@pikaa-ai/pikaa 0.3.1 → 0.3.4
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/dist/cli.js +1169 -601
- package/dist/index.js +525 -204
- package/package.json +5 -3
- package/skills/adaptyv/references/api-endpoints.md +0 -690
- package/skills/aeon/references/anomaly_detection.md +0 -154
- package/skills/aeon/references/classification.md +0 -144
- package/skills/aeon/references/clustering.md +0 -123
- package/skills/aeon/references/datasets_benchmarking.md +0 -392
- package/skills/aeon/references/distances.md +0 -256
- package/skills/aeon/references/forecasting.md +0 -109
- package/skills/aeon/references/networks.md +0 -289
- package/skills/aeon/references/regression.md +0 -118
- package/skills/aeon/references/segmentation.md +0 -163
- package/skills/aeon/references/similarity_search.md +0 -187
- package/skills/aeon/references/transformations.md +0 -246
- package/skills/analytical-method-validation/assets/validation-protocol-template.md +0 -106
- package/skills/analytical-method-validation/assets/validation-report-template.md +0 -116
- package/skills/analytical-method-validation/references/compendial-and-clsi.md +0 -96
- package/skills/analytical-method-validation/references/framework-selection.md +0 -87
- package/skills/analytical-method-validation/references/ich-m10-bioanalytical.md +0 -123
- package/skills/analytical-method-validation/references/ich-q2r2.md +0 -229
- package/skills/analytical-method-validation/references/source-ledger.md +0 -125
- package/skills/analytical-method-validation/references/statistics.md +0 -209
- package/skills/analytical-method-validation/scripts/_catalog.py +0 -499
- package/skills/analytical-method-validation/scripts/_common.py +0 -955
- package/skills/analytical-method-validation/scripts/check_accuracy_precision.py +0 -328
- package/skills/analytical-method-validation/scripts/check_bioanalytical_run.py +0 -293
- package/skills/analytical-method-validation/scripts/check_detection_limits.py +0 -310
- package/skills/analytical-method-validation/scripts/check_response.py +0 -243
- package/skills/analytical-method-validation/scripts/compare_methods.py +0 -215
- package/skills/analytical-method-validation/scripts/plan_validation.py +0 -381
- package/skills/anndata/references/best_practices.md +0 -532
- package/skills/anndata/references/concatenation.md +0 -399
- package/skills/anndata/references/data_structure.md +0 -314
- package/skills/anndata/references/io_operations.md +0 -466
- package/skills/anndata/references/manipulation.md +0 -516
- package/skills/arbor/references/arbor-upstream.md +0 -91
- package/skills/arbor/references/executor-brief.md +0 -68
- package/skills/arbor/references/htr-methodology.md +0 -177
- package/skills/arbor/references/report-template.md +0 -39
- package/skills/arbor/scripts/tree.py +0 -564
- package/skills/arboreto/references/algorithms.md +0 -152
- package/skills/arboreto/references/basic_inference.md +0 -181
- package/skills/arboreto/references/distributed_computing.md +0 -242
- package/skills/arboreto/scripts/basic_grn_inference.py +0 -107
- package/skills/astropy/references/coordinates.md +0 -280
- package/skills/astropy/references/cosmology.md +0 -309
- package/skills/astropy/references/fits.md +0 -398
- package/skills/astropy/references/tables.md +0 -495
- package/skills/astropy/references/time.md +0 -412
- package/skills/astropy/references/units.md +0 -178
- package/skills/astropy/references/wcs_and_other_modules.md +0 -377
- package/skills/autoskill/config.yaml +0 -53
- package/skills/autoskill/references/https-proxy.md +0 -62
- package/skills/autoskill/references/screenpipe-config.yaml +0 -61
- package/skills/autoskill/scripts/autoskill.py +0 -35
- package/skills/autoskill/scripts/backends.py +0 -116
- package/skills/autoskill/scripts/cluster.py +0 -54
- package/skills/autoskill/scripts/doctor.py +0 -108
- package/skills/autoskill/scripts/fetch_window.py +0 -33
- package/skills/autoskill/scripts/match_skills.py +0 -46
- package/skills/autoskill/scripts/promote.py +0 -58
- package/skills/autoskill/scripts/redact.py +0 -40
- package/skills/autoskill/scripts/run.py +0 -194
- package/skills/autoskill/scripts/synthesize.py +0 -72
- package/skills/benchling-integration/references/api_endpoints.md +0 -883
- package/skills/benchling-integration/references/authentication.md +0 -390
- package/skills/benchling-integration/references/core_capabilities.md +0 -355
- package/skills/benchling-integration/references/eventbridge.md +0 -255
- package/skills/benchling-integration/references/sdk_reference.md +0 -772
- package/skills/bids/references/beps.yml +0 -637
- package/skills/bids/references/bids_schema.json +0 -21015
- package/skills/bids/references/bids_specification.md +0 -165
- package/skills/bids/references/conversion_tools.md +0 -475
- package/skills/bids/references/core_workflows.md +0 -552
- package/skills/bids/references/metadata_fields.md +0 -365
- package/skills/bids/scripts/update_schema.py +0 -89
- package/skills/biopython/references/advanced.md +0 -580
- package/skills/biopython/references/alignment.md +0 -377
- package/skills/biopython/references/blast.md +0 -463
- package/skills/biopython/references/databases.md +0 -492
- package/skills/biopython/references/phylogenetics.md +0 -566
- package/skills/biopython/references/sequence_io.md +0 -289
- package/skills/biopython/references/structure.md +0 -564
