Enforce strict mypy type checking and additional ruff rules

[FabianHofmann]

Changes proposed in this Pull Request

This PR enforces strict static type checking with mypy and enables additional ruff lint rules across the entire codebase (including test/ and doc/).

Docstrings

• Add docstrings to all functions

Mypy

• Configured strict mypy settings in pyproject.toml: disallow_incomplete_defs = true, check_untyped_defs = true
• Removed all directory exclusions from mypy — it now checks atlite/, test/, and doc/
• Updated .pre-commit-config.yaml to match
• Leveraged existing atlite/_types.py type aliases and added TypeAlias annotations where needed (e.g. csp.py, utils.py)
• Added missing type annotations to function signatures (e.g. conversion functions in convert.py)
• Fixed __all__ in __init__.py to use strings instead of object references

Ruff

Enabled 9 new rule sets and fixed all violations (~260 fixes):

• B (flake8-bugbear): Added from err/from None to re-raised exceptions, fixed mutable defaults
• SIM (flake8-simplify): Collapsed nested if statements, simplified dict operations
• RET (flake8-return): Removed superfluous else after return/raise
• C4 (flake8-comprehensions): Simplified unnecessary dict()/list() constructors
• TC (flake8-type-checking): Moved type-only imports into TYPE_CHECKING blocks
• NPY (numpy): Replaced legacy np.random.seed/np.random.rand with np.random.default_rng
• G (flake8-logging-format): Replaced f-strings in logging with lazy % formatting
• PTH (flake8-use-pathlib): Replaced os.path.* and open() with pathlib equivalents
• RUF100: Cleaned up unused # noqa comments

TODO

• replace cast() where possible, need bump python version for mypy
• add ruff check for docstring consistency

Checklist

• Code changes are sufficiently documented; i.e. new functions contain docstrings and further explanations may be given in doc.
• Unit tests for new features were added (if applicable).
• Newly introduced dependencies are added to environment.yaml, environment_docs.yaml and setup.py (if applicable).
• A note for the release notes doc/release_notes.rst of the upcoming release is included.
• I consent to the release of this PR's code under the MIT license.