[pre-commit.ci] pre-commit autoupdate

.github/workflows/publish-pypi.yml

@@ -52,4 +52,4 @@
 
       # This uses the trusted publisher workflow so no token is required.
       - name: Publish to PyPI
-        uses: pypa/gh-action-pypi-publish@release/v1
+        uses: pypa/gh-action-pypi-publish@release/v1

.github/workflows/run-tests.yml

@@ -30,4 +30,4 @@ jobs:
 
       - name: Test with tox
         run: |
-          tox
+          tox

.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: v0.14.8
   hooks:
     - id: ruff
       args: [--fix, --exit-non-zero-on-fix]

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,

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"

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
+    )

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:

tests/agg_test.py

@@ -6,4 +6,4 @@
 
 def aggfunc(x):
     print(x)
-    return np.array([np.nanmin(x), np.nansum(x)])
+    return np.array([np.nanmin(x), np.nansum(x)])

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
+    assert len(samples) == 2