- package/skills/bioservices/references/identifier_mapping.md +0 -685
- package/skills/bioservices/references/services_reference.md +0 -638
- package/skills/bioservices/references/workflow_patterns.md +0 -813
- package/skills/bioservices/scripts/batch_id_converter.py +0 -347
- package/skills/bioservices/scripts/compound_cross_reference.py +0 -387
- package/skills/bioservices/scripts/pathway_analysis.py +0 -309
- package/skills/bioservices/scripts/protein_analysis_workflow.py +0 -441
- package/skills/bulk-rnaseq/references/counts-and-handoff.md +0 -91
- package/skills/bulk-rnaseq/references/design-and-qc.md +0 -68
- package/skills/bulk-rnaseq/references/upstream-manual.md +0 -128
- package/skills/bulk-rnaseq/references/upstream-nfcore.md +0 -108
- package/skills/bulk-rnaseq/scripts/build_counts_matrix.py +0 -203
- package/skills/bulk-rnaseq/scripts/validate_samplesheet.py +0 -206
- package/skills/cellxgene-census/references/census_schema.md +0 -218
- package/skills/cellxgene-census/references/common_patterns.md +0 -368
- package/skills/cellxgene-census/references/core_workflow_patterns.md +0 -297
- package/skills/cirq/references/building.md +0 -307
- package/skills/cirq/references/experiments.md +0 -572
- package/skills/cirq/references/hardware.md +0 -527
- package/skills/cirq/references/noise.md +0 -514
- package/skills/cirq/references/simulation.md +0 -353
- package/skills/cirq/references/transformation.md +0 -416
- package/skills/citation-management/assets/bibtex_template.bib +0 -264
- package/skills/citation-management/assets/citation_checklist.md +0 -386
- package/skills/citation-management/references/best_practices.md +0 -91
- package/skills/citation-management/references/bibtex_formatting.md +0 -908
- package/skills/citation-management/references/citation_validation.md +0 -835
- package/skills/citation-management/references/core_workflow.md +0 -569
- package/skills/citation-management/references/example_workflows.md +0 -126
- package/skills/citation-management/references/google_scholar_search.md +0 -732
- package/skills/citation-management/references/metadata_extraction.md +0 -870
- package/skills/citation-management/references/pubmed_search.md +0 -839
- package/skills/citation-management/references/script_reference.md +0 -250
- package/skills/citation-management/references/search_strategies.md +0 -110
- package/skills/citation-management/scripts/_common.py +0 -331
- package/skills/citation-management/scripts/doi_to_bibtex.py +0 -204
- package/skills/citation-management/scripts/extract_metadata.py +0 -690
- package/skills/citation-management/scripts/format_bibtex.py +0 -356
- package/skills/citation-management/scripts/search_google_scholar.py +0 -268
- package/skills/citation-management/scripts/search_openalex.py +0 -297
- package/skills/citation-management/scripts/search_pubmed.py +0 -419
- package/skills/citation-management/scripts/validate_citations.py +0 -688
- package/skills/clinical-decision-support/assets/aggregate_cohort_table_template.json +0 -114
- package/skills/clinical-decision-support/assets/aggregate_model_evaluation_template.json +0 -115
- package/skills/clinical-decision-support/assets/artifact_intended_use_template.json +0 -81
- package/skills/clinical-decision-support/assets/decision_logic_traceability_template.json +0 -108
- package/skills/clinical-decision-support/assets/deidentification_checklist_template.json +0 -176
- package/skills/clinical-decision-support/assets/evidence_profile_template.json +0 -139
- package/skills/clinical-decision-support/assets/survival_analysis_plan_template.json +0 -134
- package/skills/clinical-decision-support/references/cohort_evaluation.md +0 -142
- package/skills/clinical-decision-support/references/decision_logic_traceability.md +0 -146
- package/skills/clinical-decision-support/references/evidence_profiles.md +0 -153
- package/skills/clinical-decision-support/references/model_biomarker_evaluation.md +0 -152
- package/skills/clinical-decision-support/references/privacy_and_disclosure.md +0 -144
- package/skills/clinical-decision-support/references/regulatory_and_governance.md +0 -104
- package/skills/clinical-decision-support/references/safety_and_scope.md +0 -103
- package/skills/clinical-decision-support/references/security_validation.md +0 -60
- package/skills/clinical-decision-support/references/sources.md +0 -119
- package/skills/clinical-decision-support/references/study_reporting.md +0 -134
- package/skills/clinical-decision-support/references/survival_analysis.md +0 -156
- package/skills/clinical-decision-support/scripts/_common.py +0 -223
- package/skills/clinical-decision-support/scripts/cohort_table_generator.py +0 -288
- package/skills/clinical-decision-support/scripts/decision_logic_traceability.py +0 -313
- package/skills/clinical-decision-support/scripts/deidentification_checklist.py +0 -260
- package/skills/clinical-decision-support/scripts/evidence_profile_check.py +0 -259
- package/skills/clinical-decision-support/scripts/model_biomarker_evaluation.py +0 -345
- package/skills/clinical-decision-support/scripts/survival_plan_validator.py +0 -294
- package/skills/clinical-decision-support/scripts/validate_cds_artifact.py +0 -269
- package/skills/clinical-reports/assets/adverse_event_aggregate_input_template.csv +0 -1
- package/skills/clinical-reports/assets/case_report_template.json +0 -43
- package/skills/clinical-reports/assets/clinical_trial_csr_template.json +0 -51
