/uid_mapping_validator.py +0 -240
- package/skills/pyhealth/assets/starter_pipeline.py +0 -58
- package/skills/pyhealth/references/datasets.md +0 -126
- package/skills/pyhealth/references/examples.md +0 -237
- package/skills/pyhealth/references/installation.md +0 -112
- package/skills/pyhealth/references/medcode.md +0 -94
- package/skills/pyhealth/references/models.md +0 -114
- package/skills/pyhealth/references/tasks.md +0 -143
- package/skills/pylabrobot/assets/protocol-manifest.schema.json +0 -367
- package/skills/pylabrobot/references/analytical-equipment.md +0 -200
- package/skills/pylabrobot/references/hardware-backends.md +0 -215
- package/skills/pylabrobot/references/liquid-handling.md +0 -223
- package/skills/pylabrobot/references/material-handling.md +0 -229
- package/skills/pylabrobot/references/resources.md +0 -238
- package/skills/pylabrobot/references/visualization.md +0 -187
- package/skills/pylabrobot/scripts/__init__.py +0 -1
- package/skills/pylabrobot/scripts/_common.py +0 -718
- package/skills/pylabrobot/scripts/check_deck_geometry.py +0 -52
- package/skills/pylabrobot/scripts/generate_simulation_plan.py +0 -140
- package/skills/pylabrobot/scripts/inspect_backends.py +0 -216
- package/skills/pylabrobot/scripts/plan_transfers.py +0 -59
- package/skills/pylabrobot/scripts/validate_manifest.py +0 -47
- package/skills/pymatgen/references/analysis_modules.md +0 -352
- package/skills/pymatgen/references/core_classes.md +0 -290
- package/skills/pymatgen/references/io_formats.md +0 -323
- package/skills/pymatgen/references/materials_project_api.md +0 -406
- package/skills/pymatgen/references/transformations_workflows.md +0 -385
- package/skills/pymatgen/scripts/_common.py +0 -316
- package/skills/pymatgen/scripts/artifact_manifest.py +0 -172
- package/skills/pymatgen/scripts/composition_structure_validator.py +0 -300
- package/skills/pymatgen/scripts/io_conversion_plan.py +0 -204
- package/skills/pymatgen/scripts/mp_query.py +0 -416
- package/skills/pymatgen/scripts/phase_diagram_generator.py +0 -415
- package/skills/pymatgen/scripts/structure_analyzer.py +0 -293
- package/skills/pymatgen/scripts/structure_converter.py +0 -219
- package/skills/pymatgen/scripts/symmetry_sensitivity_report.py +0 -212
- package/skills/pymc/assets/hierarchical_model_template.py +0 -332
- package/skills/pymc/assets/linear_regression_template.py +0 -244
- package/skills/pymc/references/distributions.md +0 -345
- package/skills/pymc/references/model_patterns.md +0 -130
- package/skills/pymc/references/sampling_inference.md +0 -432
- package/skills/pymc/references/standard_workflow.md +0 -176
- package/skills/pymc/references/workflows.md +0 -530
- package/skills/pymc/scripts/model_comparison.py +0 -409
- package/skills/pymc/scripts/model_diagnostics.py +0 -328
- package/skills/pymoo/references/algorithms.md +0 -232
- package/skills/pymoo/references/constraints_mcdm.md +0 -417
- package/skills/pymoo/references/operators.md +0 -345
- package/skills/pymoo/references/parallelization.md +0 -80
- package/skills/pymoo/references/problems.md +0 -265
- package/skills/pymoo/references/quick_start_workflows.md +0 -404
- package/skills/pymoo/references/visualization.md +0 -353
- package/skills/pymoo/scripts/custom_problem_example.py +0 -181
- package/skills/pymoo/scripts/decision_making_example.py +0 -161
- package/skills/pymoo/scripts/many_objective_example.py +0 -74
- package/skills/pymoo/scripts/multi_objective_example.py +0 -63
- package/skills/pymoo/scripts/single_objective_example.py +0 -59
- package/skills/pyopenms/references/data_structures.md +0 -498
- package/skills/pyopenms/references/feature_detection.md +0 -495
- package/skills/pyopenms/references/file_io.md +0 -359
- package/skills/pyopenms/references/identification.md +0 -431
- package/skills/pyopenms/references/metabolomics.md +0 -548
- package/skills/pyopenms/references/signal_processing.md +0 -444
- package/skills/pyopenms/scripts/accurate_mass_search.py +0 -111
- package/skills/pyopenms/scripts/align_link_quantify.py +0 -140
- package/skills/pyopenms/scripts/consensus_to_matrix.py +0 -70
- package/skills/pyopenms/scripts/convert_format.py +0 -95
- package/skills/pyopenms/scripts/detect_adducts.py +0 -90
- package/skills/pyopenms/scripts/detect_features_centroided.py +0 -80
- package/skills/pyopenms/scripts/detect_features_metabo.py +0 -110
- package/skills/pyopenms/scripts/digest_protein.py +0 -102
- package/skills/pyopenms/scripts/export_gnps_sirius.py +0 -90
- package/skills/pyopenms/scripts/extract_chromatograms.py +0 -105
- package/skills/pyopenms/scripts/inspect_ms_data.py +0 -167
- package/skills/pyopenms/scripts/mass_calculator.py +0 -92
- package/skills/pyopenms/scripts/plot_ms_data.py +0 -129
- package/skills/pyopenms/scripts/process_identifications.py +0 -111
- package/skills/pyopenms/scripts/process_spectra.py +0 -124
- package/skills/pyopenms/scripts/theoretical_spectrum.py +0 -75
- package/skills/pysam/references/alignment_files.md +0 -374
- package/skills/pysam/references/api_reference.md +0 -421
- package/skills/pysam/references/common_workflows.md +0 -442
- package/skills/pysam/references/coordinates_and_indexing.md +0 -318
- package/skills/pysam/references/cram_and_performance.md +0 -314
- package/skills/pysam/references/migration_to_0_24.md +0 -177
- package/skills/pysam/references/sequence_files.md +0 -316
- package/skills/pysam/references/sources.md +0 -132
- package/skills/pysam/references/variant_files.md +0 -396
- package/skills/pysam/scripts/alignment_qc.py +0 -326
- package/skills/pysam/scripts/filter_alignments.py +0 -359
- package/skills/pysam/scripts/inspect_hts.py +0 -485
- package/skills/pysam/scripts/variant_summary.py +0 -362
- package/skills/pytdc/references/datasets.md +0 -242
- package/skills/pytdc/references/oracles.md +0 -273
- package/skills/pytdc/references/sources.md +0 -165
- package/skills/pytdc/references/utilities.md +0 -364
- package/skills/pytdc/scripts/_common.py +0 -205
- package/skills/pytdc/scripts/benchmark_evaluation.py +0 -367
- package/skills/pytdc/scripts/cache_audit.py +0 -146
- package/skills/pytdc/scripts/discover_metadata.py +0 -174
- package/skills/pytdc/scripts/load_and_split_data.py +0 -374
- package/skills/pytdc/scripts/molecular_generation.py +0 -417
- package/skills/pytorch-lightning/references/best_practices.md +0 -724
- package/skills/pytorch-lightning/references/callbacks.md +0 -564
- package/skills/pytorch-lightning/references/data_module.md +0 -565
- package/skills/pytorch-lightning/references/distributed_training.md +0 -644
- package/skills/pytorch-lightning/references/lightning_module.md +0 -487
- package/skills/pytorch-lightning/references/logging.md +0 -636
- package/skills/pytorch-lightning/references/trainer.md +0 -641
- package/skills/pytorch-lightning/scripts/quick_trainer_setup.py +0 -473
- package/skills/pytorch-lightning/scripts/template_datamodule.py +0 -328
- package/skills/pytorch-lightning/scripts/template_lightning_module.py +0 -220
- package/skills/pyzotero/references/authentication.md +0 -105
- package/skills/pyzotero/references/cli.md +0 -102
- package/skills/pyzotero/references/collections.md +0 -113
- package/skills/pyzotero/references/error-handling.md +0 -108
- package/skills/pyzotero/references/exports.md +0 -102
- package/skills/pyzotero/references/files-attachments.md +0 -97
- package/skills/pyzotero/references/full-text.md +0 -68
- package/skills/pyzotero/references/mcp.md +0 -90
- package/skills/pyzotero/references/pagination.md +0 -79
- package/skills/pyzotero/references/read-api.md +0 -137
- package/skills/pyzotero/references/saved-searches.md +0 -77
- package/skills/pyzotero/references/search-params.md +0 -90
- package/skills/pyzotero/references/tags.md +0 -87
- package/skills/pyzotero/references/write-api.md +0 -123
- package/skills/qiskit/references/algorithms.md +0 -311
- package/skills/qiskit/references/backends.md +0 -382
- package/skills/qiskit/references/circuits.md +0 -319
- package/skills/qiskit/references/migration.md +0 -338
- package/skills/qiskit/references/patterns.md +0 -386
- package/skills/qiskit/references/primitives.md +0 -400
- package/skills/qiskit/references/setup.md +0 -253
- package/skills/qiskit/references/sources.md +0 -156
- package/skills/qiskit/references/testing.md +0 -428
- package/skills/qiskit/references/transpilation.md +0 -333
- package/skills/qiskit/references/visualization.md +0 -361
- package/skills/qiskit/scripts/check_environment.py +0 -260
- package/skills/qiskit/scripts/inspect_runtime.py +0 -224
- package/skills/qiskit/scripts/run_local_primitives.py +0 -200
- package/skills/qutip/references/advanced.md +0 -413
- package/skills/qutip/references/analysis.md +0 -319
- package/skills/qutip/references/core_concepts.md +0 -300
- package/skills/qutip/references/time_evolution.md +0 -373
- package/skills/qutip/references/visualization.md +0 -334
- package/skills/qutip/scripts/_common.py +0 -370
- package/skills/qutip/scripts/convergence_sweep.py +0 -358
- package/skills/qutip/scripts/qobj_model_validator.py +0 -327
- package/skills/qutip/scripts/result_audit.py +0 -395
- package/skills/qutip/scripts/solver_config_planner.py +0 -297
- package/skills/qutip/scripts/steady_state_spectrum_planner.py +0 -245
- package/skills/qutip/scripts/two_level_simulation.py +0 -394
- package/skills/rdkit/references/api_reference.md +0 -443
- package/skills/rdkit/references/core_capabilities.md +0 -604
- package/skills/rdkit/references/descriptors_reference.md +0 -595
- package/skills/rdkit/references/smarts_patterns.md +0 -668
- package/skills/rdkit/references/workflows_and_best_practices.md +0 -169
- package/skills/rdkit/scripts/molecular_properties.py +0 -243
- package/skills/rdkit/scripts/similarity_search.py +0 -297
- package/skills/rdkit/scripts/substructure_filter.py +0 -386
- package/skills/relsa-severity-assessment/assets/example_cohort.csv +0 -55
- package/skills/relsa-severity-assessment/references/forecasting.md +0 -155
- package/skills/relsa-severity-assessment/references/relsa-method.md +0 -175
- package/skills/relsa-severity-assessment/references/thresholds-and-zones.md +0 -154
- package/skills/relsa-severity-assessment/scripts/_common.py +0 -287
- package/skills/relsa-severity-assessment/scripts/forecast_relsa.py +0 -757
- package/skills/relsa-severity-assessment/scripts/kde_thresholds.py +0 -369
- package/skills/relsa-severity-assessment/scripts/relsa_score.py +0 -488
- package/skills/research-grants/assets/budget_justification_template.md +0 -453
- package/skills/research-grants/assets/nih_specific_aims_template.md +0 -166
