v1.0.10

What's Changed

• Catch ValueError in SPIRES engine when returned value is empty in a single line by @caufieldjh in #491
• Add phenopacket extraction template by @caufieldjh in #484
• Add codespell support (config, workflow to detect/not fix) and make it fix few typos by @yarikoptic in #493
• Move codespell into main qc workflow by @caufieldjh in #494
• Build out MIC extraction template by @caufieldjh in #495
• Prep for v1.0.10 by @caufieldjh in #496

New Contributors

• @yarikoptic made their first contribution in #493

Full Changelog: v1.0.9...v1.0.10

v1.0.9

What's Changed

• Explicitly load key for groq when needed by @caufieldjh in #486
• Fix openapi key required for loading ollama models by @dnlbauer in #488
• Prep for v1.0.9 by @caufieldjh in #489

New Contributors

• @dnlbauer made their first contribution in #488

Full Changelog: v1.0.8...v1.0.9

v1.0.8

What's Changed

• Fix #475 - Handle templates without descriptions by @caufieldjh in #476
• Update dependency on python-multipart and fastapi by @caufieldjh in #478
• Expand test matrix to include Python 3.9 to 3.12 by @caufieldjh in #479
• Add more error handling by catching specific litellm exceptions by @caufieldjh in #481
• Cleanup for v1.0.8 by @caufieldjh in #483

Full Changelog: v1.0.7...v1.0.8

v1.0.7

What's Changed

• Add initial version of micronutrient extraction template (and other new templates) by @caufieldjh in #469
• Add --target-class option to web_extract command by @ptgolden in #470
• Update pathology extraction template by @caufieldjh in #472
• Prep for v1.0.7 by @caufieldjh in #473

New Contributors

• @ptgolden made their first contribution in #470

Full Changelog: v1.0.6...v1.0.7

v1.0.6

What's Changed

• More updates for pathology report extraction by @caufieldjh in #461
• Add BioEPIC demo notebook by @caufieldjh in #463
• Provide spans of named entities by @caufieldjh in #464

Full Changelog: v1.0.5...v1.0.6

v1.0.5

What's Changed

• Suppress litellm debug messages by @caufieldjh in #448
• Expand option to set token/context limit by @caufieldjh in #449
• Dependency updates and adaptations by @caufieldjh in #453
• Improvements for pathology report extractions by @caufieldjh in #452
• Remove hardcoded values and references to gpt-3.5-turbo models by @caufieldjh in #458
• Removed pydantic_version keyword in template_loader.py by @gkreder in #459
• Prep for v1.0.5 by @caufieldjh in #460

New Contributors

• @gkreder made their first contribution in #459

Full Changelog: v1.0.4...v1.0.5

v1.0.4

What's Changed

• Add system-message command by @caufieldjh in #435
• Add topic classifier by @caufieldjh in #437
• Add new food extraction template by @caufieldjh in #441
• Further development of the pathology extraction template by @caufieldjh in #444
• Update output options for multilingual analysis by @caufieldjh in #442
• Refactor file loading/parsing; add support for spreadsheets as input by @caufieldjh in #447

Full Changelog: v1.0.3...v1.0.4

v1.0.3

What's Changed

• Add template for MIRO checklist extraction by @caufieldjh in #432
• Add caching for mapper by @caufieldjh in #433
• Prep for v1.0.3 by @caufieldjh in #434

Full Changelog: v1.0.2...v1.0.3

v1.0.2

What's Changed

• Added CSV exporter by @timalamenciak in #426
• Handle HTTP 500 errors with PubmedClient by @caufieldjh in #428
• Move eliminate_empty function into utils by @caufieldjh in #429
• Replace textract with pymupdf by @caufieldjh in #430
• Prep for V1.0.2 by @caufieldjh in #431

New Contributors

• @timalamenciak made their first contribution in #426

Full Changelog: v1.0.1...v1.0.2

v1.0.1

What's Changed

• Add docs section on OpenAI-compatible Proxy Servers by @caufieldjh in #419
• Partial fix for #417 by @caufieldjh in #422
• Add JSON writer by @caufieldjh in #423
• Updates for v1.0.1 by @caufieldjh in #424

Full Changelog: v1.0.0...v1.0.1