@synsci/cli-darwin-x64-baseline 1.1.76 → 1.1.78
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/bin/skills/adaptyv/SKILL.md +114 -0
- package/bin/skills/adaptyv/reference/api_reference.md +308 -0
- package/bin/skills/adaptyv/reference/examples.md +913 -0
- package/bin/skills/adaptyv/reference/experiments.md +360 -0
- package/bin/skills/adaptyv/reference/protein_optimization.md +637 -0
- package/bin/skills/aeon/SKILL.md +374 -0
- package/bin/skills/aeon/references/anomaly_detection.md +154 -0
- package/bin/skills/aeon/references/classification.md +144 -0
- package/bin/skills/aeon/references/clustering.md +123 -0
- package/bin/skills/aeon/references/datasets_benchmarking.md +387 -0
- package/bin/skills/aeon/references/distances.md +256 -0
- package/bin/skills/aeon/references/forecasting.md +140 -0
- package/bin/skills/aeon/references/networks.md +289 -0
- package/bin/skills/aeon/references/regression.md +118 -0
- package/bin/skills/aeon/references/segmentation.md +163 -0
- package/bin/skills/aeon/references/similarity_search.md +187 -0
- package/bin/skills/aeon/references/transformations.md +246 -0
- package/bin/skills/alphafold-database/SKILL.md +513 -0
- package/bin/skills/alphafold-database/references/api_reference.md +423 -0
- package/bin/skills/anndata/SKILL.md +400 -0
- package/bin/skills/anndata/references/best_practices.md +525 -0
- package/bin/skills/anndata/references/concatenation.md +396 -0
- package/bin/skills/anndata/references/data_structure.md +314 -0
- package/bin/skills/anndata/references/io_operations.md +404 -0
- package/bin/skills/anndata/references/manipulation.md +516 -0
- package/bin/skills/arboreto/SKILL.md +243 -0
- package/bin/skills/arboreto/references/algorithms.md +138 -0
- package/bin/skills/arboreto/references/basic_inference.md +151 -0
- package/bin/skills/arboreto/references/distributed_computing.md +242 -0
- package/bin/skills/arboreto/scripts/basic_grn_inference.py +97 -0
- package/bin/skills/astropy/SKILL.md +331 -0
- package/bin/skills/astropy/references/coordinates.md +273 -0
- package/bin/skills/astropy/references/cosmology.md +307 -0
- package/bin/skills/astropy/references/fits.md +396 -0
- package/bin/skills/astropy/references/tables.md +489 -0
- package/bin/skills/astropy/references/time.md +404 -0
- package/bin/skills/astropy/references/units.md +178 -0
- package/bin/skills/astropy/references/wcs_and_other_modules.md +373 -0
- package/bin/skills/benchling-integration/SKILL.md +480 -0
- package/bin/skills/benchling-integration/references/api_endpoints.md +883 -0
- package/bin/skills/benchling-integration/references/authentication.md +379 -0
- package/bin/skills/benchling-integration/references/sdk_reference.md +774 -0
- package/bin/skills/biopython/SKILL.md +443 -0
- package/bin/skills/biopython/references/advanced.md +577 -0
- package/bin/skills/biopython/references/alignment.md +362 -0
- package/bin/skills/biopython/references/blast.md +455 -0
- package/bin/skills/biopython/references/databases.md +484 -0
- package/bin/skills/biopython/references/phylogenetics.md +566 -0
- package/bin/skills/biopython/references/sequence_io.md +285 -0
- package/bin/skills/biopython/references/structure.md +564 -0
- package/bin/skills/biorxiv-database/SKILL.md +483 -0
- package/bin/skills/biorxiv-database/references/api_reference.md +280 -0
- package/bin/skills/biorxiv-database/scripts/biorxiv_search.py +445 -0
- package/bin/skills/bioservices/SKILL.md +361 -0
- package/bin/skills/bioservices/references/identifier_mapping.md +685 -0
- package/bin/skills/bioservices/references/services_reference.md +636 -0
- package/bin/skills/bioservices/references/workflow_patterns.md +811 -0
- package/bin/skills/bioservices/scripts/batch_id_converter.py +347 -0
- package/bin/skills/bioservices/scripts/compound_cross_reference.py +378 -0
- package/bin/skills/bioservices/scripts/pathway_analysis.py +309 -0
- package/bin/skills/bioservices/scripts/protein_analysis_workflow.py +408 -0
- package/bin/skills/brenda-database/SKILL.md +719 -0
- package/bin/skills/brenda-database/references/api_reference.md +537 -0
- package/bin/skills/brenda-database/scripts/brenda_queries.py +844 -0
- package/bin/skills/brenda-database/scripts/brenda_visualization.py +772 -0
- package/bin/skills/brenda-database/scripts/enzyme_pathway_builder.py +1053 -0
- package/bin/skills/cellxgene-census/SKILL.md +511 -0
- package/bin/skills/cellxgene-census/references/census_schema.md +182 -0
- package/bin/skills/cellxgene-census/references/common_patterns.md +351 -0
- package/bin/skills/chembl-database/SKILL.md +389 -0
- package/bin/skills/chembl-database/references/api_reference.md +272 -0
- package/bin/skills/chembl-database/scripts/example_queries.py +278 -0
- package/bin/skills/cirq/SKILL.md +346 -0
- package/bin/skills/cirq/references/building.md +307 -0
- package/bin/skills/cirq/references/experiments.md +572 -0
- package/bin/skills/cirq/references/hardware.md +515 -0
- package/bin/skills/cirq/references/noise.md +515 -0
- package/bin/skills/cirq/references/simulation.md +350 -0
- package/bin/skills/cirq/references/transformation.md +416 -0
- package/bin/skills/clinicaltrials-database/SKILL.md +507 -0
- package/bin/skills/clinicaltrials-database/references/api_reference.md +358 -0
- package/bin/skills/clinicaltrials-database/scripts/query_clinicaltrials.py +215 -0
- package/bin/skills/clinpgx-database/SKILL.md +638 -0
- package/bin/skills/clinpgx-database/references/api_reference.md +757 -0
- package/bin/skills/clinpgx-database/scripts/query_clinpgx.py +518 -0
- package/bin/skills/clinvar-database/SKILL.md +362 -0
- package/bin/skills/clinvar-database/references/api_reference.md +227 -0
- package/bin/skills/clinvar-database/references/clinical_significance.md +218 -0
- package/bin/skills/clinvar-database/references/data_formats.md +358 -0
- package/bin/skills/cobrapy/SKILL.md +463 -0
- package/bin/skills/cobrapy/references/api_quick_reference.md +655 -0
- package/bin/skills/cobrapy/references/workflows.md +593 -0
- package/bin/skills/cosmic-database/SKILL.md +336 -0
- package/bin/skills/cosmic-database/references/cosmic_data_reference.md +220 -0
- package/bin/skills/cosmic-database/scripts/download_cosmic.py +231 -0
- package/bin/skills/dask/SKILL.md +456 -0
- package/bin/skills/dask/references/arrays.md +497 -0
- package/bin/skills/dask/references/bags.md +468 -0
- package/bin/skills/dask/references/best-practices.md +277 -0
- package/bin/skills/dask/references/dataframes.md +368 -0
- package/bin/skills/dask/references/futures.md +541 -0
- package/bin/skills/dask/references/schedulers.md +504 -0
- package/bin/skills/datacommons-client/SKILL.md +255 -0
- package/bin/skills/datacommons-client/references/getting_started.md +417 -0
- package/bin/skills/datacommons-client/references/node.md +250 -0
- package/bin/skills/datacommons-client/references/observation.md +185 -0
- package/bin/skills/datacommons-client/references/resolve.md +246 -0
- package/bin/skills/datamol/SKILL.md +706 -0
- package/bin/skills/datamol/references/conformers_module.md +131 -0
- package/bin/skills/datamol/references/core_api.md +130 -0
- package/bin/skills/datamol/references/descriptors_viz.md +195 -0
- package/bin/skills/datamol/references/fragments_scaffolds.md +174 -0
- package/bin/skills/datamol/references/io_module.md +109 -0
- package/bin/skills/datamol/references/reactions_data.md +218 -0
- package/bin/skills/deepchem/SKILL.md +597 -0
- package/bin/skills/deepchem/references/api_reference.md +303 -0
- package/bin/skills/deepchem/references/workflows.md +491 -0
- package/bin/skills/deepchem/scripts/graph_neural_network.py +338 -0
- package/bin/skills/deepchem/scripts/predict_solubility.py +224 -0
- package/bin/skills/deepchem/scripts/transfer_learning.py +375 -0
- package/bin/skills/deeptools/SKILL.md +531 -0
- package/bin/skills/deeptools/assets/quick_reference.md +58 -0
- package/bin/skills/deeptools/references/effective_genome_sizes.md +116 -0
- package/bin/skills/deeptools/references/normalization_methods.md +410 -0
- package/bin/skills/deeptools/references/tools_reference.md +533 -0
- package/bin/skills/deeptools/references/workflows.md +474 -0
- package/bin/skills/deeptools/scripts/validate_files.py +195 -0
- package/bin/skills/deeptools/scripts/workflow_generator.py +454 -0
- package/bin/skills/denario/SKILL.md +215 -0
- package/bin/skills/denario/references/examples.md +494 -0
- package/bin/skills/denario/references/installation.md +213 -0
- package/bin/skills/denario/references/llm_configuration.md +265 -0
- package/bin/skills/denario/references/research_pipeline.md +471 -0
- package/bin/skills/diffdock/SKILL.md +483 -0
- package/bin/skills/diffdock/assets/batch_template.csv +4 -0
- package/bin/skills/diffdock/assets/custom_inference_config.yaml +90 -0
- package/bin/skills/diffdock/references/confidence_and_limitations.md +182 -0
- package/bin/skills/diffdock/references/parameters_reference.md +163 -0
- package/bin/skills/diffdock/references/workflows_examples.md +392 -0
- package/bin/skills/diffdock/scripts/analyze_results.py +334 -0
- package/bin/skills/diffdock/scripts/prepare_batch_csv.py +254 -0
- package/bin/skills/diffdock/scripts/setup_check.py +278 -0
- package/bin/skills/dnanexus-integration/SKILL.md +383 -0
- package/bin/skills/dnanexus-integration/references/app-development.md +247 -0
- package/bin/skills/dnanexus-integration/references/configuration.md +646 -0
- package/bin/skills/dnanexus-integration/references/data-operations.md +400 -0
- package/bin/skills/dnanexus-integration/references/job-execution.md +412 -0
- package/bin/skills/dnanexus-integration/references/python-sdk.md +523 -0
- package/bin/skills/document-skills/docx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/docx/SKILL.md +233 -0
- package/bin/skills/document-skills/docx/docx-js.md +350 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/bin/skills/document-skills/docx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/pack.py +159 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/unpack.py +29 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validate.py +69 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/__init__.py +15 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/base.py +951 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/docx.py +274 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/pptx.py +315 -0
- package/bin/skills/document-skills/docx/ooxml/scripts/validation/redlining.py +279 -0
- package/bin/skills/document-skills/docx/ooxml.md +610 -0
- package/bin/skills/document-skills/docx/scripts/__init__.py +1 -0
- package/bin/skills/document-skills/docx/scripts/document.py +1276 -0
- package/bin/skills/document-skills/docx/scripts/templates/comments.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtended.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsExtensible.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/commentsIds.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/templates/people.xml +3 -0
- package/bin/skills/document-skills/docx/scripts/utilities.py +374 -0
- package/bin/skills/document-skills/pdf/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pdf/SKILL.md +330 -0
- package/bin/skills/document-skills/pdf/forms.md +205 -0
- package/bin/skills/document-skills/pdf/reference.md +612 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes.py +70 -0
- package/bin/skills/document-skills/pdf/scripts/check_bounding_boxes_test.py +226 -0
- package/bin/skills/document-skills/pdf/scripts/check_fillable_fields.py +12 -0
- package/bin/skills/document-skills/pdf/scripts/convert_pdf_to_images.py +35 -0
- package/bin/skills/document-skills/pdf/scripts/create_validation_image.py +41 -0
- package/bin/skills/document-skills/pdf/scripts/extract_form_field_info.py +152 -0
- package/bin/skills/document-skills/pdf/scripts/fill_fillable_fields.py +114 -0
- package/bin/skills/document-skills/pdf/scripts/fill_pdf_form_with_annotations.py +108 -0
- package/bin/skills/document-skills/pptx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/pptx/SKILL.md +520 -0
- package/bin/skills/document-skills/pptx/html2pptx.md +625 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chart.xsd +1499 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-chartDrawing.xsd +146 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-diagram.xsd +1085 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-lockedCanvas.xsd +11 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-main.xsd +3081 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-picture.xsd +23 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-spreadsheetDrawing.xsd +185 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/dml-wordprocessingDrawing.xsd +287 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/pml.xsd +1676 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-additionalCharacteristics.xsd +28 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-bibliography.xsd +144 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-commonSimpleTypes.xsd +174 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlDataProperties.xsd +25 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-customXmlSchemaProperties.xsd +18 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesCustom.xsd +59 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesExtended.xsd +56 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-documentPropertiesVariantTypes.xsd +195 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-math.xsd +582 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/shared-relationshipReference.xsd +25 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/sml.xsd +4439 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-main.xsd +570 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-officeDrawing.xsd +509 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-presentationDrawing.xsd +12 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-spreadsheetDrawing.xsd +108 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/vml-wordprocessingDrawing.xsd +96 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/wml.xsd +3646 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ISO-IEC29500-4_2016/xml.xsd +116 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-contentTypes.xsd +42 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-coreProperties.xsd +50 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-digSig.xsd +49 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/ecma/fouth-edition/opc-relationships.xsd +33 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/mce/mc.xsd +75 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2010.xsd +560 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2012.xsd +67 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-2018.xsd +14 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cex-2018.xsd +20 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-cid-2016.xsd +13 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-sdtdatahash-2020.xsd +4 -0
- package/bin/skills/document-skills/pptx/ooxml/schemas/microsoft/wml-symex-2015.xsd +8 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/pack.py +159 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/unpack.py +29 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validate.py +69 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validation/__init__.py +15 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validation/base.py +951 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validation/docx.py +274 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validation/pptx.py +315 -0
- package/bin/skills/document-skills/pptx/ooxml/scripts/validation/redlining.py +279 -0
- package/bin/skills/document-skills/pptx/ooxml.md +427 -0
- package/bin/skills/document-skills/pptx/scripts/html2pptx.js +979 -0
- package/bin/skills/document-skills/pptx/scripts/inventory.py +1020 -0
- package/bin/skills/document-skills/pptx/scripts/rearrange.py +231 -0
- package/bin/skills/document-skills/pptx/scripts/replace.py +385 -0
- package/bin/skills/document-skills/pptx/scripts/thumbnail.py +450 -0
- package/bin/skills/document-skills/xlsx/LICENSE.txt +30 -0
- package/bin/skills/document-skills/xlsx/SKILL.md +325 -0
- package/bin/skills/document-skills/xlsx/recalc.py +178 -0
- package/bin/skills/drugbank-database/SKILL.md +190 -0
- package/bin/skills/drugbank-database/references/chemical-analysis.md +590 -0
- package/bin/skills/drugbank-database/references/data-access.md +242 -0
- package/bin/skills/drugbank-database/references/drug-queries.md +386 -0
- package/bin/skills/drugbank-database/references/interactions.md +425 -0
- package/bin/skills/drugbank-database/references/targets-pathways.md +518 -0
- package/bin/skills/drugbank-database/scripts/drugbank_helper.py +350 -0
- package/bin/skills/ena-database/SKILL.md +204 -0
- package/bin/skills/ena-database/references/api_reference.md +490 -0
- package/bin/skills/ensembl-database/SKILL.md +311 -0
- package/bin/skills/ensembl-database/references/api_endpoints.md +346 -0
- package/bin/skills/ensembl-database/scripts/ensembl_query.py +427 -0
- package/bin/skills/esm/SKILL.md +306 -0
- package/bin/skills/esm/references/esm-c-api.md +583 -0
- package/bin/skills/esm/references/esm3-api.md +452 -0
- package/bin/skills/esm/references/forge-api.md +657 -0
- package/bin/skills/esm/references/workflows.md +685 -0
- package/bin/skills/etetoolkit/SKILL.md +623 -0
- package/bin/skills/etetoolkit/references/api_reference.md +583 -0
- package/bin/skills/etetoolkit/references/visualization.md +783 -0
- package/bin/skills/etetoolkit/references/workflows.md +774 -0
- package/bin/skills/etetoolkit/scripts/quick_visualize.py +214 -0
- package/bin/skills/etetoolkit/scripts/tree_operations.py +229 -0
- package/bin/skills/exploratory-data-analysis/SKILL.md +446 -0
- package/bin/skills/exploratory-data-analysis/assets/report_template.md +196 -0
- package/bin/skills/exploratory-data-analysis/references/bioinformatics_genomics_formats.md +664 -0
- package/bin/skills/exploratory-data-analysis/references/chemistry_molecular_formats.md +664 -0
- package/bin/skills/exploratory-data-analysis/references/general_scientific_formats.md +518 -0
- package/bin/skills/exploratory-data-analysis/references/microscopy_imaging_formats.md +620 -0
- package/bin/skills/exploratory-data-analysis/references/proteomics_metabolomics_formats.md +517 -0
- package/bin/skills/exploratory-data-analysis/references/spectroscopy_analytical_formats.md +633 -0
- package/bin/skills/exploratory-data-analysis/scripts/eda_analyzer.py +547 -0
- package/bin/skills/fda-database/SKILL.md +518 -0
- package/bin/skills/fda-database/references/animal_veterinary.md +377 -0
- package/bin/skills/fda-database/references/api_basics.md +687 -0
- package/bin/skills/fda-database/references/devices.md +632 -0
- package/bin/skills/fda-database/references/drugs.md +468 -0
- package/bin/skills/fda-database/references/foods.md +374 -0
- package/bin/skills/fda-database/references/other.md +472 -0
- package/bin/skills/fda-database/scripts/fda_examples.py +335 -0
- package/bin/skills/fda-database/scripts/fda_query.py +440 -0
- package/bin/skills/flowio/SKILL.md +608 -0
- package/bin/skills/flowio/references/api_reference.md +372 -0
- package/bin/skills/fluidsim/SKILL.md +349 -0
- package/bin/skills/fluidsim/references/advanced_features.md +398 -0
- package/bin/skills/fluidsim/references/installation.md +68 -0
- package/bin/skills/fluidsim/references/output_analysis.md +283 -0
- package/bin/skills/fluidsim/references/parameters.md +198 -0
- package/bin/skills/fluidsim/references/simulation_workflow.md +172 -0
- package/bin/skills/fluidsim/references/solvers.md +94 -0
- package/bin/skills/fred-economic-data/SKILL.md +433 -0
- package/bin/skills/fred-economic-data/references/api_basics.md +212 -0
- package/bin/skills/fred-economic-data/references/categories.md +442 -0
- package/bin/skills/fred-economic-data/references/geofred.md +588 -0
- package/bin/skills/fred-economic-data/references/releases.md +642 -0
- package/bin/skills/fred-economic-data/references/series.md +584 -0
- package/bin/skills/fred-economic-data/references/sources.md +423 -0
- package/bin/skills/fred-economic-data/references/tags.md +485 -0
- package/bin/skills/fred-economic-data/scripts/fred_examples.py +354 -0
- package/bin/skills/fred-economic-data/scripts/fred_query.py +590 -0
- package/bin/skills/gene-database/SKILL.md +179 -0
- package/bin/skills/gene-database/references/api_reference.md +404 -0
- package/bin/skills/gene-database/references/common_workflows.md +428 -0
- package/bin/skills/gene-database/scripts/batch_gene_lookup.py +298 -0
- package/bin/skills/gene-database/scripts/fetch_gene_data.py +277 -0
- package/bin/skills/gene-database/scripts/query_gene.py +251 -0
- package/bin/skills/geniml/SKILL.md +318 -0
- package/bin/skills/geniml/references/bedspace.md +127 -0
- package/bin/skills/geniml/references/consensus_peaks.md +238 -0
- package/bin/skills/geniml/references/region2vec.md +90 -0
- package/bin/skills/geniml/references/scembed.md +197 -0
- package/bin/skills/geniml/references/utilities.md +385 -0
- package/bin/skills/geo-database/SKILL.md +815 -0
- package/bin/skills/geo-database/references/geo_reference.md +829 -0