- package/skills/research-grants/assets/nsf_project_summary_template.md +0 -92
- package/skills/research-grants/references/broader_impacts.md +0 -392
- package/skills/research-grants/references/core_components.md +0 -397
- package/skills/research-grants/references/darpa_guidelines.md +0 -636
- package/skills/research-grants/references/doe_guidelines.md +0 -586
- package/skills/research-grants/references/nih_guidelines.md +0 -853
- package/skills/research-grants/references/nsf_guidelines.md +0 -570
- package/skills/research-grants/references/nstc_guidelines.md +0 -733
- package/skills/research-grants/references/proposal_types_and_resubmission.md +0 -81
- package/skills/research-grants/references/review_criteria.md +0 -93
- package/skills/research-grants/references/specific_aims_guide.md +0 -458
- package/skills/research-grants/references/writing_principles.md +0 -94
- package/skills/research-lookup/scripts/manuscript_packet.py +0 -754
- package/skills/research-lookup/scripts/research_lookup.py +0 -1204
- package/skills/rowan/references/access_and_pricing.md +0 -37
- package/skills/rowan/references/batch_and_webhooks.md +0 -255
- package/skills/rowan/references/end_to_end_example.md +0 -119
- package/skills/rowan/references/troubleshooting.md +0 -106
- package/skills/rowan/references/workflow_catalog.md +0 -308
- package/skills/scanpy/assets/analysis_template.py +0 -301
- package/skills/scanpy/assets/celltype_mapping.json +0 -10
- package/skills/scanpy/assets/gene_signatures.json +0 -9
- package/skills/scanpy/assets/pipeline_config.json +0 -19
- package/skills/scanpy/references/analysis_workflow.md +0 -236
- package/skills/scanpy/references/api_reference.md +0 -267
- package/skills/scanpy/references/plotting_guide.md +0 -365
- package/skills/scanpy/references/r_interop.md +0 -292
- package/skills/scanpy/references/standard_workflow.md +0 -223
- package/skills/scanpy/scripts/_common.py +0 -127
- package/skills/scanpy/scripts/annotate.py +0 -84
- package/skills/scanpy/scripts/batch_correct.py +0 -65
- package/skills/scanpy/scripts/cluster.py +0 -63
- package/skills/scanpy/scripts/convert.py +0 -43
- package/skills/scanpy/scripts/find_markers.py +0 -75
- package/skills/scanpy/scripts/inspect_data.py +0 -81
- package/skills/scanpy/scripts/plot.py +0 -78
- package/skills/scanpy/scripts/preprocess.py +0 -88
- package/skills/scanpy/scripts/pseudobulk.py +0 -74
- package/skills/scanpy/scripts/qc_analysis.py +0 -104
- package/skills/scanpy/scripts/reduce_dimensions.py +0 -64
- package/skills/scanpy/scripts/run_pipeline.py +0 -182
- package/skills/scanpy/scripts/score_genes.py +0 -82
- package/skills/scanpy/scripts/subset.py +0 -64
- package/skills/scholar-evaluation/assets/evaluation_template.json +0 -50
- package/skills/scholar-evaluation/assets/evidence_manifest_template.json +0 -63
- package/skills/scholar-evaluation/assets/process_checklist_template.json +0 -70
- package/skills/scholar-evaluation/assets/ratings_template.csv +0 -21
- package/skills/scholar-evaluation/assets/rubric_template.json +0 -301
- package/skills/scholar-evaluation/references/evaluation_framework.md +0 -264
- package/skills/scholar-evaluation/references/local_tooling.md +0 -232
- package/skills/scholar-evaluation/references/responsible_assessment.md +0 -196
- package/skills/scholar-evaluation/references/security_validation.md +0 -95
- package/skills/scholar-evaluation/references/source_ledger.md +0 -222
- package/skills/scholar-evaluation/scripts/_common.py +0 -986
- package/skills/scholar-evaluation/scripts/calculate_scores.py +0 -57
- package/skills/scholar-evaluation/scripts/check_process.py +0 -231
- package/skills/scholar-evaluation/scripts/check_traceability.py +0 -233
- package/skills/scholar-evaluation/scripts/generate_report_scaffold.py +0 -231
- package/skills/scholar-evaluation/scripts/summarize_agreement.py +0 -235
- package/skills/scholar-evaluation/scripts/validate_rubric.py +0 -54
- package/skills/scholar-evaluation/scripts/weight_sensitivity.py +0 -251
- package/skills/scientific-brainstorming/references/brainstorming_methods.md +0 -292
- package/skills/scientific-brainstorming/references/facilitation_workflows.md +0 -284
- package/skills/scientific-brainstorming/references/idea_evaluation.md +0 -268
- package/skills/scientific-brainstorming/references/responsible_ai.md +0 -220
- package/skills/scientific-brainstorming/references/sources.md +0 -364
- package/skills/scientific-brainstorming/scripts/_common.py +0 -307
- package/skills/scientific-brainstorming/scripts/evaluate_matrix.py +0 -518
- package/skills/scientific-brainstorming/scripts/session_scaffold.py +0 -248
- package/skills/scientific-brainstorming/scripts/validate_register.py +0 -654
- package/skills/scientific-critical-thinking/references/common_biases.md +0 -364
- package/skills/scientific-critical-thinking/references/core_capabilities.md +0 -407
- package/skills/scientific-critical-thinking/references/evidence_hierarchy.md +0 -485
- package/skills/scientific-critical-thinking/references/experimental_design.md +0 -496
- package/skills/scientific-critical-thinking/references/logical_fallacies.md +0 -478
- package/skills/scientific-critical-thinking/references/scientific_method.md +0 -169
- package/skills/scientific-critical-thinking/references/statistical_pitfalls.md +0 -506
- package/skills/scientific-schematics/references/best_practices.md +0 -574
- package/skills/scientific-schematics/references/iterative_refinement.md +0 -315
- package/skills/scientific-schematics/scripts/example_usage.sh +0 -92
- package/skills/scientific-schematics/scripts/generate_schematic.py +0 -198
- package/skills/scientific-schematics/scripts/generate_schematic_ai.py +0 -950
- package/skills/scientific-slides/assets/beamer_template_conference.tex +0 -407
- package/skills/scientific-slides/assets/beamer_template_defense.tex +0 -906
- package/skills/scientific-slides/assets/beamer_template_seminar.tex +0 -870
- package/skills/scientific-slides/assets/powerpoint_design_guide.md +0 -662
- package/skills/scientific-slides/assets/timing_guidelines.md +0 -597
- package/skills/scientific-slides/references/beamer_guide.md +0 -1019
- package/skills/scientific-slides/references/common_pitfalls.md +0 -85
- package/skills/scientific-slides/references/data_visualization_slides.md +0 -708
- package/skills/scientific-slides/references/presentation_structure.md +0 -642
- package/skills/scientific-slides/references/presentation_workflow.md +0 -196
- package/skills/scientific-slides/references/prompt_writing.md +0 -42
- package/skills/scientific-slides/references/script_reference.md +0 -143
- package/skills/scientific-slides/references/slide_capabilities.md +0 -360
- package/skills/scientific-slides/references/slide_design_principles.md +0 -849
- package/skills/scientific-slides/references/talk_types_guide.md +0 -687
- package/skills/scientific-slides/references/visual_review_workflow.md +0 -775
- package/skills/scientific-slides/scripts/generate_schematic.py +0 -198
- package/skills/scientific-slides/scripts/generate_schematic_ai.py +0 -950
- package/skills/scientific-slides/scripts/generate_slide_image.py +0 -197
- package/skills/scientific-slides/scripts/generate_slide_image_ai.py +0 -877
- package/skills/scientific-slides/scripts/pdf_to_images.py +0 -221
- package/skills/scientific-slides/scripts/slides_to_pdf.py +0 -235
- package/skills/scientific-slides/scripts/validate_presentation.py +0 -408
- package/skills/scientific-visualization/assets/color_palettes.py +0 -263
- package/skills/scientific-visualization/assets/nature.mplstyle +0 -68
- package/skills/scientific-visualization/assets/presentation.mplstyle +0 -68
- package/skills/scientific-visualization/assets/publication.mplstyle +0 -77
- package/skills/scientific-visualization/assets/publisher_profiles.json +0 -269
- package/skills/scientific-visualization/references/color_palettes.md +0 -227
- package/skills/scientific-visualization/references/journal_requirements.md +0 -169
- package/skills/scientific-visualization/references/matplotlib_examples.md +0 -336
- package/skills/scientific-visualization/references/publication_guidelines.md +0 -196
- package/skills/scientific-visualization/references/sources.md +0 -76
- package/skills/scientific-visualization/scripts/_common.py +0 -136
- package/skills/scientific-visualization/scripts/export_plan.py +0 -493
- package/skills/scientific-visualization/scripts/figure_export.py +0 -642
- package/skills/scientific-visualization/scripts/image_metadata.py +0 -731
- package/skills/scientific-visualization/scripts/palette_audit.py +0 -327
- package/skills/scientific-visualization/scripts/style_presets.py +0 -501
- package/skills/scientific-visualization/scripts/style_preview.py +0 -232
- package/skills/scientific-writing/assets/REPORT_FORMATTING_GUIDE.md +0 -60
- package/skills/scientific-writing/assets/authorship_template.json +0 -56
- package/skills/scientific-writing/assets/claim_evidence_template.csv +0 -2
- package/skills/scientific-writing/assets/consistency_manifest_template.json +0 -43
- package/skills/scientific-writing/assets/manuscript_manifest_template.json +0 -37
- package/skills/scientific-writing/assets/manuscript_scaffold.md +0 -65
- package/skills/scientific-writing/assets/reporting_coverage_template.json +0 -6
- package/skills/scientific-writing/assets/reporting_guidelines.json +0 -529
- package/skills/scientific-writing/assets/source_manifest_template.json +0 -27
- package/skills/scientific-writing/references/authorship_ai_confidentiality.md +0 -111
- package/skills/scientific-writing/references/citation_styles.md +0 -92
- package/skills/scientific-writing/references/cli_reference.md +0 -113
- package/skills/scientific-writing/references/evidence_workflow.md +0 -94
- package/skills/scientific-writing/references/figures_tables.md +0 -94
- package/skills/scientific-writing/references/imrad_structure.md +0 -114
- package/skills/scientific-writing/references/journal_policies.md +0 -56
- package/skills/scientific-writing/references/professional_report_formatting.md +0 -82
- package/skills/scientific-writing/references/reporting_guidelines.md +0 -107
- package/skills/scientific-writing/references/research_integrity_open_science.md +0 -97
- package/skills/scientific-writing/references/source_ledger.md +0 -268
- package/skills/scientific-writing/references/writing_principles.md +0 -97
- package/skills/scientific-writing/scripts/_common.py +0 -240
- package/skills/scientific-writing/scripts/audit_claims.py +0 -241
