@synsci/cli-darwin-x64 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 +1,541 @@
|
|
|
1
|
+
# Dask Futures
|
|
2
|
+
|
|
3
|
+
## Overview
|
|
4
|
+
|
|
5
|
+
Dask futures extend Python's `concurrent.futures` interface, enabling immediate (non-lazy) task execution. Unlike delayed computations (used in DataFrames, Arrays, and Bags), futures provide more flexibility in situations where computations may evolve over time or require dynamic workflow construction.
|
|
6
|
+
|
|
7
|
+
## Core Concept
|
|
8
|
+
|
|
9
|
+
Futures represent real-time task execution:
|
|
10
|
+
- Tasks execute immediately when submitted (not lazy)
|
|
11
|
+
- Each future represents a remote computation result
|
|
12
|
+
- Automatic dependency tracking between futures
|
|
13
|
+
- Enables dynamic, evolving workflows
|
|
14
|
+
- Direct control over task scheduling and data placement
|
|
15
|
+
|
|
16
|
+
## Key Capabilities
|
|
17
|
+
|
|
18
|
+
### Real-Time Execution
|
|
19
|
+
- Tasks run immediately when submitted
|
|
20
|
+
- No need for explicit `.compute()` call
|
|
21
|
+
- Get results with `.result()` method
|
|
22
|
+
|
|
23
|
+
### Automatic Dependency Management
|
|
24
|
+
When you submit tasks with future inputs, Dask automatically handles dependency tracking. Once all input futures have completed, they will be moved onto a single worker for efficient computation.
|
|
25
|
+
|
|
26
|
+
### Dynamic Workflows
|
|
27
|
+
Build computations that evolve based on intermediate results:
|
|
28
|
+
- Submit new tasks based on previous results
|
|
29
|
+
- Conditional execution paths
|
|
30
|
+
- Iterative algorithms with varying structure
|
|
31
|
+
|
|
32
|
+
## When to Use Futures
|
|
33
|
+
|
|
34
|
+
**Use Futures When**:
|
|
35
|
+
- Building dynamic, evolving workflows
|
|
36
|
+
- Need immediate task execution (not lazy)
|
|
37
|
+
- Computations depend on runtime conditions
|
|
38
|
+
- Require fine control over task placement
|
|
39
|
+
- Implementing custom parallel algorithms
|
|
40
|
+
- Need stateful computations (with actors)
|
|
41
|
+
|
|
42
|
+
**Use Other Collections When**:
|
|
43
|
+
- Static, predefined computation graphs (use delayed, DataFrames, Arrays)
|
|
44
|
+
- Simple data parallelism on large collections (use Bags, DataFrames)
|
|
45
|
+
- Standard array/dataframe operations suffice
|
|
46
|
+
|
|
47
|
+
## Setting Up Client
|
|
48
|
+
|
|
49
|
+
Futures require a distributed client:
|
|
50
|
+
|
|
51
|
+
```python
|
|
52
|
+
from dask.distributed import Client
|
|
53
|
+
|
|
54
|
+
# Local cluster (on single machine)
|
|
55
|
+
client = Client()
|
|
56
|
+
|
|
57
|
+
# Or specify resources
|
|
58
|
+
client = Client(n_workers=4, threads_per_worker=2)
|
|
59
|
+
|
|
60
|
+
# Or connect to existing cluster
|
|
61
|
+
client = Client('scheduler-address:8786')
|
|
62
|
+
```
|
|
63
|
+
|
|
64
|
+
