Merge branch 'master' into 'feature_verbose'

# Conflicts:
#   nerval/evaluate.py

README.md

@@ -7,6 +7,7 @@
 Nerval is an evaluation library written in python implementing a metric for named-entity recognition evaluation on noisy text, typically to measure NER performances on OCR or Handwritten text recognition predictions.
 
 Expected inputs are a ground truth and a prediction BIOES/BILOU files without any  ''§'' occurrences, this character having a special meaning during evaluation.
+It also works by designating a csv file with file matches (one pair per row with the annotation file in the first column and the prediction file in the second column)
 
 ## Usage
 
@@ -31,7 +32,7 @@ You can now use Nerval in command line :
 
 ```
 $ nerval -a/--annot <annot_file.bio> -p/--predict <predict-file.bio> \
-		 [-t/--threshold <threshold_value>]
+		 [-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.
@@ -58,6 +59,12 @@ We also provide two annotation and prediction toy files, which are identical for
 $ nerval -a demo/toy_test_annot.bio -p demo/toy_test_predict.bio
 ```
 
+You can also indicate a folder and a csv file to have multiple evaluation at once.
+
+```
+$ nerval -c demo/mapping_file.csv -f demo/bio_folder
+```
+
 ## Metric
 
 This metric uses string alignment at character level.

demo/bio_folder/demo_annot.bio

+Césaire B-PER
+Alphonse I-PER
+Garon I-PER
+marraine O
+Adeline B-PER
+Dionne I-PER
+, O
+soussignés O
+Lecture O
+faite O
+Adéline O
+Dionne O
+Arsène O
+Côté O
+Arpin O
+R O
+Le O
+onze B-DAT
+aout I-DAT
+mil I-DAT
+neuf I-DAT
+cent I-DAT
+un I-DAT
+nous O
+prêtre O
+soussigné O
+avons O
+baptisé O
+Marie B-PER
+Luce I-PER
+Louise I-PER
+, O
+née O
+la B-DAT
+veille I-DAT
+, O
+fille O
+légitime O
+de O
+Carmel B-PER
+Côté I-PER
+, O
+cordonnier B-OCC
+, O
+pré O
+- O
+sent O
+, O
+déclarant O
+ne O
+savoir O
+signer O
+, O
+et O
+de O
+Eugé B-PER
+nie I-PER
+Fréchette I-PER
+, O
+de O
+cette B-LOC
+paroisse I-LOC
+. O
+Parrain O
+Napoléon B-PER
+Fréchette I-PER
+, O
+marraine O
+Adeline B-PER
+Tremblay I-PER
+, O
+soussignés O
+, O
+de O
+Ste B-LOC
+Luce I-LOC
+, O
+Lec O
+- O
+ture O
+faite O
+. O

demo/bio_folder/demo_predict.bio

+Césaire B-PER
+Alphonse O
+Garon B-PER
+marraine O
+Adeline B-PER
+Dionne I-PER
+, O
+soussignés O
+Lecture O
+faite O
+Adéline O
+Dionne O
+Arsène O
+Côté O
+Arpin O
+R O
+Le O
+onze B-DAT
+aout I-DAT
+mil I-DAT
+neuf I-DAT
+cent I-DAT
+un O
+nous O
+pretre O
+soussigné O
+avons O
+baptisé O
+Marie B-PER
+Luce I-PER
+Louise I-PER
+, O
+née O
+la B-DAT
+veille I-DAT
+, O
+fille O
+légitime O
+de O
+Carmel B-PER
+Côté I-PER
+, O
+cordonnier B-OCC
+, O
+pré O
+- O
+sent O
+, O
+déclarant O
+ne O
+savoir O
+signer O
+, O
+et O
+de O
+Eugé B-PER
+nie I-PER
+Fréchette I-PER
+, O
+de O
+cette B-LOC
+paroisse I-LOC
+. O
+Parrain O
+Napoléon B-PER
+Fréchette I-PER
+, O
+marraine O
+Adéline B-PER
+Tremblay I-PER
+, O
+sousignés O
+, O
+de O
+St B-LOC
+. I-LOC
+Luce O
+, O
+Lec O
+ture O
+faite O

demo/bio_folder/toy_test_annot.bio

+John B-PER
+Ronald I-PER
+Reuel I-PER
+Tolkien I-PER
+was O
+born O
+on O
+three B-DAT
+January I-DAT
+eighteen I-DAT
+ninety I-DAT
+- I-DAT
+two I-DAT
+in O
+Bloemfontein B-LOC
+in O
+the O
+Orange B-LOC
+Free I-LOC
+State I-LOC
+, O
+to O
+Arthur B-PER
+Reuel I-PER
+Tolkien I-PER
+, O
+an O
+English O
+bank B-OCC
+manager I-OCC
+, O
+and O
+his O
+wife O
+Mabel B-PER
+, O
+née O
+Suffield B-PER
+. O

demo/bio_folder/toy_test_predict.bio

+John B-PER
+Ronald I-PER
+Reuel I-PER
+Tolkien I-PER
+was O
+born O
+on O
+three B-DAT
+January I-DAT
+eighteen I-DAT
+ninety I-DAT
+- I-DAT
+two I-DAT
+in O
+Bloemfontein B-LOC
+in O
+the O
+Orange B-LOC
+Free I-LOC
+State I-LOC
+, O
+to O
+Arthur B-PER
+Reuel I-PER
+Tolkien I-PER
+, O
+an O
+English O
+bank B-OCC
+manager I-OCC
+, O
+and O
+his O
+wife O
+Mabel B-PER
+, O
+née O
+Suffield B-PER
+. O

