[pre-commit.ci] auto fixes from pre-commit.com hooks

pre-commit-ci[bot] · pre-commit-ci[bot] · commit efe0aff52909 · 2025-03-17T16:29:58.000Z
for more information, see https://pre-commit.ci
diff --git a/bioframe/__init__.py b/bioframe/__init__.py
@@ -9,7 +9,25 @@
     __version__ = "unknown"
 
 __all__ = [
+    "SCHEMAS",
+    "UCSCClient",
     "arrops",
+    "assemblies_available",
+    "assembly_info",
+    "assign_view",
+    "binnify",
+    "closest",
+    "cluster",
+    "complement",
+    "count_overlaps",
+    "coverage",
+    "digest",
+    "expand",
+    "fetch_centromeres",
+    "fetch_chromsizes",
+    "frac_gc",
+    "frac_gene_coverage",
+    "frac_mapped",
     "from_any",
     "from_dict",
     "from_list",
@@ -24,27 +42,17 @@
     "is_sorted",
     "is_tiling",
     "is_viewframe",
+    "load_fasta",
+    "make_chromarms",
     "make_viewframe",
+    "mark_runs",
+    "merge",
+    "merge_runs",
+    "overlap",
+    "pair_by_distance",
     "parse_region",
     "parse_region_string",
-    "sanitize_bedframe",
-    "to_ucsc_string",
-    "update_default_colnames",
-    "binnify",
-    "digest",
-    "frac_gc",
-    "frac_gene_coverage",
-    "frac_mapped",
-    "make_chromarms",
-    "pair_by_distance",
-    "seq_gc",
-    "SCHEMAS",
-    "UCSCClient",
-    "assemblies_available",
-    "assembly_info",
-    "fetch_centromeres",
-    "fetch_chromsizes",
-    "load_fasta",
+    "plot_intervals",
     "read_alignments",
     "read_bam",
     "read_bigbed",
@@ -53,30 +61,22 @@
     "read_pairix",
     "read_tabix",
     "read_table",
-    "to_bed",
-    "to_bigbed",
-    "to_bigwig",
-    "assign_view",
-    "closest",
-    "cluster",
-    "complement",
-    "count_overlaps",
-    "coverage",
-    "expand",
-    "merge",
-    "overlap",
-    "mark_runs",
-    "merge_runs",
+    "sanitize_bedframe",
     "select",
     "select_indices",
     "select_labels",
     "select_mask",
+    "seq_gc",
     "setdiff",
     "sort_bedframe",
     "subtract",
-    "trim",
-    "plot_intervals",
+    "to_bed",
+    "to_bigbed",
+    "to_bigwig",
     "to_ucsc_colorstring",
+    "to_ucsc_string",
+    "trim",
+    "update_default_colnames",
 ]
 
 from .core import (
diff --git a/bioframe/core/__init__.py b/bioframe/core/__init__.py
@@ -27,24 +27,24 @@
 
 __all__ = [
     "arrops",
+    "from_any",
+    "from_dict",
+    "from_list",
+    "from_series",
     "is_bedframe",
     "is_cataloged",
+    "is_chrom_dtype",
+    "is_complete_ucsc_string",
     "is_contained",
     "is_covering",
     "is_overlapping",
     "is_sorted",
     "is_tiling",
     "is_viewframe",
-    "from_any",
-    "from_dict",
-    "from_list",
-    "from_series",
     "make_viewframe",
-    "sanitize_bedframe",
-    "is_chrom_dtype",
-    "update_default_colnames",
-    "is_complete_ucsc_string",
     "parse_region",
     "parse_region_string",
+    "sanitize_bedframe",
     "to_ucsc_string",
+    "update_default_colnames",
 ]
diff --git a/bioframe/core/checks.py b/bioframe/core/checks.py
@@ -8,12 +8,12 @@
 __all__ = [
     "is_bedframe",
     "is_cataloged",
-    "is_overlapping",
-    "is_viewframe",
     "is_contained",
     "is_covering",
-    "is_tiling",
+    "is_overlapping",
     "is_sorted",
+    "is_tiling",
+    "is_viewframe",
 ]
 
 
diff --git a/bioframe/core/construction.py b/bioframe/core/construction.py
@@ -6,10 +6,10 @@
 from .stringops import is_complete_ucsc_string, parse_region_string, to_ucsc_string
 
 __all__ = [
+    "from_any",
     "from_dict",
-    "from_series",
     "from_list",
-    "from_any",
+    "from_series",
     "make_viewframe",
     "sanitize_bedframe",
 ]
diff --git a/bioframe/core/specs.py b/bioframe/core/specs.py
@@ -4,8 +4,8 @@
 import pandas as pd
 
 __all__ = [
-    "update_default_colnames",
     "is_chrom_dtype",
+    "update_default_colnames",
 ]
 
 _rc = {"colnames": {"chrom": "chrom", "start": "start", "end": "end"}}
diff --git a/bioframe/core/stringops.py b/bioframe/core/stringops.py
@@ -4,9 +4,9 @@
 import pandas as pd
 
