refactor: pyproject.toml migration + ruff lint clean-up - #13
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- Replace setup.py with PEP 621 pyproject.toml (setuptools backend) - Add environment.yml for conda/mamba (conda-forge + nodefaults, python=3.11) - Migrate CI to use environment.yml via setup-miniconda@v3 (single 3.11 job) - All Python deps (core + jupyter/dev extras) now in pyproject.toml as SSOT - Update README.md and AGENTS.md with conda + pip install tracks
- Add [tool.ruff] config to pyproject.toml (extend-exclude Tutorials) - Auto-fix: import sorting (I001), unused imports (F401), deprecated typing imports (UP006/UP035), unnecessary list() in sorted() (C414) - Manual: narrow exception catches (BLE001/E722/S110), ValueError→TypeError for type validation (TRY004), mutable default args (B006), uncaptured loop variable (B023), unused unpacked variables (RUF059/F841), ClassVar annotations (RUF012), nested with collapse (SIM117), subprocess check (PLW1510) - Add __all__ to __init__.py for explicit public API re-exports - Fix test_grid_extraction.py expected exception (ValueError→TypeError)
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Summary
Replaces
setup.pywith PEP 621pyproject.tomlas the single source of truth for all Python dependencies, addsenvironment.ymlfor conda/mamba users, migrates CI to the env file, and cleans up all 118 ruff lint issues to zero.Changes
Dependency management overhaul (6 files)
[jupyter]+[dev](ruff) extraspip: -e ".[jupyter,dev]"setup-miniconda@v3with env file, single 3.11 jobRuff lint clean-up (25 files)
ruff check .→ 0 errors (was 118)list()insorted()(C414)ValueError→TypeErrorfor type validation (TRY004), mutable default args (B006), uncaptured loop variable (B023), unused unpacked/dead variables (RUF059/F841),ClassVarannotations (RUF012), nestedwithcollapse (SIM117), subprocess check (PLW1510)__all__to__init__.pyfor explicit public API re-exports[tool.ruff]config withextend-exclude = ["Tutorials"]Verification
ruff check .→ 0 errorspython3 -m unittest discover tests→ 88 tests OK, 1 skipped (live Julia test)