Modernize packaging, CI, and documentation

[soraros]

Summary

Replaces setup.py, .github/workflows/pytest.yml, and .github/workflows/documentation.yml with pyproject.toml (PEP 621, hatchling), uv, and .github/workflows/ci.yml. Local development, Read the Docs, and CI all use uv; runtime and dev tools via uv sync, documentation via uv sync --extra docs (CI and RTD add --no-dev).

Changes

• Python: CI matrix 3.11–3.13; 3.9 and 3.10 removed (version schedule).
• CI: Single workflow with four jobs; runs on every branch push and on pull requests to main (previously only main).
• Tests: pytest and coverage (replaces unittest discover); installs the full runtime set from pyproject.toml, including PySide6 (omitted in the old workflow).
• Dependencies: uv sync replaces a shorter ad hoc pip install list in the old workflow (now includes VTK and PySide6 explicitly).
• Release: uv build and a wheel smoke test in a .wheel-check venv.
• Docs: sphinx-autoapi on Sphinx with Furo (replaces sphinx-rtd-theme); output under doc/_build/html (was repo-root _build/); removed doc/Makefile, doc/requirements.txt, and manual API stubs. Read the Docs remains the primary docs site.
• Pages: upload-pages-artifact + deploy-pages on main (replaces peaceiris/actions-gh-pages → gh-pages). If Settings → Pages still deploys from gh-pages, switch Source to GitHub Actions (publishing source).

Commands

With uv installed, from the repo root. After uv sync, use uv run … without activating .venv.

# Install the package, runtime deps, and dev tools (pytest, coverage, ruff)
uv sync

# Run entry points from pyproject.toml
uv run pyfem --help
uv run pyfem-gui

# Tests
uv run pytest
uv run coverage run -m pytest -q  # CI
uv run coverage report            # CI

# Documentation
uv sync --extra docs              # `docs` extra (CI / RTD: add `--no-dev`)
uv run sphinx-build -M html doc doc/_build

# Wheel and sdist
uv build

[soraros]

Gentle ping @jjcremmers