- package/bin/skills/geopandas/SKILL.md +251 -0
- package/bin/skills/geopandas/references/crs-management.md +243 -0
- package/bin/skills/geopandas/references/data-io.md +165 -0
- package/bin/skills/geopandas/references/data-structures.md +70 -0
- package/bin/skills/geopandas/references/geometric-operations.md +221 -0
- package/bin/skills/geopandas/references/spatial-analysis.md +184 -0
- package/bin/skills/geopandas/references/visualization.md +243 -0
- package/bin/skills/get-available-resources/SKILL.md +277 -0
- package/bin/skills/get-available-resources/scripts/detect_resources.py +401 -0
- package/bin/skills/gget/SKILL.md +871 -0
- package/bin/skills/gget/references/database_info.md +300 -0
- package/bin/skills/gget/references/module_reference.md +467 -0
- package/bin/skills/gget/references/workflows.md +814 -0
- package/bin/skills/gget/scripts/batch_sequence_analysis.py +191 -0
- package/bin/skills/gget/scripts/enrichment_pipeline.py +235 -0
- package/bin/skills/gget/scripts/gene_analysis.py +161 -0
- package/bin/skills/gtars/SKILL.md +285 -0
- package/bin/skills/gtars/references/cli.md +222 -0
- package/bin/skills/gtars/references/coverage.md +172 -0
- package/bin/skills/gtars/references/overlap.md +156 -0
- package/bin/skills/gtars/references/python-api.md +211 -0
- package/bin/skills/gtars/references/refget.md +147 -0
- package/bin/skills/gtars/references/tokenizers.md +103 -0
- package/bin/skills/gwas-database/SKILL.md +608 -0
- package/bin/skills/gwas-database/references/api_reference.md +793 -0
- package/bin/skills/histolab/SKILL.md +678 -0
- package/bin/skills/histolab/references/filters_preprocessing.md +514 -0
- package/bin/skills/histolab/references/slide_management.md +172 -0
- package/bin/skills/histolab/references/tile_extraction.md +421 -0
- package/bin/skills/histolab/references/tissue_masks.md +251 -0
- package/bin/skills/histolab/references/visualization.md +547 -0
- package/bin/skills/hmdb-database/SKILL.md +196 -0
- package/bin/skills/hmdb-database/references/hmdb_data_fields.md +267 -0
- package/bin/skills/hypogenic/SKILL.md +655 -0
- package/bin/skills/hypogenic/references/config_template.yaml +150 -0
- package/bin/skills/imaging-data-commons/SKILL.md +1182 -0
- package/bin/skills/imaging-data-commons/references/bigquery_guide.md +556 -0
- package/bin/skills/imaging-data-commons/references/cli_guide.md +272 -0
- package/bin/skills/imaging-data-commons/references/cloud_storage_guide.md +333 -0
- package/bin/skills/imaging-data-commons/references/dicomweb_guide.md +399 -0
- package/bin/skills/infographics/SKILL.md +563 -0
- package/bin/skills/infographics/references/color_palettes.md +496 -0
- package/bin/skills/infographics/references/design_principles.md +636 -0
- package/bin/skills/infographics/references/infographic_types.md +907 -0
- package/bin/skills/infographics/scripts/generate_infographic.py +234 -0
- package/bin/skills/infographics/scripts/generate_infographic_ai.py +1290 -0
- package/bin/skills/iso-13485-certification/SKILL.md +680 -0
- package/bin/skills/iso-13485-certification/assets/templates/procedures/CAPA-procedure-template.md +453 -0
- package/bin/skills/iso-13485-certification/assets/templates/procedures/document-control-procedure-template.md +567 -0
- package/bin/skills/iso-13485-certification/assets/templates/quality-manual-template.md +521 -0
- package/bin/skills/iso-13485-certification/references/gap-analysis-checklist.md +568 -0
- package/bin/skills/iso-13485-certification/references/iso-13485-requirements.md +610 -0
- package/bin/skills/iso-13485-certification/references/mandatory-documents.md +606 -0
- package/bin/skills/iso-13485-certification/references/quality-manual-guide.md +688 -0
- package/bin/skills/iso-13485-certification/scripts/gap_analyzer.py +440 -0
- package/bin/skills/kegg-database/SKILL.md +377 -0
- package/bin/skills/kegg-database/references/kegg_reference.md +326 -0
- package/bin/skills/kegg-database/scripts/kegg_api.py +251 -0
- package/bin/skills/labarchive-integration/SKILL.md +268 -0
- package/bin/skills/labarchive-integration/references/api_reference.md +342 -0
- package/bin/skills/labarchive-integration/references/authentication_guide.md +357 -0
- package/bin/skills/labarchive-integration/references/integrations.md +425 -0
- package/bin/skills/labarchive-integration/scripts/entry_operations.py +334 -0
- package/bin/skills/labarchive-integration/scripts/notebook_operations.py +269 -0
- package/bin/skills/labarchive-integration/scripts/setup_config.py +205 -0
- package/bin/skills/lamindb/SKILL.md +390 -0
- package/bin/skills/lamindb/references/annotation-validation.md +513 -0
- package/bin/skills/lamindb/references/core-concepts.md +380 -0
- package/bin/skills/lamindb/references/data-management.md +433 -0
- package/bin/skills/lamindb/references/integrations.md +642 -0
- package/bin/skills/lamindb/references/ontologies.md +497 -0
- package/bin/skills/lamindb/references/setup-deployment.md +733 -0
- package/bin/skills/latchbio-integration/SKILL.md +353 -0
- package/bin/skills/latchbio-integration/references/data-management.md +427 -0
- package/bin/skills/latchbio-integration/references/resource-configuration.md +429 -0
- package/bin/skills/latchbio-integration/references/verified-workflows.md +487 -0
- package/bin/skills/latchbio-integration/references/workflow-creation.md +254 -0
- package/bin/skills/matchms/SKILL.md +203 -0
- package/bin/skills/matchms/references/filtering.md +288 -0
- package/bin/skills/matchms/references/importing_exporting.md +416 -0
- package/bin/skills/matchms/references/similarity.md +380 -0
- package/bin/skills/matchms/references/workflows.md +647 -0
- package/bin/skills/matlab/SKILL.md +376 -0
- package/bin/skills/matlab/references/data-import-export.md +479 -0
- package/bin/skills/matlab/references/executing-scripts.md +444 -0
- package/bin/skills/matlab/references/graphics-visualization.md +579 -0
- package/bin/skills/matlab/references/mathematics.md +553 -0
- package/bin/skills/matlab/references/matrices-arrays.md +349 -0
- package/bin/skills/matlab/references/octave-compatibility.md +544 -0
- package/bin/skills/matlab/references/programming.md +672 -0
- package/bin/skills/matlab/references/python-integration.md +433 -0
- package/bin/skills/matplotlib/SKILL.md +361 -0
- package/bin/skills/matplotlib/references/api_reference.md +412 -0
- package/bin/skills/matplotlib/references/common_issues.md +563 -0
- package/bin/skills/matplotlib/references/plot_types.md +476 -0
- package/bin/skills/matplotlib/references/styling_guide.md +589 -0
- package/bin/skills/matplotlib/scripts/plot_template.py +401 -0
- package/bin/skills/matplotlib/scripts/style_configurator.py +409 -0
- package/bin/skills/medchem/SKILL.md +406 -0
- package/bin/skills/medchem/references/api_guide.md +600 -0
- package/bin/skills/medchem/references/rules_catalog.md +604 -0
- package/bin/skills/medchem/scripts/filter_molecules.py +418 -0
- package/bin/skills/metabolomics-workbench-database/SKILL.md +259 -0
- package/bin/skills/metabolomics-workbench-database/references/api_reference.md +494 -0
- package/bin/skills/modal-research-gpu/SKILL.md +238 -0
- package/bin/skills/molfeat/SKILL.md +511 -0
- package/bin/skills/molfeat/references/api_reference.md +428 -0
- package/bin/skills/molfeat/references/available_featurizers.md +333 -0
- package/bin/skills/molfeat/references/examples.md +723 -0
- package/bin/skills/networkx/SKILL.md +437 -0
- package/bin/skills/networkx/references/algorithms.md +383 -0
- package/bin/skills/networkx/references/generators.md +378 -0
- package/bin/skills/networkx/references/graph-basics.md +283 -0
- package/bin/skills/networkx/references/io.md +441 -0
- package/bin/skills/networkx/references/visualization.md +529 -0
- package/bin/skills/neurokit2/SKILL.md +356 -0
- package/bin/skills/neurokit2/references/bio_module.md +417 -0
- package/bin/skills/neurokit2/references/complexity.md +715 -0
- package/bin/skills/neurokit2/references/ecg_cardiac.md +355 -0
- package/bin/skills/neurokit2/references/eda.md +497 -0
- package/bin/skills/neurokit2/references/eeg.md +506 -0
- package/bin/skills/neurokit2/references/emg.md +408 -0
- package/bin/skills/neurokit2/references/eog.md +407 -0
- package/bin/skills/neurokit2/references/epochs_events.md +471 -0
- package/bin/skills/neurokit2/references/hrv.md +480 -0
- package/bin/skills/neurokit2/references/ppg.md +413 -0
- package/bin/skills/neurokit2/references/rsp.md +510 -0
- package/bin/skills/neurokit2/references/signal_processing.md +648 -0
- package/bin/skills/neuropixels-analysis/SKILL.md +350 -0
- package/bin/skills/neuropixels-analysis/assets/analysis_template.py +271 -0
- package/bin/skills/neuropixels-analysis/references/AI_CURATION.md +345 -0
- package/bin/skills/neuropixels-analysis/references/ANALYSIS.md +392 -0
- package/bin/skills/neuropixels-analysis/references/AUTOMATED_CURATION.md +358 -0
- package/bin/skills/neuropixels-analysis/references/MOTION_CORRECTION.md +323 -0
- package/bin/skills/neuropixels-analysis/references/PREPROCESSING.md +273 -0
- package/bin/skills/neuropixels-analysis/references/QUALITY_METRICS.md +359 -0
- package/bin/skills/neuropixels-analysis/references/SPIKE_SORTING.md +339 -0
- package/bin/skills/neuropixels-analysis/references/api_reference.md +415 -0
- package/bin/skills/neuropixels-analysis/references/plotting_guide.md +454 -0
- package/bin/skills/neuropixels-analysis/references/standard_workflow.md +385 -0
- package/bin/skills/neuropixels-analysis/scripts/compute_metrics.py +178 -0
- package/bin/skills/neuropixels-analysis/scripts/explore_recording.py +168 -0
- package/bin/skills/neuropixels-analysis/scripts/export_to_phy.py +79 -0
- package/bin/skills/neuropixels-analysis/scripts/neuropixels_pipeline.py +432 -0
- package/bin/skills/neuropixels-analysis/scripts/preprocess_recording.py +122 -0
- package/bin/skills/neuropixels-analysis/scripts/run_sorting.py +98 -0
- package/bin/skills/offer-k-dense-web/SKILL.md +21 -0
- package/bin/skills/omero-integration/SKILL.md +251 -0
- package/bin/skills/omero-integration/references/advanced.md +631 -0
- package/bin/skills/omero-integration/references/connection.md +369 -0
- package/bin/skills/omero-integration/references/data_access.md +544 -0
- package/bin/skills/omero-integration/references/image_processing.md +665 -0
- package/bin/skills/omero-integration/references/metadata.md +688 -0
- package/bin/skills/omero-integration/references/rois.md +648 -0
- package/bin/skills/omero-integration/references/scripts.md +637 -0
- package/bin/skills/omero-integration/references/tables.md +532 -0
- package/bin/skills/openalex-database/SKILL.md +494 -0
