Merge pull request #22 from yfpeng/v2

v0.9.4

Author: Yifan Peng

environment2.7.yml

@@ -13,7 +13,6 @@ dependencies:
   - ply=3.10
   - tqdm=4.19.5
   - nltk=3.2.4
-  - pytest=3.1.3
   - pathlib2=2.3.3
   - numpy=1.15.4
   - jpype1=0.6.3

environment3.7.yml

@@ -0,0 +1,21 @@
+name: negbio3.7
+channels:
+  - anaconda
+  - conda-forge
+  - auto
+dependencies:
+  - python=3.7
+  - docutils=0.14
+  - docopt=0.6.2
+  - pytest=4.2.0
+  - networkx=2.2
+  - ply=3.11
+  - tqdm=4.31
+  - nltk=3.4
+  - numpy=1.16
+  - jpype1=0.6.3
+  - pip:
+    - bioc==1.3.1
+    - pystanforddependencies==0.3.1
+    - bllipparser==2016.9.11
+    - pymetamap==0.1

negbio/pipeline/cleanup.py

@@ -12,12 +12,14 @@ def clean_sentences(document, sort_anns=False):
     try:
         for passage in document.passages:
             del passage.sentences[:]
-            if sort_anns:
-                id = 0
-                for ann in sorted(passage.annotations, key=lambda ann: ann.get_total_location().offset):
+
+        if sort_anns:
+            key_func = lambda ann: ann.get_total_location().offset
+            id = 0
+            for passage in document.passages:
+                for ann in sorted(passage.annotations, key=key_func):
                     ann.id = str(id)
                     id += 1
     except:
         logging.exception("Cannot process %s", document.id)
     return document
-

requirements.txt

@@ -6,7 +6,6 @@ networkx==1.11
 ply==3.10
 tqdm==4.19.5
 nltk==3.2.4
-pytest==3.1.3
 bioc==1.1.dev3
 pystanforddependencies==0.3.1
 bllipparser==2016.9.11

setup.py

@@ -63,7 +63,7 @@ def run(self):
     # Versions should comply with PEP440.  For a discussion on single-sourcing
     # the version across setup.py and the project code, see
     # https://packaging.python.org/en/latest/single_source_version.html
-    version='0.9.3',
+    version='0.9.4',
 
     description='NegBio: a tool for negation and uncertainty detection',
     long_description=readme(),

tests/negbio/pipeline/test_parse.py

@@ -3,12 +3,12 @@
 from negbio.pipeline.parse import Bllip
 
 
-def test_parse():
+def test_Bllip():
     b = Bllip()
     t = b.parse('hello world!')
     assert str(t) == '(S1 (S (NP (NN hello) (NN world) (NN !))))'
 
 
 if __name__ == '__main__':
     logging.basicConfig(level=logging.WARNING)
-    test_parse()
+    test_Bllip()