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Restructure and linting - #36
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Major overhaul of project infrastructure. Packaging & Dependencies - Add joblib and vtk to core dependencies - Add optional extras: [memd] (chaospy, numba) and [cluster] (pycircstat) - Move docs deps from [project.optional-dependencies] to [dependency-groups] docs - Add ruff, pytest, deptry to dev dependency group - Add deptry config with package_module_name_map (sklearn, skimage, gdist) - Add ruff config: line-length 100, extend-select I, isort first-party - Remove Development Status classifier CI/CD - Add ruff lint job to tests.yml - Add reusable docs-build.yml workflow (sphinx-gallery, caching, libgl1) - Add docs.yml workflow for PR/push verification - Gate release publish on docs-build job - Add deptry step to tests.yml (Python 3.13) Documentation - Switch to Sphinx-Gallery: all 8 examples converted to executable scripts - Gated slow example sections behind BUILDING_DOCS env var - Fixed Sphinx-Gallery __file__ issue via WAVEDATA_EXAMPLE_DIR env var - Fixed literal \\n corruption in EMD.py - Added plot_gallery=True, Agg backend, ExampleData symlink in conf.py - Switched RTD to uv sync with docs dependency group - Added libgl1 to RTD apt packages - Updated docs/index.rst with toctree for auto_examples - Removed old RST tutorials (docs/source/tutorials/) Examples - Separated ExampleData into inputs (ExampleData/) and outputs (ExampleData/Output/) - All examples now write generated files (pkl, gifs) to Output/ directory - Added output_dir + mkdir to Simulations, OpticalFlow, FrequencyDecomposition, CircLinCorr - Updated .gitignore: removed global *.gif rule, added Output/ ignore - Added env-var-based data_dir path in all 8 examples Core Library - Sorted imports across all WaveSpace modules (isort) - Added try/except guards for optional deps: EMD.py (memd), ClusterGradient.py (pycircstat) - Fixed Plotting.py r'$\\mu' escape, mutable default args - Added SimulationFuns.py np.real() for array outputs - Prefixed unused variables with underscore across codebase - Fixed SensorLayout plotting parameter type Testing - Added UnitTest/conftest.py for matplotlib Agg backend - Removed .vscode/settings.json
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pyproject.tomland adopteduvfor development, documentation, and CI environments.joblibandvtkas declared runtime dependencies.ClusterGradient,MEMD_Matlab_translation, andgenerateFromLog.