Refacto of the extensions

[percevalw]

Description

This PR refactors the extensions of several pipelines to conform with #47.
The current changes are the following (this is still a draft):

Added

• New to_duration method to convert an absolute date into a date relative to the note_datetime (or None)

Changes

• Score / disorders / behaviors entities now have a hardcoded label, instead of being dynamically set from the component name. The following scores may have a different name than the current one in your pipelines:
  • eds.emergency.gemsa → emergency.gemsa
  • eds.emergency.ccmu → emergency.ccmu
  • eds.emergency.priority → emergency.priority
  • eds.charlson → charlson
  • eds.elston-ellis → elston-ellis
  • eds.SOFA → sofa
  • eds.adicap → adicap
  • eds.adicap → adicap
• eds.dates now separate dates from durations. Each entity has its own label:
  • spans["dates"] → entities labelled as date with a span._.date parsed object
  • spans["durations"] → entities labelled as duration with a span._.duration parsed object
• the "relative" / "absolute" / "duration" mode of the time entity is now stored in
  the mode attribute of the span._.date/duration
• the "from" / "until" period bound, if any, is now stored in the span._.date.bound attribute
• to_datetime now only return absolute dates, converts relative dates into absolute if doc._.note_datetime is given, and None otherwise

Checklist

• If this PR is a bug fix, the bug is documented in the test suite.
• Changes were documented in the changelog (pending section).
• If necessary, changes were made to the documentation (eg new pipeline).
• Refactor eds.measurements
• Refactor eds.consultation-dates
• Add value extension

(this PR has integrated the changes of #83)

[codecov]

Codecov Report

Patch coverage is 95.30% of modified lines.

Files Changed	Coverage
edsnlp/patch_spacy_dot_components.py	ø
edsnlp/pipelines/core/context/context.py	ø
edsnlp/pipelines/core/endlines/model.py	ø
edsnlp/pipelines/core/sentences/factory.py	ø
...pipelines/misc/dates/patterns/atomic/directions.py	ø
...snlp/pipelines/misc/dates/patterns/atomic/modes.py	ø
edsnlp/pipelines/misc/dates/patterns/relative.py	ø
edsnlp/pipelines/misc/measurements/patterns.py	ø
edsnlp/pipelines/ner/disorders/aids/patterns.py	ø
edsnlp/pipelines/ner/disorders/ckd/patterns.py	ø
... and 120 more

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