[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>

.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

src/sourmash/sbt.py

@@ -763,7 +763,9 @@ def save(self, path, storage=None, sparseness=0.0, structure_only=False):
                     manifest_rows.append(row)
 
             if n % 100 == 0:
-                notify(f"{format(n+1)} of {format(total_nodes)} nodes saved", end="\r")
+                notify(
+                    f"{format(n + 1)} of {format(total_nodes)} nodes saved", end="\r"
+                )
 
         # now, save the index file and manifests.
         #

src/sourmash/sig/__main__.py

@@ -1298,7 +1298,7 @@ def kmers(args):
     found_hashes = set(found_mh.hashes)
     cont = len(query_hashes.intersection(found_hashes)) / len(query_hashes)
 
-    notify(f"found {len(found_mh)} distinct matching hashes ({cont*100:.1f}%)")
+    notify(f"found {len(found_mh)} distinct matching hashes ({cont * 100:.1f}%)")
 
     if not kmer_w and not save_seqs:
         notify("NOTE: see --save-kmers or --save-sequences for output options.")

src/sourmash/tax/__main__.py

@@ -93,7 +93,7 @@ def metagenome(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -284,7 +284,7 @@ def genome(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -345,7 +345,7 @@ def genome(args):
     else:
         classif_perc = (float(n_classified) / float(n_total)) * 100
         notify(
-            f"classified {n_classified}/{n_total} queries ({classif_perc :.2f}%). Writing results"
+            f"classified {n_classified}/{n_total} queries ({classif_perc:.2f}%). Writing results"
         )
 
     # write outputs
@@ -442,7 +442,7 @@ def annotate(args):
 
     if not tax_assign:
         error(
-            f'ERROR: No taxonomic assignments loaded from {",".join(args.taxonomy_csv)}. Exiting.'
+            f"ERROR: No taxonomic assignments loaded from {','.join(args.taxonomy_csv)}. Exiting."
         )
         sys.exit(-1)
 
@@ -518,7 +518,7 @@ def annotate(args):
                         )
                     else:
                         notify(
-                            f"Annotated {rows_annotated} of {n+1} total rows from '{in_csv}'."
+                            f"Annotated {rows_annotated} of {n + 1} total rows from '{in_csv}'."
                         )
 
         except ValueError as exc:

src/sourmash/tax/tax_utils.py

@@ -22,8 +22,8 @@
     "ascending_taxlist",
     "collect_gather_csvs",
     "load_gather_results",
-    "check_and_load_gather_csvs" "report_missing_and_skipped_identities",
-    "aggregate_by_lineage_at_rank" "format_for_krona",
+    "check_and_load_gather_csvsreport_missing_and_skipped_identities",
+    "aggregate_by_lineage_at_rankformat_for_krona",
     "write_output",
     "write_bioboxes",
     "parse_lingroups",
@@ -793,7 +793,7 @@ def read_lingroups(lingroup_csv):
     if n is None:
         raise ValueError(f"No lingroups loaded from {lingroup_csv}.")
     n_lg = len(lingroupD.keys())
-    notify(f"Read {n+1} lingroup rows and found {n_lg} distinct lingroup prefixes.")
+    notify(f"Read {n + 1} lingroup rows and found {n_lg} distinct lingroup prefixes.")
     return lingroupD
 
 
@@ -978,7 +978,7 @@ def report_missing_and_skipped_identities(gather_results):
             f"of {total_taxresults} gather results, lineage assignments for {total_n_missed} results were missed."
         )
         notify(
-            f'The following are missing from the taxonomy information: {", ".join(ident_missed)}'
+            f"The following are missing from the taxonomy information: {', '.join(ident_missed)}"
         )
 
 
@@ -2106,9 +2106,9 @@ def as_summary_dict(self, query_info, limit_float=False, lingroups=None):
 
     def as_human_friendly_dict(self, query_info):
         sD = self.as_summary_dict(query_info=query_info, limit_float=True)
-        sD["f_weighted_at_rank"] = f"{self.f_weighted_at_rank*100:>4.1f}%"
+        sD["f_weighted_at_rank"] = f"{self.f_weighted_at_rank * 100:>4.1f}%"
         if self.query_ani_at_rank is not None:
-            sD["query_ani_at_rank"] = f"{self.query_ani_at_rank*100:>3.1f}%"
+            sD["query_ani_at_rank"] = f"{self.query_ani_at_rank * 100:>3.1f}%"
         else:
             sD["query_ani_at_rank"] = "-    "
         return sD

tests/test_sourmash_compute.py

@@ -453,8 +453,7 @@ def test_do_sourmash_compute_multik_with_hp():
             in_directory=location,
         )
         assert (
-            "Computing only hp-encoded protein (and not nucleotide) "
-            "signatures." in err
+            "Computing only hp-encoded protein (and not nucleotide) signatures." in err
         )
         outfile = os.path.join(location, "short.fa.sig")
         assert os.path.exists(outfile)

tests/test_tax_utils.py

@@ -2221,7 +2221,7 @@ def test_RankLineageInfo_init_lineage_str_2():
     taxinf = RankLineageInfo(lineage_str=x)
     print(taxinf.lineage)
     print(taxinf.lineage_str)
-    assert taxinf.zip_lineage() == ["a", "b", "", "c" "", "", "", "", ""]
+    assert taxinf.zip_lineage() == ["a", "b", "", "c", "", "", "", ""]
 
 
 def test_RankLineageInfo_init_lineage_str_2_truncate():