From 15946a89532856c6800c42e026ca8622b6de8ef8 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Wed, 27 Dec 2023 19:26:27 +0000
Subject: [PATCH] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/summarizedexperiment/BaseSE.py            |  2 +-
 .../RangedSummarizedExperiment.py             | 16 ++++++++--------
 .../SummarizedExperiment.py                   | 16 ++++++++--------
 tests/test_SE_combine_cols.py                 | 19 +++++++++++++++----
 4 files changed, 32 insertions(+), 21 deletions(-)

diff --git a/src/summarizedexperiment/BaseSE.py b/src/summarizedexperiment/BaseSE.py
index 4845e0e..14229e2 100644
--- a/src/summarizedexperiment/BaseSE.py
+++ b/src/summarizedexperiment/BaseSE.py
@@ -1062,4 +1062,4 @@ def to_anndata(self):
             layers=layers,
         )
 
-        return obj
\ No newline at end of file
+        return obj
diff --git a/src/summarizedexperiment/RangedSummarizedExperiment.py b/src/summarizedexperiment/RangedSummarizedExperiment.py
index 8386902..735b509 100644
--- a/src/summarizedexperiment/RangedSummarizedExperiment.py
+++ b/src/summarizedexperiment/RangedSummarizedExperiment.py
@@ -967,10 +967,10 @@ def combine_columns(*x: RangedSummarizedExperiment) -> RangedSummarizedExperimen
 
 @ut.relaxed_combine_rows.register(RangedSummarizedExperiment)
 def relaxed_combine_rows(*x: RangedSummarizedExperiment) -> RangedSummarizedExperiment:
-    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_rows` method for :py:class:`~RangedSummarizedExperiment`
-    objects.  Whereas ``combine_rows`` expects that all objects have the same columns, ``relaxed_combine_rows`` allows
-    for different columns. Absent columns in any object are filled in with appropriate placeholder values before
-    combining.
+    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_rows` method for
+    :py:class:`~RangedSummarizedExperiment` objects.  Whereas ``combine_rows`` expects that all objects have the same
+    columns, ``relaxed_combine_rows`` allows for different columns. Absent columns in any object are filled in with
+    appropriate placeholder values before combining.
 
     Args:
         x:
@@ -1008,10 +1008,10 @@ def relaxed_combine_rows(*x: RangedSummarizedExperiment) -> RangedSummarizedExpe
 def relaxed_combine_columns(
     *x: RangedSummarizedExperiment,
 ) -> RangedSummarizedExperiment:
-    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_columns` method for :py:class:`~RangedSummarizedExperiment`
-    objects.  Whereas ``combine_columns`` expects that all objects have the same rows, ``relaxed_combine_columns`` allows
-    for different rows. Absent columns in any object are filled in with appropriate placeholder values before
-    combining.
+    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_columns` method for
+    :py:class:`~RangedSummarizedExperiment` objects.  Whereas ``combine_columns`` expects that all objects have the same
+    rows, ``relaxed_combine_columns`` allows for different rows. Absent columns in any object are filled in with
+    appropriate placeholder values before combining.
 
     Args:
         x:
diff --git a/src/summarizedexperiment/SummarizedExperiment.py b/src/summarizedexperiment/SummarizedExperiment.py
index b0d04f3..ebdc718 100644
--- a/src/summarizedexperiment/SummarizedExperiment.py
+++ b/src/summarizedexperiment/SummarizedExperiment.py
@@ -163,10 +163,10 @@ def combine_columns(*x: SummarizedExperiment) -> SummarizedExperiment:
 
 @ut.relaxed_combine_rows.register(SummarizedExperiment)
 def relaxed_combine_rows(*x: SummarizedExperiment) -> SummarizedExperiment:
-    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_rows` method for :py:class:`~SummarizedExperiment`
-    objects.  Whereas ``combine_rows`` expects that all objects have the same columns, ``relaxed_combine_rows`` allows
-    for different columns. Absent columns in any object are filled in with appropriate placeholder values before
-    combining.
+    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_rows` method for
+    :py:class:`~SummarizedExperiment` objects.  Whereas ``combine_rows`` expects that all objects have the same columns,
+    ``relaxed_combine_rows`` allows for different columns. Absent columns in any object are filled in with appropriate
+    placeholder values before combining.
 
     Args:
         x:
@@ -198,10 +198,10 @@ def relaxed_combine_rows(*x: SummarizedExperiment) -> SummarizedExperiment:
 
 @ut.relaxed_combine_columns.register(SummarizedExperiment)
 def relaxed_combine_columns(*x: SummarizedExperiment) -> SummarizedExperiment:
-    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_columns` method for :py:class:`~SummarizedExperiment`
-    objects.  Whereas ``combine_columns`` expects that all objects have the same rows, ``relaxed_combine_columns`` allows
-    for different rows. Absent columns in any object are filled in with appropriate placeholder values before
-    combining.
+    """A relaxed version of the :py:func:`~biocutils.combine_rows.combine_columns` method for
+    :py:class:`~SummarizedExperiment` objects.  Whereas ``combine_columns`` expects that all objects have the same rows,
+    ``relaxed_combine_columns`` allows for different rows. Absent columns in any object are filled in with appropriate
+    placeholder values before combining.
 
     Args:
         x:
diff --git a/tests/test_SE_combine_cols.py b/tests/test_SE_combine_cols.py
index 71be166..4aafc22 100644
--- a/tests/test_SE_combine_cols.py
+++ b/tests/test_SE_combine_cols.py
@@ -43,7 +43,11 @@ def test_SE_combine_cols_with_names_mixed(summarized_experiments):
     assert combined.shape == (3, 6)
     assert set(combined.assay_names).issubset(["counts", "lognorm"])
     assert list(combined.row_data.column_names) == ["seqnames", "start", "end"]
-    assert list(combined.column_data.column_names) == ['sample', 'disease', 'doublet_score']
+    assert list(combined.column_data.column_names) == [
+        "sample",
+        "disease",
+        "doublet_score",
+    ]
     assert combined.row_names is not None
     assert len(combined.row_names) == 3
     assert combined.column_names is not None
@@ -58,7 +62,11 @@ def test_SE_combine_cols_with_names_mixed(summarized_experiments):
     assert combined.shape == (3, 6)
     assert set(combined.assay_names).issubset(["counts", "lognorm"])
     assert list(combined.row_data.column_names) == ["seqnames", "start", "end"]
-    assert list(combined.column_data.column_names) == ['sample', 'disease', 'doublet_score']
+    assert list(combined.column_data.column_names) == [
+        "sample",
+        "disease",
+        "doublet_score",
+    ]
     assert combined.row_names is not None
     assert len(combined.row_names) == 3
     assert combined.column_names is not None
@@ -77,7 +85,11 @@ def test_SE_both_combine_cols_with_names(summarized_experiments):
     assert combined.shape == (3, 6)
     assert set(combined.assay_names).issubset(["counts", "lognorm"])
     assert list(combined.row_data.column_names) == ["seqnames", "start", "end"]
-    assert list(combined.column_data.column_names) == ['sample', 'disease', 'doublet_score']
+    assert list(combined.column_data.column_names) == [
+        "sample",
+        "disease",
+        "doublet_score",
+    ]
     assert combined.row_names is not None
     assert len(combined.row_names) == 3
     assert combined.column_names is not None
@@ -95,4 +107,3 @@ def test_SE_both_combine_cols_with_names(summarized_experiments):
     assert len(combined.column_data.column_names) > 2
     assert combined.row_names is not None
     assert combined.column_names is not None
-