- package/skills/scientific-writing/scripts/check_consistency.py +0 -408
- package/skills/scientific-writing/scripts/check_references.py +0 -219
- package/skills/scientific-writing/scripts/lint_manuscript.py +0 -171
- package/skills/scientific-writing/scripts/scaffold_manuscript.py +0 -143
- package/skills/scientific-writing/scripts/select_reporting_guidelines.py +0 -214
- package/skills/scientific-writing/scripts/validate_authorship.py +0 -322
- package/skills/scientific-writing/scripts/validate_manifest.py +0 -460
- package/skills/scikit-bio/references/api_reference.md +0 -766
- package/skills/scikit-learn/references/common_workflows.md +0 -107
- package/skills/scikit-learn/references/core_capabilities.md +0 -133
- package/skills/scikit-learn/references/model_evaluation.md +0 -592
- package/skills/scikit-learn/references/pipelines_and_composition.md +0 -612
- package/skills/scikit-learn/references/preprocessing.md +0 -606
- package/skills/scikit-learn/references/quick_reference.md +0 -436
- package/skills/scikit-learn/references/supervised_learning.md +0 -379
- package/skills/scikit-learn/references/unsupervised_learning.md +0 -517
- package/skills/scikit-learn/scripts/classification_pipeline.py +0 -257
- package/skills/scikit-learn/scripts/clustering_analysis.py +0 -386
- package/skills/scikit-survival/references/competing-risks.md +0 -302
- package/skills/scikit-survival/references/cox-models.md +0 -252
- package/skills/scikit-survival/references/data-handling.md +0 -278
- package/skills/scikit-survival/references/ensemble-models.md +0 -287
- package/skills/scikit-survival/references/evaluation-metrics.md +0 -391
- package/skills/scikit-survival/references/svm-models.md +0 -277
- package/skills/scikit-survival/scripts/_common.py +0 -456
- package/skills/scikit-survival/scripts/competing_risk_cif.py +0 -286
- package/skills/scikit-survival/scripts/evaluate_survival_metrics.py +0 -296
- package/skills/scikit-survival/scripts/model_report.py +0 -297
- package/skills/scikit-survival/scripts/train_survival_model.py +0 -583
- package/skills/scikit-survival/scripts/validate_survival_csv.py +0 -172
- package/skills/scvelo/references/velocity_models.md +0 -168
- package/skills/scvelo/scripts/rna_velocity_workflow.py +0 -240
- package/skills/scvi-tools/references/differential-expression.md +0 -597
- package/skills/scvi-tools/references/models-atac-seq.md +0 -329
- package/skills/scvi-tools/references/models-multimodal.md +0 -400
- package/skills/scvi-tools/references/models-scrna-seq.md +0 -333
- package/skills/scvi-tools/references/models-spatial.md +0 -432
- package/skills/scvi-tools/references/models-specialized.md +0 -376
- package/skills/scvi-tools/references/theoretical-foundations.md +0 -438
- package/skills/scvi-tools/references/workflows.md +0 -559
- package/skills/seaborn/references/examples.md +0 -824
- package/skills/seaborn/references/function_reference.md +0 -772
- package/skills/seaborn/references/grids_and_levels.md +0 -85
- package/skills/seaborn/references/objects_interface.md +0 -963
- package/skills/seaborn/references/palettes_and_theming.md +0 -110
- package/skills/seaborn/references/patterns_and_troubleshooting.md +0 -114
- package/skills/seaborn/references/plotting_functions.md +0 -178
- package/skills/shap/references/data-maskers.md +0 -287
- package/skills/shap/references/explainers.md +0 -376
- package/skills/shap/references/migration.md +0 -415
- package/skills/shap/references/modalities.md +0 -353
- package/skills/shap/references/plots.md +0 -406
- package/skills/shap/references/theory.md +0 -352
- package/skills/shap/references/troubleshooting.md +0 -442
- package/skills/shap/references/workflows.md +0 -565
- package/skills/shap/scripts/tabular_report.py +0 -326
- package/skills/simpy/references/cli-guide.md +0 -266
- package/skills/simpy/references/events.md +0 -225
- package/skills/simpy/references/monitoring.md +0 -260
- package/skills/simpy/references/process-interaction.md +0 -269
- package/skills/simpy/references/real-time.md +0 -174
- package/skills/simpy/references/resources.md +0 -274
- package/skills/simpy/references/simulation-methodology.md +0 -293
- package/skills/simpy/references/sources.md +0 -167
- package/skills/simpy/scripts/_common.py +0 -473
- package/skills/simpy/scripts/basic_simulation_template.py +0 -415
- package/skills/simpy/scripts/bounded_queue_scenario.py +0 -126
- package/skills/simpy/scripts/event_trace_summary.py +0 -296
- package/skills/simpy/scripts/replication_runner.py +0 -194
- package/skills/simpy/scripts/resource_monitor.py +0 -474
- package/skills/simpy/scripts/validate_simulation_config.py +0 -111
- package/skills/stable-baselines3/references/algorithms.md +0 -348
- package/skills/stable-baselines3/references/callbacks.md +0 -571
- package/skills/stable-baselines3/references/custom_environments.md +0 -528
- package/skills/stable-baselines3/references/vectorized_envs.md +0 -580
- package/skills/stable-baselines3/scripts/custom_env_template.py +0 -314
- package/skills/stable-baselines3/scripts/evaluate_agent.py +0 -245
- package/skills/stable-baselines3/scripts/train_rl_agent.py +0 -165
- package/skills/statistical-analysis/references/assumptions_and_diagnostics.md +0 -379
- package/skills/statistical-analysis/references/bayesian_statistics.md +0 -686
- package/skills/statistical-analysis/references/effect_sizes_and_power.md +0 -649
- package/skills/statistical-analysis/references/reporting_standards.md +0 -482
- package/skills/statistical-analysis/references/test_selection_guide.md +0 -129
- package/skills/statistical-analysis/scripts/assumption_checks.py +0 -652
- package/skills/statistical-power/references/closed_form_recipes.md +0 -174
- package/skills/statistical-power/references/effect_sizes.md +0 -121
- package/skills/statistical-power/references/simulation_based_power.md +0 -101
- package/skills/statistical-power/scripts/power.py +0 -320
- package/skills/statistical-power/scripts/simulate_power.py +0 -217
- package/skills/statsmodels/references/discrete_choice.md +0 -669
- package/skills/statsmodels/references/glm.md +0 -619
- package/skills/statsmodels/references/linear_models.md +0 -447
- package/skills/statsmodels/references/model_selection.md +0 -99
- package/skills/statsmodels/references/modeling_capabilities.md +0 -168
- package/skills/statsmodels/references/quick_start_guide.md +0 -154
- package/skills/statsmodels/references/stats_diagnostics.md +0 -859
- package/skills/statsmodels/references/time_series.md +0 -723
- package/skills/sympy/references/advanced-topics.md +0 -635
- package/skills/sympy/references/code-generation-printing.md +0 -628
- package/skills/sympy/references/core-capabilities.md +0 -348
- package/skills/sympy/references/core_capabilities.md +0 -190
- package/skills/sympy/references/matrices-linear-algebra.md +0 -526
- package/skills/sympy/references/physics-mechanics.md +0 -592
- package/skills/tamarind/references/api_reference.md +0 -165
- package/skills/tamarind/references/examples.md +0 -132
- package/skills/tamarind/references/tool_catalog.md +0 -66
- package/skills/tamarind/references/workflows.md +0 -263
- package/skills/timesfm-forecasting/examples/anomaly-detection/detect_anomalies.py +0 -524
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.json +0 -448
- package/skills/timesfm-forecasting/examples/anomaly-detection/output/anomaly_detection.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/demo_covariates.py +0 -568
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_data.png +0 -0
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/covariates_metadata.json +0 -59
- package/skills/timesfm-forecasting/examples/covariates-forecasting/output/sales_with_covariates.csv +0 -109
- package/skills/timesfm-forecasting/examples/global-temperature/generate_animation_data.py +0 -147
- package/skills/timesfm-forecasting/examples/global-temperature/generate_gif.py +0 -248
- package/skills/timesfm-forecasting/examples/global-temperature/generate_html.py +0 -544
- package/skills/timesfm-forecasting/examples/global-temperature/output/animation_data.json +0 -5441
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_animation.gif +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.csv +0 -13
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_output.json +0 -188
- package/skills/timesfm-forecasting/examples/global-temperature/output/forecast_visualization.png +0 -0
- package/skills/timesfm-forecasting/examples/global-temperature/output/interactive_forecast.html +0 -5939
- package/skills/timesfm-forecasting/examples/global-temperature/run_example.sh +0 -53
- package/skills/timesfm-forecasting/examples/global-temperature/run_forecast.py +0 -167
- package/skills/timesfm-forecasting/examples/global-temperature/temperature_anomaly.csv +0 -37
- package/skills/timesfm-forecasting/examples/global-temperature/visualize_forecast.py +0 -123
- package/skills/timesfm-forecasting/references/api_reference.md +0 -231
- package/skills/timesfm-forecasting/references/data_preparation.md +0 -272
- package/skills/timesfm-forecasting/references/examples_and_validation.md +0 -103
- package/skills/timesfm-forecasting/references/output_and_config.md +0 -93
- package/skills/timesfm-forecasting/references/performance_tuning.md +0 -80
- package/skills/timesfm-forecasting/references/system_requirements.md +0 -201
- package/skills/timesfm-forecasting/references/workflows.md +0 -126
- package/skills/timesfm-forecasting/scripts/check_system.py +0 -521
- package/skills/timesfm-forecasting/scripts/forecast_csv.py +0 -269
- package/skills/torch-geometric/references/custom_datasets.md +0 -239
- package/skills/torch-geometric/references/explainability.md +0 -208
- package/skills/torch-geometric/references/heterogeneous.md +0 -241
- package/skills/torch-geometric/references/link_prediction.md +0 -226
- package/skills/torch-geometric/references/message_passing.md +0 -121
- package/skills/torch-geometric/references/scaling.md +0 -269
- package/skills/torchdrug/references/core_concepts.md +0 -241
- package/skills/torchdrug/references/datasets.md +0 -179
- package/skills/torchdrug/references/knowledge_graphs.md +0 -226
- package/skills/torchdrug/references/models_architectures.md +0 -223
- package/skills/torchdrug/references/molecular_generation.md +0 -246
- package/skills/torchdrug/references/molecular_property_prediction.md +0 -239
- package/skills/torchdrug/references/protein_modeling.md +0 -221
- package/skills/torchdrug/references/retrosynthesis.md +0 -247
- package/skills/transformers/references/generation.md +0 -473
