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[pre-commit.ci] pre-commit autoupdate #64

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0ff8979
[pre-commit.ci] pre-commit autoupdate
pre-commit-ci[bot] Jan 19, 2026
6266c91
[pre-commit.ci] auto fixes from pre-commit.com hooks
pre-commit-ci[bot] Jan 19, 2026
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14 changes: 7 additions & 7 deletions .pre-commit-config.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -6,20 +6,20 @@ default_stages:
- pre-push
minimum_pre_commit_version: 2.16.0
repos:
- repo: https://github.com/psf/black
rev: 25.1.0
- repo: https://github.com/psf/black-pre-commit-mirror
rev: 26.1.0
hooks:
- id: black
- repo: https://github.com/pre-commit/mirrors-prettier
rev: v4.0.0-alpha.8
hooks:
- id: prettier
- repo: https://github.com/asottile/blacken-docs
rev: 1.19.1
rev: 1.20.0
hooks:
- id: blacken-docs
- repo: https://github.com/PyCQA/isort
rev: 6.0.0
rev: 7.0.0
hooks:
- id: isort
- repo: https://github.com/asottile/yesqa
Expand All @@ -34,7 +34,7 @@ repos:
- flake8-bugbear
- flake8-blind-except
- repo: https://github.com/pre-commit/pre-commit-hooks
rev: v5.0.0
rev: v6.0.0
hooks:
- id: detect-private-key
- id: check-ast
Expand All @@ -53,7 +53,7 @@ repos:
- --remove-unused-variable
- --ignore-init-module-imports
- repo: https://github.com/PyCQA/flake8
rev: 7.1.2
rev: 7.3.0
hooks:
- id: flake8
additional_dependencies:
Expand All @@ -64,7 +64,7 @@ repos:
- flake8-bugbear
- flake8-blind-except
- repo: https://github.com/asottile/pyupgrade
rev: v3.19.1
rev: v3.21.2
hooks:
- id: pyupgrade
args: [--py3-plus, --py38-plus, --keep-runtime-typing]
2 changes: 1 addition & 1 deletion ALLCools/clustering/feature_selection/feature_enrichment.py
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Expand Up @@ -241,7 +241,7 @@ def cluster_enriched_features(
null_values = null_enrichment.iloc[row, :].sort_values()
values = enrichment.iloc[row, :]
pvals = 1 - np.searchsorted(null_values, values) / values.shape[0]
(_, q, _, _) = multipletests(pvals, alpha, method="fdr_bh")
_, q, _, _ = multipletests(pvals, alpha, method="fdr_bh")
qvals[row, :] = q
qvals = pd.DataFrame(qvals, index=enrichment.index, columns=enrichment.columns)

Expand Down
5 changes: 1 addition & 4 deletions ALLCools/plot/genome_track/GtfTrack.py
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Expand Up @@ -181,9 +181,7 @@ class GtfTrack(BedTrack):

SUPPORTED_ENDINGS = ["gtf", "gtf.gz", "gtf.db"]
TRACK_TYPE = "gtf"
OPTIONS_TXT = (
GenomeTrack.OPTIONS_TXT
+ f"""
OPTIONS_TXT = GenomeTrack.OPTIONS_TXT + f"""
# By default the transcript_name is used.
# If you want to use the gene_name:
# prefered_name = gene_name
Expand Down Expand Up @@ -255,7 +253,6 @@ class GtfTrack(BedTrack):
# optional. If not given is guessed from the file ending.
file_type = {TRACK_TYPE}
"""
)

DEFAULTS_PROPERTIES = {
"fontsize": 12,
Expand Down
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