- package/skills/clinical-reports/assets/clinical_trial_results_template.json +0 -66
- package/skills/clinical-reports/assets/clinical_trial_safety_aggregate_template.json +0 -49
- package/skills/clinical-reports/assets/consistency_manifest_template.json +0 -15
- package/skills/clinical-reports/assets/deidentification_process_checklist.json +0 -56
- package/skills/clinical-reports/assets/lab_report_template.json +0 -36
- package/skills/clinical-reports/assets/pathology_report_template.json +0 -36
- package/skills/clinical-reports/assets/provenance_manifest_template.json +0 -17
- package/skills/clinical-reports/assets/quality_review_checklist.json +0 -34
- package/skills/clinical-reports/assets/radiology_report_template.json +0 -34
- package/skills/clinical-reports/assets/research_summary_template.json +0 -36
- package/skills/clinical-reports/assets/terminology_manifest_template.json +0 -11
- package/skills/clinical-reports/assets/trial_protocol_reporting_checklist.json +0 -70
- package/skills/clinical-reports/references/case_report_guidelines.md +0 -72
- package/skills/clinical-reports/references/clinical_trial_reporting.md +0 -97
- package/skills/clinical-reports/references/data_presentation.md +0 -92
- package/skills/clinical-reports/references/diagnostic_reports_standards.md +0 -76
- package/skills/clinical-reports/references/medical_terminology.md +0 -84
- package/skills/clinical-reports/references/privacy_and_deidentification.md +0 -84
- package/skills/clinical-reports/references/professional_review.md +0 -78
- package/skills/clinical-reports/references/report_type_routing.md +0 -57
- package/skills/clinical-reports/references/safety_reporting.md +0 -109
- package/skills/clinical-reports/references/sources.md +0 -75
- package/skills/clinical-reports/scripts/_common.py +0 -263
- package/skills/clinical-reports/scripts/check_deidentification.py +0 -298
- package/skills/clinical-reports/scripts/consistency_checker.py +0 -390
- package/skills/clinical-reports/scripts/format_adverse_events.py +0 -455
- package/skills/clinical-reports/scripts/generate_report_template.py +0 -115
- package/skills/clinical-reports/scripts/provenance_validator.py +0 -263
- package/skills/clinical-reports/scripts/terminology_validator.py +0 -277
- package/skills/clinical-reports/scripts/validate_case_report.py +0 -278
- package/skills/clinical-reports/scripts/validate_trial_report.py +0 -534
- package/skills/cobrapy/references/api_quick_reference.md +0 -665
- package/skills/cobrapy/references/workflows.md +0 -600
- package/skills/consciousness-council/references/advanced-configurations.md +0 -96
- package/skills/dask/references/arrays.md +0 -495
- package/skills/dask/references/bags.md +0 -468
- package/skills/dask/references/best-practices.md +0 -277
- package/skills/dask/references/dataframes.md +0 -370
- package/skills/dask/references/futures.md +0 -541
- package/skills/dask/references/schedulers.md +0 -517
- package/skills/database-lookup/references/addgene.md +0 -38
- package/skills/database-lookup/references/alphafold.md +0 -52
- package/skills/database-lookup/references/alphavantage.md +0 -261
- package/skills/database-lookup/references/bea.md +0 -409
- package/skills/database-lookup/references/bindingdb.md +0 -85
- package/skills/database-lookup/references/biogrid.md +0 -110
- package/skills/database-lookup/references/bls.md +0 -235
- package/skills/database-lookup/references/brenda.md +0 -71
- package/skills/database-lookup/references/cbioportal.md +0 -206
- package/skills/database-lookup/references/census.md +0 -251
- package/skills/database-lookup/references/chebi.md +0 -103
- package/skills/database-lookup/references/chembl.md +0 -80
- package/skills/database-lookup/references/clinicaltrials.md +0 -86
- package/skills/database-lookup/references/clinpgx.md +0 -64
- package/skills/database-lookup/references/clinvar.md +0 -91
- package/skills/database-lookup/references/cod.md +0 -121
- package/skills/database-lookup/references/cosmic.md +0 -59
- package/skills/database-lookup/references/dailymed.md +0 -65
- package/skills/database-lookup/references/database_selection_guide.md +0 -166
- package/skills/database-lookup/references/datacommons.md +0 -237
- package/skills/database-lookup/references/dbsnp.md +0 -143
- package/skills/database-lookup/references/disgenet.md +0 -52
- package/skills/database-lookup/references/drugbank.md +0 -54
- package/skills/database-lookup/references/ecb.md +0 -191
- package/skills/database-lookup/references/emdb.md +0 -37
- package/skills/database-lookup/references/ena.md +0 -372
- package/skills/database-lookup/references/encode.md +0 -47
- package/skills/database-lookup/references/ensembl.md +0 -539
- package/skills/database-lookup/references/epa.md +0 -232
- package/skills/database-lookup/references/eurostat.md +0 -237
- package/skills/database-lookup/references/fda.md +0 -64
- package/skills/database-lookup/references/federal-reserve.md +0 -216
- package/skills/database-lookup/references/fred.md +0 -297
- package/skills/database-lookup/references/gene-ontology.md +0 -147
- package/skills/database-lookup/references/geo.md +0 -130
- package/skills/database-lookup/references/gnomad.md +0 -93
- package/skills/database-lookup/references/gtex.md +0 -136
- package/skills/database-lookup/references/gwas-catalog.md +0 -46
- package/skills/database-lookup/references/hca.md +0 -35
