Update package installation files and development environment

[tieneupin]

Partially addresses issue #194 .

• Updated [options.extras_require] table in setup.cfg to include dependencies for client, server, and developer installations of Murfey. More than one can be called during pip installation (e.g. to install all three for development use, input pip install -e .[client,server,developer]).
• Imported configuration settings from setup.cfg to pyproject.toml. Pip can now successfully install Murfey solely off pyproject.toml.
  • Python versions tested:
    • 3.12.2
    • 3.11.8
    • 3.10.14
    • 3.9.19

[tieneupin]

• Updated pre-commit-config.yaml to use the latest versions of pre-commit-hooks, isort, black, flake8, and mirrors-mypy for its checks.
• Added Flake8-pyproject as a Flake8 dependency, which allows it to read Flake8 configuration settings from the pyproject.toml file.
• Current results when running pre-commit:
  • check for merge conflicts....................................Passed
  • check python ast.................................................Passed
  • check json...........................................................Passed
  • check for added large files..................................Passed
  • check yaml..........................................................Passed
  • isort.....................................................................Passed
  • black....................................................................Passed
  • flake8...................................................................Passed
  • mypy....................................................................Failed
    • hook id: mypy
    • exit code: 1

[tieneupin]

• Started addressing errors revealed by pre-commit:
  • src/murfey/util/eer.py:14: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type]
  • src/murfey/util/eer.py:21: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type]
  • src/murfey/util/eer.py:23: error: Argument 2 to "from_bytes" of "int" has incompatible type "str"; expected "Literal['little', 'big']" [arg-type]
  • src/murfey/client/tui/__main__.py:3: error: Module "murfey.client.tui" has no attribute "MurfeyTUI" [attr-defined]
  • src/murfey/server/__init__.py:2712: error: Item "None" of "TransportManager | None" has no attribute "do_create_ispyb_job" [union-attr]
  • src/murfey/server/api.py:709: error: Value of type "Coroutine[Any, Any, None]" must be used [unused-coroutine]
• All MyPy errors resolved.

[tieneupin]

• Compared Ruff pre-commit hook against the combination of Black, Isort, and Flake8 hooks.
  • Ruff formatting deviates from Black's in certain ways (https://docs.astral.sh/ruff/formatter/black/).
  • Ruff linter doesn't yet cover all the Flake8 rules selected/ignored in this project.
    • VSCode throws up a warning only when certain codes are added to the select/ignore lists for Ruff in the pyproject.toml file. Other codes are fine.
  • Given our current project size, both sets of hooks complete at roughly the same speed.
• Updated MyPy pre-commit hook settings to include arguments to install missing type dependencies, and to ignore non-critical warnings.

[tieneupin]

• Removal of setup.cfg broke Azure's Flake8 checks (Flake8 cannot read pyproject.toml by default).
  • Fixed by Dan via installing pyproject-flake8 extension when setting up Azure's tests.

[tieneupin]

Added Prettier pre-commit hook to standardise formatting of non-Python files.