Clinlp

Changed
* :exclamation: Renamed the `clinlp_entity_matcher` to `clinlp_rule_based_entity_matcher`
* :exclamation: `clinlp` now stores entities in `doc.spans['ents']` rather than `doc.ents`, allowing for overlap
* :exclamation: Overlap in entities found by the entity matcher is no longer resolved by default (replacing old behaviour). To remove overlap, pass `resolve_overlap=True`.
* Refactored tests to use `pytest` best practices
* Changed `clinlp_autocomponent` to `clinlp_component`, which automatically registers your component with spaCy
* Codebase and linting improvements
* Renamed the `other_threshold` config to `family_threshold` in the `clinlp_experiencer_transformer` component

Fixed
* The `clinlp_rule_based_entity_matcher` no longer overwrites entities detected by other components (but appends them)

Added
* Integrated the clin_nlp_metrics package in this repository, specifically in `clinlp.metrics.ie`
* Support for non-binary qualifier in the Context Algorithm (e.g. 'Change', with values Decreasing, Stable and Increasing)
* Support for bidirectional qualifier patterns

Changed
* :exclamation: Moved all components related to information extraction to `clinlp.ie`. Please update imports accordingly (e.g. `from clinlp.ie import Term`).
* :exclamation: Updated the framework for qualifiers, to now have three qualifier classes: Presence, Temporality and Experiencer. For more details, see docs.

Added
* Support for Python 3.12

Added
* A component for transformer-based detection of Experiencer qualifiers (Patient/Other) (`clinlp_experiencer_transformer`)

Added
* A way to use a csv file as input for a conceptlist, using `create_concept_dict`

Fixed
* Fix a bug with termination trigger directly next to context trigger