# 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.

### Changed
- Upgraded to [zensols.mednlp] version 1.8.0.


## [1.7.1] - 2024-05-11
### Added
- Database count database methods in persistence layer.
- Name to ID and ID to name transform methods for notes and sections.
- Admission listing by note count.
- Get note IDs by `hadm_id` and category.

### Changes
- Fix admission existence checks.


## [1.7.0] - 2024-04-14
### Changed
- Upgrade to [zensols.mednlp] 1.7.0.


## [1.6.0] - 2024-02-27
### Added
- Better MIMIC paragraph chunker using additional features from [zensols.nlp].
- CLI action to remove cached files.

### Changed
- Upgrade to [zensols.mednlp] 1.6.0.


## [1.5.2] - 2024-02-08
### Removed
- The [zensols.dbpg] dependency for PostgreSQL MIMIC-III DB access.

### Changed
- SQLite is now the default database for MIMIC-III DB access.  This removes
  this package [zensols.mimicsid] from needing the PostgreSQL driver from being
  install.


## [1.5.1] - 2024-01-17
### Changed
- Fix "missing `zensols.dbpg` package error" by pinning requirements to
  PostgreSQL db package as there is no clean way of separating the DB access
  logic without a large overhaul.


## [1.5.0] - 2023-12-05
### Changed
- Upgrade to [zensols.mednlp] version 1.5.0.
- Fix SQLite admission ID types.

### Added
- Support for Python 3.11.
- Added note ID access for admissions.

### Removed
- Support for Python 3.9.


## [1.4.3] - 2023-09-08
### Removed
- `NoteFactor`'s `section` parameter has been removed in favor of creating
  default notes with `create_default`.  This is a lower risk change given how
  deep in the framework this class is used.

### Added
- A new `DefaultNoteFactory` that always creates default/no-section notes.

### Changed
- Faster note to admission ID resolution in database for faster preemptive note
  parsing.
- `NoteFactory.create_default` to create new default/no-section notes.


## [1.4.2] - 2023-08-25
### Changed
- Switch to `MultiProcessDefaultStash`, which allows for swapping in other
  multiprocessing implementations.


## [1.4.1] - 2023-08-16
### Changed
- PostreSQL is now optional, and to use it, the [zensols.dbpg] needs to be
  installed (see the [README](README.md)].


## [1.4.0] - 2023-08-15
Downstream moderate risk update release.

### Changes
- A cleaner CLI for MIMIC note access.
- Default to section based `Note.write`.
- `NoteStash` is now primed by upstream stashes for [zensols.mimicsid] MedSecId
  model install.
- Tokenzier separates on commas to find more MIMIC-III masks.
- More MIMIC-III mask tags created and others regular expressions fixed.
- Update to [zensols.mednlp] 1.4.0.

### Added
- SQLite support for the MIMIC-III database.
- Feature to clear cached notes from the `Corpus` class.
- CLI actions to write an admission to disk an to get random `hadm_ids`.


## [1.3.1] - 2023-06-25
### Changed
- Add default and settings for changing the MIMIC-III database name.


## [1.3.0] - 2023-06-20
### Changed
- Upgrade to [zensols.mednlp] 1.3.0.


## [1.2.0] - 2023-06-09
### Changed
- Upgrade to [zensols.mednlp] 1.2.0.
- Move admission sample to `Admission` persister.
- Narrow body `FeatureDocument`s using right exclusive spans.

### Added
- `Note.annotator` property.
- `Note` and `Admission` accessors to `Corpus` container class.
- SQL `Note` counts.


## [1.1.0] - 2023-04-05
### Changed
- MIMIC notes write changes
- Move application methods from `Corpus` to the application.
- Fixed procedure data to hospital admission class.


### Changed
- Admission and note write semantics.


## [1.0.0] - 2023-02-02
### Changed
- Updated [zensols.mednlp] to 1.0.0.


## [0.1.1] - 2022-10-02
### Changed
- Upgrade dependencies.


## [0.1.0] - 2022-10-01
Significant feature release.

### Added
- Special MIMIC-III tokenization to deal with pseudo tokens.
- Add spaCy `._.` token features extracted from MIMIC-III pseudo tokens.
- Combine [zensols.mednlp] document parser with MIMIC-III features.
- Build out MIMIC-III container classes.
- Add section and paragraph segmentation code and container classes.
- Add reusable/shared data space for parsed documents.
- Add Postgres database support.


## [0.0.1] - 2022-05-04
### Added
- Initial version.


<!-- links -->
[Unreleased]: https://github.com/plandes/mimic/compare/v1.8.0...HEAD
[1.8.0]: https://github.com/plandes/mimic/compare/v1.7.1...v1.8.0
[1.7.1]: https://github.com/plandes/mimic/compare/v1.7.0...v1.7.1
[1.7.0]: https://github.com/plandes/mimic/compare/v1.6.0...v1.7.0
[1.6.0]: https://github.com/plandes/mimic/compare/v1.5.2...v1.6.0
[1.5.2]: https://github.com/plandes/mimic/compare/v1.5.1...v1.5.2
[1.5.1]: https://github.com/plandes/mimic/compare/v1.5.0...v1.5.1
[1.5.0]: https://github.com/plandes/mimic/compare/v1.4.3...v1.5.0
[1.4.3]: https://github.com/plandes/mimic/compare/v1.4.2...v1.4.3
[1.4.2]: https://github.com/plandes/mimic/compare/v1.4.1...v1.4.2
[1.4.1]: https://github.com/plandes/mimic/compare/v1.4.0...v1.4.1
[1.4.0]: https://github.com/plandes/mimic/compare/v1.3.1...v1.4.0
[1.3.1]: https://github.com/plandes/mimic/compare/v1.3.0...v1.3.1
[1.3.0]: https://github.com/plandes/mimic/compare/v1.2.0...v1.3.0
[1.2.0]: https://github.com/plandes/mimic/compare/v1.1.0...v1.2.0
[1.1.0]: https://github.com/plandes/mimic/compare/v1.0.0...v1.1.0
[1.0.0]: https://github.com/plandes/mimic/compare/v0.1.1...v1.0.0
[0.1.1]: https://github.com/plandes/mimic/compare/v0.1.0...v0.1.1
[0.1.0]: https://github.com/plandes/mimic/compare/v0.0.1...v0.1.0
[0.0.1]: https://github.com/plandes/mimic/compare/v0.0.0...v0.0.1

[zensols.mednlp]: https://github.com/plandes/mednlp
[zensols.mimicsid]: https://github.com/plandes/mimicsid
[zensols.dbpg]: https://github.com/plandes/dbutilpg
[zensols.nlp]:  https://github.com/plandes/nlparse