## Submitting Tasks
|
|
65
|
+
|
|
66
|
+
### Basic Submit
|
|
67
|
+
```python
|
|
68
|
+
from dask.distributed import Client
|
|
69
|
+
|
|
70
|
+
client = Client()
|
|
71
|
+
|
|
72
|
+
# Submit single task
|
|
73
|
+
def add(x, y):
|
|
74
|
+
return x + y
|
|
75
|
+
|
|
76
|
+
future = client.submit(add, 1, 2)
|
|
77
|
+
|
|
78
|
+
# Get result
|
|
79
|
+
result = future.result() # Blocks until complete
|
|
80
|
+
print(result) # 3
|
|
81
|
+
```
|
|
82
|
+
|
|
83
|
+
### Multiple Tasks
|
|
84
|
+
```python
|
|
85
|
+
# Submit multiple independent tasks
|
|
86
|
+
futures = []
|
|
87
|
+
for i in range(10):
|
|
88
|
+
future = client.submit(add, i, i)
|
|
89
|
+
futures.append(future)
|
|
90
|
+
|
|
91
|
+
# Gather results
|
|
92
|
+
results = client.gather(futures) # Efficient parallel gathering
|
|
93
|
+
```
|
|
94
|
+
|
|
95
|
+
### Map Over Inputs
|
|
96
|
+
```python
|
|
97
|
+
# Apply function to multiple inputs
|
|
98
|
+
def square(x):
|
|
99
|
+
return x ** 2
|
|
100
|
+
|
|
101
|
+
# Submit batch of tasks
|
|
102
|
+
futures = client.map(square, range(100))
|
|
103
|
+
|
|
104
|
+
# Gather results
|
|
105
|
+
results = client.gather(futures)
|
|
106
|
+
```
|
|
107
|
+
|
|
108
|
+
**Note**: Each task carries ~1ms overhead, making `map` less suitable for millions of tiny tasks. For massive datasets, use Bags or DataFrames instead.
|
|
109
|
+
|
|
110
|
+
## Working with Futures
|
|
111
|
+
|
|
112
|
+
### Check Status
|
|
113
|
+
```python
|
|
114
|
+
future = client.submit(expensive_function, arg)
|
|
115
|
+
|
|
116
|
+
# Check if complete
|
|
117
|
+
print(future.done()) # False or True
|
|
118
|
+
|
|
119
|
+
# Check status
|
|
120
|
+
print(future.status) # 'pending', 'running', 'finished', or 'error'
|
|
121
|
+
```
|
|
122
|
+
|
|
123
|
+
### Non-Blocking Result Retrieval
|
|
124
|
+
```python
|
|
125
|
+
# Non-blocking check
|
|
126
|
+
if future.done():
|
|
127
|
+
result = future.result()
|
|
128
|
+
else:
|
|
129
|
+
print("Still computing...")
|
|
130
|
+
|
|
131
|
+
# Or use callbacks
|
|
132
|
+
def handle_result(future):
|
|
133
|
+
print(f"Result: {future.result()}")
|
|
134
|
+
|
|
135
|
+
future.add_done_callback(handle_result)
|
|
136
|
+
```
|
|
137
|
+
|
|
138
|
+
### Error Handling
|
|
139
|
+
```python
|
|
140
|
+
def might_fail(x):
|
|
141
|
+
if x < 0:
|
|
142
|
+
raise ValueError("Negative value")
|
|
143
|
+
return x ** 2
|
|
144
|
+
|
|
145
|
+
future = client.submit(might_fail, -5)
|
|
146
|
+
|
|
147
|
+
try:
|
|
148
|
+
result = future.result()
|
|
149
|
+
except ValueError as e:
|
|
150
|
+
print(f"Task failed: {e}")
|
|
151
|
+
```
|
|
152
|
+
|
|
153
|
+
## Task Dependencies
|
|
154
|
+
|
|
155
|
+
### Automatic Dependency Tracking
|
|
156
|
+
```python
|
|
157
|
+
# Submit task
|
|
158
|
+
future1 = client.submit(add, 1, 2)
|
|
159
|
+
|
|
160
|
+
