Update pre-commit hooks (#4359)

Co-authored-by: mashehu <mashehu3@gmail.com>

Author: renovate[bot]

.pre-commit-config.yaml

@@ -1,6 +1,6 @@
 repos:
   - repo: https://github.com/astral-sh/ruff-pre-commit
-    rev: v0.15.16
+    rev: v0.15.22
     hooks:
       - id: ruff-check # linter
         args: [--fix, --exit-non-zero-on-fix] # sort imports and fix
@@ -36,7 +36,7 @@ repos:
               tests/pipelines/__snapshots__/.*
           )$
   - repo: https://github.com/pre-commit/mirrors-mypy
-    rev: "v2.1.0"
+    rev: "v2.3.0"
     hooks:
       - id: mypy
         args: [--ignore-missing-imports, --scripts-are-modules, -n4]
@@ -49,7 +49,7 @@ repos:
           - types-setuptools
           - pydantic
   - repo: https://github.com/astral-sh/uv-pre-commit
-    rev: 0.11.19
+    rev: 0.11.30
     hooks:
       - id: uv-lock
         priority: 20

nf_core/pipelines/download/docker.py

@@ -287,15 +287,17 @@ def _run_docker_command(
             # - read lines if there are any,
             # - check if we should kill it,
             # - update the progress bar
+            assert proc.stdout is not None
+            stdout = proc.stdout
             lines = []
             while True:
                 if self.kill_with_fire:
                     proc.kill()
                     raise KeyboardInterrupt("Docker command was cancelled by user")
 
-                rlist, _, _ = select.select([proc.stdout], [], [], 0.1)
-                if rlist and proc.stdout is not None:
-                    line = proc.stdout.readline()
+                rlist, _, _ = select.select([stdout], [], [], 0.1)
+                if rlist:
+                    line = stdout.readline()
                     if line:
                         lines.append(line)
                         self.progress.update(progress_task, current_log=line.strip())