- package/skills/transformers/references/models.md +0 -371
- package/skills/transformers/references/pipelines.md +0 -334
- package/skills/transformers/references/tokenizers.md +0 -449
- package/skills/transformers/references/training.md +0 -504
- package/skills/treatment-plans/assets/clinician_authored_intervention_template.json +0 -11
- package/skills/treatment-plans/assets/goals_monitoring_checkpoint_template.json +0 -13
- package/skills/treatment-plans/assets/informed_preference_shared_decision_template.json +0 -11
- package/skills/treatment-plans/assets/intended_use_handoff_template.json +0 -83
- package/skills/treatment-plans/assets/source_fact_manifest_template.json +0 -11
- package/skills/treatment-plans/assets/transition_reconciliation_template.json +0 -27
- package/skills/treatment-plans/references/documentation_workflow.md +0 -165
- package/skills/treatment-plans/references/privacy_governance.md +0 -119
- package/skills/treatment-plans/references/safety_scope.md +0 -101
- package/skills/treatment-plans/references/security_validation.md +0 -68
- package/skills/treatment-plans/references/shared_decision_handoff.md +0 -138
- package/skills/treatment-plans/references/source_boundaries.md +0 -127
- package/skills/treatment-plans/references/source_ledger.md +0 -131
- package/skills/treatment-plans/scripts/_common.py +0 -1160
- package/skills/treatment-plans/scripts/check_completeness.py +0 -572
- package/skills/treatment-plans/scripts/check_consistency.py +0 -386
- package/skills/treatment-plans/scripts/generate_template.py +0 -133
- package/skills/treatment-plans/scripts/privacy_process_check.py +0 -213
- package/skills/treatment-plans/scripts/timeline_generator.py +0 -260
- package/skills/treatment-plans/scripts/validate_traceability.py +0 -147
- package/skills/treatment-plans/scripts/validate_treatment_plan.py +0 -95
- package/skills/umap-learn/references/api_reference.md +0 -574
- package/skills/uncertainty-and-units/references/domain-conversions.md +0 -188
- package/skills/uncertainty-and-units/references/gum-methodology.md +0 -219
- package/skills/uncertainty-and-units/references/pint-recipes.md +0 -228
- package/skills/uncertainty-and-units/references/plausibility-scales.md +0 -168
- package/skills/uncertainty-and-units/references/reporting-rules.md +0 -133
- package/skills/uncertainty-and-units/references/uncertainties-recipes.md +0 -167
- package/skills/uncertainty-and-units/scripts/_common.py +0 -666
- package/skills/uncertainty-and-units/scripts/audit_units.py +0 -575
- package/skills/uncertainty-and-units/scripts/check_plausibility.py +0 -894
- package/skills/uncertainty-and-units/scripts/convert_units.py +0 -280
- package/skills/uncertainty-and-units/scripts/format_result.py +0 -326
- package/skills/uncertainty-and-units/scripts/propagate_uncertainty.py +0 -662
- package/skills/uncertainty-and-units/scripts/uncertainty_budget.py +0 -363
- package/skills/usfiscaldata/references/api-basics.md +0 -105
- package/skills/usfiscaldata/references/datasets-debt.md +0 -166
- package/skills/usfiscaldata/references/datasets-fiscal.md +0 -212
- package/skills/usfiscaldata/references/datasets-interest-rates.md +0 -188
- package/skills/usfiscaldata/references/datasets-securities.md +0 -238
- package/skills/usfiscaldata/references/examples.md +0 -258
- package/skills/usfiscaldata/references/parameters.md +0 -182
- package/skills/usfiscaldata/references/response-format.md +0 -178
- package/skills/vaex/references/core_dataframes.md +0 -373
- package/skills/vaex/references/data_processing.md +0 -555
- package/skills/vaex/references/io_operations.md +0 -718
- package/skills/vaex/references/machine_learning.md +0 -728
- package/skills/vaex/references/performance.md +0 -571
- package/skills/vaex/references/visualization.md +0 -644
- package/skills/venue-templates/assets/examples/cell_summary_example.md +0 -247
- package/skills/venue-templates/assets/examples/medical_structured_abstract.md +0 -313
- package/skills/venue-templates/assets/examples/nature_abstract_examples.md +0 -213
- package/skills/venue-templates/assets/examples/neurips_introduction_example.md +0 -245
- package/skills/venue-templates/assets/grants/nih_specific_aims.tex +0 -237
- package/skills/venue-templates/assets/grants/nsf_proposal_template.tex +0 -384
- package/skills/venue-templates/assets/journals/elsarticle-harv.bst +0 -1598
- package/skills/venue-templates/assets/journals/elsarticle-num-names.bst +0 -1535
- package/skills/venue-templates/assets/journals/elsarticle-num.bst +0 -1509
- package/skills/venue-templates/assets/journals/elsarticle-template-harv.tex +0 -286
- package/skills/venue-templates/assets/journals/elsarticle-template-num-names.tex +0 -284
- package/skills/venue-templates/assets/journals/elsarticle-template-num.tex +0 -286
- package/skills/venue-templates/assets/journals/nature_article.tex +0 -174
- package/skills/venue-templates/assets/journals/neurips_article.tex +0 -292
- package/skills/venue-templates/assets/journals/plos_one.tex +0 -320
- package/skills/venue-templates/assets/posters/beamerposter_academic.tex +0 -312
- package/skills/venue-templates/references/cell_press_style.md +0 -486
- package/skills/venue-templates/references/conferences_formatting.md +0 -175
- package/skills/venue-templates/references/cs_conference_style.md +0 -465
- package/skills/venue-templates/references/grants_requirements.md +0 -267
- package/skills/venue-templates/references/journals_formatting.md +0 -200
- package/skills/venue-templates/references/medical_journal_styles.md +0 -536
- package/skills/venue-templates/references/ml_conference_style.md +0 -562
- package/skills/venue-templates/references/nature_science_style.md +0 -407
- package/skills/venue-templates/references/posters_guidelines.md +0 -630
- package/skills/venue-templates/references/reviewer_expectations.md +0 -422
- package/skills/venue-templates/references/venue_writing_styles.md +0 -323
- package/skills/venue-templates/scripts/customize_template.py +0 -206
- package/skills/venue-templates/scripts/query_template.py +0 -202
- package/skills/venue-templates/scripts/validate_format.py +0 -321
- package/skills/waypoint-bio/references/cli-reference.md +0 -210
- package/skills/waypoint-bio/references/compass-benchmark.md +0 -124
- package/skills/waypoint-bio/references/data-preparation.md +0 -200
- package/skills/waypoint-bio/references/python-api.md +0 -219
- package/skills/waypoint-bio/scripts/profiler_to_waypoint.py +0 -481
- package/skills/waypoint-bio/scripts/vocab_coverage.py +0 -235
- package/skills/what-if-oracle/references/scenario-templates.md +0 -137
- package/skills/xlsx/LICENSE.txt +0 -30
- package/skills/xlsx/scripts/office/helpers/__init__.py +0 -111
- package/skills/xlsx/scripts/office/helpers/pptx_chart.py +0 -170
- package/skills/xlsx/scripts/office/helpers/pptx_slide.py +0 -60
- package/skills/xlsx/scripts/office/helpers/pptx_theme.py +0 -114
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +0 -1499
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +0 -146
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +0 -1085
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +0 -11
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-main.xsd +0 -3081
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +0 -23
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +0 -185
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +0 -287
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/pml.xsd +0 -1676
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +0 -28
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +0 -144
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +0 -174
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +0 -25
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +0 -18
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +0 -59
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +0 -56
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +0 -195
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-math.xsd +0 -582
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +0 -25
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/sml.xsd +0 -4439
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-main.xsd +0 -570
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +0 -509
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +0 -12
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +0 -108
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +0 -96
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/wml.xsd +0 -3646
- package/skills/xlsx/scripts/office/schemas/ISO-IEC29500-4_2016/xml.xsd +0 -116
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-contentTypes.xsd +0 -42
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-coreProperties.xsd +0 -50
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-digSig.xsd +0 -49
- package/skills/xlsx/scripts/office/schemas/ecma/fouth-edition/opc-relationships.xsd +0 -33
- package/skills/xlsx/scripts/office/schemas/mce/mc.xsd +0 -75
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2010.xsd +0 -560
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2012.xsd +0 -67
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-2018.xsd +0 -14
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cex-2018.xsd +0 -20
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/xlsx/scripts/office/soffice.py +0 -232
- package/skills/xlsx/scripts/office/validate.py +0 -173
- package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
- package/skills/xlsx/scripts/office/validators/base.py +0 -875
- package/skills/xlsx/scripts/office/validators/docx.py +0 -466
- package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
- package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
- package/skills/xlsx/scripts/recalc.py +0 -308
- package/skills/zarr-python/references/api_reference.md +0 -162
- package/skills/zarr-python/references/chunking_and_compression.md +0 -138
- package/skills/zarr-python/references/integration.md +0 -147
- package/skills/zarr-python/references/performance_and_patterns.md +0 -198
- package/skills/zarr-python/references/storage_backends.md +0 -91
- package/skills/zarr-python/references/v3_migration.md +0 -127
|
@@ -1,264 +0,0 @@
|
|
|
1
|
-
# Evaluation Framework
|
|
2
|
-
|
|
3
|
-
## What ScholarEval is—and is not
|
|
4
|
-
|
|
5
|
-
The paper currently referenced by this skill is Moussa et al.,
|
|
6
|
-
[*ScholarEval: Research Idea Evaluation Grounded in
|
|
7
|
-
Literature*](https://arxiv.org/abs/2510.16234), arXiv:2510.16234v2,
|
|
8
|
-
revised 2026-02-28.