# Use future as input (creates dependency)
|
|
161
|
+
future2 = client.submit(add, future1, 10) # Depends on future1
|
|
162
|
+
|
|
163
|
+
# Chain dependencies
|
|
164
|
+
future3 = client.submit(add, future2, 100) # Depends on future2
|
|
165
|
+
|
|
166
|
+
# Get final result
|
|
167
|
+
result = future3.result() # 113
|
|
168
|
+
```
|
|
169
|
+
|
|
170
|
+
### Complex Dependencies
|
|
171
|
+
```python
|
|
172
|
+
# Multiple dependencies
|
|
173
|
+
a = client.submit(func1, x)
|
|
174
|
+
b = client.submit(func2, y)
|
|
175
|
+
c = client.submit(func3, a, b) # Depends on both a and b
|
|
176
|
+
|
|
177
|
+
result = c.result()
|
|
178
|
+
```
|
|
179
|
+
|
|
180
|
+
## Data Movement Optimization
|
|
181
|
+
|
|
182
|
+
### Scatter Data
|
|
183
|
+
Pre-scatter important data to avoid repeated transfers:
|
|
184
|
+
|
|
185
|
+
```python
|
|
186
|
+
# Upload data to cluster once
|
|
187
|
+
large_dataset = client.scatter(big_data) # Returns future
|
|
188
|
+
|
|
189
|
+
# Use scattered data in multiple tasks
|
|
190
|
+
futures = [client.submit(process, large_dataset, i) for i in range(100)]
|
|
191
|
+
|
|
192
|
+
# Each task uses the same scattered data without re-transfer
|
|
193
|
+
results = client.gather(futures)
|
|
194
|
+
```
|
|
195
|
+
|
|
196
|
+
### Efficient Gathering
|
|
197
|
+
Use `client.gather()` for concurrent result collection:
|
|
198
|
+
|
|
199
|
+
```python
|
|
200
|
+
# Better: Gather all at once (parallel)
|
|
201
|
+
results = client.gather(futures)
|
|
202
|
+
|
|
203
|
+
# Worse: Sequential result retrieval
|
|
204
|
+
results = [f.result() for f in futures]
|
|
205
|
+
```
|
|
206
|
+
|
|
207
|
+
## Fire-and-Forget
|
|
208
|
+
|
|
209
|
+
For side-effect tasks without needing the result:
|
|
210
|
+
|
|
211
|
+
```python
|
|
212
|
+
from dask.distributed import fire_and_forget
|
|
213
|
+
|
|
214
|
+
def log_to_database(data):
|
|
215
|
+
# Write to database, no return value needed
|
|
216
|
+
database.write(data)
|
|
217
|
+
|
|
218
|
+
# Submit without keeping reference
|
|
219
|
+
future = client.submit(log_to_database, data)
|
|
220
|
+
fire_and_forget(future)
|
|
221
|
+
|
|
222
|
+
# Dask won't abandon this computation even without active future reference
|
|
223
|
+
```
|
|
224
|
+
|
|
225
|
+
## Performance Characteristics
|
|
226
|
+
|
|
227
|
+
### Task Overhead
|
|
228
|
+
- ~1ms overhead per task
|
|
229
|
+
- Good for: Thousands of tasks
|
|
230
|
+
- Not suitable for: Millions of tiny tasks
|
|
231
|
+
|
|
232
|
+
### Worker-to-Worker Communication
|
|
233
|
+
- Direct worker-to-worker data transfer
|
|
234
|
+
- Roundtrip latency: ~1ms
|
|
235
|
+
- Efficient for task dependencies
|
|
236
|
+
|
|
237
|
+
### Memory Management
|
|
238
|
+
Dask tracks active futures locally. When a future is garbage collected by your local Python session, Dask will feel free to delete that data.
