Refacto of the extensions

.github/workflows/documentation.yml

@@ -13,7 +13,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install '.[docs]'
+        pip install '.[dev]'
     - name: Set up Git
       run: |
         git config user.name ${{ github.actor }}

.github/workflows/release.yml

@@ -72,7 +72,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install '.[docs]'
+        pip install '.[dev]'
     - name: Set up Git
       run: |
         git config user.name ${{ github.actor }}

.github/workflows/tests.yml

@@ -7,22 +7,17 @@ on:
 
 jobs:
   Linting:
+    if: github.event_name == 'pull_request'
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
-      - name: Set PY variable
-        run: echo "PY=$(python -VV | sha256sum | cut -d' ' -f1)" >> $GITHUB_ENV
-      - uses: actions/cache@v2
+      - uses: actions/checkout@v3
         with:
-          path: ~/.cache/pre-commit
-          key: pre-commit|${{ env.PY }}|${{ hashFiles('.pre-commit-config.yaml') }}
-      - name: Install pre-commit
-        run: |
-          pip install pre-commit
-          pre-commit install
-      - name: Run pre-commit
-        run: SKIP=no-commit-to-branch pre-commit run --all-files
+          # requites to grab the history of the PR
+          fetch-depth: 0
+      - uses: actions/setup-python@v3
+      - uses: pre-commit/[email protected]
+        with:
+          extra_args: --color=always --from-ref ${{ github.event.pull_request.base.sha }} --to-ref ${{ github.event.pull_request.head.sha }}
 
   Pytest:
     runs-on: ubuntu-latest
@@ -79,7 +74,7 @@ jobs:
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install '.[docs]'
+        pip install '.[dev]'
     - name: Build documentation
       run: |
         mkdocs build --clean

.pre-commit-config.yaml

@@ -17,24 +17,15 @@ repos:
       - id: check-toml
       - id: check-json
       - id: check-symlinks
-      - id: check-docstring-first
       - id: check-added-large-files
       - id: detect-private-key
-  - repo: https://github.com/pycqa/isort
-    rev: 5.11.5
+  # ruff
+  - repo: https://github.com/charliermarsh/ruff-pre-commit
+    # Ruff version.
+    rev: 'v0.0.288'
     hooks:
-      - id: isort
-        name: isort (python)
-        args: ["--profile", "black"]
-      - id: isort
-        name: isort (cython)
-        types: [cython]
-        args: ["--profile", "black"]
-      - id: isort
-        name: isort (pyi)
-        types: [pyi]
-        args: ["--profile", "black"]
-
+      - id: ruff
+        args: ['--config', 'pyproject.toml']
   - repo: https://github.com/psf/black
     rev: 22.3.0
     hooks:
@@ -45,10 +36,6 @@ repos:
       - id: blacken-docs
         additional_dependencies: [black==20.8b1]
         exclude: notebooks/
-  - repo: https://github.com/pycqa/flake8
-    rev: 4.0.1
-    hooks:
-      - id: flake8
   - repo: https://github.com/econchick/interrogate
     rev: 1.5.0
     hooks:

Makefile

@@ -14,14 +14,14 @@ create-env: .venv
 
 install : .venv
 	. .venv/bin/activate
-	pip install -r '.[dev,docs,setup]'.txt
+	pip install -r '.[dev,setup]'.txt
 	python scripts/conjugate_verbs.py
 	pip install -e .
 	pre-commit install
 
 documentation: .venv
 	. .venv/bin/activate
-	pip install -e '.[docs]'
+	pip install -e '.[dev]'
 	mkdocs serve
 
 test: .venv

README.md

@@ -36,7 +36,7 @@ Once you've installed the library, let's begin with a very simple example that e
 ```python
 import spacy
 
-nlp = spacy.blank("fr")
+nlp = spacy.blank("eds")
 
 terms = dict(
     covid=["covid", "coronavirus"],

changelog.md

@@ -1,6 +1,30 @@
 # Changelog
 
-## Pending
+## Unreleased
+
+### Added
+
+- New `to_duration` method to convert an absolute date into a date relative to the note_datetime (or None)
+
+### Changes
+
+- Input and output of components are now specified by `span_getter` and `span_setter` arguments.
+- :boom: Score / disorders / behaviors entities now have a fixed label (passed as an argument), 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.measuremets` → `size`, `weight`, ... instead of `eds.size`, `eds.weight`, ...
+- `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
 
 ### Fixed
 - `export_to_brat` issue with spans of entities on multiple lines.
@@ -300,9 +324,7 @@ Fix release to allow installation from source
 
 - Renamed `generic` to `matcher`. This is a non-breaking change for the average user, adding the pipeline is still :
 
-  <!-- no-check -->
-
-  ```python
+  ```{ .python .no-check }
   nlp.add_pipe("matcher", config=dict(terms=dict(maladie="maladie")))
   ```
 

contributing.md

@@ -24,7 +24,7 @@ $ python -m venv venv
 $ source venv/bin/activate
 
 # Install the package with common, dev, setup dependencies in editable mode
-$ pip install -e '.[dev,docs,setup]'
+$ pip install -e '.[dev,setup]'
 # And build resources
 $ python scripts/conjugate_verbs.py
 ```
@@ -113,7 +113,7 @@ We use `MkDocs` for EDS-NLP's documentation. You can checkout the changes you ma
 
 ```console
 # Install the requirements
-$ pip install -e '.[docs]'
+$ pip install -e '.[dev]'
 ---> 100%
 color:green Installation successful