|
|
9
|
-
|
|
10
|
-
The preprint describes an experimental retrieval-augmented system for evaluating
|
|
11
|
-
research ideas on:
|
|
12
|
-
|
|
13
|
-
- **soundness:** whether existing literature empirically supports proposed
|
|
14
|
-
methods; and
|
|
15
|
-
- **contribution:** how an idea advances beyond prior work along comparison
|
|
16
|
-
dimensions.
|
|
17
|
-
|
|
18
|
-
It reports a 117-idea, four-discipline dataset, coverage comparisons with
|
|
19
|
-
expert-annotated review points, and a user study. Those studies evaluate that
|
|
20
|
-
framework. They do **not** validate the generalized rubric in this skill as a
|
|
21
|
-
psychometric instrument, establish stable score meaning across disciplines, or
|
|
22
|
-
authorize use in consequential decisions.
|
|
23
|
-
|
|
24
|
-
As of the dated source review, arXiv and the official project repository were
|
|
25
|
-
the verified primary publication records. No peer-reviewed publication status
|
|
26
|
-
was verified. Cite it as an arXiv preprint unless a later primary record is
|
|
27
|
-
checked. See `references/source_ledger.md`.
|
|
28
|
-
|
|
29
|
-
## Relationship to this skill
|
|
30
|
-
|
|
31
|
-
This skill borrows the useful discipline of:
|
|
32
|
-
|
|
33
|
-
1. defining what is being assessed;
|
|
34
|
-
2. grounding judgments in traceable literature and work evidence;
|
|
35
|
-
3. separating soundness-like questions from contribution-like questions; and
|
|
36
|
-
4. auditing whether generated feedback covers expert concerns.
|
|
37
|
-
|
|
38
|
-
It does not reproduce ScholarEval's model pipeline, prompts, retrieval system,
|
|
39
|
-
dataset, or reported metrics. The bundled scripts do not call ScholarEval,
|
|
40
|
-
search the web, invoke a model, or evaluate private documents.
|
|
41
|
-
|
|
42
|
-
The template is a **locally governed developmental rubric**. Its default
|
|
43
|
-
construct is:
|
|
44
|
-
|
|
45
|
-
> Traceable support for a scholarly work's claims and methods: the degree to
|
|
46
|
-
> which a work states a bounded question, situates its contribution, uses
|
|
47
|
-
> fit-for-purpose methods, aligns analysis with claims, and documents
|
|
48
|
-
> transparent and responsible practices using traceable evidence.
|
|
49
|
-
|
|
50
|
-
This construct must be reviewed and adapted by relevant disciplinary experts.
|
|
51
|
-
|
|
52
|
-
## Five template criteria
|
|
53
|
-
|
|
54
|
-
### 1. Question and scope
|
|
55
|
-
|
|
56
|
-
Review:
|
|
57
|
-
|
|
58
|
-
- a clear, bounded question or objective;
|
|
59
|
-
- significance rationale appropriate to the field and work stage;
|
|
60
|
-
- assumptions, boundary conditions, and success conditions; and
|
|
61
|
-
- feasibility of the proposed or reported scope.
|
|
62
|
-
|
|
63
|
-
Do not treat fashionable topics, institutional affiliation, or venue
|
|
64
|
-
expectations as evidence of significance.
|
|
65
|
-
|
|
66
|
-
### 2. Literature grounding and contribution claim
|
|
67
|
-
|
|
68
|
-
Review:
|
|
69
|
-
|
|
70
|
-
- source-selection or search boundaries;
|
|
71
|
-
- engagement with relevant and contrary evidence;
|
|
72
|
-
- traceable primary sources for comparison claims;
|
|
73
|
-
- comparison dimensions used to define the contribution; and
|
|
74
|
-
- limits on novelty or advancement claims.
|
|
75
|
-
|
|
76
|
-
Failure to find prior work does not establish novelty. Search coverage varies by
|
|
77
|
-
database, language, date, indexing, terminology, discipline, and access.
|
|
78
|
-
|
|
79
|
-
### 3. Method and design fit
|
|
80
|
-
|
|
81
|
-
Review:
|
|
82
|
-
|
|
83
|
-
- alignment between question, design, data or materials, and method;
|
|
84
|
-
- sampling, corpus, inclusion, exclusion, and measurement choices;
|
|
85
|
-
- alternatives and design rationale;
|
|
86
|
-
- validity threats, bias, and mitigation;
|
|
87
|
-
- ethics, consent, privacy, safety, and governance; and
|
|
88
|
-
- detail sufficient for appropriate checking or reproduction.
|
|
89
|
-
|
|
90
|
-
Use discipline-specific reporting and methods standards. Do not reward
|
|
91
|
-
complexity for its own sake.
|
|
92
|
-
|
|
93
|
-
### 4. Analysis, claims, and uncertainty
|
|
94
|
-
|
|
95
|
-
Review:
|
|
96
|
-
|
|
97
|
-
- fit of analytical methods to data and inferential target;
|
|
98
|
-
- assumptions and diagnostics;
|
|
99
|
-
- robustness, sensitivity, negative cases, and alternative explanations;
|
|
100
|
-
- appropriate statistical or qualitative uncertainty;
|
|
101
|
-
- alignment between results and claims; and
|
|
102
|
-
- explicit limits on generalization and causal language.
|
|
103
|
-
|
|
104
|
-
The rubric's `uncertainty` value is a rater-supplied bounded judgment range. It
|
|
105
|
-
is not a sampling confidence interval, posterior interval, or standard error.
|
|
106
|
-
|
|
107
|
-
### 5. Transparency, integrity, and reproducibility
|
|
108
|
-
|
|
109
|
-
Review:
|
|
110
|
-
|
|
111
|
-
- complete reporting, provenance, and stable evidence locators;
|
|
112
|
-
- protocols, registrations, data, code, materials, and justified restrictions;
|
|
113
|
-
- negative, null, and contradictory findings where relevant;
|
|
114
|
-
- conflicts, limitations, corrections, and research-integrity safeguards;
|
|
115
|
-
- accessible communication; and
|
|
116
|
-
- transparent attribution of contributions.
|
|
117
|
-
|
|
118
|
-
Open practice is not an absolute requirement when privacy, consent, safety,
|
|
119
|
-
security, Indigenous data governance, commercial constraints, or other
|
|
120
|
-
legitimate restrictions apply. Assess whether restrictions are justified and
|
|
121
|
-
whether safe access or metadata alternatives are provided.
|
|
122
|
-
|
|
123
|
-
## Scale semantics
|
|
124
|
-
|
|
125
|
-
The template uses an ordinal 0–4 scale:
|
|
126
|
-
|
|
127
|
-
- **0 — no assessable evidence**
|
|
128
|
-
- **1 — limited support**
|
|
129
|
-
- **2 — mixed support**
|
|
130
|
-
- **3 — substantial support**
|
|
131
|
-
- **4 — strong support**
|
|
132
|
-
|
|
133
|
-
These are evidence anchors, not labels of a person or universal levels of
|
|
134
|
-
research quality. The rubric defines criterion-specific anchors. Raters must use
|
|
135
|
-
the anchor text, not intuition about what a number “usually means.”
|
|
136
|
-
|
|
137
|
-
Do not convert the score to:
|
|
138
|
-
|
|
139
|
-
- accept/reject or publication readiness;
|
|
140
|
-
- exceptional/poor labels;
|
|
141
|
-
- predicted success or impact;
|
|
142
|
-
- person ranking; or
|
|
143
|
-
- funding, hiring, promotion, tenure, admissions, award, or discipline advice.
|
|
144
|
-
|
|
145
|
-
## Rating statuses
|
|
146
|
-
|
|
147
|
-
Each criterion has exactly one status:
|
|
148
|
-
|
|
149
|
-
- `rated`: score, uncertainty, evidence identifiers, and rationale reference
|
|
150
|
-
are required;
|
|
151
|
-
- `missing`: evidence needed for assessment is absent or unavailable; score and
|
|
152
|
-
uncertainty are null; or
|
|
153
|
-
- `not_applicable`: the criterion does not apply to this work under a documented
|
|
154
|
-
rationale; score and uncertainty are null.
|
|
155
|
-
|
|
156
|
-
Do not encode missing or not-applicable as zero.
