Biomedicus

Support for deploying the e2e pipeline using the docker image.

Added the End-to-end REST pipeline service, described here: https://nlpie.github.io/biomedicus/docs/deploy-pipeline.html.

What's Changed

* Updated concepts to UMLS 2023AA
* Fixed an issue with overlapping annotations for the same concepts
* Dependency Updates

Breaking Changes
* Removed support for Python 3.8 from biomedicus (deprecated, numpy no longer receiving updates on 3.8)

**Full Changelog**: https://github.com/nlpie/biomedicus/compare/v3.2.1...v3.3.0

What's Changed
- Dependency Updates (Torch 2.0, rocksdb 8.0)
- Supports Python 3.8-3.11 now
- Switched to performing negation detection using only negex by default.
- Updated to [MTAP 1.2.1](https://github.com/nlpie/mtap/releases/tag/v1.2.1). This introduces some breaking changes, click on the link for more info.
- Moved everything in biomedicus_client.pipeline to biomedicus_client package.
- Renamed some built-in pipeline and deployment configuration files (-conf.yml to .yml)

**Release Milestone**: https://github.com/nlpie/biomedicus/milestone/15?closed=1
**Full Changelog**: https://github.com/nlpie/biomedicus/compare/v3.1.0...v3.2.1

What's Changed
* Dependencies for release versions are now pinned for more stable releases.
* Fix for a number of RTF reader formatting issues. (140, 141)
* Fixed an issue where the sentences processor would fail when CUDA is available (142)
* Fixed an issue where deepen was failing due to incorrect offset indices on dependencies (138)

**Full Changelog**: https://github.com/nlpie/biomedicus/compare/v3.0.0...v3.1.0

Initial public release.