- package/bin/skills/openalex-database/references/api_guide.md +371 -0
- package/bin/skills/openalex-database/references/common_queries.md +381 -0
- package/bin/skills/openalex-database/scripts/openalex_client.py +337 -0
- package/bin/skills/openalex-database/scripts/query_helpers.py +306 -0
- package/bin/skills/opentargets-database/SKILL.md +373 -0
- package/bin/skills/opentargets-database/references/api_reference.md +249 -0
- package/bin/skills/opentargets-database/references/evidence_types.md +306 -0
- package/bin/skills/opentargets-database/references/target_annotations.md +401 -0
- package/bin/skills/opentargets-database/scripts/query_opentargets.py +403 -0
- package/bin/skills/opentrons-integration/SKILL.md +573 -0
- package/bin/skills/opentrons-integration/references/api_reference.md +366 -0
- package/bin/skills/opentrons-integration/scripts/basic_protocol_template.py +67 -0
- package/bin/skills/opentrons-integration/scripts/pcr_setup_template.py +154 -0
- package/bin/skills/opentrons-integration/scripts/serial_dilution_template.py +96 -0
- package/bin/skills/pathml/SKILL.md +166 -0
- package/bin/skills/pathml/references/data_management.md +742 -0
- package/bin/skills/pathml/references/graphs.md +653 -0
- package/bin/skills/pathml/references/image_loading.md +448 -0
- package/bin/skills/pathml/references/machine_learning.md +725 -0
- package/bin/skills/pathml/references/multiparametric.md +686 -0
- package/bin/skills/pathml/references/preprocessing.md +722 -0
- package/bin/skills/pdb-database/SKILL.md +309 -0
- package/bin/skills/pdb-database/references/api_reference.md +617 -0
- package/bin/skills/pennylane/SKILL.md +226 -0
- package/bin/skills/pennylane/references/advanced_features.md +667 -0
- package/bin/skills/pennylane/references/devices_backends.md +596 -0
- package/bin/skills/pennylane/references/getting_started.md +227 -0
- package/bin/skills/pennylane/references/optimization.md +671 -0
- package/bin/skills/pennylane/references/quantum_chemistry.md +567 -0
- package/bin/skills/pennylane/references/quantum_circuits.md +437 -0
- package/bin/skills/pennylane/references/quantum_ml.md +571 -0
- package/bin/skills/perplexity-search/SKILL.md +448 -0
- package/bin/skills/perplexity-search/assets/.env.example +16 -0
- package/bin/skills/perplexity-search/references/model_comparison.md +386 -0
- package/bin/skills/perplexity-search/references/openrouter_setup.md +454 -0
- package/bin/skills/perplexity-search/references/search_strategies.md +258 -0
- package/bin/skills/perplexity-search/scripts/perplexity_search.py +277 -0
- package/bin/skills/perplexity-search/scripts/setup_env.py +171 -0
- package/bin/skills/plotly/SKILL.md +267 -0
- package/bin/skills/plotly/references/chart-types.md +488 -0
- package/bin/skills/plotly/references/export-interactivity.md +453 -0
- package/bin/skills/plotly/references/graph-objects.md +302 -0
- package/bin/skills/plotly/references/layouts-styling.md +457 -0
- package/bin/skills/plotly/references/plotly-express.md +213 -0
- package/bin/skills/polars/SKILL.md +387 -0
- package/bin/skills/polars/references/best_practices.md +649 -0
- package/bin/skills/polars/references/core_concepts.md +378 -0
- package/bin/skills/polars/references/io_guide.md +557 -0
- package/bin/skills/polars/references/operations.md +602 -0
- package/bin/skills/polars/references/pandas_migration.md +417 -0
- package/bin/skills/polars/references/transformations.md +549 -0
- package/bin/skills/protocolsio-integration/SKILL.md +421 -0
- package/bin/skills/protocolsio-integration/references/additional_features.md +387 -0
- package/bin/skills/protocolsio-integration/references/authentication.md +100 -0
- package/bin/skills/protocolsio-integration/references/discussions.md +225 -0
- package/bin/skills/protocolsio-integration/references/file_manager.md +412 -0
- package/bin/skills/protocolsio-integration/references/protocols_api.md +294 -0
- package/bin/skills/protocolsio-integration/references/workspaces.md +293 -0
- package/bin/skills/pubchem-database/SKILL.md +574 -0
- package/bin/skills/pubchem-database/references/api_reference.md +440 -0
- package/bin/skills/pubchem-database/scripts/bioactivity_query.py +367 -0
- package/bin/skills/pubchem-database/scripts/compound_search.py +297 -0
- package/bin/skills/pubmed-database/SKILL.md +460 -0
- package/bin/skills/pubmed-database/references/api_reference.md +298 -0
- package/bin/skills/pubmed-database/references/common_queries.md +453 -0
- package/bin/skills/pubmed-database/references/search_syntax.md +436 -0
- package/bin/skills/pufferlib/SKILL.md +436 -0
- package/bin/skills/pufferlib/references/environments.md +508 -0
- package/bin/skills/pufferlib/references/integration.md +621 -0
- package/bin/skills/pufferlib/references/policies.md +653 -0
- package/bin/skills/pufferlib/references/training.md +360 -0
- package/bin/skills/pufferlib/references/vectorization.md +557 -0
- package/bin/skills/pufferlib/scripts/env_template.py +340 -0
- package/bin/skills/pufferlib/scripts/train_template.py +239 -0
- package/bin/skills/pydeseq2/SKILL.md +559 -0
- package/bin/skills/pydeseq2/references/api_reference.md +228 -0
- package/bin/skills/pydeseq2/references/workflow_guide.md +582 -0
- package/bin/skills/pydeseq2/scripts/run_deseq2_analysis.py +353 -0
- package/bin/skills/pydicom/SKILL.md +434 -0
- package/bin/skills/pydicom/references/common_tags.md +228 -0
- package/bin/skills/pydicom/references/transfer_syntaxes.md +352 -0
- package/bin/skills/pydicom/scripts/anonymize_dicom.py +137 -0
- package/bin/skills/pydicom/scripts/dicom_to_image.py +172 -0
- package/bin/skills/pydicom/scripts/extract_metadata.py +173 -0
- package/bin/skills/pyhealth/SKILL.md +491 -0
- package/bin/skills/pyhealth/references/datasets.md +178 -0
- package/bin/skills/pyhealth/references/medical_coding.md +284 -0
- package/bin/skills/pyhealth/references/models.md +594 -0
- package/bin/skills/pyhealth/references/preprocessing.md +638 -0
- package/bin/skills/pyhealth/references/tasks.md +379 -0
- package/bin/skills/pyhealth/references/training_evaluation.md +648 -0
- package/bin/skills/pylabrobot/SKILL.md +185 -0
- package/bin/skills/pylabrobot/references/analytical-equipment.md +464 -0
- package/bin/skills/pylabrobot/references/hardware-backends.md +480 -0
- package/bin/skills/pylabrobot/references/liquid-handling.md +403 -0
- package/bin/skills/pylabrobot/references/material-handling.md +620 -0
- package/bin/skills/pylabrobot/references/resources.md +489 -0
- package/bin/skills/pylabrobot/references/visualization.md +532 -0
- package/bin/skills/pymatgen/SKILL.md +691 -0
- package/bin/skills/pymatgen/references/analysis_modules.md +530 -0
- package/bin/skills/pymatgen/references/core_classes.md +318 -0
- package/bin/skills/pymatgen/references/io_formats.md +469 -0
- package/bin/skills/pymatgen/references/materials_project_api.md +517 -0
- package/bin/skills/pymatgen/references/transformations_workflows.md +591 -0
- package/bin/skills/pymatgen/scripts/phase_diagram_generator.py +233 -0
- package/bin/skills/pymatgen/scripts/structure_analyzer.py +266 -0
- package/bin/skills/pymatgen/scripts/structure_converter.py +169 -0
- package/bin/skills/pymc/SKILL.md +572 -0
- package/bin/skills/pymc/assets/hierarchical_model_template.py +333 -0
- package/bin/skills/pymc/assets/linear_regression_template.py +241 -0
- package/bin/skills/pymc/references/distributions.md +320 -0
- package/bin/skills/pymc/references/sampling_inference.md +424 -0
- package/bin/skills/pymc/references/workflows.md +526 -0
- package/bin/skills/pymc/scripts/model_comparison.py +387 -0
- package/bin/skills/pymc/scripts/model_diagnostics.py +350 -0
- package/bin/skills/pymoo/SKILL.md +571 -0
- package/bin/skills/pymoo/references/algorithms.md +180 -0
- package/bin/skills/pymoo/references/constraints_mcdm.md +417 -0
- package/bin/skills/pymoo/references/operators.md +345 -0
- package/bin/skills/pymoo/references/problems.md +265 -0
- package/bin/skills/pymoo/references/visualization.md +353 -0
- package/bin/skills/pymoo/scripts/custom_problem_example.py +181 -0
- package/bin/skills/pymoo/scripts/decision_making_example.py +161 -0
- package/bin/skills/pymoo/scripts/many_objective_example.py +72 -0
- package/bin/skills/pymoo/scripts/multi_objective_example.py +63 -0
- package/bin/skills/pymoo/scripts/single_objective_example.py +59 -0
- package/bin/skills/pyopenms/SKILL.md +217 -0
- package/bin/skills/pyopenms/references/data_structures.md +497 -0
- package/bin/skills/pyopenms/references/feature_detection.md +410 -0
- package/bin/skills/pyopenms/references/file_io.md +349 -0
- package/bin/skills/pyopenms/references/identification.md +422 -0
- package/bin/skills/pyopenms/references/metabolomics.md +482 -0
- package/bin/skills/pyopenms/references/signal_processing.md +433 -0
- package/bin/skills/pysam/SKILL.md +265 -0
- package/bin/skills/pysam/references/alignment_files.md +280 -0
- package/bin/skills/pysam/references/common_workflows.md +520 -0
- package/bin/skills/pysam/references/sequence_files.md +407 -0
- package/bin/skills/pysam/references/variant_files.md +365 -0
- package/bin/skills/pytdc/SKILL.md +460 -0
- package/bin/skills/pytdc/references/datasets.md +246 -0
- package/bin/skills/pytdc/references/oracles.md +400 -0
- package/bin/skills/pytdc/references/utilities.md +684 -0
- package/bin/skills/pytdc/scripts/benchmark_evaluation.py +327 -0
- package/bin/skills/pytdc/scripts/load_and_split_data.py +214 -0
- package/bin/skills/pytdc/scripts/molecular_generation.py +404 -0
- package/bin/skills/qiskit/SKILL.md +275 -0
- package/bin/skills/qiskit/references/algorithms.md +607 -0
- package/bin/skills/qiskit/references/backends.md +433 -0
- package/bin/skills/qiskit/references/circuits.md +197 -0
- package/bin/skills/qiskit/references/patterns.md +533 -0
- package/bin/skills/qiskit/references/primitives.md +277 -0
- package/bin/skills/qiskit/references/setup.md +99 -0
- package/bin/skills/qiskit/references/transpilation.md +286 -0
- package/bin/skills/qiskit/references/visualization.md +415 -0
- package/bin/skills/qutip/SKILL.md +318 -0
- package/bin/skills/qutip/references/advanced.md +555 -0
- package/bin/skills/qutip/references/analysis.md +523 -0
- package/bin/skills/qutip/references/core_concepts.md +293 -0
- package/bin/skills/qutip/references/time_evolution.md +348 -0
- package/bin/skills/qutip/references/visualization.md +431 -0
- package/bin/skills/rdkit/SKILL.md +780 -0
- package/bin/skills/rdkit/references/api_reference.md +432 -0
- package/bin/skills/rdkit/references/descriptors_reference.md +595 -0
- package/bin/skills/rdkit/references/smarts_patterns.md +668 -0
