Clean up code and modernize - #58
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…on-cleanup-b355a0 # Conflicts: # CI/unit_tests/particle/test_particle.py # CI/unit_tests/visualizer/test_visualizer.py # znvis/particle/particle.py # znvis/visualizer/visualizer.py
Update the JOSS paper and bibliography, and perform a cleanup pass over the codebase for publication readiness. Paper: - Reflect merged features in paper.md (headless/parallel offscreen rendering, programmable camera paths, memory-efficient mesh caching). - Add and cite the published SwarmRL reference (EPJ E 2025). Code cleanups: - Fix broken examples/export_scene.py (removed invalid `colour=` kwarg passed to Sphere; colour is a Material field) and correct its docstring. - Fix Mitsuba shared-mutable default: deep-copy default_scene_dict so separate instances no longer mutate the same module-level dict. - Rename misspelled _toogle_play_direction -> _toggle_play_direction. - Expose znvis.__version__ via importlib.metadata. - Fix headless_visualizer copy-paste docstrings, an "occured" typo, and a leftover commented-out debug print; label the current-frame print. - Remove stray committed examples/example_data/__temp_ipython__.png. JOSS readiness: - Add CONTRIBUTING.md with contribution, testing, and support guidelines. - Add README sections for documentation, contributing, license, citation. - Add a draft-pdf GitHub Action to compile the JOSS paper. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Add Jannik Drotleff, Christoph Lohrmann, and David Zimmer as authors. Mark Samuel Tovey and Jannik Drotleff as equal first authors (equal-contrib), with Samuel Tovey as corresponding author. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
Consolidate the toolchain onto a single tool. Ruff replaces black (formatting), isort (import sorting), and flake8 (linting), run via one command. - pyproject.toml: drop [tool.black]/[tool.isort], add [tool.ruff] with rule set E, W, F, I, UP, B (line length 88, target py311); swap the dev dependencies to ruff. - Remove now-redundant .flake8 and .isort.cfg config files. - .pre-commit-config.yaml: replace the three hooks with ruff + ruff-format. - .github/workflows/lint.yaml: replace the black/isort/flake8 jobs with a single ruff job (ruff check + ruff format --check). - Apply the resulting fixes: modernize type annotations to PEP 585/604 (list[...], X | None), add `raise ... from e` in except blocks, add strict=True to zip() calls, and drop unused loop variables. - Update CONTRIBUTING.md and the README badge to reference ruff. All 151 tests pass; ruff check and ruff format are clean. Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
jdrotleff
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Jul 13, 2026
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LGTM
Thanks for all the updates, cleanups and catching the toogle typo. I never noticed 😄
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