[pre-commit.ci] pre-commit autoupdate (#3492)

<!--pre-commit.ci start-->
updates:
- [github.com/astral-sh/ruff-pre-commit: v0.8.6 →
v0.9.1](astral-sh/ruff-pre-commit@v0.8.6...v0.9.1)
<!--pre-commit.ci end-->

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

Author: pre-commit-ci[bot]

.pre-commit-config.yaml

@@ -10,7 +10,7 @@ repos:
       - id: check-toml
       - id: debug-statements
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.8.6
+    rev: v0.9.1
     hooks:
       - id: ruff-format
       - id: ruff

src/sourmash/cli/compare.py

@@ -92,7 +92,7 @@ def subparser(subparsers):
     subparser.add_argument(
         "--csv",
         metavar="F",
-        help="write matrix to specified file in CSV format (with column " "headers)",
+        help="write matrix to specified file in CSV format (with column headers)",
     )
     subparser.add_argument(
         "--labels-to",

src/sourmash/cli/compute.py

@@ -105,7 +105,7 @@ def subparser(subparsers):
         type=str,
         default="",
         metavar="FILE",
-        help="merge all input files into one signature file with the " "specified name",
+        help="merge all input files into one signature file with the specified name",
     )
     file_args.add_argument(
         "--name-from-first",

src/sourmash/cli/gather.py

@@ -100,8 +100,7 @@ def subparser(subparsers):
     subparser.add_argument(
         "--save-matches",
         metavar="FILE",
-        help="save gather matched signatures from the database to the "
-        "specified file",
+        help="save gather matched signatures from the database to the specified file",
     )
     subparser.add_argument(
         "--save-prefetch",

src/sourmash/cli/prefetch.py

@@ -58,12 +58,12 @@ def subparser(subparsers):
     subparser.add_argument(
         "--save-unmatched-hashes",
         metavar="FILE",
-        help="output unmatched query hashes as a signature to the " "specified file",
+        help="output unmatched query hashes as a signature to the specified file",
     )
     subparser.add_argument(
         "--save-matching-hashes",
         metavar="FILE",
-        help="output matching query hashes as a signature to the " "specified file",
+        help="output matching query hashes as a signature to the specified file",
     )
     subparser.add_argument(
         "--md5", default=None, help="select the signature with this md5 as query"

src/sourmash/command_compute.py

@@ -78,10 +78,10 @@ def compute(args):
         notify("Computing both nucleotide and protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna and args.dayhoff:
-        notify("Computing both nucleotide and Dayhoff-encoded protein " "signatures.")
+        notify("Computing both nucleotide and Dayhoff-encoded protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna and args.hp:
-        notify("Computing both nucleotide and hp-encoded protein " "signatures.")
+        notify("Computing both nucleotide and hp-encoded protein signatures.")
         num_sigs = 2 * len(ksizes)
     elif args.dna:
         notify("Computing only nucleotide (and not protein) signatures.")
@@ -91,11 +91,11 @@ def compute(args):
         num_sigs = len(ksizes)
     elif args.dayhoff:
         notify(
-            "Computing only Dayhoff-encoded protein (and not nucleotide) " "signatures."
+            "Computing only Dayhoff-encoded protein (and not nucleotide) signatures."
         )
         num_sigs = len(ksizes)
     elif args.hp:
-        notify("Computing only hp-encoded protein (and not nucleotide) " "signatures.")
+        notify("Computing only hp-encoded protein (and not nucleotide) signatures.")
         num_sigs = len(ksizes)
 
     if args.protein or args.dayhoff or args.hp:
@@ -269,7 +269,7 @@ def _compute_individual(args, signatures_factory):
                 save_sigs_to_location(sigs, save_sigs)
 
                 notify(
-                    f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                    f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
                 )
 
         # if not args.output, close output for every input filename.
@@ -443,7 +443,7 @@ def to_param_str(self):
             kstr = [f"k={k}" for k in self.ksizes]
         else:
             # for protein, divide ksize by three.
-            kstr = [f"k={k//3}" for k in self.ksizes]
+            kstr = [f"k={k // 3}" for k in self.ksizes]
         assert kstr
         pi.extend(kstr)
 

src/sourmash/command_sketch.py

@@ -207,7 +207,7 @@ def _execute_sketch(args, signatures_factory):
         error("error: sourmash only supports CC0-licensed signatures. sorry!")
         sys.exit(-1)
 
-    notify(f'computing signatures for files: {", ".join(args.filenames)}')
+    notify(f"computing signatures for files: {', '.join(args.filenames)}")
 
     if args.merge and not args.output:
         error("ERROR: must specify -o with --merge")
@@ -353,7 +353,7 @@ def _compute_sigs(to_build, output, *, check_sequence=False):
                 save_sigs.add(sig)
 
             notify(
-                f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
             )
 
     save_sigs.close()
@@ -768,7 +768,7 @@ def _compute_individual(args, signatures_factory):
                 save_sigs_to_location(sigs, save_sigs)
 
                 notify(
-                    f"calculated {len(sigs)} signatures for {n+1} sequences in {filename}"
+                    f"calculated {len(sigs)} signatures for {n + 1} sequences in {filename}"
                 )
 
         # if not args.output, close output for every input filename.
@@ -942,7 +942,7 @@ def to_param_str(self):
             kstr = [f"k={k}" for k in self.ksizes]
         else:
             # for protein, divide ksize by three.
-            kstr = [f"k={k//3}" for k in self.ksizes]
+            kstr = [f"k={k // 3}" for k in self.ksizes]
         assert kstr
         pi.extend(kstr)
 

src/sourmash/commands.py

@@ -1077,7 +1077,7 @@ def gather(args):
             )
 
         print_results(
-            f"the recovered matches hit {sum_f_uniq_found*100:.1f}% of the query k-mers (unweighted)."
+            f"the recovered matches hit {sum_f_uniq_found * 100:.1f}% of the query k-mers (unweighted)."
         )
 
     print_results("")
@@ -1345,7 +1345,7 @@ def multigather(args):
                 )
 
             print_results(
-                f"the recovered matches hit {sum_f_uniq_found*100:.1f}% of the query k-mers (unweighted)."
+                f"the recovered matches hit {sum_f_uniq_found * 100:.1f}% of the query k-mers (unweighted)."
             )
             print_results("")
 

src/sourmash/distance_utils.py

@@ -16,7 +16,7 @@
 
 def check_distance(dist):
     if not 0 <= dist <= 1:
-        raise ValueError(f"Error: distance value {dist :.4f} is not between 0 and 1!")
+        raise ValueError(f"Error: distance value {dist:.4f} is not between 0 and 1!")
     else:
         return dist
 

src/sourmash/plugins.py

@@ -198,7 +198,7 @@ def list_all_plugins():
     notify(
         f"{'plugin type':<20s} {'from python module':<30s} {'v':<5s} {'entry point name':<20s}"
     )
-    notify(f"{'-'*20} {'-'*30} {'-'*5} {'-'*20}")
+    notify(f"{'-' * 20} {'-' * 30} {'-' * 5} {'-' * 20}")
 
     for plugin in plugins:
         name = plugin.name