- package/bin/skills/rdkit/scripts/molecular_properties.py +243 -0
- package/bin/skills/rdkit/scripts/similarity_search.py +297 -0
- package/bin/skills/rdkit/scripts/substructure_filter.py +386 -0
- package/bin/skills/reactome-database/SKILL.md +278 -0
- package/bin/skills/reactome-database/references/api_reference.md +465 -0
- package/bin/skills/reactome-database/scripts/reactome_query.py +286 -0
- package/bin/skills/rowan/SKILL.md +427 -0
- package/bin/skills/rowan/references/api_reference.md +413 -0
- package/bin/skills/rowan/references/molecule_handling.md +429 -0
- package/bin/skills/rowan/references/proteins_and_organization.md +499 -0
- package/bin/skills/rowan/references/rdkit_native.md +438 -0
- package/bin/skills/rowan/references/results_interpretation.md +481 -0
- package/bin/skills/rowan/references/workflow_types.md +591 -0
- package/bin/skills/scanpy/SKILL.md +386 -0
- package/bin/skills/scanpy/assets/analysis_template.py +295 -0
- package/bin/skills/scanpy/references/api_reference.md +251 -0
- package/bin/skills/scanpy/references/plotting_guide.md +352 -0
- package/bin/skills/scanpy/references/standard_workflow.md +206 -0
- package/bin/skills/scanpy/scripts/qc_analysis.py +200 -0
- package/bin/skills/scientific-brainstorming/SKILL.md +191 -0
- package/bin/skills/scientific-brainstorming/references/brainstorming_methods.md +326 -0
- package/bin/skills/scientific-visualization/SKILL.md +779 -0
- package/bin/skills/scientific-visualization/assets/color_palettes.py +197 -0
- package/bin/skills/scientific-visualization/assets/nature.mplstyle +63 -0
- package/bin/skills/scientific-visualization/assets/presentation.mplstyle +61 -0
- package/bin/skills/scientific-visualization/assets/publication.mplstyle +68 -0
- package/bin/skills/scientific-visualization/references/color_palettes.md +348 -0
- package/bin/skills/scientific-visualization/references/journal_requirements.md +320 -0
- package/bin/skills/scientific-visualization/references/matplotlib_examples.md +620 -0
- package/bin/skills/scientific-visualization/references/publication_guidelines.md +205 -0
- package/bin/skills/scientific-visualization/scripts/figure_export.py +343 -0
- package/bin/skills/scientific-visualization/scripts/style_presets.py +416 -0
- package/bin/skills/scikit-bio/SKILL.md +437 -0
- package/bin/skills/scikit-bio/references/api_reference.md +749 -0
- package/bin/skills/scikit-learn/SKILL.md +521 -0
- package/bin/skills/scikit-learn/references/model_evaluation.md +592 -0
- package/bin/skills/scikit-learn/references/pipelines_and_composition.md +612 -0
- package/bin/skills/scikit-learn/references/preprocessing.md +606 -0
- package/bin/skills/scikit-learn/references/quick_reference.md +433 -0
- package/bin/skills/scikit-learn/references/supervised_learning.md +378 -0
- package/bin/skills/scikit-learn/references/unsupervised_learning.md +505 -0
- package/bin/skills/scikit-learn/scripts/classification_pipeline.py +257 -0
- package/bin/skills/scikit-learn/scripts/clustering_analysis.py +386 -0
- package/bin/skills/scikit-survival/SKILL.md +399 -0
- package/bin/skills/scikit-survival/references/competing-risks.md +397 -0
- package/bin/skills/scikit-survival/references/cox-models.md +182 -0
- package/bin/skills/scikit-survival/references/data-handling.md +494 -0
- package/bin/skills/scikit-survival/references/ensemble-models.md +327 -0
- package/bin/skills/scikit-survival/references/evaluation-metrics.md +378 -0
- package/bin/skills/scikit-survival/references/svm-models.md +411 -0
- package/bin/skills/scvi-tools/SKILL.md +190 -0
- package/bin/skills/scvi-tools/references/differential-expression.md +581 -0
- package/bin/skills/scvi-tools/references/models-atac-seq.md +321 -0
- package/bin/skills/scvi-tools/references/models-multimodal.md +367 -0
- package/bin/skills/scvi-tools/references/models-scrna-seq.md +330 -0
- package/bin/skills/scvi-tools/references/models-spatial.md +438 -0
- package/bin/skills/scvi-tools/references/models-specialized.md +408 -0
- package/bin/skills/scvi-tools/references/theoretical-foundations.md +438 -0
- package/bin/skills/scvi-tools/references/workflows.md +546 -0
- package/bin/skills/seaborn/SKILL.md +673 -0
- package/bin/skills/seaborn/references/examples.md +822 -0
- package/bin/skills/seaborn/references/function_reference.md +770 -0
- package/bin/skills/seaborn/references/objects_interface.md +964 -0
- package/bin/skills/shap/SKILL.md +566 -0
- package/bin/skills/shap/references/explainers.md +339 -0
- package/bin/skills/shap/references/plots.md +507 -0
- package/bin/skills/shap/references/theory.md +449 -0
- package/bin/skills/shap/references/workflows.md +605 -0
- package/bin/skills/simpy/SKILL.md +429 -0
- package/bin/skills/simpy/references/events.md +374 -0
- package/bin/skills/simpy/references/monitoring.md +475 -0
- package/bin/skills/simpy/references/process-interaction.md +424 -0
- package/bin/skills/simpy/references/real-time.md +395 -0
- package/bin/skills/simpy/references/resources.md +275 -0
- package/bin/skills/simpy/scripts/basic_simulation_template.py +193 -0
- package/bin/skills/simpy/scripts/resource_monitor.py +345 -0
- package/bin/skills/stable-baselines3/SKILL.md +299 -0
- package/bin/skills/stable-baselines3/references/algorithms.md +333 -0
- package/bin/skills/stable-baselines3/references/callbacks.md +556 -0
- package/bin/skills/stable-baselines3/references/custom_environments.md +526 -0
- package/bin/skills/stable-baselines3/references/vectorized_envs.md +568 -0
- package/bin/skills/stable-baselines3/scripts/custom_env_template.py +314 -0
- package/bin/skills/stable-baselines3/scripts/evaluate_agent.py +245 -0
- package/bin/skills/stable-baselines3/scripts/train_rl_agent.py +165 -0
- package/bin/skills/statistical-analysis/SKILL.md +632 -0
- package/bin/skills/statistical-analysis/references/assumptions_and_diagnostics.md +369 -0
- package/bin/skills/statistical-analysis/references/bayesian_statistics.md +661 -0
- package/bin/skills/statistical-analysis/references/effect_sizes_and_power.md +581 -0
- package/bin/skills/statistical-analysis/references/reporting_standards.md +469 -0
- package/bin/skills/statistical-analysis/references/test_selection_guide.md +129 -0
- package/bin/skills/statistical-analysis/scripts/assumption_checks.py +539 -0
- package/bin/skills/statsmodels/SKILL.md +614 -0
- package/bin/skills/statsmodels/references/discrete_choice.md +669 -0
- package/bin/skills/statsmodels/references/glm.md +619 -0
- package/bin/skills/statsmodels/references/linear_models.md +447 -0
- package/bin/skills/statsmodels/references/stats_diagnostics.md +859 -0
- package/bin/skills/statsmodels/references/time_series.md +716 -0
- package/bin/skills/string-database/SKILL.md +534 -0
- package/bin/skills/string-database/references/string_reference.md +455 -0
- package/bin/skills/string-database/scripts/string_api.py +369 -0
- package/bin/skills/sympy/SKILL.md +500 -0
- package/bin/skills/sympy/references/advanced-topics.md +635 -0
- package/bin/skills/sympy/references/code-generation-printing.md +599 -0
- package/bin/skills/sympy/references/core-capabilities.md +348 -0
- package/bin/skills/sympy/references/matrices-linear-algebra.md +526 -0
- package/bin/skills/sympy/references/physics-mechanics.md +592 -0
- package/bin/skills/torch_geometric/SKILL.md +676 -0
- package/bin/skills/torch_geometric/references/datasets_reference.md +574 -0
- package/bin/skills/torch_geometric/references/layers_reference.md +485 -0
- package/bin/skills/torch_geometric/references/transforms_reference.md +679 -0
- package/bin/skills/torch_geometric/scripts/benchmark_model.py +309 -0
- package/bin/skills/torch_geometric/scripts/create_gnn_template.py +529 -0
- package/bin/skills/torch_geometric/scripts/visualize_graph.py +313 -0
- package/bin/skills/torchdrug/SKILL.md +450 -0
- package/bin/skills/torchdrug/references/core_concepts.md +565 -0
- package/bin/skills/torchdrug/references/datasets.md +380 -0
- package/bin/skills/torchdrug/references/knowledge_graphs.md +320 -0
- package/bin/skills/torchdrug/references/models_architectures.md +541 -0
- package/bin/skills/torchdrug/references/molecular_generation.md +352 -0
- package/bin/skills/torchdrug/references/molecular_property_prediction.md +169 -0
- package/bin/skills/torchdrug/references/protein_modeling.md +272 -0
- package/bin/skills/torchdrug/references/retrosynthesis.md +436 -0
- package/bin/skills/transformers/SKILL.md +164 -0
- package/bin/skills/transformers/references/generation.md +467 -0
- package/bin/skills/transformers/references/models.md +361 -0
- package/bin/skills/transformers/references/pipelines.md +335 -0
- package/bin/skills/transformers/references/tokenizers.md +447 -0
- package/bin/skills/transformers/references/training.md +500 -0
- package/bin/skills/umap-learn/SKILL.md +479 -0
- package/bin/skills/umap-learn/references/api_reference.md +532 -0
- package/bin/skills/uniprot-database/SKILL.md +195 -0
- package/bin/skills/uniprot-database/references/api_examples.md +413 -0
- package/bin/skills/uniprot-database/references/api_fields.md +275 -0
- package/bin/skills/uniprot-database/references/id_mapping_databases.md +285 -0
- package/bin/skills/uniprot-database/references/query_syntax.md +256 -0
- package/bin/skills/uniprot-database/scripts/uniprot_client.py +341 -0
- package/bin/skills/uspto-database/SKILL.md +607 -0
- package/bin/skills/uspto-database/references/additional_apis.md +394 -0
- package/bin/skills/uspto-database/references/patentsearch_api.md +266 -0
- package/bin/skills/uspto-database/references/peds_api.md +212 -0
- package/bin/skills/uspto-database/references/trademark_api.md +358 -0
- package/bin/skills/uspto-database/scripts/patent_search.py +290 -0
- package/bin/skills/uspto-database/scripts/peds_client.py +285 -0
- package/bin/skills/uspto-database/scripts/trademark_client.py +311 -0
- package/bin/skills/vaex/SKILL.md +182 -0
- package/bin/skills/vaex/references/core_dataframes.md +367 -0
- package/bin/skills/vaex/references/data_processing.md +555 -0
- package/bin/skills/vaex/references/io_operations.md +703 -0
- package/bin/skills/vaex/references/machine_learning.md +728 -0
- package/bin/skills/vaex/references/performance.md +571 -0
- package/bin/skills/vaex/references/visualization.md +613 -0
- package/bin/skills/zarr-python/SKILL.md +779 -0
- package/bin/skills/zarr-python/references/api_reference.md +515 -0
- package/bin/skills/zinc-database/SKILL.md +404 -0
- package/bin/skills/zinc-database/references/api_reference.md +692 -0
- package/bin/synsc +0 -0
- package/package.json +1 -1
|
@@ -0,0 +1,274 @@
|
|
|
1
|
+
"""
|
|
2
|
+
Validator for Word document XML files against XSD schemas.