- package/skills/database-lookup/references/hpo.md +0 -48
- package/skills/database-lookup/references/human-protein-atlas.md +0 -57
- package/skills/database-lookup/references/interpro.md +0 -120
- package/skills/database-lookup/references/jaspar.md +0 -50
- package/skills/database-lookup/references/kegg.md +0 -78
- package/skills/database-lookup/references/lincs-l1000.md +0 -68
- package/skills/database-lookup/references/materials-project.md +0 -123
- package/skills/database-lookup/references/metabolomics-workbench.md +0 -98
- package/skills/database-lookup/references/monarch.md +0 -46
- package/skills/database-lookup/references/mousemine.md +0 -40
- package/skills/database-lookup/references/nasa-exoplanet-archive.md +0 -112
- package/skills/database-lookup/references/nasa.md +0 -121
- package/skills/database-lookup/references/ncbi-gene.md +0 -64
- package/skills/database-lookup/references/ncbi-protein.md +0 -104
- package/skills/database-lookup/references/ncbi-taxonomy.md +0 -121
- package/skills/database-lookup/references/nist.md +0 -105
- package/skills/database-lookup/references/noaa.md +0 -199
- package/skills/database-lookup/references/omim.md +0 -114
- package/skills/database-lookup/references/opentargets.md +0 -459
- package/skills/database-lookup/references/openweathermap.md +0 -255
- package/skills/database-lookup/references/pdb.md +0 -121
- package/skills/database-lookup/references/pride.md +0 -74
- package/skills/database-lookup/references/pubchem.md +0 -145
- package/skills/database-lookup/references/quickgo.md +0 -45
- package/skills/database-lookup/references/reactome.md +0 -140
- package/skills/database-lookup/references/retrieval-contract.md +0 -123
- package/skills/database-lookup/references/rummageo.md +0 -32
- package/skills/database-lookup/references/sdss.md +0 -130
- package/skills/database-lookup/references/sec-edgar.md +0 -315
- package/skills/database-lookup/references/simbad.md +0 -405
- package/skills/database-lookup/references/sra.md +0 -149
- package/skills/database-lookup/references/string.md +0 -283
- package/skills/database-lookup/references/tcga-gdc.md +0 -58
- package/skills/database-lookup/references/treasury.md +0 -215
- package/skills/database-lookup/references/ucsc-genome.md +0 -135
- package/skills/database-lookup/references/uniprot.md +0 -283
- package/skills/database-lookup/references/usgs.md +0 -260
- package/skills/database-lookup/references/uspto.md +0 -130
- package/skills/database-lookup/references/who.md +0 -283
- package/skills/database-lookup/references/worldbank.md +0 -239
- package/skills/database-lookup/references/zinc.md +0 -202
- package/skills/datamol/references/conformers_module.md +0 -131
- package/skills/datamol/references/core_api.md +0 -136
- package/skills/datamol/references/core_workflows.md +0 -451
- package/skills/datamol/references/descriptors_viz.md +0 -195
- package/skills/datamol/references/fragments_scaffolds.md +0 -174
- package/skills/datamol/references/io_module.md +0 -112
- package/skills/datamol/references/reactions_data.md +0 -218
- package/skills/datamol/references/workflow_patterns.md +0 -104
- package/skills/deepchem/references/api_reference.md +0 -305
- package/skills/deepchem/references/core_capabilities.md +0 -276
- package/skills/deepchem/references/typical_workflows.md +0 -109
- package/skills/deepchem/references/workflows.md +0 -491
- package/skills/deepchem/scripts/graph_neural_network.py +0 -350
- package/skills/deepchem/scripts/predict_solubility.py +0 -223
- package/skills/deepchem/scripts/transfer_learning.py +0 -443
- package/skills/deepspot-m/references/api.md +0 -186
- package/skills/deepspot-m/references/whole_slide.md +0 -174
- package/skills/deeptools/assets/quick_reference.md +0 -65
- package/skills/deeptools/references/core_workflows.md +0 -134
- package/skills/deeptools/references/effective_genome_sizes.md +0 -118
- package/skills/deeptools/references/normalization_methods.md +0 -424
- package/skills/deeptools/references/tools_reference.md +0 -569
- package/skills/deeptools/references/workflows.md +0 -476
- package/skills/deeptools/scripts/validate_files.py +0 -195
- package/skills/deeptools/scripts/workflow_generator.py +0 -520
- package/skills/depmap/references/dependency_analysis.md +0 -178
- package/skills/dhdna-profiler/references/advanced-profiling.md +0 -72
- package/skills/diffdock/assets/batch_template.csv +0 -4
- package/skills/diffdock/assets/custom_inference_config.yaml +0 -94
- package/skills/diffdock/references/confidence_and_limitations.md +0 -182
- package/skills/diffdock/references/parameters_reference.md +0 -173
- package/skills/diffdock/references/workflows_examples.md +0 -401
- package/skills/diffdock/scripts/analyze_results.py +0 -346
- package/skills/diffdock/scripts/prepare_batch_csv.py +0 -257
- package/skills/diffdock/scripts/setup_check.py +0 -283
- package/skills/dnanexus-integration/references/app-development.md +0 -371
- package/skills/dnanexus-integration/references/authentication.md +0 -226
- package/skills/dnanexus-integration/references/configuration.md +0 -444
- package/skills/dnanexus-integration/references/data-operations.md +0 -474
- package/skills/dnanexus-integration/references/job-execution.md +0 -482
- package/skills/dnanexus-integration/references/operations-and-troubleshooting.md +0 -506
- package/skills/dnanexus-integration/references/python-sdk.md +0 -548
