style: Fix bugbear errors

docs/make_cli_rst.py

@@ -52,7 +52,7 @@ def _write_opts(opts):
     if opt.default is not None and opt.show_default:
         extra.append(
             "default: {}".format(
-                ", ".join("%s" % d for d in opt.default)
+                ", ".join(f"{d}" for d in opt.default)
                 if isinstance(opt.default, (list, tuple))
                 else opt.default
             )
@@ -161,7 +161,7 @@ def _format_envvar(param):
 
 def _format_envvars(ctx):
     """Format all envvars for a `click.Command`."""
-    params = [x for x in ctx.command.params if getattr(x, "envvar")]
+    params = [x for x in ctx.command.params if x.envvar]
 
     for param in params:
         yield ".. _{command_name}-{param_name}-{envvar}:".format(

pyproject.toml

@@ -96,6 +96,7 @@ cooler = "cooler.cli:cli"
 path = "src/cooler/_version.py"
 
 [tool.ruff]
+src = ["src"]
 exclude = [
     ".venv",
     "__init__.py",

src/cooler/balance.py

@@ -111,7 +111,9 @@ def _balance_genomewide(
             break
     else:
         warnings.warn(
-            "Iteration limit reached without convergence.", ConvergenceWarning
+            "Iteration limit reached without convergence.",
+            ConvergenceWarning,
+            stacklevel=1,
         )
 
     scale = nzmarg.mean()
@@ -180,6 +182,7 @@ def _balance_cisonly(
             warnings.warn(
                 f"Iteration limit reached without convergence on {chroms[cid]}.",
                 ConvergenceWarning,
+                stacklevel=1,
             )
 
         scale = nzmarg.mean()
@@ -244,7 +247,9 @@ def _balance_transonly(
             break
     else:
         warnings.warn(
-            "Iteration limit reached without convergence.", ConvergenceWarning
+            "Iteration limit reached without convergence.",
+            ConvergenceWarning,
+            stacklevel=1,
         )
 
     scale = nzmarg.mean()

src/cooler/cli/zoomify.py

@@ -197,7 +197,8 @@ def zoomify(
             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."
+                    "explicitly if you want to coarsen more.",
+                    stacklevel=1,
                 )
             if res == "n":
                 r = preferred_sequence(curres, maxres, "nice")

src/cooler/core/_rangequery.py

@@ -97,7 +97,7 @@ def sparray_slice_from_dict(
         raise ImportError(
             "The 'sparse' package is required for pydata/sparse output. "
             "You can install it with 'pip install sparse'."
-        )
+        ) from None
 
     shape = (row_stop - row_start, col_stop - col_start)
     return COO(
@@ -355,7 +355,7 @@ def to_delayed(self) -> list:
         except ImportError:
             raise ImportError(
                 "The 'dask' package is required for `dask.delayed` output."
-            )
+            ) from None
 
         out = []
         for task in self.tasks:
@@ -383,7 +383,7 @@ def to_dask_frame(self) -> Any:
             raise ImportError(
                 "The 'dask' package is required for dask DataFrame output. "
                 "Install dask[dataframe] or dask[complete] with pip."
-            )
+            ) from None
 
         meta = self.reader.get_frame_meta(self.field)
         tasks = self.tasks

src/cooler/create/_create.py

@@ -429,7 +429,9 @@ def _get_dtypes_arg(
     if "dtype" in kwargs:
         if dtypes is None:
             dtypes = kwargs.pop("dtype")
-            warnings.warn("Use dtypes= instead of dtype=", FutureWarning)
+            warnings.warn(
+                "Use dtypes= instead of dtype=", FutureWarning, stacklevel=2
+            )
         else:
             raise ValueError(
                 'Received both "dtypes" and "dtype" arguments. '
@@ -593,7 +595,8 @@ def create(
     if not symmetric_upper and triucheck:
         warnings.warn(
             "Creating a non-symmetric matrix, but `triucheck` was set to "
-            "True. Changing to False."
+            "True. Changing to False.",
+            stacklevel=2,
         )
         triucheck = False
 

