Change Log

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

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

Unreleased

1.8.0 - 2025-01-11

Removed

  • Support for Python 3.10.

Changed

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

1.6.0 - 2024-02-27

Added

  • Better MIMIC paragraph chunker using additional features from zensols.nlp.

  • CLI action to remove cached files.

Changed

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].

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

1.2.0 - 2023-06-09

Changed

  • Upgrade to zensols.mednlp 1.2.0.

  • Move admission sample to Admission persister.

  • Narrow body FeatureDocuments 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

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.