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Fix #70: stop calling logging.basicConfig() at import time #71

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Merged
iskandr merged 3 commits into from
Jul 8, 2026
Merged

Fix #70: stop calling logging.basicConfig() at import time #71

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9e9222d
Fix #70: stop calling logging.basicConfig() at import time
iskandr Jul 8, 2026
2f24147
Use lazy logging args instead of eager % interpolation
iskandr Jul 8, 2026
89869f1
Bump version to 2.7.2
iskandr Jul 8, 2026
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2 changes: 1 addition & 1 deletion gtfparse/__init__.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,7 +23,7 @@
read_gtf,
)

__version__ = "2.7.1"
__version__ = "2.7.2"

__all__ = [
"GENCODE_BIOTYPE_ALIASES",
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3 changes: 1 addition & 2 deletions gtfparse/attribute_parsing.py
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Expand Up @@ -14,7 +14,6 @@
from collections import OrderedDict
from sys import intern

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -103,5 +102,5 @@ def expand_attribute_strings(attribute_strings, quote_char="'", missing_value=""
extra_columns[column_name] = column
column_order.append(column_name)

logging.info("Extracted GTF attributes: %s" % column_order)
logger.info("Extracted GTF attributes: %s", column_order)
return OrderedDict((column_name, extra_columns[column_name]) for column_name in column_order)
5 changes: 2 additions & 3 deletions gtfparse/create_missing_features.py
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Expand Up @@ -15,7 +15,6 @@

import pandas as pd

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -58,9 +57,9 @@ def create_missing_features(dataframe, unique_keys={}, extra_columns={}, missing

for feature_name, groupby_key in unique_keys.items():
if feature_name in existing_features:
logging.info("Feature '%s' already exists in GTF data" % feature_name)
logger.info("Feature '%s' already exists in GTF data", feature_name)
continue
logging.info("Creating rows for missing feature '%s'" % feature_name)
logger.info("Creating rows for missing feature '%s'", feature_name)

# don't include rows where the groupby key was missing
missing = pd.Series([x is None or x == "" for x in dataframe[groupby_key]])
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5 changes: 2 additions & 3 deletions gtfparse/read_gtf.py
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Expand Up @@ -19,7 +19,6 @@
from .attribute_parsing import expand_attribute_strings
from .parsing_error import ParsingError

logging.basicConfig(level=logging.INFO)
logger = logging.getLogger(__name__)


Expand Down Expand Up @@ -406,10 +405,10 @@ def wrapped_fn(x):
# the 2nd column is the transcript_biotype (otherwise, it's the
# gene_biotype)
if "gene_biotype" not in column_names:
logging.info("Using column 'source' to replace missing 'gene_biotype'")
logger.info("Using column 'source' to replace missing 'gene_biotype'")
result_df["gene_biotype"] = result_df["source"]
if "transcript_biotype" not in column_names:
logging.info("Using column 'source' to replace missing 'transcript_biotype'")
logger.info("Using column 'source' to replace missing 'transcript_biotype'")
result_df["transcript_biotype"] = result_df["source"]

if usecols is not None:
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