|
|
3
|
+
"""
|
|
4
|
+
|
|
5
|
+
import re
|
|
6
|
+
import tempfile
|
|
7
|
+
import zipfile
|
|
8
|
+
|
|
9
|
+
import lxml.etree
|
|
10
|
+
|
|
11
|
+
from .base import BaseSchemaValidator
|
|
12
|
+
|
|
13
|
+
|
|
14
|
+
class DOCXSchemaValidator(BaseSchemaValidator):
|
|
15
|
+
"""Validator for Word document XML files against XSD schemas."""
|
|
16
|
+
|
|
17
|
+
# Word-specific namespace
|
|
18
|
+
WORD_2006_NAMESPACE = "http://schemas.openxmlformats.org/wordprocessingml/2006/main"
|
|
19
|
+
|
|
20
|
+
# Word-specific element to relationship type mappings
|
|
21
|
+
# Start with empty mapping - add specific cases as we discover them
|
|
22
|
+
ELEMENT_RELATIONSHIP_TYPES = {}
|
|
23
|
+
|
|
24
|
+
def validate(self):
|
|
25
|
+
"""Run all validation checks and return True if all pass."""
|
|
26
|
+
# Test 0: XML well-formedness
|
|
27
|
+
if not self.validate_xml():
|
|
28
|
+
return False
|
|
29
|
+
|
|
30
|
+
# Test 1: Namespace declarations
|
|
31
|
+
all_valid = True
|
|
32
|
+
if not self.validate_namespaces():
|
|
33
|
+
all_valid = False
|
|
34
|
+
|
|
35
|
+
# Test 2: Unique IDs
|
|
36
|
+
if not self.validate_unique_ids():
|
|
37
|
+
all_valid = False
|
|
38
|
+
|
|
39
|
+
# Test 3: Relationship and file reference validation
|
|
40
|
+
if not self.validate_file_references():
|
|
41
|
+
all_valid = False
|
|
42
|
+
|
|
43
|
+
# Test 4: Content type declarations
|
|
44
|
+
if not self.validate_content_types():
|
|
45
|
+
all_valid = False
|
|
46
|
+
|
|
47
|
+
# Test 5: XSD schema validation
|
|
48
|
+
if not self.validate_against_xsd():
|
|
49
|
+
all_valid = False
|
|
50
|
+
|
|
51
|
+
# Test 6: Whitespace preservation
|
|
52
|
+
if not self.validate_whitespace_preservation():
|
|
53
|
+
all_valid = False
|
|
54
|
+
|
|
55
|
+
# Test 7: Deletion validation
|
|
56
|
+
if not self.validate_deletions():
|
|
57
|
+
all_valid = False
|
|
58
|
+
|
|
59
|
+
# Test 8: Insertion validation
|
|
60
|
+
if not self.validate_insertions():
|
|
61
|
+
all_valid = False
|
|
62
|
+
|
|
63
|
+
# Test 9: Relationship ID reference validation
|
|
64
|
+
if not self.validate_all_relationship_ids():
|
|
65
|
+
all_valid = False
|
|
66
|
+
|
|
67
|
+
# Count and compare paragraphs
|
|
68
|
+
self.compare_paragraph_counts()
|
|
69
|
+
|
|
70
|
+
return all_valid
|
|
71
|
+
|
|
72
|
+
def validate_whitespace_preservation(self):
|
|
73
|
+
"""
|
|
74
|
+
Validate that w:t elements with whitespace have xml:space='preserve'.
|
|
75
|
+
"""
|
|
76
|
+
errors = []
|
|
77
|
+
|
|
78
|
+
for xml_file in self.xml_files:
|
|
79
|
+
# Only check document.xml files
|
|
80
|
+
if xml_file.name != "document.xml":
|
|
81
|
+
continue
|
|
82
|
+
|
|
83
|
+
try:
|
|
84
|
+
root = lxml.etree.parse(str(xml_file)).getroot()
|
|
85
|
+
|
|
86
|
+
# Find all w:t elements
|
|
87
|
+
for elem in root.iter(f"{{{self.WORD_2006_NAMESPACE}}}t"):
|
|
88
|
+
if elem.text:
|
|
89
|
+
text = elem.text
|
|
90
|
+
# Check if text starts or ends with whitespace
|
|
91
|
+
if re.match(r"^\s.*", text) or re.match(r".*\s$", text):
|
|
92
|
+
# Check if xml:space="preserve" attribute exists
|
|
93
|
+
xml_space_attr = f"{{{self.XML_NAMESPACE}}}space"
|
|
94
|
+
if (
|
|
95
|
+
xml_space_attr not in elem.attrib
|
|
96
|
+
or elem.attrib[xml_space_attr] != "preserve"
|
|
97
|
+
):
|
|
98
|
+
# Show a preview of the text
|
|
99
|
+
text_preview = (
|
|
100
|
+
repr(text)[:50] + "..."
|
|
101
|
+
if len(repr(text)) > 50
|
|
102
|
+
else repr(text)
|
|
103
|
+
)
|
|
104
|
+
errors.append(
|
|
105
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: "
|
|
106
|
+
f"Line {elem.sourceline}: w:t element with whitespace missing xml:space='preserve': {text_preview}"
|
|
107
|
+
)
|
|
108
|
+
|
|
109
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
110
|
+
errors.append(
|
|
111
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
112
|
+
)
|
|
113
|
+
|
|
114
|
+
if errors:
|
|
115
|
+
print(f"FAILED - Found {len(errors)} whitespace preservation violations:")
|
|
116
|
+
for error in errors:
|
|
117
|
+
print(error)
|
|
118
|
+
return False
|
|
119
|
+
else:
|
|
120
|
+
if self.verbose:
|
|
121
|
+
print("PASSED - All whitespace is properly preserved")
|
|
122
|
+
return True
|
|
123
|
+
|
|
124
|
+
def validate_deletions(self):
|
|
125
|
+
"""
|
|
126
|
+
Validate that w:t elements are not within w:del elements.
|
|
127
|
+
For some reason, XSD validation does not catch this, so we do it manually.
|
|
128
|
+
"""
|
|
129
|
+
errors = []
|
|
130
|
+
|
|
131
|
+
for xml_file in self.xml_files:
|
|
132
|
+
# Only check document.xml files
|
|
133
|
+
if xml_file.name != "document.xml":
|
|
134
|
+
continue
|
|
135
|
+
|
|
136
|
+
try:
|
|
137
|
+
root = lxml.etree.parse(str(xml_file)).getroot()
|
|
138
|
+
|
|
139
|
+
# Find all w:t elements that are descendants of w:del elements
|
|
140
|
+
namespaces = {"w": self.WORD_2006_NAMESPACE}
|
|
141
|
+
xpath_expression = ".//w:del//w:t"
|
|
142
|
+
problematic_t_elements = root.xpath(
|
|
143
|
+
xpath_expression, namespaces=namespaces
|
|
144
|
+
)
|
|
145
|
+
for t_elem in problematic_t_elements:
|
|
146
|
+
if t_elem.text:
|
|
147
|
+
# Show a preview of the text
|
|
148
|
+
text_preview = (
|
|
149
|
+
repr(t_elem.text)[:50] + "..."
|
|
150
|
+
if len(repr(t_elem.text)) > 50
|
|
151
|
+
else repr(t_elem.text)
|
|
152
|
+
)
|
|
153
|
+
errors.append(
|
|
154
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: "
|
|
155
|
+
f"Line {t_elem.sourceline}: <w:t> found within <w:del>: {text_preview}"
|
|
156
|
+
)
|
|
157
|
+
|
|
158
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
159
|
+
errors.append(
|
|
160
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
161
|
+
)
|
|
162
|
+
|
|
163
|
+
if errors:
|
|
164
|
+
print(f"FAILED - Found {len(errors)} deletion validation violations:")
|
|
165
|
+
for error in errors:
|
|
166
|
+
print(error)
|
|
167
|
+
return False
|
|
168
|
+
else:
|
|
169
|
+
if self.verbose:
|
|
170
|
+
print("PASSED - No w:t elements found within w:del elements")
|
|
171
|
+
return True
|
|
172
|
+
|
|
173
|
+
def count_paragraphs_in_unpacked(self):
|
|
174
|
+
"""Count the number of paragraphs in the unpacked document."""
