Set default distance threshold to `0` instead of `0.3`

README.md

@@ -35,7 +35,7 @@ $ nerval -a/--annot <annot_file.bio> -p/--predict <predict-file.bio> \
 		 [-t/--threshold <threshold_value>] [-c/--csv <correspondence_file.csv>]
 ```
 
-The threshold value should be between 0 and 1. It designates the acceptable number of characters differing between an annotated and a predicted entity - over the number of characters in the annotated entity - to consider it as a match. Default value is 0.30. 0 would impose perfect matches, 1 would allow completely different strings to be considered as a match.
+The threshold value should be between 0 and 1. It designates the acceptable number of characters differing between an annotated and a predicted entity - over the number of characters in the annotated entity - to consider it as a match. Default value is 0. 0 would impose perfect matches, 1 would allow completely different strings to be considered as a match.
 
 For instance, if we consider the following case:
 

nerval/cli.py

@@ -3,7 +3,7 @@ from pathlib import Path
 
 from nerval.evaluate import run, run_multiple
 
-THRESHOLD = 0.30
+THRESHOLD = 0
 
 
 def threshold_float_type(arg):

tests/__init__.py

+TEST_THRESHOLD = 0.3

tests/test_compute_matches.py

 import pytest
 
 from nerval import ALL_ENTITIES, evaluate
-
-THRESHOLD = 0.30
-
+from tests import TEST_THRESHOLD
 
 fake_tags_aligned_nested_perfect = [
     # Labels 1
@@ -368,7 +366,7 @@ fake_predict_tags_bk_boundary_2 = [
                 "G*rard de *N*erval ----bo*rn in Paris in 1833 *.",
                 fake_annot_tags_aligned,
                 fake_predict_tags_aligned,
-                THRESHOLD,
+                TEST_THRESHOLD,
             ),
             {ALL_ENTITIES: 1, "PER": 1, "LOC": 0, "DAT": 0},
         ),
@@ -378,7 +376,7 @@ fake_predict_tags_bk_boundary_2 = [
                 "Louis par la grâce de Dieu roy de France et de Navarre.",
                 fake_tags_aligned_nested_perfect,
                 fake_tags_aligned_nested_perfect,
-                THRESHOLD,
+                TEST_THRESHOLD,
             ),
             {ALL_ENTITIES: 3, "PER": 1, "LOC": 2},
         ),
@@ -388,7 +386,7 @@ fake_predict_tags_bk_boundary_2 = [
                 "Louis par la grâce de Dieu roy de France et de Navarre.",
                 fake_tags_aligned_nested_perfect,
                 fake_tags_aligned_nested_false,
-                THRESHOLD,
+                TEST_THRESHOLD,
             ),
             {ALL_ENTITIES: 2, "PER": 1, "LOC": 1},
         ),
@@ -398,7 +396,7 @@ fake_predict_tags_bk_boundary_2 = [
                 "The red dragon",
                 fake_annot_tags_bk_boundary,
                 fake_predict_tags_bk_boundary,
-                THRESHOLD,
+                TEST_THRESHOLD,
             ),
             {ALL_ENTITIES: 0, "PER": 0},
         ),
@@ -408,7 +406,7 @@ fake_predict_tags_bk_boundary_2 = [
                 "A red dragon",
                 fake_annot_tags_bk_boundary_2,
                 fake_predict_tags_bk_boundary_2,
-                THRESHOLD,
+                TEST_THRESHOLD,
             ),
             {ALL_ENTITIES: 1, "PER": 1},
         ),

tests/test_run.py

@@ -4,6 +4,7 @@ from pathlib import Path
 import pytest
 
 from nerval import ALL_ENTITIES, evaluate
+from tests import TEST_THRESHOLD
 
 
 @pytest.mark.parametrize(
@@ -92,7 +93,7 @@ def test_run(annotation, prediction, expected):
         evaluate.run(
             annotation=annotation,
             prediction=prediction,
-            threshold=0.3,
+            threshold=TEST_THRESHOLD,
             verbose=False,
         )
         == expected
@@ -104,7 +105,7 @@ def test_run_empty_bio(empty_bio):
         Exception,
         match="No content found in annotation or prediction files.",
     ):
-        evaluate.run(empty_bio, empty_bio, 0.3, False)
+        evaluate.run(empty_bio, empty_bio, TEST_THRESHOLD, False)
 
 
 def test_run_empty_entry():
@@ -112,7 +113,7 @@ def test_run_empty_entry():
         AssertionError,
         match=re.escape("Error: Input file invalid.bio does not exist"),
     ):
-        evaluate.run(Path("invalid.bio"), Path("invalid.bio"), 0.3, False)
+        evaluate.run(Path("invalid.bio"), Path("invalid.bio"), TEST_THRESHOLD, False)
 
 
 def test_run_invalid_header(csv_file_error, folder_bio):
@@ -120,7 +121,7 @@ def test_run_invalid_header(csv_file_error, folder_bio):
         Exception,
         match="Columns in the CSV mapping should be: Annotation,Prediction",
     ):
-        evaluate.run_multiple(csv_file_error, folder_bio, 0.3, False)
+        evaluate.run_multiple(csv_file_error, folder_bio, TEST_THRESHOLD, False)
 
 
 def test_run_multiple(csv_file, folder_bio):
@@ -128,4 +129,4 @@ def test_run_multiple(csv_file, folder_bio):
         Exception,
         match="No file found for files demo_annot.bio, demo_predict.bio",
     ):
-        evaluate.run_multiple(csv_file, folder_bio, 0.3, False)
+        evaluate.run_multiple(csv_file, folder_bio, TEST_THRESHOLD, False)