src/cooler/create/_ingest.py

@@ -691,13 +691,15 @@ def __init__(
         for chrom in self.gs.contigs:
             if chrom not in self.file_contigs:
                 warnings.warn(
-                    "Did not find contig " + f" '{chrom}' in contact list file."
+                    "Did not find contig " + f" '{chrom}' in contact list file.",
+                    stacklevel=2,
                 )
 
         warnings.warn(
             "NOTE: When using the Tabix aggregator, make sure the order of "
             "chromosomes in the provided chromsizes agrees with the chromosome "
-            "ordering of read ends in the contact list file."
+            "ordering of read ends in the contact list file.",
+            stacklevel=2,
         )
 
     def aggregate(
@@ -871,7 +873,8 @@ def __init__(
         for chrom in self.gs.contigs:
             if chrom not in self.file_contigs:
                 warnings.warn(
-                    "Did not find contig " + f" '{chrom}' in contact list file."
+                    "Did not find contig " + f" '{chrom}' in contact list file.",
+                    stacklevel=2,
                 )
 
     def aggregate(
@@ -991,7 +994,10 @@ def select_block(self, chrom1, chrom2):
             try:
                 block = self.mapping[chrom2, chrom1].T
             except KeyError:
-                warnings.warn(f"Block for {{{chrom1}, {chrom2}}} not found")
+                warnings.warn(
+                    f"Block for {{{chrom1}, {chrom2}}} not found",
+                    stacklevel=2,
+                )
                 raise
         return block
 
@@ -1097,7 +1103,10 @@ def select_block(self, chrom1, chrom2):
             try:
                 block = self.mapping[chrom2, chrom1].T
             except KeyError:
-                warnings.warn(f"Block for {{{chrom1}, {chrom2}}} not found")
+                warnings.warn(
+                    f"Block for {{{chrom1}, {chrom2}}} not found",
+                    stacklevel=2,
+                )
                 raise
         return block
 

src/cooler/fileops.py

@@ -118,7 +118,10 @@ def _is_cooler(grp: h5py.Group) -> bool:
     if fmt == MAGIC:
         keys = ("chroms", "bins", "pixels", "indexes")
         if not all(name in grp.keys() for name in keys):
-            warnings.warn(f"Cooler path {grp.name} appears to be corrupt")
+            warnings.warn(
+                f"Cooler path {grp.name} appears to be corrupt",
+                stacklevel=2,
+            )
         return True
     return False
 
@@ -172,7 +175,10 @@ def is_scool_file(filepath: str) -> bool:
         if fmt == MAGIC_SCOOL:
             keys = ("chroms", "bins", "cells")
             if not all(name in f.keys() for name in keys):
-                warnings.warn("Scool file appears to be corrupt")
+                warnings.warn(
+                    "Scool file appears to be corrupt",
+                    stacklevel=2,
+                )
                 return False
             if "cells" in f.keys() and len(f["cells"].keys()) > 0:
                 for cells in f["cells"].keys():

src/cooler/reduce.py

@@ -125,7 +125,8 @@ def merge_breakpoints(
     if n_over > 0:
         warnings.warn(
             f"{n_over} merge epochs will require buffering more than {bufsize} "
-            f"pixel records, with as many as {nrecords_per_epoch.max():g}."
+            f"pixel records, with as many as {nrecords_per_epoch.max():g}.",
+            stacklevel=2,
         )
 
     return bin1_partition, cum_nrecords

tests/test_fileops.py

@@ -160,6 +160,4 @@ def test_list_scool_cells():
     ]
     cell_paths = fileops.list_scool_cells(src_file)
     assert len(cell_paths) == 5
-    for cell in paths:
-        if cell not in cell_paths:
-            assert False
+    assert all([cell in paths for cell in cell_paths])