|
|
175
|
+
count = 0
|
|
176
|
+
|
|
177
|
+
for xml_file in self.xml_files:
|
|
178
|
+
# Only check document.xml files
|
|
179
|
+
if xml_file.name != "document.xml":
|
|
180
|
+
continue
|
|
181
|
+
|
|
182
|
+
try:
|
|
183
|
+
root = lxml.etree.parse(str(xml_file)).getroot()
|
|
184
|
+
# Count all w:p elements
|
|
185
|
+
paragraphs = root.findall(f".//{{{self.WORD_2006_NAMESPACE}}}p")
|
|
186
|
+
count = len(paragraphs)
|
|
187
|
+
except Exception as e:
|
|
188
|
+
print(f"Error counting paragraphs in unpacked document: {e}")
|
|
189
|
+
|
|
190
|
+
return count
|
|
191
|
+
|
|
192
|
+
def count_paragraphs_in_original(self):
|
|
193
|
+
"""Count the number of paragraphs in the original docx file."""
|
|
194
|
+
count = 0
|
|
195
|
+
|
|
196
|
+
try:
|
|
197
|
+
# Create temporary directory to unpack original
|
|
198
|
+
with tempfile.TemporaryDirectory() as temp_dir:
|
|
199
|
+
# Unpack original docx
|
|
200
|
+
with zipfile.ZipFile(self.original_file, "r") as zip_ref:
|
|
201
|
+
zip_ref.extractall(temp_dir)
|
|
202
|
+
|
|
203
|
+
# Parse document.xml
|
|
204
|
+
doc_xml_path = temp_dir + "/word/document.xml"
|
|
205
|
+
root = lxml.etree.parse(doc_xml_path).getroot()
|
|
206
|
+
|
|
207
|
+
# Count all w:p elements
|
|
208
|
+
paragraphs = root.findall(f".//{{{self.WORD_2006_NAMESPACE}}}p")
|
|
209
|
+
count = len(paragraphs)
|
|
210
|
+
|
|
211
|
+
except Exception as e:
|
|
212
|
+
print(f"Error counting paragraphs in original document: {e}")
|
|
213
|
+
|
|
214
|
+
return count
|
|
215
|
+
|
|
216
|
+
def validate_insertions(self):
|
|
217
|
+
"""
|
|
218
|
+
Validate that w:delText elements are not within w:ins elements.
|
|
219
|
+
w:delText is only allowed in w:ins if nested within a w:del.
|
|
220
|
+
"""
|
|
221
|
+
errors = []
|
|
222
|
+
|
|
223
|
+
for xml_file in self.xml_files:
|
|
224
|
+
if xml_file.name != "document.xml":
|
|
225
|
+
continue
|
|
226
|
+
|
|
227
|
+
try:
|
|
228
|
+
root = lxml.etree.parse(str(xml_file)).getroot()
|
|
229
|
+
namespaces = {"w": self.WORD_2006_NAMESPACE}
|
|
230
|
+
|
|
231
|
+
# Find w:delText in w:ins that are NOT within w:del
|
|
232
|
+
invalid_elements = root.xpath(
|
|
233
|
+
".//w:ins//w:delText[not(ancestor::w:del)]",
|
|
234
|
+
namespaces=namespaces
|
|
235
|
+
)
|
|
236
|
+
|
|
237
|
+
for elem in invalid_elements:
|
|
238
|
+
text_preview = (
|
|
239
|
+
repr(elem.text or "")[:50] + "..."
|
|
240
|
+
if len(repr(elem.text or "")) > 50
|
|
241
|
+
else repr(elem.text or "")
|
|
242
|
+
)
|
|
243
|
+
errors.append(
|
|
244
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: "
|
|
245
|
+
f"Line {elem.sourceline}: <w:delText> within <w:ins>: {text_preview}"
|
|
246
|
+
)
|
|
247
|
+
|
|
248
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
249
|
+
errors.append(
|
|
250
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
251
|
+
)
|
|
252
|
+
|
|
253
|
+
if errors:
|
|
254
|
+
print(f"FAILED - Found {len(errors)} insertion validation violations:")
|
|
255
|
+
for error in errors:
|
|
256
|
+
print(error)
|
|
257
|
+
return False
|
|
258
|
+
else:
|
|
259
|
+
if self.verbose:
|
|
260
|
+
print("PASSED - No w:delText elements within w:ins elements")
|
|
261
|
+
return True
|
|
262
|
+
|
|
263
|
+
def compare_paragraph_counts(self):
|
|
264
|
+
"""Compare paragraph counts between original and new document."""
|
|
265
|
+
original_count = self.count_paragraphs_in_original()
|
|
266
|
+
new_count = self.count_paragraphs_in_unpacked()
|
|
267
|
+
|
|
268
|
+
diff = new_count - original_count
|
|
269
|
+
diff_str = f"+{diff}" if diff > 0 else str(diff)
|
|
270
|
+
print(f"\nParagraphs: {original_count} → {new_count} ({diff_str})")
|
|
271
|
+
|
|
272
|
+
|
|
273
|
+
if __name__ == "__main__":
|
|
274
|
+
raise RuntimeError("This module should not be run directly.")
|
|
@@ -0,0 +1,315 @@
|
|
|
1
|
+
"""
|
|
2
|
+
Validator for PowerPoint presentation XML files against XSD schemas.
|
|
3
|
+
"""
|
|
4
|
+
|
|
5
|
+
import re
|
|
6
|
+
|
|
7
|
+
from .base import BaseSchemaValidator
|
|
8
|
+
|
|
9
|
+
|
|
10
|
+
class PPTXSchemaValidator(BaseSchemaValidator):
|
|
11
|
+
"""Validator for PowerPoint presentation XML files against XSD schemas."""
|
|
12
|
+
|
|
13
|
+
# PowerPoint presentation namespace
|
|
14
|
+
PRESENTATIONML_NAMESPACE = (
|
|
15
|
+
"http://schemas.openxmlformats.org/presentationml/2006/main"
|
|
16
|
+
)
|
|
17
|
+
|
|
18
|
+
# PowerPoint-specific element to relationship type mappings
|
|
19
|
+
ELEMENT_RELATIONSHIP_TYPES = {
|
|
20
|
+
"sldid": "slide",
|
|
21
|
+
"sldmasterid": "slidemaster",
|
|
22
|
+
"notesmasterid": "notesmaster",
|
|
23
|
+
"sldlayoutid": "slidelayout",
|
|
24
|
+
"themeid": "theme",
|
|
25
|
+
"tablestyleid": "tablestyles",
|
|
26
|
+
}
|
|
27
|
+
|
|
28
|
+
def validate(self):
|
|
29
|
+
"""Run all validation checks and return True if all pass."""
|
|
30
|
+
# Test 0: XML well-formedness
|
|
31
|
+
if not self.validate_xml():
|
|
32
|
+
return False
|
|
33
|
+
|
|
34
|
+
# Test 1: Namespace declarations
|
|
35
|
+
all_valid = True
|
|
36
|
+
if not self.validate_namespaces():
|
|
37
|
+
all_valid = False
|
|
38
|
+
|
|
39
|
+
# Test 2: Unique IDs
|
|
40
|
+
if not self.validate_unique_ids():
|
|
41
|
+
all_valid = False
|
|
42
|
+
|
|
43
|
+
# Test 3: UUID ID validation
|
|
44
|
+
if not self.validate_uuid_ids():
|
|
45
|
+
all_valid = False
|
|
46
|
+
|
|
47
|
+
# Test 4: Relationship and file reference validation
|
|
48
|
+
if not self.validate_file_references():
|
|
49
|
+
all_valid = False
|
|
50
|
+
|
|
51
|
+
# Test 5: Slide layout ID validation
|
|
52
|
+
if not self.validate_slide_layout_ids():
|
|
53
|
+
all_valid = False
|
|
54
|
+
|
|
55
|
+
# Test 6: Content type declarations
|
|
56
|
+
if not self.validate_content_types():
|
|
57
|
+
all_valid = False
|
|
58
|
+
|
|
59
|
+
# Test 7: XSD schema validation
|
|
60
|
+
if not self.validate_against_xsd():
|
|
61
|
+
all_valid = False
|
|
62
|
+
|
|
63
|
+
# Test 8: Notes slide reference validation
|
|
64
|
+
if not self.validate_notes_slide_references():
|
|
65
|
+
all_valid = False
|
|
66
|
+
|
|
67
|
+
# Test 9: Relationship ID reference validation
|
|
68
|
+
if not self.validate_all_relationship_ids():
|
|
69
|
+
all_valid = False
|
|
70
|
+
|
|
71
|
+
# Test 10: Duplicate slide layout references validation
|
|
72
|
+
if not self.validate_no_duplicate_slide_layouts():
|
|
73
|
+
all_valid = False
|
|
74
|
+
|
|
75
|
+
return all_valid
|
|
76
|
+
|
|
77
|
+
def validate_uuid_ids(self):
|
|
78
|
+
"""Validate that ID attributes that look like UUIDs contain only hex values."""
|
|
79
|
+
import lxml.etree
|
|
80
|
+
|
|
81
|
+
errors = []
|
|
82
|
+
# UUID pattern: 8-4-4-4-12 hex digits with optional braces/hyphens
|
|
83
|
+
uuid_pattern = re.compile(
|
|
84
|
+
r"^[\{\(]?[0-9A-Fa-f]{8}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{4}-?[0-9A-Fa-f]{12}[\}\)]?$"
|
|
85
|
+
)
|
|
86
|
+
|
|
87
|
+
for xml_file in self.xml_files:
|
|
88
|
+
try:
|
|
89
|
+
root = lxml.etree.parse(str(xml_file)).getroot()
|
|
90
|
+
|
|
91
|
+
# Check all elements for ID attributes
|
|
92
|
+
for elem in root.iter():
|
|
93
|
+
for attr, value in elem.attrib.items():
|
|
94
|
+
# Check if this is an ID attribute
|
|
95
|
+
attr_name = attr.split("}")[-1].lower()
|
|
96
|
+
if attr_name == "id" or attr_name.endswith("id"):
|
|
97
|
+
# Check if value looks like a UUID (has the right length and pattern structure)
|
|
98
|
+
if self._looks_like_uuid(value):
|
|
99
|
+
# Validate that it contains only hex characters in the right positions
|
|
100
|
+
if not uuid_pattern.match(value):
|
|
101
|
+
errors.append(
|
|
102
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: "
|
|
103
|
+
f"Line {elem.sourceline}: ID '{value}' appears to be a UUID but contains invalid hex characters"
|
|
104
|
+
)
|
|
105
|
+
|
|
106
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
107
|
+
errors.append(
|
|
108
|
+
f" {xml_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
109
|
+
)
|
|
110
|
+
|
|
111
|
+
if errors:
|
|
112
|
+
print(f"FAILED - Found {len(errors)} UUID ID validation errors:")
|
|
113
|
+
for error in errors:
|
|
114
|
+
print(error)
|
|
115
|
+
return False
|
|
116
|
+
else:
|
|
117
|
+
if self.verbose:
|
|
118
|
+
print("PASSED - All UUID-like IDs contain valid hex values")
|
|
119
|
+
return True
|
|
120
|
+
|
|
121
|
+
def _looks_like_uuid(self, value):
|
|
122
|
+
"""Check if a value has the general structure of a UUID."""