- package/skills/dnanexus-integration/references/sources.md +0 -168
- package/skills/dnanexus-integration/references/workflow-languages.md +0 -292
- package/skills/dnanexus-integration/scripts/inspect_dxpy.py +0 -366
- package/skills/dnanexus-integration/scripts/validate_dxapp.py +0 -796
- package/skills/docx/LICENSE.txt +0 -30
- package/skills/docx/scripts/__init__.py +0 -1
- package/skills/docx/scripts/accept_changes.py +0 -135
- package/skills/docx/scripts/comment.py +0 -368
- package/skills/docx/scripts/merge_runs.py +0 -310
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- package/skills/xlsx/scripts/office/schemas/microsoft/wml-cid-2016.xsd +0 -13
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-sdtdatahash-2020.xsd +0 -4
- package/skills/xlsx/scripts/office/schemas/microsoft/wml-symex-2015.xsd +0 -8
- package/skills/xlsx/scripts/office/soffice.py +0 -232
- package/skills/xlsx/scripts/office/validate.py +0 -173
- package/skills/xlsx/scripts/office/validators/__init__.py +0 -15
- package/skills/xlsx/scripts/office/validators/base.py +0 -875
- package/skills/xlsx/scripts/office/validators/docx.py +0 -466
- package/skills/xlsx/scripts/office/validators/pptx.py +0 -441
- package/skills/xlsx/scripts/office/validators/redlining.py +0 -299
- package/skills/xlsx/scripts/recalc.py +0 -308
- package/skills/zarr-python/references/api_reference.md +0 -162
- package/skills/zarr-python/references/chunking_and_compression.md +0 -138
- package/skills/zarr-python/references/integration.md +0 -147
- package/skills/zarr-python/references/performance_and_patterns.md +0 -198
- package/skills/zarr-python/references/storage_backends.md +0 -91
- package/skills/zarr-python/references/v3_migration.md +0 -127
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# Vision, OCR, and Azure Extraction
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This guide distinguishes four different features that are often conflated:
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1. Built-in image metadata/description
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2. Official `markitdown-ocr` vision plugin
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3. Azure Document Intelligence
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4. Azure Content Understanding
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All examples target MarkItDown 0.1.6.
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## Decision Guide
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| Requirement | Best fit |
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| Describe a standalone JPEG/PNG or images on PPTX slides | Built-in `llm_client` path |
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| Read text from PDF/DOCX/PPTX/XLSX embedded images | `markitdown-ocr` |
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| OCR scanned PDFs with Azure layout extraction | Document Intelligence |
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| Custom fields, YAML front matter, video, or richer multimodal analysis | Content Understanding |
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| Data must remain local | Use a separate local OCR/layout parser |
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None of the first four options is a local Tesseract workflow.
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## Data-Handling Rule
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Before using an external service:
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- Identify the exact provider, endpoint, region, account, and model/analyzer.
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- Tell the user which source bytes, images, audio, video, and prompts will leave the machine.
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- Confirm that the provider is approved for the source's classification and regulatory requirements.
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- Estimate cost and retention implications.
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- Send only the required files/pages.
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- Never log API keys, bearer tokens, source bytes, or full base64 payloads.
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## Built-in Image Descriptions
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The built-in JPEG/PNG and PPTX paths can call an OpenAI-compatible client. MarkItDown encodes image bytes as a data URI and calls:
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```text
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client.chat.completions.create(model=..., messages=...)
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```
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Install a reviewed client version:
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```bash
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```
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```python
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from markitdown import MarkItDown
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from openai import OpenAI
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# The SDK obtains only its named provider credential through its normal
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# configuration. The image and prompt are sent to that provider.
