From ad29708f6d5d16746e3102140977a1ca0846460d Mon Sep 17 00:00:00 2001
From: manonBlanco <blanco@teklia.com>
Date: Fri, 24 Nov 2023 10:01:23 +0100
Subject: [PATCH] Use prettytable instead of termtables
---
.isort.cfg | 2 +-
README.md | 6 +++---
nerval/evaluate.py | 15 ++++++++-------
nerval/utils.py | 16 +++++++++++++---
requirements.txt | 2 +-
5 files changed, 26 insertions(+), 15 deletions(-)
diff --git a/.isort.cfg b/.isort.cfg
index 5cf2203..4fec7ef 100644
--- a/.isort.cfg
+++ b/.isort.cfg
@@ -7,4 +7,4 @@ use_parentheses = True
line_length = 120
default_section=FIRSTPARTY
-known_third_party = editdistance,edlib,pytest,setuptools,termtables
+known_third_party = editdistance,edlib,pytest,setuptools,prettytable
diff --git a/README.md b/README.md
index 31bb747..be8e0ee 100644
--- a/README.md
+++ b/README.md
@@ -50,7 +50,7 @@ Counting the spaces, 7 characters differ over 24 characters in the reference ent
### Demo
```
-$ nerval -a demo/bio_folder/demo_annot.bio -p demo/bio_folder/demo_predict.bio
+$ nerval -a demo/demo_annot.bio -p demo/demo_predict.bio
```
We also provide two annotation and prediction toy files, which are identical for now and produce perfect scores. Feel free to play with the the text and entity tags in the prediction file to see the impact on the score.
@@ -62,13 +62,13 @@ $ 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
+$ nerval -c demo/mapping_file.csv -f demo
```
And with the verbose option that's triggered by -v
```
-$ nerval -a demo/bio_folder/demo_annot.bio -p demo/bio_folder/demo_predict.bio -v
+$ nerval -a demo/demo_annot.bio -p demo/demo_predict.bio -v
```
## Metric
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 5cbe3ab..a2af0bd 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -1,6 +1,5 @@
# -*- coding: utf-8 -*-
-import glob
import logging
import os
from csv import reader
@@ -8,7 +7,7 @@ from pathlib import Path
import editdistance
import edlib
-import termtables as tt
+from prettytable import MARKDOWN, PrettyTable
from nerval.parse import (
BEGINNING_POS,
@@ -324,7 +323,7 @@ def run_multiple(file_csv, folder, threshold, verbose):
list_cor = list(csv_reader)
if os.path.isdir(folder):
- list_bio_file = glob.glob(str(folder) + "/**/*.bio", recursive=True)
+ list_bio_file = list(folder.rglob("*.bio"))
count = 0
precision = 0
@@ -351,17 +350,19 @@ def run_multiple(file_csv, folder, threshold, verbose):
raise Exception(f"No file found for files {annot}, {predict}")
if count:
logger.info("Average score on all corpus")
- tt.print(
+ table = PrettyTable()
+ table.field_names = ["Precision", "Recall", "F1"]
+ table.set_style(MARKDOWN)
+ table.add_rows(
[
[
round(precision / count, 3),
round(recall / count, 3),
round(f1 / count, 3),
]
- ],
- ["Precision", "Recall", "F1"],
- style=tt.styles.markdown,
+ ]
)
+ print(table)
else:
raise Exception("No file were counted")
else:
diff --git a/nerval/utils.py b/nerval/utils.py
index 595299e..21c6c20 100644
--- a/nerval/utils.py
+++ b/nerval/utils.py
@@ -1,5 +1,5 @@
# -*- coding: utf-8 -*-
-import termtables as tt
+from prettytable import MARKDOWN, PrettyTable
def print_results(scores: dict):
@@ -25,7 +25,12 @@ def print_results(scores: dict):
scores[tag]["Support"],
]
)
- tt.print(results, header, style=tt.styles.markdown)
+
+ table = PrettyTable()
+ table.field_names = header
+ table.set_style(MARKDOWN)
+ table.add_rows(results)
+ print(table)
def print_result_compact(scores: dict):
@@ -41,4 +46,9 @@ def print_result_compact(scores: dict):
scores["All"]["Support"],
]
]
- tt.print(result, header, style=tt.styles.markdown)
+
+ table = PrettyTable()
+ table.field_names = header
+ table.set_style(MARKDOWN)
+ table.add_rows(result)
+ print(table)
diff --git a/requirements.txt b/requirements.txt
index 56ec7b8..ec0fabe 100644
--- a/requirements.txt
+++ b/requirements.txt
@@ -1,3 +1,3 @@
editdistance==0.6.2
edlib==1.3.9
-termtables==0.2.4
+prettytable==3.9.0
--
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