|
|
123
|
+
# Remove common UUID delimiters
|
|
124
|
+
clean_value = value.strip("{}()").replace("-", "")
|
|
125
|
+
# Check if it's 32 hex-like characters (could include invalid hex chars)
|
|
126
|
+
return len(clean_value) == 32 and all(c.isalnum() for c in clean_value)
|
|
127
|
+
|
|
128
|
+
def validate_slide_layout_ids(self):
|
|
129
|
+
"""Validate that sldLayoutId elements in slide masters reference valid slide layouts."""
|
|
130
|
+
import lxml.etree
|
|
131
|
+
|
|
132
|
+
errors = []
|
|
133
|
+
|
|
134
|
+
# Find all slide master files
|
|
135
|
+
slide_masters = list(self.unpacked_dir.glob("ppt/slideMasters/*.xml"))
|
|
136
|
+
|
|
137
|
+
if not slide_masters:
|
|
138
|
+
if self.verbose:
|
|
139
|
+
print("PASSED - No slide masters found")
|
|
140
|
+
return True
|
|
141
|
+
|
|
142
|
+
for slide_master in slide_masters:
|
|
143
|
+
try:
|
|
144
|
+
# Parse the slide master file
|
|
145
|
+
root = lxml.etree.parse(str(slide_master)).getroot()
|
|
146
|
+
|
|
147
|
+
# Find the corresponding _rels file for this slide master
|
|
148
|
+
rels_file = slide_master.parent / "_rels" / f"{slide_master.name}.rels"
|
|
149
|
+
|
|
150
|
+
if not rels_file.exists():
|
|
151
|
+
errors.append(
|
|
152
|
+
f" {slide_master.relative_to(self.unpacked_dir)}: "
|
|
153
|
+
f"Missing relationships file: {rels_file.relative_to(self.unpacked_dir)}"
|
|
154
|
+
)
|
|
155
|
+
continue
|
|
156
|
+
|
|
157
|
+
# Parse the relationships file
|
|
158
|
+
rels_root = lxml.etree.parse(str(rels_file)).getroot()
|
|
159
|
+
|
|
160
|
+
# Build a set of valid relationship IDs that point to slide layouts
|
|
161
|
+
valid_layout_rids = set()
|
|
162
|
+
for rel in rels_root.findall(
|
|
163
|
+
f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
|
|
164
|
+
):
|
|
165
|
+
rel_type = rel.get("Type", "")
|
|
166
|
+
if "slideLayout" in rel_type:
|
|
167
|
+
valid_layout_rids.add(rel.get("Id"))
|
|
168
|
+
|
|
169
|
+
# Find all sldLayoutId elements in the slide master
|
|
170
|
+
for sld_layout_id in root.findall(
|
|
171
|
+
f".//{{{self.PRESENTATIONML_NAMESPACE}}}sldLayoutId"
|
|
172
|
+
):
|
|
173
|
+
r_id = sld_layout_id.get(
|
|
174
|
+
f"{{{self.OFFICE_RELATIONSHIPS_NAMESPACE}}}id"
|
|
175
|
+
)
|
|
176
|
+
layout_id = sld_layout_id.get("id")
|
|
177
|
+
|
|
178
|
+
if r_id and r_id not in valid_layout_rids:
|
|
179
|
+
errors.append(
|
|
180
|
+
f" {slide_master.relative_to(self.unpacked_dir)}: "
|
|
181
|
+
f"Line {sld_layout_id.sourceline}: sldLayoutId with id='{layout_id}' "
|
|
182
|
+
f"references r:id='{r_id}' which is not found in slide layout relationships"
|
|
183
|
+
)
|
|
184
|
+
|
|
185
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
186
|
+
errors.append(
|
|
187
|
+
f" {slide_master.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
188
|
+
)
|
|
189
|
+
|
|
190
|
+
if errors:
|
|
191
|
+
print(f"FAILED - Found {len(errors)} slide layout ID validation errors:")
|
|
192
|
+
for error in errors:
|
|
193
|
+
print(error)
|
|
194
|
+
print(
|
|
195
|
+
"Remove invalid references or add missing slide layouts to the relationships file."
|
|
196
|
+
)
|
|
197
|
+
return False
|
|
198
|
+
else:
|
|
199
|
+
if self.verbose:
|
|
200
|
+
print("PASSED - All slide layout IDs reference valid slide layouts")
|
|
201
|
+
return True
|
|
202
|
+
|
|
203
|
+
def validate_no_duplicate_slide_layouts(self):
|
|
204
|
+
"""Validate that each slide has exactly one slideLayout reference."""
|
|
205
|
+
import lxml.etree
|
|
206
|
+
|
|
207
|
+
errors = []
|
|
208
|
+
slide_rels_files = list(self.unpacked_dir.glob("ppt/slides/_rels/*.xml.rels"))
|
|
209
|
+
|
|
210
|
+
for rels_file in slide_rels_files:
|
|
211
|
+
try:
|
|
212
|
+
root = lxml.etree.parse(str(rels_file)).getroot()
|
|
213
|
+
|
|
214
|
+
# Find all slideLayout relationships
|
|
215
|
+
layout_rels = [
|
|
216
|
+
rel
|
|
217
|
+
for rel in root.findall(
|
|
218
|
+
f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
|
|
219
|
+
)
|
|
220
|
+
if "slideLayout" in rel.get("Type", "")
|
|
221
|
+
]
|
|
222
|
+
|
|
223
|
+
if len(layout_rels) > 1:
|
|
224
|
+
errors.append(
|
|
225
|
+
f" {rels_file.relative_to(self.unpacked_dir)}: has {len(layout_rels)} slideLayout references"
|
|
226
|
+
)
|
|
227
|
+
|
|
228
|
+
except Exception as e:
|
|
229
|
+
errors.append(
|
|
230
|
+
f" {rels_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
231
|
+
)
|
|
232
|
+
|
|
233
|
+
if errors:
|
|
234
|
+
print("FAILED - Found slides with duplicate slideLayout references:")
|
|
235
|
+
for error in errors:
|
|
236
|
+
print(error)
|
|
237
|
+
return False
|
|
238
|
+
else:
|
|
239
|
+
if self.verbose:
|
|
240
|
+
print("PASSED - All slides have exactly one slideLayout reference")
|
|
241
|
+
return True
|
|
242
|
+
|
|
243
|
+
def validate_notes_slide_references(self):
|
|
244
|
+
"""Validate that each notesSlide file is referenced by only one slide."""
|
|
245
|
+
import lxml.etree
|
|
246
|
+
|
|
247
|
+
errors = []
|
|
248
|
+
notes_slide_references = {} # Track which slides reference each notesSlide
|
|
249
|
+
|
|
250
|
+
# Find all slide relationship files
|
|
251
|
+
slide_rels_files = list(self.unpacked_dir.glob("ppt/slides/_rels/*.xml.rels"))
|
|
252
|
+
|
|
253
|
+
if not slide_rels_files:
|
|
254
|
+
if self.verbose:
|
|
255
|
+
print("PASSED - No slide relationship files found")
|
|
256
|
+
return True
|
|
257
|
+
|
|
258
|
+
for rels_file in slide_rels_files:
|
|
259
|
+
try:
|
|
260
|
+
# Parse the relationships file
|
|
261
|
+
root = lxml.etree.parse(str(rels_file)).getroot()
|
|
262
|
+
|
|
263
|
+
# Find all notesSlide relationships
|
|
264
|
+
for rel in root.findall(
|
|
265
|
+
f".//{{{self.PACKAGE_RELATIONSHIPS_NAMESPACE}}}Relationship"
|
|
266
|
+
):
|
|
267
|
+
rel_type = rel.get("Type", "")
|
|
268
|
+
if "notesSlide" in rel_type:
|
|
269
|
+
target = rel.get("Target", "")
|
|
270
|
+
if target:
|
|
271
|
+
# Normalize the target path to handle relative paths
|
|
272
|
+
normalized_target = target.replace("../", "")
|
|
273
|
+
|
|
274
|
+
# Track which slide references this notesSlide
|
|
275
|
+
slide_name = rels_file.stem.replace(
|
|
276
|
+
".xml", ""
|
|
277
|
+
) # e.g., "slide1"
|
|
278
|
+
|
|
279
|
+
if normalized_target not in notes_slide_references:
|
|
280
|
+
notes_slide_references[normalized_target] = []
|
|
281
|
+
notes_slide_references[normalized_target].append(
|
|
282
|
+
(slide_name, rels_file)
|
|
283
|
+
)
|
|
284
|
+
|
|
285
|
+
except (lxml.etree.XMLSyntaxError, Exception) as e:
|
|
286
|
+
errors.append(
|
|
287
|
+
f" {rels_file.relative_to(self.unpacked_dir)}: Error: {e}"
|
|
288
|
+
)
|
|
289
|
+
|
|
290
|
+
# Check for duplicate references
|
|
291
|
+
for target, references in notes_slide_references.items():
|
|
292
|
+
if len(references) > 1:
|
|
293
|
+
slide_names = [ref[0] for ref in references]
|
|
294
|
+
errors.append(
|
|
295
|
+
f" Notes slide '{target}' is referenced by multiple slides: {', '.join(slide_names)}"
|
|
296
|
+
)
|
|
297
|
+
for slide_name, rels_file in references:
|
|
298
|
+
errors.append(f" - {rels_file.relative_to(self.unpacked_dir)}")
|
|
299
|
+
|
|
300
|
+
if errors:
|
|
301
|
+
print(
|
|
302
|
+
f"FAILED - Found {len([e for e in errors if not e.startswith(' ')])} notes slide reference validation errors:"
|
|
303
|
+
)
|
|
304
|
+
for error in errors:
|
|
305
|
+
print(error)
|
|
306
|
+
print("Each slide may optionally have its own slide file.")
|
|
307
|
+
return False
|
|
308
|
+
else:
|
|
309
|
+
if self.verbose:
|
|
310
|
+
print("PASSED - All notes slide references are unique")
|
|
311
|
+
return True
|
|
312
|
+
|
|
313
|
+
|
|
314
|
+
if __name__ == "__main__":
|
|
315
|
+
raise RuntimeError("This module should not be run directly.")
|