[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: v0.14.14
+    rev: v0.16.2
     hooks:
       - id: ruff
         args: [--fix, --show-fixes, --exit-non-zero-on-fix]

src/cooler/_reduce.py

@@ -314,7 +314,7 @@ def _greedy_prune_partition(edges: np.ndarray, maxlen: int) -> np.ndarray:
     edges = np.asarray(edges)
     assert len(edges) >= 2 and edges[0] == 0
     cumlen = np.r_[0, np.cumsum(np.diff(edges))]
-    cuts = [maxlen * i for i in range(0, int(np.ceil(cumlen[-1] / maxlen)))]
+    cuts = [maxlen * i for i in range(int(np.ceil(cumlen[-1] / maxlen)))]
     cuts.append(cumlen[-1])
     idx = np.unique(np.searchsorted(cumlen, cuts))
     return edges[idx]

src/cooler/cli/dump.py

@@ -300,5 +300,4 @@ def dump(
             na_rep=na_rep,
         )
 
-    else:
-        f.flush()
+    f.flush()

src/cooler/core/_rangequery.py

@@ -295,7 +295,7 @@ def __call__(
 
         # Concatenate outputs
         if len(result["bin1_id"]):
-            for key in result.keys():
+            for key in result:
                 result[key] = np.concatenate(result[key], axis=0)
 
             if reflect:

src/cooler/create/_create.py

@@ -457,7 +457,7 @@ def _set_h5opts(h5opts: dict[str, Any]) -> dict[str, Any]:
         "fillvalue",
         "track_times",
     }
-    for key in result.keys():
+    for key in result:
         if key not in available_opts:
             raise ValueError(f"Unknown storage option '{key}'.")
     result.setdefault("compression", "gzip")

src/cooler/sandbox/dask.py

@@ -117,7 +117,7 @@ def read_table(group_uri, keys=None, chunksize=10_000_000, index=None, lock=None
 
     # Build the task graph
     dsk = {}
-    for i in range(0, ceil(nrows / chunksize)):
+    for i in range(ceil(nrows / chunksize)):
         slc = slice(i * chunksize, (i + 1) * chunksize)
         data_dict = (_slice_group, filepath, grouppath, keys, slc, lock)
         if categoricals:

src/cooler/util.py

@@ -189,7 +189,7 @@ def parse_region(
     return chrom, start, end
 
 
-def natsort_key(s: str, _NS_REGEX=re.compile(r"(\d+)", re.U)) -> tuple:
+def natsort_key(s: str, _NS_REGEX=re.compile(r"(\d+)", re.UNICODE)) -> tuple:
     return tuple([int(x) if x.isdigit() else x for x in _NS_REGEX.split(s) if x])
 
 

tests/test_util.py

@@ -267,15 +267,13 @@ def test_hdf5_contextmanagers():
     assert f.id
 
     # can't change mode on open file
-    with pytest.raises(ValueError):
-        with util.open_hdf5(f, "r+"):
-            pass
+    with pytest.raises(ValueError), util.open_hdf5(f, "r+"):
+        pass
 
     # not allowed on open files
     for mode in ["w", "w-", "x"]:
-        with pytest.raises(ValueError):
-            with util.open_hdf5(f, mode):
-                pass
+        with pytest.raises(ValueError), util.open_hdf5(f, mode):
+            pass
 
     # group's parent file gets closed on teardown
     with util.closing_hdf5(f["chroms"]):