From 674d7e14a0d524cc286b16629d56e72836fb7030 Mon Sep 17 00:00:00 2001
From: manonBlanco <blanco@teklia.com>
Date: Fri, 24 Nov 2023 12:32:19 +0100
Subject: [PATCH] Comply with ruff's PTH rule
---
nerval/evaluate.py | 11 +++++------
pyproject.toml | 2 ++
setup.py | 2 +-
3 files changed, 8 insertions(+), 7 deletions(-)
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index e72fd08..7feec7b 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -1,5 +1,4 @@
import logging
-import os
from csv import reader
from pathlib import Path
from typing import List
@@ -343,14 +342,14 @@ def run(annotation: Path, prediction: Path, threshold: int, verbose: bool) -> di
return scores
-def run_multiple(file_csv, folder, threshold, verbose):
+def run_multiple(file_csv: Path, folder: Path, threshold: int, verbose: bool):
"""Run the program for multiple files (correlation indicated in the csv file)"""
# Read the csv in a list
- with open(file_csv) as read_obj:
+ with file_csv.open() as read_obj:
csv_reader = reader(read_obj)
list_cor = list(csv_reader)
- if os.path.isdir(folder):
+ if folder.is_dir():
list_bio_file = list(folder.rglob("*.bio"))
count = 0
@@ -362,10 +361,10 @@ def run_multiple(file_csv, folder, threshold, verbose):
predict = None
for file in list_bio_file:
- if row[0] == os.path.basename(file):
+ if row[0] == file.name:
annot = file
for file in list_bio_file:
- if row[1] == os.path.basename(file):
+ if row[1] == file.name:
predict = file
if annot and predict:
diff --git a/pyproject.toml b/pyproject.toml
index 447804e..28ef1df 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -33,4 +33,6 @@ select = [
"Q",
# flake8-unused-arguments
"ARG",
+ # flake8-use-pathlib
+ "PTH",
]
diff --git a/setup.py b/setup.py
index c15ce58..611c366 100644
--- a/setup.py
+++ b/setup.py
@@ -27,7 +27,7 @@ def parse_requirements():
setup(
name="nerval",
- version=open("VERSION").read(),
+ version=Path("VERSION").read_text(),
description="Tool to evaluate NER on noisy text.",
author="Teklia",
author_email="contact@teklia.com",
--
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