|
|
157
|
-
|
|
158
|
-
## Transparent score math
|
|
159
|
-
|
|
160
|
-
For rated criteria \(R\), score \(s_i\), and predeclared weight \(w_i\):
|
|
161
|
-
|
|
162
|
-
\[
|
|
163
|
-
\text{descriptive score}
|
|
164
|
-
=
|
|
165
|
-
\frac{\sum_{i \in R} w_i s_i}
|
|
166
|
-
{\sum_{i \in R} w_i}
|
|
167
|
-
\]
|
|
168
|
-
|
|
169
|
-
The score report separately provides:
|
|
170
|
-
|
|
171
|
-
- total, applicable, rated, missing, and not-applicable weight;
|
|
172
|
-
- coverage of applicable weight;
|
|
173
|
-
- each weighted contribution;
|
|
174
|
-
- the normalized descriptive score; and
|
|
175
|
-
- a bounded aggregation of criterion uncertainty ranges.
|
|
176
|
-
|
|
177
|
-
The uncertainty aggregation is not a confidence interval. Normalization does
|
|
178
|
-
not make incomplete evaluations comparable. Review missingness before looking
|
|
179
|
-
at any score.
|
|
180
|
-
|
|
181
|
-
## Rubric development record
|
|
182
|
-
|
|
183
|
-
Before replacing `content_validity_status: not_established`, document:
|
|
184
|
-
|
|
185
|
-
1. the exact discipline, work type, language, stage, and intended use;
|
|
186
|
-
2. construct definition and excluded constructs;
|
|
187
|
-
3. literature and standard review used to draft criteria;
|
|
188
|
-
4. disciplinary expert and stakeholder selection;
|
|
189
|
-
5. systematic mapping of criteria to construct components;
|
|
190
|
-
6. cognitive interviews or rater response-process evidence;
|
|
191
|
-
7. accessibility and translation review;
|
|
192
|
-
8. pilot sample and evidence-availability analysis;
|
|
193
|
-
9. revisions, dissent, unresolved gaps, and approval; and
|
|
194
|
-
10. the limits of any validity claim.
|
|
195
|
-
|
|
196
|
-
Rubric provenance must identify the version, owner role, source identifiers,
|
|
197
|
-
review date, and content-evidence reference.
|
|
198
|
-
|
|
199
|
-
## Rater protocol
|
|
200
|
-
|
|
201
|
-
At minimum:
|
|
202
|
-
|
|
203
|
-
1. select qualified raters with relevant disciplinary and methods expertise;
|
|
204
|
-
2. disclose conflicts and recuse where required;
|
|
205
|
-
3. train on construct boundaries, anchors, evidence rules, missingness,
|
|
206
|
-
accessibility, bias, and privacy;
|
|
207
|
-
4. calibrate on synthetic or authorized examples;
|
|
208
|
-
5. rate independently before discussion;
|
|
209
|
-
6. record evidence identifiers and uncertainty;
|
|
210
|
-
7. summarize agreement and investigate systematic disagreements;
|
|
211
|
-
8. resolve only through documented evidence and rationale, not forced averaging;
|
|
212
|
-
9. monitor drift over time; and
|
|
213
|
-
10. retrain, revise, or suspend the rubric when evidence warrants.
|
|
214
|
-
|
|
215
|
-
The bundled agreement script reports exact agreement, within-one-step agreement,
|
|
216
|
-
and mean absolute difference. Those summaries do not replace a
|
|
217
|
-
design-appropriate reliability analysis. The rubric therefore separately
|
|
218
|
-
records `inter_rater_reliability_status` and
|
|
219
|
-
`inter_rater_reliability_ref`; the template leaves reliability not established.
|
|
220
|
-
|
|
221
|
-
## Evidence traceability
|
|
222
|
-
|
|
223
|
-
Each rated criterion must point to one or more entries in the evidence manifest.
|
|
224
|
-
Each entry records:
|
|
225
|
-
|
|
226
|
-
- pseudonymous evidence identifier;
|
|
227
|
-
- linked criterion identifiers;
|
|
228
|
-
- source type;
|
|
229
|
-
- local stable locator;
|
|
230
|
-
- local claim reference;
|
|
231
|
-
- access status; and
|
|
232
|
-
- verification status.
|
|
233
|
-
|
|
234
|
-
Never place an excerpt or raw private document in the manifest. Keep source
|
|
235
|
-
content in the authorized source system.
|
|
236
|
-
|
|
237
|
-
## Weight sensitivity and order instability
|
|
238
|
-
|
|
239
|
-
Weights are value judgments. Predeclare and justify them. Run
|
|
240
|
-
`scripts/weight_sensitivity.py` before interpreting a composite.
|
|
241
|
-
|
|
242
|
-
The script increases and decreases one weight at a time and renormalizes the
|
|
243
|
-
weights. It reports score ranges and whether pairwise ordinal relationships
|
|
244
|
-
among scholarly works change. Instability is evidence that an apparent order
|
|
245
|
-
depends on contestable weights.
|
|
246
|
-
|
|
247
|
-
The output must not be used to rank people or decide a high-impact outcome.
|
|
248
|
-
Even stable ordering does not establish validity.
|
|
249
|
-
|
|
250
|
-
## Interpretation template
|
|
251
|
-
|
|
252
|
-
For each criterion, qualified reviewers should record:
|
|
253
|
-
|
|
254
|
-
1. status and evidence references;
|
|
255
|
-
2. observed evidence;
|
|
256
|
-
3. interpretation against the anchor;
|
|
257
|
-
4. score and uncertainty, if rated;
|
|
258
|
-
5. missing or not-applicable rationale;
|
|
259
|
-
6. disciplinary and stage context;
|
|
260
|
-
7. strengths and limitations; and
|
|
261
|
-
8. non-prescriptive improvement options.
|
|
262
|
-
|
|
263
|
-
Conclude with construct, provenance, coverage, agreement, sensitivity, bias,
|
|
264
|
-
privacy, accessibility, and validity limitations—not a decision recommendation.
|
|
@@ -1,232 +0,0 @@
|
|
|
1
|
-
# Local Deterministic Tooling
|
|
2
|
-
|
|
3
|
-
## Security properties
|
|
4
|
-
|
|
5
|
-
Every bundled script:
|
|
6
|
-
|
|
7
|
-
- uses only the Python standard library;
|
|
8
|
-
- reads bounded local `.json` or `.csv` files;
|
|
9
|
-
- rejects symbolic-link inputs, duplicate JSON keys, excessive depth or size,
|
|
10
|
-
non-finite numbers, unknown schema fields, and common private-application
|
|
11
|
-
fields;
|
|
12
|
-
- uses fixed schemas and never executes supplied text;
|
|
13
|
-
- has no network, model, credential, environment-file, dynamic-code,
|
|
14
|
-
executable-serialization, or child-process behavior;
|
|
15
|
-
- writes only minimized JSON reports and refuses to overwrite by default; and
|
|
16
|
-
- does not copy evidence excerpts or raw source documents.
|
|
17
|
-
|
|
18
|
-
Inputs are limited to 2 MiB, JSON depth 20, 25,000 structure nodes, 50 rubric
|
|
19
|
-
criteria, 50 comparison evaluations, and 20,000 agreement rows. Outputs are
|
|
20
|
-
limited to 2 MiB.
|
|
21
|
-
|
|
22
|
-
Use an authorized local directory. Keep private source documents in the
|
|
23
|
-
institution's records system and reference them with opaque local identifiers.
|
|
24
|
-
|
|
25
|
-
## Templates
|
|
26
|
-
|
|
27
|
-
- `assets/rubric_template.json` — valid structure, but deliberately records
|
|
28
|
-
content validity as not established.
|
|
29
|
-
- `assets/evaluation_template.json` — structurally valid all-missing example.
|
|
30
|
-
- `assets/evidence_manifest_template.json` — synthetic local-reference records.
|
|
31
|
-
- `assets/process_checklist_template.json` — fail-closed unconfirmed controls.
|
|
32
|
-
- `assets/ratings_template.csv` — pseudonymous synthetic agreement data.
|
|
33
|
-
|
|
34
|
-
Copy a template into an authorized working directory before editing it. Do not
|
|
35
|
-
replace synthetic identifiers with names or contact information.
|
|
36
|
-
|
|
37
|
-
## 1. Rubric schema validation
|
|
38
|
-
|
|
39
|
-
```bash
|
|
40
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/validate_rubric.py \
|
|
41
|
-
--rubric assets/rubric_template.json
|
|
42
|
-
```
|
|
43
|
-
|
|
44
|
-
The validator checks:
|
|
45
|
-
|
|
46
|
-
- fixed intended use and scholarly-work unit;
|
|
47
|
-
- complete prohibited-use list;
|
|
48
|
-
- construct, boundaries, limitations, and provenance;
|
|
49
|
-
- content-validity status and reference;
|
|
50
|
-
- bounded scale and complete anchors;
|
|
51
|
-
- unique criteria and weights summing to one;
|
|
52
|
-
- absence of common scored proxy measures;
|
|
53
|
-
- required rater training, calibration, agreement, separately recorded
|
|
54
|
-
inter-rater reliability status, and drift controls; and
|
|
55
|
-
- committee, conflict, appeal, accessibility, data-protection, subgroup, and
|
|
56
|
-
review-cycle governance.
|
|
57
|
-
|
|
58
|
-
A rubric can be structurally `valid` while warning that content validity is not
|
|
59
|
-
documented. Structural validity is not psychometric validity.
|
|
60
|
-
|
|
61
|
-
## 2. Bounded descriptive scoring
|
|
62
|
-
|
|
63
|
-
```bash
|
|
64
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/calculate_scores.py \
|
|
65
|
-
--rubric assets/rubric_template.json \
|
|
66
|
-
--evaluation assets/evaluation_template.json \
|
|
67
|
-
--output /tmp/scholar-score.json
|
|
68
|
-
```
|
|
69
|
-
|
|
70
|
-
The evaluation contains one entry for every criterion:
|
|
71
|
-
|
|
72
|
-
```json
|
|
73
|
-
{
|
|
74
|
-
"criterion_id": "method_design",
|
|
75
|
-
"status": "rated",
|
|
76
|
-
"score": 3,
|
|
77
|
-
"uncertainty": 0.5,
|
|
78
|
-
"evidence_ids": ["EVIDENCE-SYNTHETIC-METHOD"],
|
|
79
|
-
"rationale_ref": "LOCAL-RATING-RATIONALE-METHOD"
|
|
80
|
-
}
|
|
81
|
-
```
|
|
82
|
-
|
|
83
|
-
For `missing` or `not_applicable`, `score` and `uncertainty` must be null and
|
|
84
|
-
`evidence_ids` must be empty. A local rationale reference remains required.