 __all__ = [
+    "is_complete_ucsc_string",
     "parse_region",
     "parse_region_string",
-    "is_complete_ucsc_string",
     "to_ucsc_string",
 ]
 
diff --git a/bioframe/extras.py b/bioframe/extras.py
@@ -7,16 +7,16 @@
 from .core.specs import _get_default_colnames, _verify_columns
 
 __all__ = [
-    "make_chromarms",
     "binnify",
     "digest",
-    "frac_mapped",
     "frac_gc",
-    "seq_gc",
     "frac_gene_coverage",
-    "pair_by_distance",
+    "frac_mapped",
+    "make_chromarms",
     "mark_runs",
-    "merge_runs"
+    "merge_runs",
+    "pair_by_distance",
+    "seq_gc"
 ]
 
 
diff --git a/bioframe/io/__init__.py b/bioframe/io/__init__.py
@@ -17,22 +17,22 @@
 from .schemas import SCHEMAS
 
 __all__ = [
+    "SCHEMAS",
+    "UCSCClient",
     "assemblies_available",
     "assembly_info",
-    "read_table",
-    "read_chromsizes",
-    "read_tabix",
-    "read_pairix",
-    "read_bam",
-    "read_alignments",
+    "fetch_centromeres",
+    "fetch_chromsizes",
     "load_fasta",
+    "read_alignments",
+    "read_bam",
+    "read_bigbed",
     "read_bigwig",
+    "read_chromsizes",
+    "read_pairix",
+    "read_tabix",
+    "read_table",
     "to_bed",
-    "to_bigwig",
-    "read_bigbed",
     "to_bigbed",
-    "UCSCClient",
-    "fetch_centromeres",
-    "fetch_chromsizes",
-    "SCHEMAS",
+    "to_bigwig",
 ]
diff --git a/bioframe/io/fileops.py b/bioframe/io/fileops.py
@@ -26,16 +26,16 @@
 from .schemas import BAM_FIELDS, SCHEMAS
 
 __all__ = [
-    "read_table",
-    "read_chromsizes",
-    "read_tabix",
-    "read_pairix",
-    "read_alignments",
     "load_fasta",
-    "read_bigwig",
-    "to_bigwig",
+    "read_alignments",
     "read_bigbed",
+    "read_bigwig",
+    "read_chromsizes",
+    "read_pairix",
+    "read_tabix",
+    "read_table",
     "to_bigbed",
+    "to_bigwig",
 ]
 
 
diff --git a/bioframe/io/resources.py b/bioframe/io/resources.py
@@ -11,9 +11,9 @@
 from .schemas import SCHEMAS
 
 __all__ = [
-    "fetch_chromsizes",
-    "fetch_centromeres",
     "UCSCClient",
+    "fetch_centromeres",
+    "fetch_chromsizes",
 ]
 
 
diff --git a/bioframe/ops.py b/bioframe/ops.py
@@ -6,23 +6,23 @@
 from .core.stringops import parse_region
 
 __all__ = [
+    "assign_view",
+    "closest",
+    "cluster",
+    "complement",
+    "count_overlaps",
+    "coverage",
+    "expand",
+    "merge",
+    "overlap",
     "select",
-    "select_mask",
     "select_indices",
     "select_labels",
-    "expand",
-    "overlap",
-    "cluster",
-    "merge",
-    "coverage",
-    "closest",
-    "subtract",
+    "select_mask",
     "setdiff",
-    "count_overlaps",
-    "trim",
-    "complement",
     "sort_bedframe",
-    "assign_view",
+    "subtract",
+    "trim",
 ]
 
 

Original file line number	Diff line number	Diff line change
`@@ -4,8 +4,8 @@`
`4`	`4`	`import pandas as pd`
`5`	`5`
`6`	`6`	`__all__ = [`
`7`		`- "update_default_colnames",`
`8`	`7`	`"is_chrom_dtype",`
	`8`	`+ "update_default_colnames",`
`9`	`9`	`]`
`10`	`10`
`11`	`11`	`_rc = {"colnames": {"chrom": "chrom", "start": "start", "end": "end"}}`
Original file line number	Diff line number	Diff line change
`@@ -4,9 +4,9 @@`
`4`	`4`	`import pandas as pd`
`5`	`5`
`6`	`6`	`__all__ = [`
	`7`	`+ "is_complete_ucsc_string",`
`7`	`8`	`"parse_region",`
`8`	`9`	`"parse_region_string",`
`9`		`- "is_complete_ucsc_string",`
`10`	`10`	`"to_ucsc_string",`
`11`	`11`	`]`
`12`	`12`
Original file line number	Diff line number	Diff line change
`@@ -11,9 +11,9 @@`
`11`	`11`	`from .schemas import SCHEMAS`
`12`	`12`
`13`	`13`	`__all__ = [`
`14`		`- "fetch_chromsizes",`
`15`		`- "fetch_centromeres",`
`16`	`14`	`"UCSCClient",`
	`15`	`+ "fetch_centromeres",`
	`16`	`+ "fetch_chromsizes",`
`17`	`17`	`]`
`18`	`18`
`19`	`19`