From 0941889630b2798392b9c6cada19a85004db2729 Mon Sep 17 00:00:00 2001
From: manonBlanco <blanco@teklia.com>
Date: Fri, 24 Nov 2023 10:13:38 +0100
Subject: [PATCH] Apply suggestions
---
nerval/evaluate.py | 7 ++-----
tests/test_parse_bio.py | 3 +--
2 files changed, 3 insertions(+), 7 deletions(-)
diff --git a/nerval/evaluate.py b/nerval/evaluate.py
index 7a1d2c4..0efe5b4 100644
--- a/nerval/evaluate.py
+++ b/nerval/evaluate.py
@@ -309,10 +309,7 @@ def run(annotation: Path, prediction: Path, threshold: int, verbose: bool) -> di
# Get string and list of labels per character
def read_file(path: Path) -> List[str]:
assert path.exists(), f"Error: Input file {path} does not exist"
-
- with open(path, "r") as fd:
- lines = list(filter(lambda x: x != "\n", fd.readlines()))
- return lines
+ return path.read_text().strip().splitlines()
logger.info(f"Parsing file @ {annotation}")
annot = parse_bio(read_file(annotation))
@@ -320,7 +317,7 @@ def run(annotation: Path, prediction: Path, threshold: int, verbose: bool) -> di
logger.info(f"Parsing file @ {prediction}")
predict = parse_bio(read_file(prediction))
- if not annot or not predict:
+ if not (annot and predict):
raise Exception("No content found in annotation or prediction files.")
scores = evaluate(annot, predict, threshold)
diff --git a/tests/test_parse_bio.py b/tests/test_parse_bio.py
index 71868fc..1089795 100644
--- a/tests/test_parse_bio.py
+++ b/tests/test_parse_bio.py
@@ -179,8 +179,7 @@ expected_parsed_end_of_file = {
],
)
def test_parse_bio(test_input, expected):
- with open(test_input, "r") as fd:
- lines = list(filter(lambda x: x != "\n", fd.readlines()))
+ lines = test_input.read_text().strip().splitlines()
assert evaluate.parse_bio(lines) == expected
--
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