diff --git a/.github/workflows/publish-pypi.yml b/.github/workflows/publish-pypi.yml
index 796105b..1760f1d 100644
--- a/.github/workflows/publish-pypi.yml
+++ b/.github/workflows/publish-pypi.yml
@@ -52,4 +52,4 @@ jobs:
# This uses the trusted publisher workflow so no token is required.
- name: Publish to PyPI
- uses: pypa/gh-action-pypi-publish@release/v1
\ No newline at end of file
+ uses: pypa/gh-action-pypi-publish@release/v1
diff --git a/.github/workflows/run-tests.yml b/.github/workflows/run-tests.yml
index 4e9342f..90aa16a 100644
--- a/.github/workflows/run-tests.yml
+++ b/.github/workflows/run-tests.yml
@@ -30,4 +30,4 @@ jobs:
- name: Test with tox
run: |
- tox
\ No newline at end of file
+ tox
diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 8d2a1c7..03b8f5b 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -2,7 +2,7 @@ exclude: '^docs/conf.py'
repos:
- repo: https://github.com/pre-commit/pre-commit-hooks
- rev: v5.0.0
+ rev: v6.0.0
hooks:
- id: trailing-whitespace
- id: check-added-large-files
@@ -33,7 +33,7 @@ repos:
- repo: https://github.com/astral-sh/ruff-pre-commit
# Ruff version.
- rev: v0.8.6
+ rev: v0.14.9
hooks:
- id: ruff
args: [--fix, --exit-non-zero-on-fix]
diff --git a/README.md b/README.md
index b428ba7..cc20fb7 100644
--- a/README.md
+++ b/README.md
@@ -82,7 +82,7 @@ dataset = garr.build_genomicarray(
```
> [!NOTE]
-> - The aggregate function is expected to return either a scalar value or a 1-dimensional NumPy ndarray. If the later, users need to specify the expected dimension of the return array. e.g.
+> - The aggregate function is expected to return either a scalar value or a 1-dimensional NumPy ndarray. If the later, users need to specify the expected dimension of the return array. e.g.
> ```python
> feature_annotation_options=garr.FeatureAnnotationOptions(
> aggregate_function = my_custom_func,
diff --git a/assets/genarr.svg b/assets/genarr.svg
index 1bd5617..f13ef20 100644
--- a/assets/genarr.svg
+++ b/assets/genarr.svg
@@ -1 +1 @@
-
\ No newline at end of file
+
diff --git a/src/genomicarrays/GenomicArrayDatasetSlice.py b/src/genomicarrays/GenomicArrayDatasetSlice.py
index 8b58aa1..605793f 100644
--- a/src/genomicarrays/GenomicArrayDatasetSlice.py
+++ b/src/genomicarrays/GenomicArrayDatasetSlice.py
@@ -29,10 +29,7 @@
from dataclasses import dataclass
from typing import Any
-import anndata
-import genomicranges as gr
import pandas as pd
-import summarizedexperiment as se
__author__ = "Jayaram Kancherla"
__copyright__ = "Jayaram Kancherla"
diff --git a/src/genomicarrays/build_genomicarray.py b/src/genomicarrays/build_genomicarray.py
index cf5214f..5f3dd20 100644
--- a/src/genomicarrays/build_genomicarray.py
+++ b/src/genomicarrays/build_genomicarray.py
@@ -315,4 +315,6 @@ def _write_intervals_to_tiledb(outpath, intervals, bwpath, bwidx, agg_func, tota
def _wrapper_extract_bwinfo(args):
"""Wrapper for multiprocessing multiple files and intervals."""
counts_uri, input_intervals, bwpath, idx, agg_func, total_length, outsize_per_feature = args
- return _write_intervals_to_tiledb(counts_uri, input_intervals, bwpath, idx, agg_func, total_length, outsize_per_feature)
+ return _write_intervals_to_tiledb(
+ counts_uri, input_intervals, bwpath, idx, agg_func, total_length, outsize_per_feature
+ )
diff --git a/src/genomicarrays/build_options.py b/src/genomicarrays/build_options.py
index a7b00da..19accb6 100644
--- a/src/genomicarrays/build_options.py
+++ b/src/genomicarrays/build_options.py
@@ -125,7 +125,7 @@ class FeatureAnnotationOptions:
interval. The aggregate function is expected to
return either a scalar value or a 1-dimensional
NumPy `ndarray`.
-
+
Defaults to None.
expected_agg_function_length:
diff --git a/tests/agg_test.py b/tests/agg_test.py
index 262b68f..948c9a6 100644
--- a/tests/agg_test.py
+++ b/tests/agg_test.py
@@ -6,4 +6,4 @@
def aggfunc(x):
print(x)
- return np.array([np.nanmin(x), np.nansum(x)])
\ No newline at end of file
+ return np.array([np.nanmin(x), np.nansum(x)])
diff --git a/tests/test_ingest.py b/tests/test_ingest.py
index 3e9a6ed..07337d4 100644
--- a/tests/test_ingest.py
+++ b/tests/test_ingest.py
@@ -113,4 +113,4 @@ def test_ingest_bigwigs_agg_not_scalar():
sfp = tiledb.open(f"{tempdir}/sample_metadata", "r")
samples = sfp.df[:]
- assert len(samples) == 2
\ No newline at end of file
+ assert len(samples) == 2