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client = OpenAI()
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converter = MarkItDown(
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llm_client=client,
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llm_model="gpt-4o",
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llm_prompt=(
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"Describe the scientific figure. Transcribe visible labels, identify "
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),
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)
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result = converter.convert_local("figure.png")
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print(result.markdown)
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```
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Use a provider/model approved by the user; model identifiers and availability are provider-specific.
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### Limitations
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## Official `markitdown-ocr` Plugin
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Version 0.1.6 introduced the official monorepo plugin. The published plugin version is 0.1.0.
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Install exact versions:
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```bash
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```
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Review discovery before activation:
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markitdown --list-plugins
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```
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Configure through Python:
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```python
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converter = MarkItDown(
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llm_client=OpenAI(),
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llm_model="gpt-4o",
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llm_prompt=(
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"Extract all visible text exactly. Preserve table rows, columns, "
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"symbols, signs, decimal points, and units. Do not summarize."
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),
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)
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result = converter.convert_local("scanned-paper.pdf")
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print(result.markdown)
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```
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### Supported plugin paths
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- DOCX embedded images
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- XLSX worksheet images
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OCR blocks are inserted using markers similar to:
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```text
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*[Image OCR]
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<extracted text>
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[End OCR]*
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The plugin README shows `--llm-client` and `--llm-model`, but MarkItDown 0.1.6's core CLI parser does not define those options. Use the Python API above rather than copying that CLI example.
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## Azure Document Intelligence
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Install:
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```bash
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```
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The converter sends the complete file to Azure's `prebuilt-layout` analyzer and requests Markdown output. For PDF/images it enables formula extraction, high-resolution OCR, and font-style analysis.
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### Authentication
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### CLI
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--use-docintel \
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--endpoint "https://RESOURCE.cognitiveservices.azure.com/" \
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```
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### Python
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converter = MarkItDown(
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Restrict routing:
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```python
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from markitdown.converters import DocumentIntelligenceFileType
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DocumentIntelligenceFileType.PDF,
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Supported enum values include DOCX, PPTX, XLSX, HTML, PDF, JPEG, PNG, BMP, and TIFF. The default list excludes HTML.
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The 0.1.6 default Document Intelligence API version is `2024-07-31-preview`; override it with `docintel_api_version` only after checking Azure compatibility.
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## Azure Content Understanding
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Install:
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```bash
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```
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Content Understanding provides:
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- Prebuilt analyzer auto-routing
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- Optional custom analyzers
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- One endpoint across supported modalities
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Every routed `convert()`/`convert_local()` call is an Azure API call and may be billable.
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### CLI
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```bash
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markitdown interview.mp4 \
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--use-cu \
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--cu-endpoint "https://RESOURCE.cognitiveservices.azure.com/" \
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--cu-file-types mp4 \
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```
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With a custom analyzer:
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```bash
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markitdown invoice.pdf \
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--use-cu \
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--cu-endpoint "https://RESOURCE.cognitiveservices.azure.com/" \
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--cu-analyzer "my-invoice-analyzer" \
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--cu-file-types pdf \
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-o invoice.md
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```
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### Python
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from markitdown import MarkItDown
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from markitdown.converters import ContentUnderstandingFileType
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converter = MarkItDown(
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cu_endpoint="https://RESOURCE.cognitiveservices.azure.com/",
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cu_file_types=[
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ContentUnderstandingFileType.PDF,
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result = converter.convert_local("report.pdf")
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print(result.markdown)
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```
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Custom analyzer:
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```python
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converter = MarkItDown(
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cu_endpoint="https://RESOURCE.cognitiveservices.azure.com/",
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cu_credential=DefaultAzureCredential(),
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cu_analyzer_id="my-contract-analyzer",
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cu_file_types=[ContentUnderstandingFileType.PDF],
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)
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```
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When the custom analyzer's modality is incompatible with an input, the converter falls back to the matching prebuilt analyzer.
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### Default prebuilt routing
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| Modality | Analyzer |
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|---|---|
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| Document | `prebuilt-documentSearch` |
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| Image | `prebuilt-documentSearch` |
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| Audio | `prebuilt-audioSearch` |
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| Video | `prebuilt-videoSearch` |
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## Choosing Between Azure Services
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| Capability | Built-in | Document Intelligence | Content Understanding |
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|---|---|---|---|
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| Local text extraction | Yes | No | No |
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| Scanned PDF OCR | No | Yes | Yes |
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| Office conversion | Yes | Yes | Yes |
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| Structured custom fields | No | Not exposed by this integration | Yes |
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| Video | No | No | Yes |
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| Custom analyzer | No | Not exposed by this integration | Yes |
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| YAML field front matter | No | No | Yes |
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| External cost | No for local-only paths | Yes | Yes |
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## Validation for OCR/Cloud Output
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1. Record the package/plugin version, provider, model/analyzer, endpoint region, and date.
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2. Compare a sample of pages against the source.
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3. Check minus signs, decimal points, Greek letters, superscripts, units, and table boundaries.
