style: Linting with ruff

pyproject.toml

@@ -118,6 +118,21 @@ ignore = [
     "W503", # line break before binary operator
 ]
 
+[tool.ruff]
+exclude = [
+    "__init__.py",
+    "__main__.py",
+]
+extend-select = [
+    "E",  # style errors
+    # "D",  # pydocstyle
+    "F",  # pyflakes
+    "I",  # isort
+    "RUF", # ruff-specific rules
+    "UP", # pyupgrade
+    "W",  # style  warnings
+]
+
 [tool.isort]
 profile = "black"
 skip_gitignore = true

src/cooler/_logging.py

@@ -79,11 +79,14 @@ def configure(
     """
     if handlers is None:
         if stream is not None and filename is not None:
-            raise ValueError("'stream' and 'filename' should not be specified together")
+            raise ValueError(
+                "'stream' and 'filename' should not be specified together"
+            )
     else:
         if stream is not None or filename is not None:
             raise ValueError(
-                "'stream' or 'filename' should not be specified together with 'handlers'"
+                "'stream' or 'filename' should not be specified together with "
+                "'handlers'"
             )
 
     # Set up the new handlers
@@ -125,7 +128,9 @@ def set_logging_context(ctx):
 
     if _logging_context != ctx:
         if ctx == "lib":
-            configure(logger, stream=sys.stdout, level=logging.WARNING, format="{message}")
+            configure(
+                logger, stream=sys.stdout, level=logging.WARNING, format="{message}"
+            )
             logging.captureWarnings(False)
         elif ctx == "cli":
             configure(logger, stream=sys.stderr, level=logging.INFO)

src/cooler/balance.py

@@ -81,7 +81,7 @@ def _balance_genomewide(
 
     for _ in range(max_iters):
         marg = (
-            split(clr, spans=spans, map=map, use_lock=use_lock)  # noqa
+            split(clr, spans=spans, map=map, use_lock=use_lock)
             .prepare(_init)
             .pipe(filters)
             .pipe(_timesouterproduct, bias)
@@ -146,7 +146,7 @@ def _balance_cisonly(
         var = np.nan
         for _ in range(max_iters):
             marg = (
-                split(clr, spans=spans, map=map, use_lock=use_lock)  # noqa
+                split(clr, spans=spans, map=map, use_lock=use_lock)
                 .prepare(_init)
                 .pipe(filters)
                 .pipe(_timesouterproduct, bias)
@@ -215,7 +215,7 @@ def _balance_transonly(
 
     for _ in range(max_iters):
         marg = (
-            split(clr, spans=spans, map=map, use_lock=use_lock)  # noqa
+            split(clr, spans=spans, map=map, use_lock=use_lock)
             .prepare(_init)
             .pipe(filters)
             .pipe(_zero_cis)
@@ -365,9 +365,9 @@ def balance_cooler(
 
     # Drop bins with too few nonzeros from bias
     if min_nnz > 0:
-        filters = [_binarize] + base_filters
+        filters = [_binarize, *base_filters]
         marg_nnz = (
-            split(clr, spans=spans, map=map, use_lock=use_lock)  # noqa
+            split(clr, spans=spans, map=map, use_lock=use_lock)
             .prepare(_init)
             .pipe(filters)
             .pipe(_marginalize)
@@ -377,7 +377,7 @@ def balance_cooler(
 
     filters = base_filters
     marg = (
-        split(clr, spans=spans, map=map, use_lock=use_lock)  # noqa
+        split(clr, spans=spans, map=map, use_lock=use_lock)
         .prepare(_init)
         .pipe(filters)
         .pipe(_marginalize)

src/cooler/cli/csort.py

@@ -140,7 +140,7 @@ def make_index_command(index, fields, zero_based, outfile):
         index_cmd = shlex.split(INDEX_PX2.format(**fields))
     if zero_based:
         index_cmd += ["-0"]
-    return index_cmd + [outfile]
+    return [*index_cmd, outfile]
 
 
 @cli.command()
@@ -323,7 +323,7 @@ def csort(
     signal(SIGPIPE, SIG_DFL)
 
     # Check for required Unix tools
-    for tool in ["sort", "bgzip"] + [index]:
+    for tool in ["sort", "bgzip", index]:
         if not cmd_exists(tool):
             print(f"Command {tool} not found", file=sys.stderr)
             sys.exit(1)

src/cooler/cli/show.py

@@ -28,7 +28,9 @@ def load_matrix(c, row_region, col_region, field, balanced, scale):
     return mat
 
 
-def interactive(ax, c, row_chrom, col_chrom, field, balanced, scale):  # pragma: no cover
+def interactive(
+    ax, c, row_chrom, col_chrom, field, balanced, scale
+):  # pragma: no cover
     import matplotlib.pyplot as plt
 