|
|
85
|
-
|
|
86
|
-
The output reports weighted contributions, coverage, missing and
|
|
87
|
-
not-applicable weight, normalized score, and a bounded uncertainty range. It
|
|
88
|
-
contains no quality label, threshold, decision, or recommendation.
|
|
89
|
-
|
|
90
|
-
## 3. Evidence traceability
|
|
91
|
-
|
|
92
|
-
```bash
|
|
93
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_traceability.py \
|
|
94
|
-
--rubric assets/rubric_template.json \
|
|
95
|
-
--evaluation assets/evaluation_template.json \
|
|
96
|
-
--evidence assets/evidence_manifest_template.json
|
|
97
|
-
```
|
|
98
|
-
|
|
99
|
-
The checker verifies that:
|
|
100
|
-
|
|
101
|
-
- manifest, evaluation, work, and classification identifiers match;
|
|
102
|
-
- every evidence identifier is unique;
|
|
103
|
-
- every rated evidence reference resolves;
|
|
104
|
-
- evidence is linked to the criterion that cites it;
|
|
105
|
-
- source and access types are allowed; and
|
|
106
|
-
- evidence is available and verified.
|
|
107
|
-
|
|
108
|
-
It reports identifiers, paths, and counts only. It never opens or copies the
|
|
109
|
-
referenced source.
|
|
110
|
-
|
|
111
|
-
## 4. Weight sensitivity and rank instability
|
|
112
|
-
|
|
113
|
-
Provide two to 50 evaluation JSON files for distinct scholarly works:
|
|
114
|
-
|
|
115
|
-
```bash
|
|
116
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/weight_sensitivity.py \
|
|
117
|
-
--rubric assets/rubric_template.json \
|
|
118
|
-
--evaluation /tmp/work-a-evaluation.json \
|
|
119
|
-
--evaluation /tmp/work-b-evaluation.json \
|
|
120
|
-
--delta 0.2 \
|
|
121
|
-
--output /tmp/weight-sensitivity.json
|
|
122
|
-
```
|
|
123
|
-
|
|
124
|
-
For each criterion, the script multiplies its weight by `1-delta` and
|
|
125
|
-
`1+delta`, renormalizes all weights to one, and recomputes descriptive scores.
|
|
126
|
-
It reports:
|
|
127
|
-
|
|
128
|
-
- every scenario and its exact weights;
|
|
129
|
-
- each work's score and coverage per scenario;
|
|
130
|
-
- score ranges;
|
|
131
|
-
- base ordinal order; and
|
|
132
|
-
- pairwise order changes.
|
|
133
|
-
|
|
134
|
-
The base order is included solely to detect instability. It is not a ranking
|
|
135
|
-
recommendation and must never be used for people or high-impact decisions.
|
|
136
|
-
|
|
137
|
-
## 5. Inter-rater agreement summaries
|
|
138
|
-
|
|
139
|
-
The CSV header must be exactly:
|
|
140
|
-
|
|
141
|
-
```text
|
|
142
|
-
evaluation_id,work_id,rater_id,criterion_id,status,score
|
|
143
|
-
```
|
|
144
|
-
|
|
145
|
-
Use pseudonymous rater identifiers. Run:
|
|
146
|
-
|
|
147
|
-
```bash
|
|
148
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/summarize_agreement.py \
|
|
149
|
-
--rubric assets/rubric_template.json \
|
|
150
|
-
--ratings assets/ratings_template.csv \
|
|
151
|
-
--output /tmp/agreement-summary.json
|
|
152
|
-
```
|
|
153
|
-
|
|
154
|
-
For each criterion and overall, the report includes:
|
|
155
|
-
|
|
156
|
-
- pair observations;
|
|
157
|
-
- exact agreement rate;
|
|
158
|
-
- within-one-scale-step agreement rate;
|
|
159
|
-
- mean absolute difference;
|
|
160
|
-
- overlap, rated, missing, and not-applicable counts.
|
|
161
|
-
|
|
162
|
-
Rater identifiers are not emitted. These are descriptive agreement summaries,
|
|
163
|
-
not chance-corrected reliability, generalizability, validity, or fairness
|
|
164
|
-
evidence.
|
|
165
|
-
|
|
166
|
-
## 6. Bias and process checklist
|
|
167
|
-
|
|
168
|
-
```bash
|
|
169
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/check_process.py \
|
|
170
|
-
--process assets/process_checklist_template.json
|
|
171
|
-
```
|
|
172
|
-
|
|
173
|
-
The template is intentionally unconfirmed and therefore does not pass. Complete
|
|
174
|
-
it only from documented local records. The checker covers:
|
|
175
|
-
|
|
176
|
-
- qualified committee and training;
|
|
177
|
-
- conflicts and recusal;
|
|
178
|
-
- appeal and correction;
|
|
179
|
-
- accessibility and accommodations;
|
|
180
|
-
- purpose limitation, minimization, access, retention, and output controls;
|
|
181
|
-
- construct, provenance, content evidence, rater quality, agreement,
|
|
182
|
-
inter-rater reliability review, uncertainty, missingness, traceability, and
|
|
183
|
-
sensitivity;
|
|
184
|
-
- stakeholder, disciplinary, subgroup, and protected-attribute safeguards;
|
|
185
|
-
- no automation, person ranking, or decision recommendation; and
|
|
186
|
-
- drift, unintended-consequence, and periodic review.
|
|
187
|
-
|
|
188
|
-
`high_impact_use: true` or any unconfirmed decision control blocks the process.
|
|
189
|
-
The checklist does not authorize a prohibited use.
|
|
190
|
-
|
|
191
|
-
## 7. Report scaffold
|
|
192
|
-
|
|
193
|
-
Generate a minimized scaffold:
|
|
194
|
-
|
|
195
|
-
```bash
|
|
196
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_scaffold.py \
|
|
197
|
-
--rubric assets/rubric_template.json \
|
|
198
|
-
--evaluation assets/evaluation_template.json \
|
|
199
|
-
--output /tmp/developmental-report-scaffold.json
|
|
200
|
-
```
|
|
201
|
-
|
|
202
|
-
Optional companion reports:
|
|
203
|
-
|
|
204
|
-
```bash
|
|
205
|
-
PYTHONDONTWRITEBYTECODE=1 python3 scripts/generate_report_scaffold.py \
|
|
206
|
-
--rubric assets/rubric_template.json \
|
|
207
|
-
--evaluation /tmp/work-a-evaluation.json \
|
|
208
|
-
--traceability /tmp/traceability.json \
|
|
209
|
-
--agreement /tmp/agreement-summary.json \
|
|
210
|
-
--sensitivity /tmp/weight-sensitivity.json \
|
|
211
|
-
--process /tmp/process-check.json \
|
|
212
|
-
--output /tmp/developmental-report-scaffold.json
|
|
213
|
-
```
|
|
214
|
-
|
|
215
|
-
The scaffold includes:
|
|
216
|
-
|
|
217
|
-
- construct and provenance status;
|
|
218
|
-
- descriptive scores and uncertainty;
|
|
219
|
-
- empty local-reference slots for evidence, strengths, limitations, and
|
|
220
|
-
improvement options;
|
|
221
|
-
- minimized quality-assurance statuses; and
|
|
222
|
-
- fixed limitations and human-review fields.
|
|
223
|
-
|
|
224
|
-
It does not draft findings from source documents or issue a decision.
|
|
225
|
-
|
|
226
|
-
## Exit behavior
|
|
227
|
-
|
|
228
|
-
- exit `0`: requested calculation or validation completed successfully;
|
|
229
|
-
- exit `2`: invalid, blocked, incomplete, failed traceability, or unsafe input.
|
|
230
|
-
|
|
231
|
-
Errors contain only stable codes and JSON paths, never supplied values. Use
|
|
232
|
-
`--force` only when replacing a known local report.
|
|
@@ -1,196 +0,0 @@
|
|
|
1
|
-
# Responsible Assessment and Safety Boundary
|
|
2
|
-
|
|
3
|
-
## Non-negotiable boundary
|
|
4
|
-
|
|
5
|
-
This skill is for **developmental review of scholarly works** and for auditing a
|
|
6
|
-
low-stakes assessment process. It must not automate, recommend, materially
|
|
7
|
-
influence, or provide a score for:
|
|
8
|
-
|
|
9
|
-
- hiring, promotion, or tenure;
|
|
10
|
-
- admissions;
|
|
11
|
-
- grant or other funding decisions;
|
|
12
|
-
- prizes, honors, or awards;
|
|
13
|
-
- discipline, dismissal, or sanctions; or
|
|
14
|
-
- any other high-impact personnel decision.
|
|
15
|
-
|
|
16
|
-
Do not rank people. Do not convert several judgments into a single composite
|
|
17
|
-
person score. Do not infer a person's ability, character, integrity, future
|
|
18
|
-
performance, protected characteristics, or institutional worth.
|
|
19
|
-
|
|
20
|
-
This boundary remains in force when a human is nominally “in the loop.”
|
|
21
|
-
Checklists, committees, or disclaimers do not make a prohibited workflow safe.
|
|
22
|
-
If a request crosses the boundary, stop and offer one of these alternatives:
|
|
23
|
-
|
|
24
|
-
1. developmental comments on a public or authorized scholarly work, with no
|
|
25
|
-
person comparison or decision advice;
|
|
26
|
-
2. an audit of whether an existing assessment process follows responsible
|
|
27
|
-
assessment principles, without processing applications or recommending an
|
|
28
|
-
outcome; or
|
|
29
|
-
3. neutral documentation of criteria for review by the organization's legal,
|
|
30
|
-
privacy, accessibility, labor, ethics, and disciplinary experts.
