[pre-commit.ci] pre-commit autoupdate (#440)

* [pre-commit.ci] pre-commit autoupdate updates: - [github.com/astral-sh/ruff-pre-commit: v0.7.0 → v0.8.3](astral-sh/ruff-pre-commit@v0.7.0...v0.8.3) * [pre-commit.ci] auto fixes from pre-commit.com hooks for more information, see https://pre-commit.ci * Fix grouping --------- Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com> Co-authored-by: Nezar Abdennur <[email protected]>
open2c · Dec 19, 2024 · b75ba11 · b75ba11
1 parent c5a0684
commit b75ba11
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Showing 10 changed files with 33 additions and 33 deletions.
diff --git a/.pre-commit-config.yaml b/.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: v0.8.3
     hooks:
       - id: ruff
         args: [--fix, --show-fixes, --exit-non-zero-on-fix]
diff --git a/docs/make_cli_rst.py b/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
 

diff --git a/src/cooler/__init__.py b/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",
 ]
diff --git a/src/cooler/_reduce.py b/src/cooler/_reduce.py
@@ -20,7 +20,7 @@
 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__)

diff --git a/src/cooler/_typing.py b/src/cooler/_typing.py
@@ -13,4 +13,4 @@
 GenomicRangeTuple = tuple[str, int, int]
 Tabular = Union[pd.DataFrame, dict[str, np.ndarray]]
 
-__all__ = ["MapFunctor", "GenomicRangeSpecifier", "GenomicRangeTuple", "Tabular"]
+__all__ = ["GenomicRangeSpecifier", "GenomicRangeTuple", "MapFunctor", "Tabular"]
diff --git a/src/cooler/cli/zoomify.py b/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.",

diff --git a/src/cooler/core/__init__.py b/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",
 ]
diff --git a/src/cooler/create/__init__.py b/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",

diff --git a/src/cooler/fileops.py b/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:

diff --git a/src/cooler/parallel.py b/src/cooler/parallel.py
@@ -16,7 +16,7 @@
 from .core import get
 from .util import partition
 
-__all__ = ["partition", "split", "lock"]
+__all__ = ["lock", "partition", "split"]
 
 """
 Two possible reasons for using a lock