     # The code is heavily insired by
@@ -72,7 +74,7 @@ def update_heatmap(event):
             im.set_data(np.ones(1)[:, None] * np.nan)
 
             if not plotstate["placeholders"]:
-                box, = plt.plot(
+                (box,) = plt.plot(
                     [0, col_chrom_len, col_chrom_len, 0, 0, col_chrom_len],
                     [0, row_chrom_len, 0, 0, row_chrom_len, row_chrom_len],
                     c="k",
@@ -109,49 +111,44 @@ def update_heatmap(event):
 
 
 @cli.command()
-@click.argument(
-    "cool_uri",
-    metavar="COOL_PATH"
-)
-@click.argument(
-    "range",
-    type=str
-)
+@click.argument("cool_uri", metavar="COOL_PATH")
+@click.argument("range", type=str)
 @click.option(
-    "--range2", "-r2",
+    "--range2",
+    "-r2",
     type=str,
     help="The coordinates of a genomic region shown along the column dimension. "
     "If omitted, the column range is the same as the row range. "
     "Use to display asymmetric matrices or trans interactions.",
 )
 @click.option(
-    "--balanced", "-b",
+    "--balanced",
+    "-b",
     is_flag=True,
     default=False,
     help="Show the balanced contact matrix. "
     "If not provided, display the unbalanced counts.",
 )
 @click.option(
-    "--out", "-o",
+    "--out",
+    "-o",
     help="Save the image of the contact matrix to a file. "
     "If not specified, the matrix is displayed in an interactive window. "
     "The figure format is deduced from the extension of the file, "
     "the supported formats are png, jpg, svg, pdf, ps and eps.",
 )
+@click.option("--dpi", type=int, help="The DPI of the figure, if saving to a file")
 @click.option(
-    "--dpi",
-    type=int,
-    help="The DPI of the figure, if saving to a file"
-)
-@click.option(
-    "--scale", "-s",
+    "--scale",
+    "-s",
     type=click.Choice(["linear", "log2", "log10"]),
     help="Scale transformation of the colormap: linear, log2 or log10. "
     "Default is log10.",
     default="log10",
 )
 @click.option(
-    "--force", "-f",
+    "--force",
+    "-f",
     is_flag=True,
     default=False,
     help="Force display very large matrices (>=10^8 pixels). "
@@ -160,13 +157,15 @@ def update_heatmap(event):
 @click.option(
     "--zmin",
     type=float,
-    help="The minimal value of the color scale. Units must match those of the colormap scale. "
+    help="The minimal value of the color scale. "
+    "Units must match those of the colormap scale. "
     "To provide a negative value use a equal sign and quotes, e.g. -zmin='-0.5'",
 )
 @click.option(
     "--zmax",
     type=float,
-    help="The maximal value of the color scale. Units must match those of the colormap scale. "
+    help="The maximal value of the color scale. "
+    "Units must match those of the colormap scale. "
     "To provide a negative value use a equal sign and quotes, e.g. -zmax='-0.5'",
 )
 @click.option(

src/cooler/cli/zoomify.py

@@ -35,7 +35,7 @@ def invoke_balance(args, resolutions, outfile):
 
         try:
             balance_cmd.main(
-                args=[uri] + args, prog_name='cooler'
+                args=[uri, *args], prog_name='cooler'
             )
         except SystemExit as e:
             # exc_info = sys.exc_info()
@@ -84,9 +84,10 @@ def invoke_balance(args, resolutions, outfile):
 )
 @click.option(
     "--balance-args",
-    help="Additional arguments to pass to cooler balance. To deal with space ambiguity, "
-    "use quotes to pass multiple arguments, e.g. --balance-args '--nproc 8 --ignore-diags 3' "
-    "Note that nproc for balancing must be specified independently of zoomify arguments.",
+    help="Additional arguments to pass to cooler balance. "
+    "To deal with space ambiguity, use quotes to pass multiple arguments, "
+    "e.g. --balance-args '--nproc 8 --ignore-diags 3'. Note that nproc for "
+    "balancing must be specified independently of zoomify arguments.",
     type=str
 )
 @click.option(
@@ -164,7 +165,7 @@ def zoomify(
                 logger.info(f"Balancing zoom level {level}, bin size {res}")
                 try:
                     balance_cmd.main(
-                        args=[uri] + balance_args, prog_name='cooler'
+                        args=[uri, *balance_args], prog_name='cooler'
                     )
                 except SystemExit as e:
                     # exc_info = sys.exc_info()
@@ -208,7 +209,7 @@ def zoomify(
             elif res == 'b':
                 r = preferred_sequence(curres, maxres, 'binary')
             elif res == '4dn':
-                r = [1000, 2000] + preferred_sequence(5000, maxres, 'nice')
+                r = [1000, 2000, *preferred_sequence(5000, maxres, 'nice')]
             elif res.endswith('n'):
                 res = int(res.split('n')[0])
                 r = preferred_sequence(res, maxres, 'nice')
@@ -235,7 +236,7 @@ def zoomify(
         # logger.info("Applying resolutions {}".format(resolutions))
 
         zoomify_cooler(
-            [cool_uri] + list(base_uri),
+            [cool_uri, *list(base_uri)],
             outfile,
             resolutions,
             chunksize,