Update contributing guide, remove dev-facing ci optional dependency

[DanielYang59]

Summary

• Migrate test/lint workflow to uv
• Remove dev-facing ci optional dependency group as it's not user facing and we're not including tests in the wheels anyway:

  • pymatgen/pyproject.toml

    Lines 139 to 141 in f01009c

    	[tool.setuptools.packages.find]
    	where = ["src"]
    	include = ["pymatgen", "pymatgen.*"]

[DanielYang59]

uv would only install dev by default, linting tools then would not be available by uv sync (one would need uv sync --group lint, but I assume there isn't any reason not to install linting tools for development?):

By default, uv includes the dev dependency group in the environment (e.g., during uv run or uv sync).

pymatgen/pyproject.toml

Lines 328 to 345 in f9d9fe8

	[dependency-groups]
	dev = [
	"invoke>=2.2.0",
	"jupyter>=1.1.1",
	"pre-commit>=4.2.0",
	"pytest>=8.3.5",
	"pytest-cov>=6.0.0",
	"pytest-split>=0.10.0",
	"ruff>=0.11.3",
	"sphinx>=8.1.3",
	"sphinx-markdown-builder>=0.6.8",
	"sphinx-rtd-theme>=3.0.2",
	]
	lint = [
	"mypy>=1.15.0",
	"pyright>=1.1.398",
	"ruff>=0.11.2",
	]

[DanielYang59]

Looks like this install step isn't really runninng as our test matrix only has python 3.13 for Ubuntu:

pymatgen/.github/workflows/test.yml

Lines 32 to 48 in f9d9fe8

	config:
	- os: windows-latest
	python: "3.11"
	resolution: highest
	extras: ci,optional,prototypes
	- os: windows-latest
	python: "3.11"
	resolution: highest
	extras: ci,prototypes,optional,numpy-v1 # Test NP1 on Windows (quite buggy ATM)
	- os: ubuntu-latest
	python: "3.13"
	resolution: lowest-direct
	extras: ci,prototypes,optional
	- os: macos-latest
	python: "3.12"
	resolution: lowest-direct
	extras: ci,prototypes # test with only required dependencies installed

For example https://github.com/materialsproject/pymatgen/actions/runs/16538944868/job/46777460136:

[DanielYang59]

I just noticed there's another docs/contributing.md...I'm a bit confused here, which should be the main doc (invoke make-doc doesn't seem to sync these two)