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4. Flag uncertain or illegible spans instead of silently normalizing them.
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5. Reconcile page counts and section headings.
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6. Keep the original artifact and provider response provenance.
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## Sources
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- MarkItDown 0.1.6 guide: https://github.com/microsoft/markitdown/blob/v0.1.6/README.md
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- OCR plugin 0.1.0: https://github.com/microsoft/markitdown/tree/v0.1.6/packages/markitdown-ocr
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- Document Intelligence converter: https://github.com/microsoft/markitdown/blob/v0.1.6/packages/markitdown/src/markitdown/converters/_doc_intel_converter.py
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# File Formats and Conversion Behavior
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This reference targets Microsoft MarkItDown 0.1.6. "Built-in" means the converter ships in the `markitdown` package; some built-ins still require an optional dependency extra.
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## Installation by Format
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```bash
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# Full built-in feature set
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uv pip install "markitdown[all]==0.1.6"
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# Common document subset
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uv pip install "markitdown[pdf,docx,pptx,xlsx]==0.1.6"
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# Minimal package; suitable for core text/HTML/CSV/ZIP/EPUB/IPYNB paths
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uv pip install "markitdown==0.1.6"
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```
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## Built-in Converter Matrix
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| Input | Typical extensions/source | Extra | Main behavior | Important limitations/network |
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| Plain text | `.txt`, `.md`, recognized text, JSON/XML text | Core | Decodes text while preserving content | JSON/XML are not guaranteed to be normalized or pretty-printed |
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| CSV | `.csv`, `text/csv` | Core | Dedicated CSV-to-Markdown table conversion | Very wide/large tables can create large Markdown |
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| HTML | `.html`, `.htm` | Core | Headings, links, lists, tables, and readable text | CSS layout, client-side rendering, and visual fidelity are not preserved |
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| RSS/Atom-like XML | feed content/URLs | Core | Feed-focused Markdown | Remote retrieval uses network if a URI is supplied |
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| Wikipedia page | Wikipedia URL | Core | Page-oriented Markdown | Network; URL-specific converter |
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| Bing result page | Bing search-result URL | Core | Search-result-oriented Markdown | Network; HTML and service behavior can change |
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| YouTube | `https://www.youtube.com/watch?...` | `youtube-transcription` for transcript | Metadata, description, and available transcript | Fetches YouTube page/transcript; captions may be absent or restricted |
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| ZIP | `.zip` | Core | Iterates members and invokes nested converters | Treat untrusted archives as hostile; output can expand substantially |
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| EPUB | `.epub` | Core | Book metadata and structured text | Complex styling, fixed layout, DRM, and interactive content are not preserved |
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| Jupyter Notebook | `.ipynb` | Core | Notebook cells and content to Markdown | Runtime state is not reproduced; cells remain inert text during conversion |
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| PDF | `.pdf` | `pdf` | Extracts existing text and tables | No built-in local OCR for scanned pages; multi-column order and complex tables require validation |
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| Word | `.docx` | `docx` | Headings, lists, links, tables, images/alt text, and OMML math | Track changes, floating layout, and visual pagination are not faithfully reproduced |
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| PowerPoint | `.pptx` | `pptx` | Slide text, tables, notes, and shape ordering | Animations and layout fidelity are lost; image description requires an LLM client |
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| Excel | `.xlsx` | `xlsx` | Worksheets rendered as Markdown tables | Formulas, charts, merged cells, and formatting require source-level validation |
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| Legacy Excel | `.xls` | `xls` | Worksheets rendered as Markdown tables | Legacy parser limitations; no visual workbook fidelity |
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| Outlook message | `.msg` | `outlook` | Message headers and body | Attachments and rich formatting may need separate handling |
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| Image | `.jpg`, `.jpeg`, `.png` | Core | Selected ExifTool metadata; optional LLM description | Built-in converter does not locally OCR text; image may be sent to an external LLM |
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| Audio/video-audio | `.wav`, `.mp3`, `.m4a`, `.mp4` | `audio-transcription` | Metadata plus speech transcript | Transcription uses Google Web Speech through `SpeechRecognition`; content leaves the machine |
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### Formats commonly overstated
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- The 0.1.6 built-in `ImageConverter` accepts JPEG and PNG, not GIF or WebP.
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- Built-in PDF conversion extracts a text layer; Tesseract is not part of MarkItDown's PDF path.
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- The package does not promise page ranges, bounding boxes, coordinates, or pixel-faithful output.
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- JSON and XML are text-based inputs, not schema-aware transformations.
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- A successful conversion does not imply complete figure, equation, table, or reading-order recovery.
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## PDF
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### Built-in extraction
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```python
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from markitdown import MarkItDown
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result = MarkItDown().convert_local("paper.pdf")
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print(result.markdown)
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```
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Use for born-digital PDFs where text is selectable. MarkItDown 0.1.5 improved aligned/wide table output and partially numbered lists; 0.1.6 fixed linear memory growth across PDF pages.
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### Scanned PDFs
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Choose one:
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1. `markitdown-ocr==0.1.0` with an approved vision provider
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2. Azure Document Intelligence
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3. Azure Content Understanding
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4. A local OCR/layout parser when content cannot leave the environment
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Do not claim OCR was performed unless the selected path actually supplied it.
