# Change Log

All notable changes to this project will be documented in this file.

The format is based on [Keep a Changelog](http://keepachangelog.com/)

and this project adheres to [Semantic Versioning](http://semver.org/).

## [Unreleased]

## [1.8.0] - 2025-01-11

### Removed

- Support for Python 3.10.

### Added

- Clinical [PubMedBert SBERT embeddings] configuration.

- [PyRuSH] Clincal clinical sententence chunker

### Changed

- Upgraded to [zensols.util] version 1.15.

## [1.7.0] - 2024-04-14

### Removed

- Deprecated feature document parser `mednlp_combine_medfirst_doc_parser` from

  resource library.

### Changed

- Renamed `MeddicalFeatureDocumentParser` to `MedCatFeatureDocumentParser`

  since the parser only adds MedCAT CUIs.

- Fixed the configured parser that adds both ScispaCy biomed entities and

  MedCAT CUIs in `mednlp_combine_biomed_doc_parser`.

- Separated combiner with non-combiner models in configuration space.  The

  non-combiners (biomed ScispaCy and MedCAT) are parses that are used in their

  respective combiners.  These are then used by a new composite parser that

  uses both (`mednlp_combine_biomed_doc_parser`).  Unit test case added for

  all configured parsers.

## [1.6.0] - 2024-02-27

### Added

- Added a ScispaCy biomedical document parser, which is enabled by setting

  `mednlp_default:doc_parser = mednlp_combine_biomed_doc_parser`.  This uses

  better linguistic features and detects more entity span(s).

### Changed

- Fixed normalize token and sentence/token indexes from being clobbered by

  combined medical parsers.

- Fixed numeric entity feature from the combined medical parser is non-zero

  for medical entities.

- Combined medical parser defines linguistic and medical features in the

  document parser object instance.

## [1.5.0] - 2023-12-05

### Changed

- Upgrade libraries: `numpy`, `lxml`, `scikitlearn`, `scipy`, `medcat`.

- Added `scispacy` dependency.

### Added

- Support for Python 3.11.

### Removed

- Support for Python 3.9.

## [1.4.1] - 2023-09-08

### Changed

- Fix unit tests using the model provided for the MedCAT tutorials.

- Re-enable GitHub workflow unit tests CI.

## [1.4.0] - 2023-08-16

Downstream moderate risk update release.

### Changed

- Switch order of medical specific and general spaCy language parsing and

  chunking.  Now the medical parser is the source parser and the default spaCy

  parser is the target in `MappingCombinerFeatureDocumentParser`.  This was

  done to get better sentence chunking as MedCAT (used in the medical parser)

  does not sentence chunk well as it was not designed for it.

- Upgrade to [zensols.util] 1.13.0

- Fix `cui2vec` weight archive re-download on each access.

- Mapping combiner default is to use token's character absolute index.

## [1.3.2] - 2023-06-29

### Added

- Feature document parser shortcut from application factory.

### Changed

- Resource library configuration to clean up model resources after download.

## [1.3.1] - 2023-06-27

### Changed

- Updated to [zensols.nlp] to 1.7.2 and use its new feature to auto load any

  missing spaCy base model(s).

- Remove configuration file requirement from the CLI.

- Fix spaCy dependency requirement to align with `scipy` and  [zensols.nlp].

## [1.3.0] - 2023-06-20

### Changed

- Fix contraction tokenization.  This was done by swapping the target and

  source parser in the `lang.conf:mednlp_combine_doc_parser` resource library

  configuration.

## [1.2.0] - 2023-06-09

### Changed

- Upgrade to [medcat] 1.7.0.

- Better UTS error handling with raised exceptions and messages.

## [1.1.0] - 2023-04-05

### Changed

- Install missing models and packages on start up.

- Updated [zensols.install] to 0.2.1

- Updated [zensols.nlp] to 1.6.0.

## [1.0.0] - 2023-02-02

### Changed

- Updated [zensols.util] to 1.12.1.

- Updated [zensols.nlp] to 1.5.0.

## [0.1.1] - 2022-10-02

### Removed

- Make scispacy optional and remove the dependency.  See the test cases in

  [test](test/entlink).

## [0.1.0] - 2022-10-01

### Added

- Unit test in GitHub CI.

### Changed

- Upgrade to spaCy 2.2, MedCAT 3.0, `zensols.nlp` 1.4.0.

- Make `cui2vec` a standard word embedding with vectorizer and layer.

- Replace entity splitter by not embedding named entities as default

  configuration.

### Removed

- Support for Python 3.7, 3.8 from dropped support in `zensols.util`.

## [0.0.2] - 2022-05-04

### Added

- A CSV features dump example.

### Changed

- Use token instead of sentence level mapping in cases where MedCAT creates

  unaligned sentence boundaries.

- Make medical parser stand-alone and use delegate mapping combiner instead of

  using a class hierarchy.

- Entity linker is now a token decorator.

- Protect against `unk` (unknown) keys in TUIs.

## [0.0.1] - 2022-01-30

### Added

- Initial version.

<!-- links -->

[Unreleased]: https://github.com/Paul Landes/mednlp/compare/v1.8.0...HEAD

[1.8.0]: https://github.com/Paul Landes/mednlp/compare/v1.7.0...v1.8.0

[1.7.0]: https://github.com/Paul Landes/mednlp/compare/v1.6.0...v1.7.0

[1.6.0]: https://github.com/Paul Landes/mednlp/compare/v1.5.0...v1.6.0

[1.5.0]: https://github.com/Paul Landes/mednlp/compare/v1.4.1...v1.5.0

[1.4.1]: https://github.com/Paul Landes/mednlp/compare/v1.4.0...v1.4.1

[1.4.0]: https://github.com/Paul Landes/mednlp/compare/v1.3.2...v1.4.0

[1.3.2]: https://github.com/Paul Landes/mednlp/compare/v1.3.1...v1.3.2

[1.3.1]: https://github.com/Paul Landes/mednlp/compare/v1.3.0...v1.3.1

[1.3.0]: https://github.com/Paul Landes/mednlp/compare/v1.2.0...v1.3.0

[1.2.0]: https://github.com/Paul Landes/mednlp/compare/v1.1.0...v1.2.0

[1.1.0]: https://github.com/Paul Landes/mednlp/compare/v1.0.0...v1.1.0

[1.0.0]: https://github.com/Paul Landes/mednlp/compare/v0.1.1...v1.0.0

[0.1.1]: https://github.com/Paul Landes/mednlp/compare/v0.1.0...v0.1.1

[0.1.0]: https://github.com/Paul Landes/mednlp/compare/v0.0.2...v0.1.0

[0.0.2]: https://github.com/Paul Landes/mednlp/compare/v0.0.1...v0.0.2

[0.0.1]: https://github.com/Paul Landes/mednlp/compare/v0.0.0...v0.0.1

[zensols.util]: https://github.com/plandes/util

[zensols.nlp]: https://github.com/plandes/nlparse

[zensols.install]: https://github.com/plandes/install

[medcat]: https://github.com/CogStack/MedCAT

[PyRuSH]: https://github.com/jianlins/PyRuSH

[PubMedBert SBERT embeddings]: https://huggingface.co/pritamdeka/S-PubMedBert-MS-MARCO