[pre-commit.ci] pre-commit autoupdate

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: check-case-conflict
 
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.7.0
+    rev: v0.8.0
     hooks:
       - id: ruff
         args: [--fix, --show-fixes, --exit-non-zero-on-fix]

docs/make_cli_rst.py

@@ -60,7 +60,7 @@ def _write_opts(opts):
     if opt.required:
         extra.append("required")
     if extra:
-        help = "{}[{}]".format(help and help + "  " or "", "; ".join(extra))
+        help = "{}[{}]".format((help and help + "  ") or "", "; ".join(extra))
 
     return ", ".join(rv), help
 

src/cooler/__init__.py

@@ -19,21 +19,21 @@
 
 __all__ = [
     "Cooler",
+    "__format_version__",
+    "__version__",
     "annotate",
     "balance_cooler",
+    "binnify",
+    "coarsen_cooler",
     "create_cooler",
     "create_scool",
-    "rename_chroms",
-    "coarsen_cooler",
-    "merge_coolers",
-    "zoomify_cooler",
+    "fetch_chromsizes",
     "fileops",
+    "get_verbosity_level",
+    "merge_coolers",
     "parallel",
-    "binnify",
-    "fetch_chromsizes",
     "read_chromsizes",
-    "get_verbosity_level",
+    "rename_chroms",
     "set_verbosity_level",
-    "__version__",
-    "__format_version__",
+    "zoomify_cooler",
 ]

src/cooler/_reduce.py

@@ -19,7 +19,7 @@
 from .parallel import lock
 from .util import GenomeSegmentation, parse_cooler_uri
 
-__all__ = ["merge_coolers", "coarsen_cooler", "zoomify_cooler"]
+__all__ = ["coarsen_cooler", "merge_coolers", "zoomify_cooler"]
 
 
 logger = get_logger(__name__)

src/cooler/_typing.py

@@ -12,4 +12,4 @@
 GenomicRangeTuple = Tuple[str, int, int]
 Tabular = Union[pd.DataFrame, Dict[str, np.ndarray]]
 
-__all__ = ["MapFunctor", "GenomicRangeSpecifier", "GenomicRangeTuple", "Tabular"]
+__all__ = ["GenomicRangeSpecifier", "GenomicRangeTuple", "MapFunctor", "Tabular"]

src/cooler/cli/zoomify.py

@@ -194,7 +194,7 @@ def zoomify(
         # Parse and expand user-provided resolutions
         resolutions, rstring = [], resolutions
         for res in [s.strip().lower() for s in rstring.split(",")]:
-            if "n" in res or "b" in res and maxres < curres:
+            if "n" in res or ("b" in res and maxres < curres):
                 warnings.warn(
                     "Map is already < 256 x 256. Provide resolutions "
                     "explicitly if you want to coarsen more.",

src/cooler/core/__init__.py

@@ -14,9 +14,9 @@
     "FillLowerRangeQuery2D",
     "RangeSelector1D",
     "RangeSelector2D",
-    "region_to_extent",
-    "region_to_offset",
     "delete",
     "get",
     "put",
+    "region_to_extent",
+    "region_to_offset",
 ]

src/cooler/create/__init__.py

@@ -36,33 +36,33 @@
 )
 
 __all__ = [
-    "MAGIC",
-    "MAGIC_SCOOL",
-    "MAGIC_MCOOL",
-    "URL",
-    "CHROM_DTYPE",
+    "BIN1OFFSET_DTYPE",
+    "BIN_DTYPE",
     "CHROMID_DTYPE",
+    "CHROMOFFSET_DTYPE",
     "CHROMSIZE_DTYPE",
+    "CHROM_DTYPE",
     "COORD_DTYPE",
-    "BIN_DTYPE",
     "COUNT_DTYPE",
-    "CHROMOFFSET_DTYPE",
-    "BIN1OFFSET_DTYPE",
-    "PIXEL_FIELDS",
+    "MAGIC",
+    "MAGIC_MCOOL",
+    "MAGIC_SCOOL",
     "PIXEL_DTYPES",
-    "append",
-    "create",
-    "create_cooler",
-    "create_from_unordered",
-    "create_scool",
-    "rename_chroms",
+    "PIXEL_FIELDS",
+    "URL",
     "ArrayLoader",
     "BadInputError",
     "ContactBinner",
     "HDF5Aggregator",
     "PairixAggregator",
     "TabixAggregator",
     "aggregate_records",
+    "append",
+    "create",
+    "create_cooler",
+    "create_from_unordered",
+    "create_scool",
+    "rename_chroms",
     "sanitize_pixels",
     "sanitize_records",
     "validate_pixels",

src/cooler/fileops.py

@@ -24,7 +24,7 @@
 from .create import MAGIC, MAGIC_SCOOL
 from .util import natsorted, parse_cooler_uri
 
-__all__ = ["is_cooler", "is_multires_file", "list_coolers", "cp", "mv", "ln"]
+__all__ = ["cp", "is_cooler", "is_multires_file", "list_coolers", "ln", "mv"]
 
 
 def json_dumps(o: object) -> str:

src/cooler/parallel.py

@@ -15,7 +15,7 @@
 from .core import get
 from .util import partition
 
-__all__ = ["partition", "split", "lock"]
+__all__ = ["lock", "partition", "split"]
 
 """
 Two possible reasons for using a lock