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### Validate
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- Reading order in multi-column papers
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- Equations, superscripts, and symbols
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- Table headers and row alignment
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- Figure captions and footnotes
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- References and hyperlinks
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- Missing pages or empty scanned sections
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## DOCX
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Install:
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```
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Version 0.1.2 added DOCX math-equation rendering. Conversion is semantic, not page-layout preserving.
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Validate:
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- Tracked changes and comments
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For custom Mammoth mapping:
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converter = MarkItDown(style_map="p[style-name='Abstract'] => blockquote.abstract")
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result = converter.convert_local("manuscript.docx")
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```
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## PPTX
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Install:
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```
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The converter orders shapes to approximate reading order and extracts textual slide content. Optional `llm_client`, `llm_model`, and `llm_prompt` values can describe image content.
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Validate:
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- Speaker notes
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- Content conveyed only by position, color, or animation
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## XLSX and XLS
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```
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The result is useful for textual review and LLM ingestion, but it is not a workbook round trip.
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Validate:
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- Charts, images, comments, and conditional formatting
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For numeric analysis, read the workbook directly with a dataframe or spreadsheet library after using MarkItDown for orientation.
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## Images
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The built-in converter supports `.jpg`, `.jpeg`, and `.png`.
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Without an LLM client, output may contain only selected metadata and can be empty when ExifTool is unavailable or the file has no relevant metadata.
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```python
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result = MarkItDown(exiftool_path="/opt/homebrew/bin/exiftool").convert_local(
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"figure.png"
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```
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Use only a trusted ExifTool executable. MarkItDown 0.1.3 added a safety requirement for ExifTool 12.24 or later.
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Vision descriptions and OCR are external-processing paths; see `cloud_and_ocr.md`.
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## Audio
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Accepted extensions are `.wav`, `.mp3`, `.m4a`, and `.mp4`.
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```
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The implementation converts supported audio to a `SpeechRecognition` input and calls `recognize_google()`. This is not offline transcription. Obtain approval before converting confidential recordings.
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The converter does not provide speaker diarization, timestamps, confidence values, or domain adaptation.
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## YouTube
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```
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Behavior:
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- Downloads the page
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- Extracts title, description, and selected metadata
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- Requests an available transcript
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- Prefers English, then an available language, with translation fallback
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Availability depends on YouTube, the video, geography, cookies/network policy, and transcript permissions.
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## CSV, JSON, and XML
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CSV has a dedicated table converter:
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result = MarkItDown().convert_local("measurements.csv")
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```
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JSON and XML are generally handled as text-like formats. If downstream work needs validated records, parse with `json`, `defusedxml`, or a schema-aware library rather than parsing the generated Markdown.
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## ZIP and EPUB
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ZIP conversion invokes MarkItDown recursively for archive members. Apply:
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- Maximum archive size
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- Maximum member count
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- Maximum nested depth
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- Compression-ratio limits
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Do not use conversion as an archive-security boundary.
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EPUB conversion targets textual book structure. DRM-protected or fixed-layout publications may fail or lose essential visual information.
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## Remote and Special Sources
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`convert_uri()` accepts:
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- `file:`
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- `data:`
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- `http:`
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- `https:`
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`file:` and `data:` are still potentially dangerous when user-controlled. `http:` and `https:` require SSRF, redirect, size, and timeout controls. See `security.md`.
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## Azure Document Intelligence Format Set
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The 0.1.6 integration supports:
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- Documents: DOCX, PPTX, XLSX
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- OCR/layout: PDF, JPEG, PNG, BMP, TIFF
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- HTML is represented in the enum but is not in the converter's default file-type list
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The default API version is `2024-07-31-preview`. Document bytes are sent to Azure.
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## Azure Content Understanding Format Set
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The 0.1.6 integration can route:
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- Documents: PDF, DOCX, PPTX, XLSX, HTML, TXT, Markdown, RTF, XML
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- Email: EML, MSG
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- Images: JPEG, PNG, BMP, TIFF, HEIF/HEIC
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- Video: MP4, M4V, MOV, AVI, MKV, WebM, FLV, WMV
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- Audio: WAV, MP3, M4A, FLAC, OGG, AAC, WMA
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Support here means Azure Content Understanding routing, not local built-in parsing. Each routed conversion is an external, potentially billable operation.
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## Format Hints
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When bytes lack a meaningful filename:
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```python
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from markitdown import MarkItDown, StreamInfo
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with open("upload.bin", "rb") as stream:
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result = MarkItDown().convert_stream(
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stream,
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stream_info=StreamInfo(
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extension=".pdf",
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mimetype="application/pdf",
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filename="upload.pdf",
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),
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```
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CLI equivalents:
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```bash
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```
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## Source Basis
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- Official 0.1.6 README: https://github.com/microsoft/markitdown/blob/v0.1.6/README.md
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- Built-in converter registry: https://github.com/microsoft/markitdown/blob/v0.1.6/packages/markitdown/src/markitdown/_markitdown.py
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- Release history: https://github.com/microsoft/markitdown/releases
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