demo/mapping_file.csv

+demo_annot.bio,demo_predict.bio
+toy_test_annot.bio,toy_test_predict.bio
\ No newline at end of file

tests/test_folder/test_demo_annot.bio

+Césaire B-PER
+Alphonse I-PER
+Garon I-PER
+marraine O
+Adeline B-PER
+Dionne I-PER
+, O
+soussignés O
+Lecture O
+faite O
+Adéline O
+Dionne O
+Arsène O
+Côté O
+Arpin O
+R O
+Le O
+onze B-DAT
+aout I-DAT
+mil I-DAT
+neuf I-DAT
+cent I-DAT
+un I-DAT
+nous O
+prêtre O
+soussigné O
+avons O
+baptisé O
+Marie B-PER
+Luce I-PER
+Louise I-PER
+, O
+née O
+la B-DAT
+veille I-DAT
+, O
+fille O
+légitime O
+de O
+Carmel B-PER
+Côté I-PER
+, O
+cordonnier B-OCC
+, O
+pré O
+- O
+sent O
+, O
+déclarant O
+ne O
+savoir O
+signer O
+, O
+et O
+de O
+Eugé B-PER
+nie I-PER
+Fréchette I-PER
+, O
+de O
+cette B-LOC
+paroisse I-LOC
+. O
+Parrain O
+Napoléon B-PER
+Fréchette I-PER
+, O
+marraine O
+Adeline B-PER
+Tremblay I-PER
+, O
+soussignés O
+, O
+de O
+Ste B-LOC
+Luce I-LOC
+, O
+Lec O
+- O
+ture O
+faite O
+. O

tests/test_folder/test_demo_predict.bio

+Césaire B-PER
+Alphonse O
+Garon B-PER
+marraine O
+Adeline B-PER
+Dionne I-PER
+, O
+soussignés O
+Lecture O
+faite O
+Adéline O
+Dionne O
+Arsène O
+Côté O
+Arpin O
+R O
+Le O
+onze B-DAT
+aout I-DAT
+mil I-DAT
+neuf I-DAT
+cent I-DAT
+un O
+nous O
+pretre O
+soussigné O
+avons O
+baptisé O
+Marie B-PER
+Luce I-PER
+Louise I-PER
+, O
+née O
+la B-DAT
+veille I-DAT
+, O
+fille O
+légitime O
+de O
+Carmel B-PER
+Côté I-PER
+, O
+cordonnier B-OCC
+, O
+pré O
+- O
+sent O
+, O
+déclarant O
+ne O
+savoir O
+signer O
+, O
+et O
+de O
+Eugé B-PER
+nie I-PER
+Fréchette I-PER
+, O
+de O
+cette B-LOC
+paroisse I-LOC
+. O
+Parrain O
+Napoléon B-PER
+Fréchette I-PER
+, O
+marraine O
+Adéline B-PER
+Tremblay I-PER
+, O
+sousignés O
+, O
+de O
+St B-LOC
+. I-LOC
+Luce O
+, O
+Lec O
+ture O
+faite O

tests/test_folder/test_toy_annot.bio

+John B-PER
+Ronald I-PER
+Reuel I-PER
+Tolkien I-PER
+was O
+born O
+on O
+three B-DAT
+January I-DAT
+eighteen I-DAT
+ninety I-DAT
+- I-DAT
+two I-DAT
+in O
+Bloemfontein B-LOC
+in O
+the O
+Orange B-LOC
+Free I-LOC
+State I-LOC
+, O
+to O
+Arthur B-PER
+Reuel I-PER
+Tolkien I-PER
+, O
+an O
+English O
+bank B-OCC
+manager I-OCC
+, O
+and O
+his O
+wife O
+Mabel B-PER
+, O
+née O
+Suffield B-PER
+. O

tests/test_folder/test_toy_predict.bio

+John B-PER
+Ronald I-PER
+Reuel I-PER
+Tolkien I-PER
+was O
+born O
+on O
+three B-DAT
+January I-DAT
+eighteen I-DAT
+ninety I-DAT
+- I-DAT
+two I-DAT
+in O
+Bloemfontein B-LOC
+in O
+the O
+Orange B-LOC
+Free I-LOC
+State I-LOC
+, O
+to O
+Arthur B-PER
+Reuel I-PER
+Tolkien I-PER
+, O
+an O
+English O
+bank B-OCC
+manager I-OCC
+, O
+and O
+his O
+wife O
+Mabel B-PER
+, O
+née O
+Suffield B-PER
+. O

tests/test_mapping_file.csv

+demo_annot.bio,demo_predict.bio
+toy_test_annot.bio,toy_test_predict.bio
\ No newline at end of file

tests/test_run.py

@@ -9,6 +9,8 @@ FAKE_ANNOT_BIO = "tests/test_annot.bio"
 FAKE_PREDICT_BIO = "tests/test_predict.bio"
 EMPTY_BIO = "tests/test_empty.bio"
 FAKE_BIO_NESTED = "tests/test_nested.bio"
+BIO_FOLDER = "test_folder"
+CSV_FILE = "test_mapping_file.csv"
 
 expected_scores_nested = {
     "All": {
@@ -81,3 +83,8 @@ def test_run_empty_bio():
 def test_run_empty_entry():
     with pytest.raises(TypeError):
         evaluate.run(None, None, THRESHOLD)
+
+
+def test_run_multiple():
+    with pytest.raises(Exception):
+        evaluate.run_multiple(CSV_FILE, BIO_FOLDER, THRESHOLD)