Update precommit config inside package (neuroinformatics-unit#128)

* Update ruff precommit following PR neuroinformatics-unit#127

* Update pre-commit hooks version to match outer precommit file

* Update mypy and check-manifest in template precommit file (they dont get update by precommit bot)

Author: sfmig

{{cookiecutter.package_name}}/.pre-commit-config.yaml

@@ -8,7 +8,7 @@ ci:
 
 repos:
     - repo: https://github.com/pre-commit/pre-commit-hooks
-      rev: v4.6.0
+      rev: v5.0.0
       hooks:
           - id: check-docstring-first
           - id: check-executables-have-shebangs
@@ -19,19 +19,21 @@ repos:
             args: [--fix=lf]
           - id: requirements-txt-fixer
           - id: trailing-whitespace
-    - repo: https://github.com/charliermarsh/ruff-pre-commit
-      rev: v0.6.3
+    - repo: https://github.com/astral-sh/ruff-pre-commit
+      rev: v0.7.2
       hooks:
         - id: ruff
+          args: [ --config=pyproject.toml ]
         - id: ruff-format
+          args: [ --config=pyproject.toml ]
     - repo: https://github.com/pre-commit/mirrors-mypy
-      rev: v1.10.1
+      rev: v1.13.0
       hooks:
           - id: mypy
             additional_dependencies:
                 - types-setuptools
     - repo: https://github.com/mgedmin/check-manifest
-      rev: "0.49"
+      rev: "0.50"
       hooks:
           - id: check-manifest
             args: [--no-build-isolation]