v1.0.13

What's Changed

• Fix for edge cases with creating new LLMClient and SPIRESEngine by @caufieldjh in #520
• Prep for 1.0.13 by @caufieldjh in #521

Full Changelog: v1.0.12...v1.0.13

v1.0.12

What's Changed

• Improve handling of missing root class definition by @caufieldjh in #514
• Prep for v1.0.12 by @caufieldjh in #515

Full Changelog: v1.0.11...v1.0.12

v1.0.11

What's Changed

• draft schemas for table extraction by @realmarcin in #501
• Improvements for the biotic interaction extraction template by @caufieldjh in #503
• CLI cleanup by @caufieldjh in #506
• Refresh dependencies and update re: poetry dev group by @caufieldjh in #508
• Fix errors in CLI by @caufieldjh in #509
• Updates to MIC extraction template by @caufieldjh in #504
• Bump version to 1.0.11 by @caufieldjh in #510

Full Changelog: v1.0.10...v1.0.11

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