|
|
239
|
+
|
|
240
|
+
**Keep References**:
|
|
241
|
+
```python
|
|
242
|
+
# Keep reference to prevent deletion
|
|
243
|
+
important_result = client.submit(expensive_calc, data)
|
|
244
|
+
|
|
245
|
+
# Use result multiple times
|
|
246
|
+
future1 = client.submit(process1, important_result)
|
|
247
|
+
future2 = client.submit(process2, important_result)
|
|
248
|
+
```
|
|
249
|
+
|
|
250
|
+
## Advanced Coordination
|
|
251
|
+
|
|
252
|
+
### Distributed Primitives
|
|
253
|
+
|
|
254
|
+
**Queues**:
|
|
255
|
+
```python
|
|
256
|
+
from dask.distributed import Queue
|
|
257
|
+
|
|
258
|
+
queue = Queue()
|
|
259
|
+
|
|
260
|
+
def producer():
|
|
261
|
+
for i in range(10):
|
|
262
|
+
queue.put(i)
|
|
263
|
+
|
|
264
|
+
def consumer():
|
|
265
|
+
results = []
|
|
266
|
+
for _ in range(10):
|
|
267
|
+
results.append(queue.get())
|
|
268
|
+
return results
|
|
269
|
+
|
|
270
|
+
# Submit tasks
|
|
271
|
+
client.submit(producer)
|
|
272
|
+
result_future = client.submit(consumer)
|
|
273
|
+
results = result_future.result()
|
|
274
|
+
```
|
|
275
|
+
|
|
276
|
+
**Locks**:
|
|
277
|
+
```python
|
|
278
|
+
from dask.distributed import Lock
|
|
279
|
+
|
|
280
|
+
lock = Lock()
|
|
281
|
+
|
|
282
|
+
def critical_section():
|
|
283
|
+
with lock:
|
|
284
|
+
# Only one task executes this at a time
|
|
285
|
+
shared_resource.update()
|
|
286
|
+
```
|
|
287
|
+
|
|
288
|
+
**Events**:
|
|
289
|
+
```python
|
|
290
|
+
from dask.distributed import Event
|
|
291
|
+
|
|
292
|
+
event = Event()
|
|
293
|
+
|
|
294
|
+
def waiter():
|
|
295
|
+
event.wait() # Blocks until event is set
|
|
296
|
+
return "Event occurred"
|
|
297
|
+
|
|
298
|
+
def setter():
|
|
299
|
+
time.sleep(5)
|
|
300
|
+
event.set()
|
|
301
|
+
|
|
302
|
+
# Start both tasks
|
|
303
|
+
wait_future = client.submit(waiter)
|
|
304
|
+
set_future = client.submit(setter)
|
|
305
|
+
|
|
306
|
+
result = wait_future.result() # Waits for setter to complete
|
|
307
|
+
```
|
|
308
|
+
|
|
309
|
+
**Variables**:
|
|
310
|
+
```python
|
|
311
|
+
from dask.distributed import Variable
|
|
312
|
+
|
|
313
|
+
var = Variable('my-var')
|
|
314
|
+
|
|
315
|
+
# Set value
|
|
316
|
+
var.set(42)
|
|
317
|
+
|
|
318
|
+
# Get value from tasks
|
|
319
|
+
def reader():
|
|
320
|
+
return var.get()
|
|
321
|
+
|
|
322
|
+
future = client.submit(reader)
|
|
323
|
+
print(future.result()) # 42
|
|
324
|
+
```
|
|
325
|
+
|
|
326
|
+
## Actors
|
|
327
|
+
|
|
328
|
+
For stateful, rapidly-changing workflows, actors enable worker-to-worker roundtrip latency around 1ms while bypassing scheduler coordination.
