fix CI

.github/workflows/documentation.yml

@@ -13,7 +13,7 @@ env:
 
 jobs:
   Documentation:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v2
 

.github/workflows/release.yml

@@ -24,7 +24,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-22.04, windows-latest, macos-latest]
 
     steps:
       - uses: actions/checkout@v4
@@ -42,7 +42,7 @@ jobs:
 
   build_sdist:
     name: Build source distribution
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
 
@@ -58,7 +58,7 @@ jobs:
     name: Upload to PyPI
 
     needs: [build_wheels, build_sdist]
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
 
     steps:
     - uses: actions/download-artifact@v4
@@ -76,7 +76,7 @@ jobs:
         # repository_url: https://test.pypi.org/legacy/
 
   Documentation:
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v3
 

.github/workflows/test-build.yml

@@ -17,7 +17,7 @@ jobs:
     runs-on: ${{ matrix.os }}
     strategy:
       matrix:
-        os: [ubuntu-latest, windows-latest, macos-latest]
+        os: [ubuntu-22.04, windows-latest, macos-latest]
 
     steps:
       - uses: actions/checkout@v2
@@ -30,7 +30,7 @@ jobs:
 
   build_sdist:
     name: Build source distribution
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v2
 

.github/workflows/tests.yml

@@ -15,7 +15,7 @@ jobs:
   linting:
     name: Linting
     if: github.event_name == 'pull_request'
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
       - uses: actions/checkout@v3
         with:
@@ -32,7 +32,7 @@ jobs:
 
   pytest:
     name: Pytest
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: true
       matrix:
@@ -120,7 +120,7 @@ jobs:
 
   documentation:
     name: Documentation
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     steps:
     - uses: actions/checkout@v2
 
@@ -150,7 +150,7 @@ jobs:
 
   simple-installation:
     name: Simple installation
-    runs-on: ubuntu-latest
+    runs-on: ubuntu-22.04
     strategy:
       fail-fast: true
       matrix:

edsnlp/pipes/ner/behaviors/alcohol/alcohol.py

@@ -118,8 +118,8 @@ def process(self, doc: Doc) -> List[Span]:
                 stopped = self.negation.process(span)
                 if not any(stopped_token.negation for stopped_token in stopped.tokens):
                     span._.status = 2
-
-            if "zero_after" in span._.assigned.keys():
-                span._.negation = True
+            else:
+                if "zero_after" in span._.assigned.keys():
+                    span._.negation = True
 
             yield span

edsnlp/pipes/qualifiers/base.py

@@ -175,8 +175,8 @@ def get_matches(self, doc: Doc) -> List[Span]:
     def ensure_doc(self, doc: Union[Doc, Span]) -> Doc:
         return doc if not hasattr(doc, "as_doc") else doc.as_doc()
 
-    def process(self, doc: Doc) -> BaseQualifierResults:
-        doc = self.ensure_doc(doc)  # pragma: no cover
+    def process(self, doc_like: Union[Doc, Span]) -> BaseQualifierResults:
+        doc_like = self.ensure_doc(doc_like)  # pragma: no cover
         raise NotImplementedError
 
     def __call__(self, doc: Doc) -> Doc:

edsnlp/pipes/qualifiers/family/family.py

@@ -187,8 +187,8 @@ def set_extensions(self) -> None:
         if not Doc.has_extension("family"):
             Doc.set_extension("family", default=[])
 
-    def process(self, doc: Doc) -> FamilyResults:
-        doc = self.ensure_doc(doc)
+    def process(self, doc_like: Union[Doc, Span]) -> FamilyResults:
+        doc = self.ensure_doc(doc_like)
         matches = self.get_matches(doc)
 
         terminations = [m for m in matches if m.label_ == "termination"]

edsnlp/pipes/qualifiers/history/history.py

@@ -326,8 +326,8 @@ def set_extensions(self) -> None:
                 getter=deprecated_getter_factory("antecedent_cues", "history_cues"),
             )
 
-    def process(self, doc: Doc) -> HistoryResults:
-        doc = self.ensure_doc(doc)
+    def process(self, doc_like: Union[Doc, Span]) -> HistoryResults:
+        doc = self.ensure_doc(doc_like)
         note_datetime = None
         if doc._.note_datetime is not None:
             try:

edsnlp/pipes/qualifiers/hypothesis/hypothesis.py

@@ -262,8 +262,8 @@ def load_verbs(
             list_hypo_verbs_following,
         )
 
-    def process(self, doc: Doc) -> HypothesisResults:
-        doc = self.ensure_doc(doc)
+    def process(self, doc_like: Union[Doc, Span]) -> HypothesisResults:
+        doc = self.ensure_doc(doc_like)
         matches = self.get_matches(doc)
 
         terminations = [m for m in matches if m.label_ == "termination"]

edsnlp/pipes/qualifiers/negation/negation.py

@@ -295,8 +295,8 @@ def __call__(self, doc: Doc) -> Doc:
                     token._.negation = True
         return doc
 
-    def process(self, doc: Doc) -> NegationResults:
-        doc = self.ensure_doc(doc)
+    def process(self, doc_like: Union[Doc, Span]) -> NegationResults:
+        doc = self.ensure_doc(doc_like)
         matches = self.get_matches(doc)
 
         terminations = [m for m in matches if m.label_ == "termination"]

edsnlp/pipes/qualifiers/reported_speech/reported_speech.py

@@ -226,8 +226,8 @@ def load_verbs(self, verbs: List[str]) -> List[str]:
 
         return list_rep_verbs
 
-    def process(self, doc: Doc) -> ReportedSpeechResults:
-        doc = self.ensure_doc(doc)
+    def process(self, doc_like: Union[Doc, Span]) -> ReportedSpeechResults:
+        doc = self.ensure_doc(doc_like)
         matches = self.get_matches(doc)
         matches += list(self.regex_matcher(doc, as_spans=True))
 

tests/pipelines/ner/disorders/alcohol.py

@@ -10,6 +10,9 @@
         True,
         True,
         True,
+        True,
+        True,
+        False,
     ],
     detailled_status=[
         None,
@@ -22,6 +25,9 @@
         "ABSTINENCE",
         None,
         None,
+        "ABSTINENCE",
+        None,
+        None,
     ],
     negation=[
         None,
@@ -34,6 +40,9 @@
         None,
         True,
         False,
+        False,
+        False,
+        None,
     ],
     assign=None,
     texts=[
@@ -47,5 +56,8 @@
         "Le patient est en cours de sevrage éthylotabagique",
         "Patient alcoolique: non.",
         "On a un alcoolique non sevré depuis 10 ans.",
+        "Alcoolisme sevré",
+        "Alcoolisme non sevré",
+        "Dosage vitamines 25-OH",
     ],
 )