Python tooling, CI, and docs modernization

[JudoWill]

Summary

This pull request modernizes the outerspace development workflow: standard pyproject.toml tool configuration, Ruff for lint and format, tox for reproducible test and doc builds, GitHub Actions for CI and PyPI publishing, MkDocs + Read the Docs for documentation, a GPL-3.0 license file, and optional pipeline extras so default installs and CI stay lighter. Default test runs and PR CI exercise unit tests only; long integration/functional tests are opt-in.

Motivation

• Align with common Python packaging and contributor workflows (pip install -e ".[dev]", tox, pre-commit, RTD).
• Keep CI fast by excluding Snakemake-heavy functional tests from the default path while still making them easy to run locally or in a dedicated tox environment.
• Document the project and installation on PyPI/RTD and reduce machine-specific makefile usage for core dev tasks.

What changed

Packaging and dependencies

• requires-python: >=3.9 (consistent with NumPy 2).
• Optional extras: dev (pytest, coverage, tox, ruff, pre-commit, build, twine), docs (mkdocs, material, pymdown-extensions), pipeline (snakemake, pulp moved out of core dependencies).
• [project.urls] for Home, Repo, Docs, Issues.
• Pipeline command: Snakemake and pulp are loaded lazily in outerspace/cli/commands/pipeline.py so importing the CLI does not require the pipeline extra; running outerspace pipeline without the extra raises a clear install hint.

Lint and tests

• Ruff configuration in pyproject.toml ([tool.ruff], [tool.ruff.lint], isort for outerspace).
• Pytest markers: integration, functional. Default addopts run not integration and not functional. test_functional_*.py modules use pytestmark = pytest.mark.functional.
• Coverage config under [tool.coverage.*] for the outerspace package.

Tox (see tox.ini)

• tox -e ruff: Ruff check + ruff format --check.
• tox -e py: Default unit suite (same marker filter as pyproject).
• tox -e functional: integration or functional tests; uses [dev,pipeline] and --override-ini so marker selection works with the default addopts.
• tox -e docs: mkdocs build --strict.

Continuous integration and release

• .github/workflows/ci.yml: Ruff job + Python 3.9–3.12 matrix for tox -e py (unit tests only).
• .github/workflows/publish.yml: Build sdist/wheel and publish to PyPI on release or v* tags (requires trusted publishing / GitHub “pypi” environment to be configured on the repo and PyPI).

Documentation site

• mkdocs.yml, Material theme, nav over existing docs/*.md plus docs/index.md landing page.
• .readthedocs.yaml: install package with the docs extra and run MkDocs.

Repository hygiene

• LICENSE: full GPL-3.0 text (matches license metadata).
• .pre-commit-config.yaml: Ruff (with fix) and Ruff format.
• .gitignore: consider adding .tox/, dist/, htmlcov/, .ruff_cache/, .mypy_cache/, and .pytest_cache/ if not already present (keeps venv ignored for local conda envs).
• makefile: VENV points at repo venv/; make test / make ruff call tox via $(VENV)/bin/python; make venv creates conda env and pip install -e ".[dev,pipeline]" + pre-commit.
• README.md: Development section (conda venv, tox, pre-commit, RTD link).

How to test this PR

# Editable install with dev (and pipeline if you use pipeline tests)
pip install -e ".[dev,pipeline]"

# Fast path (should match CI)
tox -e ruff
tox -e py

# Optional full pipeline/integration tests
tox -e functional

# Docs
tox -e docs
# or: mkdocs serve

Read the Docs: import the project and point it at this branch; build should use .readthedocs.yaml and the docs extra.

PyPI publish: merge only after OIDC / trusted publishing is configured; dry-run on TestPyPI first is recommended.

Checklist (for maintainers)

• RTD project created or updated to use the new config and default branch.
• PyPI trusted publishing linked to this GitHub repo (if publishing is intended soon).
• Changelog or release notes updated if you maintain a CHANGELOG (not required for this PR unless you add one later).