|
|
31
|
-
|
|
32
|
-
## Allowed scope
|
|
33
|
-
|
|
34
|
-
Examples of allowed uses, subject to authorization and data protection:
|
|
35
|
-
|
|
36
|
-
- feedback on a draft paper, protocol, research idea, or literature synthesis;
|
|
37
|
-
- a retrospective methods or reporting review;
|
|
38
|
-
- calibration exercises using synthetic or public scholarly works;
|
|
39
|
-
- checking evidence traceability;
|
|
40
|
-
- describing the sensitivity of work-level scores to rubric weights; and
|
|
41
|
-
- auditing a low-stakes evaluation design for missing governance controls.
|
|
42
|
-
|
|
43
|
-
“Publication readiness” and “accept/reject” recommendations are excluded.
|
|
44
|
-
Describe evidence, limitations, and improvement options instead.
|
|
45
|
-
|
|
46
|
-
## Accountable human process
|
|
47
|
-
|
|
48
|
-
For any organizational use, an accountable committee must own the process. It
|
|
49
|
-
must include relevant disciplinary and assessment-methods expertise and must:
|
|
50
|
-
|
|
51
|
-
- publish the construct, intended use, rubric, weights, evidence requirements,
|
|
52
|
-
and interpretation limits before reviewing;
|
|
53
|
-
- record member qualifications, training, calibration, and drift checks;
|
|
54
|
-
- disclose conflicts, require recusal, and maintain a conflict record;
|
|
55
|
-
- provide an understandable notice and a meaningful appeal or correction route;
|
|
56
|
-
- provide accessible materials and reasonable accommodations;
|
|
57
|
-
- define lawful purpose, access controls, minimization, retention, and deletion;
|
|
58
|
-
- review disciplinary, language, career-path, disability, and subgroup effects;
|
|
59
|
-
- document disagreements and uncertainty rather than force consensus; and
|
|
60
|
-
- periodically evaluate and revise the evaluation.
|
|
61
|
-
|
|
62
|
-
No script in this skill is the accountable reviewer. Script output is a
|
|
63
|
-
descriptive record for qualified human interpretation.
|
|
64
|
-
|
|
65
|
-
## Qualitative-first evidence
|
|
66
|
-
|
|
67
|
-
Start with the values and construct, not the data that happen to be available.
|
|
68
|
-
Use evidence that directly bears on the criterion:
|
|
69
|
-
|
|
70
|
-
- the work's questions, methods, analyses, outputs, limitations, and provenance;
|
|
71
|
-
- datasets, software, protocols, materials, registrations, replications, and
|
|
72
|
-
negative or null findings where relevant;
|
|
73
|
-
- transparent records of responsible practices and justified restrictions;
|
|
74
|
-
- contribution records, including CRediT roles when useful, without treating a
|
|
75
|
-
role as proof of quality; and
|
|
76
|
-
- influence on policy, practice, communities, teaching, infrastructure, or
|
|
77
|
-
knowledge, when this is within the stated construct and supported by evidence.
|
|
78
|
-
|
|
79
|
-
Ask what is missing, inaccessible, contested, or not applicable. A missing item
|
|
80
|
-
is not a zero. A not-applicable item is not evidence of deficiency.
|
|
81
|
-
|
|
82
|
-
## Prohibited proxies and contextual indicators
|
|
83
|
-
|
|
84
|
-
Do not score or infer quality from:
|
|
85
|
-
|
|
86
|
-
- Journal Impact Factor or other journal-level measures;
|
|
87
|
-
- h-index, i10-index, publication counts, or citation counts;
|
|
88
|
-
- altmetrics or attention counts;
|
|
89
|
-
- journal, conference, institutional, geographic, or employer prestige;
|
|
90
|
-
- venue identity or ranking; or
|
|
91
|
-
- author affiliation, career path, network, or reputation.
|
|
92
|
-
|
|
93
|
-
The bundled rubric validator rejects common proxy-measure criteria.
|
|
94
|
-
|
|
95
|
-
If a qualified reviewer has a legitimate, predeclared reason to mention a
|
|
96
|
-
quantitative indicator descriptively outside the bundled scoring tools, record:
|
|
97
|
-
|
|
98
|
-
1. the exact construct and purpose;
|
|
99
|
-
2. why the indicator bears on that construct at the correct unit of analysis;
|
|
100
|
-
3. source, version, query date, coverage, exclusions, and data quality;
|
|
101
|
-
4. field, language, output-type, career-stage, and time-window effects;
|
|
102
|
-
5. uncertainty, missingness, gaming risks, and known biases;
|
|
103
|
-
6. why qualitative evidence is insufficient by itself; and
|
|
104
|
-
7. a statement that the indicator is not a direct measure of quality.
|
|
105
|
-
|
|
106
|
-
Never use an indicator merely because it is available. Never hide several
|
|
107
|
-
different indicators inside an opaque composite.
|
|
108
|
-
|
|
109
|
-
## Rubric evidence and psychometric caution
|
|
110
|
-
|
|
111
|
-
A rubric is a measurement claim. Before operational use, record:
|
|
112
|
-
|
|
113
|
-
- **construct:** what is and is not being assessed;
|
|
114
|
-
- **intended interpretation and use:** the exact meaning claimed for scores;
|
|
115
|
-
- **provenance:** who designed and approved criteria, anchors, and weights;
|
|
116
|
-
- **content evidence:** disciplinary expert and stakeholder review of coverage;
|
|
117
|
-
- **response process:** how raters interpret anchors and use evidence;
|
|
118
|
-
- **rater protocol:** selection, training, calibration, qualification, and drift;
|
|
119
|
-
- **agreement/reliability:** a design-appropriate analysis and its uncertainty;
|
|
120
|
-
- **fairness:** accessibility, subgroup, language, and disciplinary review;
|
|
121
|
-
- **traceability:** stable evidence references for each rating;
|
|
122
|
-
- **missing/not applicable:** explicit statuses and rationales;
|
|
123
|
-
- **weight sensitivity:** whether plausible weights change descriptive results;
|
|
124
|
-
- **consequences:** gaming, burden, goal displacement, and other effects; and
|
|
125
|
-
- **revision:** review date, owner, change record, and retirement criteria.
|
|
126
|
-
|
|
127
|
-
Do not call a rubric “validated” because experts reviewed it once, raters agreed,
|
|
128
|
-
or scores correlated with another judgment. Validity concerns the evidence for a
|
|
129
|
-
specific interpretation and use. Reliability or agreement alone is not validity.
|
|
130
|
-
|
|
131
|
-
The provided rubric explicitly records `content_validity_status` as
|
|
132
|
-
`not_established`. Replace that status only when a qualified team has documented
|
|
133
|
-
appropriate evidence for the exact discipline, population, language, and use.
|
|
134
|
-
|
|
135
|
-
## Bias and subgroup review
|
|
136
|
-
|
|
137
|
-
Perform the fairness review outside these scripts in an authorized environment.
|
|
138
|
-
Do not place protected-attribute records in rubric, evaluation, evidence, or
|
|
139
|
-
ratings files.
|
|
140
|
-
|
|
141
|
-
A qualified review should examine, where lawful and appropriate:
|
|
142
|
-
|
|
143
|
-
- access to the measured construct and accommodation effectiveness;
|
|
144
|
-
- differential missingness and evidence availability;
|
|
145
|
-
- criteria that privilege particular languages, methods, fields, institutions,
|
|
146
|
-
career patterns, or resource levels;
|
|
147
|
-
- rater severity, drift, and disagreement patterns;
|
|
148
|
-
- differential effects of weights and not-applicable decisions;
|
|
149
|
-
- false precision and threshold effects;
|
|
150
|
-
- burden, gaming, and chilling of collaboration or risky research; and
|
|
151
|
-
- whether the evaluation should be redesigned or stopped.
|
|
152
|
-
|
|
153
|
-
Report sample limitations and uncertainty. Do not expose small cells or attempt
|
|
154
|
-
to infer sensitive characteristics.
|
|
155
|
-
|
|
156
|
-
## Privacy and data protection
|
|
157
|
-
|
|
158
|
-
Use only public scholarly works, synthetic records, or deidentified low-stakes
|
|
159
|
-
records processed under an approved local purpose. Do not put raw private
|
|
160
|
-
applications, CVs, recommendation letters, reviewer identities, contact
|
|
161
|
-
details, protected attributes, or source-document text into tool inputs or
|
|
162
|
-
outputs.
|
|
163
|
-
|
|
164
|
-
The bundled formats contain only:
|
|
165
|
-
|
|
166
|
-
- pseudonymous work, evaluation, rater, criterion, and evidence identifiers;
|
|
167
|
-
- bounded scores, statuses, and uncertainty;
|
|
168
|
-
- local stable references; and
|
|
169
|
-
- minimized control attestations and aggregate summaries.
|
|
170
|
-
|
|
171
|
-
Keep source documents in the authorized records system. Use local references to
|
|
172
|
-
them. Apply least privilege, retention limits, deletion, incident handling, and
|
|
173
|
-
any stricter local law or policy.
|
|
174
|
-
|
|
175
|
-
## Accessibility
|
|
176
|
-
|
|
177
|
-
Provide the rubric, evidence requirements, notices, feedback, and appeal
|
|
178
|
-
process in accessible formats. Do not penalize an accommodation, assistive
|
|
179
|
-
technology, language variant, or accessible presentation choice. Confirm that
|
|
180
|
-
the rubric measures the intended construct rather than fluency with an
|
|
181
|
-
inaccessible interface or format.
|
|
182
|
-
|
|
183
|
-
## Communicating results
|
|
184
|
-
|
|
185
|
-
Lead with qualitative, traceable findings. For every criterion:
|
|
186
|
-
|
|
187
|
-
1. cite local evidence references;
|
|
188
|
-
2. state the rating status;
|
|
189
|
-
3. distinguish observed evidence from interpretation;
|
|
190
|
-
4. report uncertainty and disagreement;
|
|
191
|
-
5. state missing or not-applicable evidence;
|
|
192
|
-
6. explain context and limitations; and
|
|
193
|
-
7. offer non-prescriptive improvement options.
|
|
194
|
-
|
|
195
|
-
Do not label a person, declare a work “top-tier,” predict success, recommend a
|
|
196
|
-
decision, or conceal uncertainty behind a decimal.
|