Bump version: 1.3.2 → 1.4.0

AstraZeneca · Dec 1, 2023 · ddca57f · ddca57f
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -7,6 +7,30 @@ and this project adheres to [Semantic Versioning](http://semver.org/).
 
 <!-- towncrier release notes start -->
 
+## 1.4.0 - 2023-12-01
+
+
+### Features
+
+- Added new curation_report.py to assist in upgrading ontologies between versions
+- New disambiguation strategy to prefer mappings that have a default label that matches an entity.
+- The OpenTargetsDiseaseOntologyParser has been heavily reworked, so that it uses the therapeutic_area concept to decide what records should be included. This has in turn yielded the subsets: measurement, medical_procedure, biological_process and phenotype. The measurement configuration is currently disabled as it requires heavy curation of the underlying strings. In addition, the OpenTargetsDiseaseOntologyParser now supports a custom ID grouping method, to make use of cross references.
+
+### Bugfixes
+
+- MemoryEfficientStringMatchingStep now only produces a single entity per class where multiple curations exist with different cases.
+- Previously, the `tested_dependencies.txt` file in the model packs included an editable install of kazu, which wasn't intended.
+  We now exclude kazu from that output.
+- Speed up model pack builds for model packs using `ExplosionStringMatchingStep`, by fixing a bug that caused the parsers to be populated twice in this case.
+
+### Deprecations and Removals
+
+- Removed pytorch-lightning as a dependency. The signatures of SapbertStringSimilarityScorer and TransformersModelForTokenClassificationNerStep have changed
+- Renamed `create_phrasematchers_using_curations` method of `OntologyMatcher` to `create_phrasematchers`. The old name will continue to work until kazu 1.6, but using it will produce a `DeprecationWarning`.
+- `MetadataDatabase.add_parser` now requires an `entity_class`.
+  This enables correct string normalisation in the `MappingStep` for the new disambiguation strategy.
+
+
 ## 1.3.2 - 2023-11-21
 
 

diff --git a/docs/_changelog.d/+create_phrasematchers_rename.removal.md b/docs/_changelog.d/+create_phrasematchers_rename.removal.md
diff --git a/docs/_changelog.d/+curationreport.feature.rst b/docs/_changelog.d/+curationreport.feature.rst
diff --git a/docs/_changelog.d/+doubleparserpopulate.bugfix.md b/docs/_changelog.d/+doubleparserpopulate.bugfix.md
diff --git a/docs/_changelog.d/+excludekazutested_dependencies.bugfix.md b/docs/_changelog.d/+excludekazutested_dependencies.bugfix.md
diff --git a/docs/_changelog.d/+metadbaddparser.removal.rst b/docs/_changelog.d/+metadbaddparser.removal.rst
diff --git a/docs/_changelog.d/+otdisease.feature.rst b/docs/_changelog.d/+otdisease.feature.rst
diff --git a/docs/_changelog.d/+pl.removal.rst b/docs/_changelog.d/+pl.removal.rst
diff --git a/docs/_changelog.d/+prefdefaultlabel.feature.rst b/docs/_changelog.d/+prefdefaultlabel.feature.rst
diff --git a/docs/_changelog.d/+stringmapper.bugfix.rst b/docs/_changelog.d/+stringmapper.bugfix.rst
diff --git a/kazu/__init__.py b/kazu/__init__.py
@@ -1 +1 @@
-__version__ = "1.3.2"
+__version__ = "1.4.0"