[pre-commit.ci] autoupdate

.pre-commit-config.yaml

@@ -1,7 +1,7 @@
 # pre-commit run --all-files
 repos:
 -   repo: https://github.com/pre-commit/pre-commit-hooks
-    rev: v5.0.0
+    rev: v6.0.0
     hooks:
     -   id: check-added-large-files
     -   id: check-case-conflict
@@ -27,7 +27,7 @@ repos:
         language: pygrep
         files: \.(py|sh|rst|yml|yaml)$
 -   repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.6.9
+    rev: v0.14.3
     hooks:
     # Run the Ruff linter (flake8 alternative):
     -   id: ruff
@@ -46,7 +46,7 @@ repos:
             '--config=format.docstring-code-format=true'
         ]
 -   repo: https://github.com/rstcheck/rstcheck
-    rev: v6.2.4
+    rev: v6.2.5
     hooks:
     -   id: rstcheck
         args: [
@@ -56,13 +56,13 @@ repos:
             --ignore-substitutions=version
         ]
 -   repo: https://github.com/PyCQA/doc8
-    rev: 'v1.1.2'
+    rev: 'v2.0.0'
     hooks:
     -   id: doc8
         additional_dependencies: [pygments]
         args: [--quiet,--ignore=D001]
 -   repo: https://github.com/codespell-project/codespell
-    rev: v2.3.0
+    rev: v2.4.1
     hooks:
     -   id: codespell
         files: \.(py|sh|rst|yml|yaml)$

primer_selection/isPcr_lineage_report.py

@@ -340,9 +340,9 @@ def report_group(
                     except KeyError:
                         local_mito[more_cut] = culled
                     assert cut_lineage not in local_mito
-                    assert (
-                        sum(local_mito.values()) == total
-                    ), "Oops - culling changed the total"
+                    assert sum(local_mito.values()) == total, (
+                        "Oops - culling changed the total"
+                    )
                     # sys.stderr.write(
                     #    f"DEBUG '{cut_lineage}' count {culled} --> {more_cut} which is now {local_mito[more_cut]}\n"
                     # )
@@ -378,7 +378,9 @@ def report_group(
         for primer_name in primer_defs:
             assert (
                 len(local_lengths[cut_lineage, primer_name]) <= local_mito[cut_lineage]
-            ), f"{cut_lineage} {primer_name}: {len(local_lengths[cut_lineage, primer_name])} products from {local_mito[cut_lineage]} mtDNA for {cut_lineage if cut_lineage else 'Other ' + root}"
+            ), (
+                f"{cut_lineage} {primer_name}: {len(local_lengths[cut_lineage, primer_name])} products from {local_mito[cut_lineage]} mtDNA for {cut_lineage if cut_lineage else 'Other ' + root}"
+            )
 
     # assert set(local_mito) == set(local_lengths)
     # print(f"{len(local_lengths)} entries for {root} level {levels}")
@@ -529,7 +531,9 @@ def report_group(
                 assert (
                     len(local_lengths[cut_lineage, primer_name])
                     <= local_mito[cut_lineage]
-                ), f"{cut_lineage} {primer_name}: {len(local_lengths[cut_lineage, primer_name])} products from {local_mito[cut_lineage]} mtDNA for {cut_lineage if cut_lineage else 'Other'}"
+                ), (
+                    f"{cut_lineage} {primer_name}: {len(local_lengths[cut_lineage, primer_name])} products from {local_mito[cut_lineage]} mtDNA for {cut_lineage if cut_lineage else 'Other'}"
+                )
         worksheet = workbook.add_worksheet(f"{root} - Percent")
         worksheet.set_column(0, 0, 43)  # column width
         worksheet.set_column(1, 1, 6.5)

primer_selection/isPcr_tally.py

@@ -91,8 +91,7 @@
     metavar="TSV",
     required=True,
     help=(
-        "Deduplicated bed output file(s) from isPcr. Only the "
-        "first 4 columns are used."
+        "Deduplicated bed output file(s) from isPcr. Only the first 4 columns are used."
     ),
 )
 parser.add_argument(
@@ -174,9 +173,9 @@ def load_fasta(fasta_files):
                 continue
             f_lengths = {len(f) for f, r in cocktail}
             r_lengths = {len(r) for f, r in cocktail}
-            assert (
-                len(f_lengths) == 1 and len(r_lengths) == 1
-            ), f"Assorted lengths in {name} cocktail"
+            assert len(f_lengths) == 1 and len(r_lengths) == 1, (
+                f"Assorted lengths in {name} cocktail"
+            )
             # Do NOT add +1, the start/end are python style, len=end-start
             product_len = (
                 int(end) - int(start) - list(f_lengths)[0] - list(r_lengths)[0]

primer_selection/primer_selection.py

@@ -48,9 +48,9 @@ def load_isprc(isprc_filename, ref_name, primer_hits):
                 left,
                 right,
             ) in primer_hits, f"Stale cache? Why {name}, {left}, {right}"
-            assert (
-                length == f"{len(seq)}bp"
-            ), f"Expected length {len(seq)} from sequence, yet {length}"
+            assert length == f"{len(seq)}bp", (
+                f"Expected length {len(seq)} from sequence, yet {length}"
+            )
             seq = seq.upper()
             # chrom, rest = region.rsplit(":", 1)
             # if "+" in rest:

snakemake/snakemake_progress_bar_demo.py

@@ -22,7 +22,6 @@
 from pathlib import Path
 
 from rich.progress import Progress  # or use tqdm, or ...
-
 from snakemake.api import DAGSettings
 from snakemake.api import ResourceSettings
 from snakemake.api import SnakemakeApi