From 63a73087971ef0d8b78c78cfdac51da52dafa8a4 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Sep 2026 18:04:19 +0000
Subject: [PATCH 1/2] [pre-commit.ci] pre-commit autoupdate
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

updates:
- [github.com/biomejs/pre-commit: v2.4.16 → v2.5.12](https://github.com/biomejs/pre-commit/compare/v2.4.16...v2.5.12)
- [github.com/tox-dev/pyproject-fmt: v2.23.0 → v2.29.3](https://github.com/tox-dev/pyproject-fmt/compare/v2.23.0...v2.29.3)
- [github.com/astral-sh/ruff-pre-commit: v0.15.15 → v0.16.6](https://github.com/astral-sh/ruff-pre-commit/compare/v0.15.15...v0.16.6)
---
 .pre-commit-config.yaml | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/.pre-commit-config.yaml b/.pre-commit-config.yaml
index 598e3b612..db6ee838f 100644
--- a/.pre-commit-config.yaml
+++ b/.pre-commit-config.yaml
@@ -31,15 +31,15 @@ exclude: |
   )
 repos:
   - repo: https://github.com/biomejs/pre-commit
-    rev: v2.4.16
+    rev: v2.5.12
     hooks:
       - id: biome-format
   - repo: https://github.com/tox-dev/pyproject-fmt
-    rev: v2.23.0
+    rev: v2.29.3
     hooks:
       - id: pyproject-fmt
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.15
+    rev: v0.16.6
     hooks:
       - id: ruff-check
         types_or: [python, pyi, jupyter]

From ead90e7c965788a1ed69ef42b025ba01b4601838 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Mon, 7 Sep 2026 18:13:26 +0000
Subject: [PATCH 2/2] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 gget/gget_virus.py | 2 +-
 pyproject.toml     | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/gget/gget_virus.py b/gget/gget_virus.py
index 7742e6a91..b030bcd1d 100644
--- a/gget/gget_virus.py
+++ b/gget/gget_virus.py
@@ -5517,7 +5517,7 @@ def merge_metadata_csvs(genbank_csv_path: str, standard_csv_path: str) -> bool:
 
         return True
 
-    except Exception as e:  # noqa: BLE001
+    except Exception as e:
         logger.warning("❌ Failed to merge metadata CSVs: %s", e)
         logger.debug("Exception details:", exc_info=True)
         return False
diff --git a/pyproject.toml b/pyproject.toml
index 81c5a2c71..06b0278b4 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -148,11 +148,11 @@ ini_options.testpaths = [ "tests" ]
 ini_options.addopts = [ "-ra" ]
 
 [tool.coverage]
+run.source = [ "gget" ]
 run.omit = [
   "**/test_*.py",
   "gget/main.py",
 ]
-run.source = [ "gget" ]
 
 # mypy-baseline grandfathers the pre-existing type errors so the pre-commit
 # mypy hook only fails on NEW errors. Refresh after fixing some with: