Merge pull request #28 from jenojp/develop

prep for 0.1.9 release

negspacy/negation.py

@@ -7,9 +7,9 @@
 
 class Negex:
     """
-	A spaCy pipeline component which identifies negated tokens in text.
+        A spaCy pipeline component which identifies negated tokens in text.
 
-	Based on: NegEx - A Simple Algorithm for Identifying Negated Findings and Diseasesin Discharge Summaries
+        Based on: NegEx - A Simple Algorithm for Identifying Negated Findings and Diseasesin Discharge Summaries
     Chapman, Bridewell, Hanbury, Cooper, Buchanan
 
     Parameters
@@ -31,7 +31,7 @@ class Negex:
     termination: list
         phrases that "terminate" a sentence for processing purposes such as "but". If empty, defaults are used
 
-	"""
+    """
 
     def __init__(
         self,
@@ -170,7 +170,7 @@ def add_patterns(
     def get_patterns(self):
         """
         returns phrase patterns used for various negation dictionaries
-        
+
         Returns
         -------
         patterns: dict
@@ -191,7 +191,7 @@ def process_negations(self, doc):
         """
         Find negations in doc and clean candidate negations to remove pseudo negations
 
-        Parameters 
+        Parameters
         ----------
         doc: object
             spaCy Doc object
@@ -282,7 +282,7 @@ def negex(self, doc):
         """
         Negates entities of interest
 
-        Parameters 
+        Parameters
         ----------
         doc: object
             spaCy Doc object

negspacy/test.py

@@ -196,7 +196,7 @@ def test_add_remove_patterns():
     )
     negex.remove_patterns(termination="but")
     negex.remove_patterns(
-        preceding_negations="wow a negation", following_negations=["extra negation"]
+        preceding_negations="wow a negation", following_negations="extra negation"
     )
     patterns_after = negex.get_patterns()
     assert (
@@ -213,11 +213,10 @@ def test_add_remove_patterns():
     )
     assert len(patterns_after["pseudo_patterns"]) == len(patterns["pseudo_patterns"])
 
+
 def test_issue_14():
     nlp = spacy.load("en_core_sci_sm")
-    negex = Negex(
-        nlp, language="en_clinical", chunk_prefix=["no", "cancer free"]
-    )
+    negex = Negex(nlp, language="en_clinical", chunk_prefix=["no", "cancer free"])
     negex.remove_patterns(following_negations="free")
     nlp.add_pipe(negex, last=True)
     print(negex.get_patterns())
@@ -227,7 +226,16 @@ def test_issue_14():
     for i, e in enumerate(doc.ents):
         print(e.text, e._.negex)
         assert e._.negex == expected[i]
-
+
+    nlp.remove_pipe("Negex")
+    negex = Negex(nlp, language="en_clinical", chunk_prefix=["no", "free"])
+    nlp.add_pipe(negex, last=True)
+    doc = nlp("The patient has a cancer free diagnosis")
+    expected = [False, False]
+    for i, e in enumerate(doc.ents):
+        print(e.text, e._.negex)
+        assert e._.negex == expected[i]
+
 
 if __name__ == "__main__":
     test()

setup.py

@@ -3,7 +3,7 @@
 
 setup(
     name = 'negspacy',
-    version = 'v0.1.8',
+    version = 'v0.1.9',
     url = 'https://github.com/jenojp/negspacy',
     author = 'Jeno Pizarro',
     author_email = 'jenopizzaro@gmail.com',