[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -9,7 +9,7 @@ repos:
       - id: check-case-conflict
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.9.3
     hooks:
       - id: ruff
         types_or: [python, pyi, jupyter]

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 (

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",
 ]

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",
 ]
 
 

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",
 ]

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"}}

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",
 ]
 

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"
 ]
 
 

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",
 ]

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",
 ]
 
 

bioframe/io/resources.py

@@ -11,9 +11,9 @@
 from .schemas import SCHEMAS
 
 __all__ = [
-    "fetch_chromsizes",
-    "fetch_centromeres",
     "UCSCClient",
+    "fetch_centromeres",
+    "fetch_chromsizes",
 ]
 
 

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",
 ]