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…d a jupyter notebook example along with sample data to run the code in the notebook.
Update README.md
…odified_by_Gabe Attach Simularium converter and ProAffinity
This directory stores pdb files downloaded when testing
Bumps [networkx](https://github.com/networkx/networkx) from 3.0 to 3.2.1. - [Release notes](https://github.com/networkx/networkx/releases) - [Commits](networkx/networkx@networkx-3.0...networkx-3.2.1) --- updated-dependencies: - dependency-name: networkx dependency-version: 3.2.1 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
Bumps [nvidia-curand-cu12](https://developer.nvidia.com/cuda-zone) from 10.3.2.106 to 10.3.10.19. --- updated-dependencies: - dependency-name: nvidia-curand-cu12 dependency-version: 10.3.10.19 dependency-type: direct:production update-type: version-update:semver-patch ... Signed-off-by: dependabot[bot] <[email protected]>
Automated release notes
Config file/template for release notes
Bumps [huggingface-hub](https://github.com/huggingface/huggingface_hub) from 0.32.2 to 0.33.2. - [Release notes](https://github.com/huggingface/huggingface_hub/releases) - [Commits](huggingface/huggingface_hub@v0.32.2...v0.33.2) --- updated-dependencies: - dependency-name: huggingface-hub dependency-version: 0.33.2 dependency-type: direct:production update-type: version-update:semver-minor ... Signed-off-by: dependabot[bot] <[email protected]>
… add 1D adaptive rates unpack Gillespie module from class; Allow changing rates in Gillespie simulation. It requires a brand new input of rate_update_rules, which is a callable. Add 1D adaptive rates in adaptive_rates. Also - renamed functions in Gillespie simulations for easier understanding, while keeping legacy API still available. - test cases updated (totally 4, old 3 + new for dimerization in 1D with adaptive rates) - Lazyloader in __init__.py of ionerdss is also changed accordingly.
…BiophysicsLab/ionerdss into Adaptive-rates-Gillespie
…spie Adaptive rates gillespie Tests about Gillepie passed. There are tests about the refactored module failed. Need attentions.
- Move networkx to core dependencies (used for graph-based molecular modeling, not just ODE) - Remove misleading 'ode' dependency group that contained networkx - Add 'docs' group for sphinx documentation dependencies (furo, nbsphinx) - Rename 'full' group to 'all' with explicit dependency list (fixes copilot self-reference issue) - Fix README documentation build path (docs → website) - Add comprehensive Examples section highlighting Jupyter notebooks in examples/ directory - Update development guidance to emphasize Jupyter for working with examples - Update all dependency references throughout codebase This creates a logical, maintainable dependency structure that reflects actual usage patterns and provides better guidance for new users and contributors.
- Remove redundant dependency installation steps in unittest workflow - Fix incorrect [tests] reference (should be [test]) - Simplify to single step using requirements-dev.txt which installs [all] - Ensures CI tests with comprehensive dependency coverage
- Update requirements-dev.txt to install [test,jupyter] for typical development needs - Update environment.yml to match typical developer requirements - Update README to distinguish typical vs comprehensive development setups - Update CI to use [test] only - appropriate for headless testing, avoids heavy ovito deps - Remove all references to deprecated [full] and [ode] groups Now the naming scheme is logical and consistent: - requirements-dev.txt → typical dev needs (test + jupyter) - [all] → comprehensive development (includes heavy deps like ovito) - CI → minimal testing dependencies, designed to handle optional deps gracefully
- Change from [all] to [test] to avoid heavy ovito installation in headless CI - Prevents OpenGL context errors in CI environment - Tests are designed to handle missing optional dependencies gracefully
PR #84 moved MoleculeTemplate, CoarseGrainedMolecule, and BindingInterfaceTemplate to components.py but didn't update the imports in pdb_model.py, causing NameError exceptions in tests. Also adds missing rigid_transform_chains import and apply_rigid_transform function.
- Add missing BindingInterface and ReactionTemplate imports - Fix rigid_transform_chains calls with Chain objects by extracting CA coordinates - Fix Reaction() constructor calls with proper arguments - Fix MoleculeType constructor parameter names - Fix attribute access in save_model method - Add coordinate alignment to handle chains with different lengths
simplify dependency and environment management
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It was a mistake to merge it here. It should be merged into the ionerdss repo in JohnsonBiophysicsLab |
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Follow the import style of scipy.
submoduledictionary to keep track of all submodules and how to import them.__dir()__for autocompletion.__getattr__()for import submodules when they are called.__init__files should also be updated in submodules (TODO). Define__dir()__if not all names should be visible for users.