|
|
329
|
+
|
|
330
|
+
### Creating Actors
|
|
331
|
+
```python
|
|
332
|
+
from dask.distributed import Client
|
|
333
|
+
|
|
334
|
+
client = Client()
|
|
335
|
+
|
|
336
|
+
class Counter:
|
|
337
|
+
def __init__(self):
|
|
338
|
+
self.count = 0
|
|
339
|
+
|
|
340
|
+
def increment(self):
|
|
341
|
+
self.count += 1
|
|
342
|
+
return self.count
|
|
343
|
+
|
|
344
|
+
def get_count(self):
|
|
345
|
+
return self.count
|
|
346
|
+
|
|
347
|
+
# Create actor on worker
|
|
348
|
+
counter = client.submit(Counter, actor=True).result()
|
|
349
|
+
|
|
350
|
+
# Call methods
|
|
351
|
+
future1 = counter.increment()
|
|
352
|
+
future2 = counter.increment()
|
|
353
|
+
result = counter.get_count().result()
|
|
354
|
+
print(result) # 2
|
|
355
|
+
```
|
|
356
|
+
|
|
357
|
+
### Actor Use Cases
|
|
358
|
+
- Stateful services (databases, caches)
|
|
359
|
+
- Rapidly changing state
|
|
360
|
+
- Complex coordination patterns
|
|
361
|
+
- Real-time streaming applications
|
|
362
|
+
|
|
363
|
+
## Common Patterns
|
|
364
|
+
|
|
365
|
+
### Embarrassingly Parallel Tasks
|
|
366
|
+
```python
|
|
367
|
+
from dask.distributed import Client
|
|
368
|
+
|
|
369
|
+
client = Client()
|
|
370
|
+
|
|
371
|
+
def process_item(item):
|
|
372
|
+
# Independent computation
|
|
373
|
+
return expensive_computation(item)
|
|
374
|
+
|
|
375
|
+
# Process many items in parallel
|
|
376
|
+
items = range(1000)
|
|
377
|
+
futures = client.map(process_item, items)
|
|
378
|
+
|
|
379
|
+
# Gather all results
|
|
380
|
+
results = client.gather(futures)
|
|
381
|
+
```
|
|
382
|
+
|
|
383
|
+
### Dynamic Task Submission
|
|
384
|
+
```python
|
|
385
|
+
def recursive_compute(data, depth):
|
|
386
|
+
if depth == 0:
|
|
387
|
+
return process(data)
|
|
388
|
+
|
|
389
|
+
# Split and recurse
|
|
390
|
+
left, right = split(data)
|
|
391
|
+
left_future = client.submit(recursive_compute, left, depth - 1)
|
|
392
|
+
right_future = client.submit(recursive_compute, right, depth - 1)
|
|
393
|
+
|
|
394
|
+
# Combine results
|
|
395
|
+
return combine(left_future.result(), right_future.result())
|
|
396
|
+
|
|
397
|
+
# Start computation
|
|
398
|
+
result_future = client.submit(recursive_compute, initial_data, 5)
|
|
399
|
+
result = result_future.result()
|
|
400
|
+
```
|
|
401
|
+
|
|
402
|
+
### Parameter Sweep
|
|
403
|
+
```python
|
|
404
|
+
from itertools import product
|
|
405
|
+
|
|
406
|
+
def run_simulation(param1, param2, param3):
|
|
407
|
+
# Run simulation with parameters
|
|
408
|
+
return simulate(param1, param2, param3)
|
|
409
|
+
|
|
410
|
+
# Generate parameter combinations
|
|
411
|
+
params = product(range(10), range(10), range(10))
|
|
412
|
+
|
|
413
|
+
# Submit all combinations
|
|
414
|
+
futures = [client.submit(run_simulation, p1, p2, p3) for p1, p2, p3 in params]
|
|
415
|
+
|
|
416
|
+
# Gather results as they complete
|
|
417
|
+
from dask.distributed import as_completed
|
|
418
|
+
|
|
419
|
+
for future in as_completed(futures):
|
|
420
|
+
result = future.result()
|
|
421
|
+
process_result(result)
|
|
422
|
+
```
|
|
423
|
+
|
|
424
|
+
### Pipeline with Dependencies
|
|
425
|
+
```python
|
|
426
|
+
# Stage 1: Load data
|
|
427
|
+
load_futures = [client.submit(load_data, file) for file in files]
|
|
428
|
+
|
|
429
|
+
# Stage 2: Process (depends on stage 1)
|
|
430
|
+
process_futures = [client.submit(process, f) for f in load_futures]
|
|
431
|
+
|
|
432
|
+
# Stage 3: Aggregate (depends on stage 2)
|
|
433
|
+
agg_future = client.submit(aggregate, process_futures)
|
|
434
|
+
|
|
435
|
+
# Get final result
|
|
436
|
+
result = agg_future.result()
|
|
437
|
+
```
|
|
438
|
+
|
|
439
|
+
### Iterative Algorithm
|
|
440
|
+
```python
|
|
441
|
+
# Initialize
|
|
442
|
+
state = client.scatter(initial_state)
|
|
443
|
+
|
|
444
|
+
# Iterate
|
|
445
|
+
for iteration in range(num_iterations):
|
|
446
|
+
# Compute update based on current state
|
|
447
|
+
state = client.submit(update_function, state)
|
|
448
|
+
|
|
449
|
+
# Check convergence
|
|
450
|
+
converged = client.submit(check_convergence, state)
|
|
451
|
+
if converged.result():
|
|
452
|
+
break
|
|
453
|
+
|
|
454
|
+
# Get final state
|
|
455
|
+
final_state = state.result()
|
|
456
|
+
```
|
|
457
|
+
|
|
458
|
+
## Best Practices
|
|
459
|
+
|
|
460
|
+
### 1. Pre-scatter Large Data
|
|
461
|
+
```python
|
|
462
|
+
# Upload once, use many times
|
|
463
|
+
large_data = client.scatter(big_dataset)
|
|
464
|
+
futures = [client.submit(process, large_data, i) for i in range(100)]
|
|
465
|
+
```
|
|
466
|
+
|
|
467
|
+
### 2. Use Gather for Bulk Retrieval
|
|
468
|
+
```python
|
|
469
|
+
# Efficient: Parallel gathering
|
|
470
|
+
results = client.gather(futures)
|
|
471
|
+
|
|
472
|
+
# Inefficient: Sequential
|
|
473
|
+
results = [f.result() for f in futures]
|
|
474
|
+
```
|
|
475
|
+
|
|
476
|
+
### 3. Manage Memory with References
|
|
477
|
+
```python
|
|
478
|
+
# Keep important futures
|
|
479
|
+
important = client.submit(expensive_calc, data)
|
|
480
|
+
|
|
481
|
+
# Use multiple times
|
|
482
|
+
f1 = client.submit(use_result, important)
|
|
483
|
+
f2 = client.submit(use_result, important)
|
|
484
|
+
|
|
485
|
+
# Clean up when done
|
|
486
|
+
del important
|
|
487
|
+
```
|
|
488
|
+
|
|
489
|
+
### 4. Handle Errors Appropriately
|
|
490
|
+
```python
|
|
491
|
+
futures = client.map(might_fail, inputs)
|
|
492
|
+
|
|
493
|
+
# Check for errors
|
|
494
|
+
results = []
|
|
495
|
+
errors = []
|
|
496
|
+
for future in as_completed(futures):
|
|
497
|
+
try:
|
|
498
|
+
results.append(future.result())
|
|
499
|
+
except Exception as e:
|
|
500
|
+
errors.append(e)
|
|
501
|
+
```
|
|
502
|
+
|
|
503
|
+
### 5. Use as_completed for Progressive Processing
|
|
504
|
+
```python
|
|
505
|
+
from dask.distributed import as_completed
|
|
506
|
+
|
|
507
|
+
futures = client.map(process, items)
|
|
508
|
+
|
|
509
|
+
# Process results as they arrive
|
|
510
|
+
for future in as_completed(futures):
|
|
511
|
+
result = future.result()
|
|
512
|
+
handle_result(result)
|
|
513
|
+
```
|
|
514
|
+
|
|
515
|
+
## Debugging Tips
|
|
516
|
+
|
|
517
|
+
### Monitor Dashboard
|
|
518
|
+
View the Dask dashboard to see:
|
|
519
|
+
- Task progress
|
|
520
|
+
- Worker utilization
|
|
521
|
+
- Memory usage
|
|
522
|
+
- Task dependencies
|
|
523
|
+
|
|
524
|
+
### Check Task Status
|
|
525
|
+
```python
|
|
526
|
+
# Inspect future
|
|
527
|
+
print(future.status)
|
|
528
|
+
print(future.done())
|
|
529
|
+
|
|
530
|
+
# Get traceback on error
|
|
531
|
+
try:
|
|
532
|
+
future.result()
|
|
533
|
+
except Exception:
|
|
534
|
+
print(future.traceback())
|
|
535
|
+
```
|
|
536
|
+
|
|
537
|
+
### Profile Tasks
|
|
538
|
+
```python
|
|
539
|
+
# Get performance data
|
|
540
|
+
client.profile(filename='profile.html')
|
|
541
|
+
```
|