pyafv 0.3.1__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- pyafv-0.3.1/LICENSE +21 -0
- pyafv-0.3.1/PKG-INFO +83 -0
- pyafv-0.3.1/README.md +140 -0
- pyafv-0.3.1/README_PyPI.md +42 -0
- pyafv-0.3.1/pyafv/__init__.py +11 -0
- pyafv-0.3.1/pyafv/backend.py +16 -0
- pyafv-0.3.1/pyafv/cell_geom.pyx +508 -0
- pyafv-0.3.1/pyafv/finite_voronoi_fallback.py +989 -0
- pyafv-0.3.1/pyafv/finite_voronoi_fast.py +802 -0
- pyafv-0.3.1/pyafv/physical_params.py +117 -0
- pyafv-0.3.1/pyafv/simulator.py +37 -0
- pyafv-0.3.1/pyafv.egg-info/PKG-INFO +83 -0
- pyafv-0.3.1/pyafv.egg-info/SOURCES.txt +19 -0
- pyafv-0.3.1/pyafv.egg-info/dependency_links.txt +1 -0
- pyafv-0.3.1/pyafv.egg-info/requires.txt +8 -0
- pyafv-0.3.1/pyafv.egg-info/top_level.txt +1 -0
- pyafv-0.3.1/pyproject.toml +46 -0
- pyafv-0.3.1/setup.cfg +4 -0
- pyafv-0.3.1/setup.py +29 -0
- pyafv-0.3.1/tests/test_core.py +47 -0
- pyafv-0.3.1/tests/test_geom.py +43 -0
pyafv-0.3.1/LICENSE
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MIT License
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Copyright (c) 2025 Wei Wang
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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pyafv-0.3.1/PKG-INFO
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Metadata-Version: 2.4
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Name: pyafv
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Version: 0.3.1
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Summary: Python implementation of the active-finite-Voronoi (AFV) model
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Author-email: "Wei Wang (汪巍)" <ww000721@gmail.com>
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License: MIT License
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Copyright (c) 2025 Wei Wang
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.
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Project-URL: Download, https://test.pypi.org/project/pyafv/#files
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Project-URL: Source Code, https://github.com/wwang721/pyafv
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Requires-Python: >=3.11.11
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Description-Content-Type: text/markdown
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License-File: LICENSE
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Requires-Dist: numpy>=2.1.3
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Requires-Dist: scipy>=1.15.3
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Requires-Dist: matplotlib>=3.10.7
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Provides-Extra: examples
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Requires-Dist: ipywidgets>=8.1.5; extra == "examples"
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Requires-Dist: jupyter>=1.1.0; extra == "examples"
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Requires-Dist: tqdm>=4.67.1; extra == "examples"
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Dynamic: license-file
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<!--[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml?query=branch:main)-->
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[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml)
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[](https://codecov.io/github/wwang721/pyafv/tree/main)
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[](https://doi.org/10.5281/zenodo.18091659)
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Python code that implements the **active-finite-Voronoi (AFV) model**.
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The AFV framework was introduced and developed in, for example, Refs. [[1](#huang2023bridging)–[3](#wang2026divergence)].
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## More information
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GitHub: [https://github.com/wwang721/pyafv](https://github.com/wwang721/pyafv)
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See important [**issues**](https://github.com/wwang721/pyafv/issues?q=is%3Aissue%20state%3Aclosed) for additional context, such as:
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* [QhullError when 3+ points are collinear #1](https://github.com/wwang721/pyafv/issues/1) [Closed - see [comments](https://github.com/wwang721/pyafv/issues/1#issuecomment-3701355742)]
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* [Add customized plotting to examples illustrating access to vertices and edges #5](https://github.com/wwang721/pyafv/issues/5) [Completed in PR [#7](https://github.com/wwang721/pyafv/pull/7)]
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* [Time step dependence of intercellular adhesion in simulations #8](https://github.com/wwang721/pyafv/issues/8) [Closed in PR [#9](https://github.com/wwang721/pyafv/pull/9)]
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## References
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<table>
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<tr>
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<td id="huang2023bridging" valign="top">[1]</td>
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<td>
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J. Huang, H. Levine, and D. Bi, <em>Bridging the gap between collective motility and epithelial-mesenchymal transitions through the active finite Voronoi model</em>, <a href="https://doi.org/10.1039/D3SM00327B">Soft Matter <strong>19</strong>, 9389 (2023)</a>.
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</td>
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</tr>
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<tr>
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<td id="teomy2018confluent" valign="top">[2]</td>
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<td>
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E. Teomy, D. A. Kessler, and H. Levine, <em>Confluent and nonconfluent phases in a model of cell tissue</em>, <a href="https://doi.org/10.1103/PhysRevE.98.042418">Phys. Rev. E <strong>98</strong>, 042418 (2018)</a>.
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</td>
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</tr>
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<tr>
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<td id="wang2026divergence" valign="top">[3]</td>
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<td>
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W. Wang (汪巍) and B. A. Camley, <em>Divergence of detachment forces in the finite-Voronoi model</em>, manuscript in preparation (2026).
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</td>
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</tr>
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</table>
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pyafv-0.3.1/README.md
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<!--[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml?query=branch:main)-->
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[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml)
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[](https://codecov.io/github/wwang721/pyafv/tree/main)
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[](https://doi.org/10.5281/zenodo.18091659)
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# PyAFV
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Python code that implements the **active-finite-Voronoi (AFV) model**.
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The AFV framework was introduced and developed in, for example, Refs. [[1](#huang2023bridging)–[3](#wang2026divergence)].
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## Installation
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This project uses [`uv`](https://docs.astral.sh/uv/) for Python package management – a single tool to replace `pip` (⚡️10-100x faster) and `venv`.
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> Python 3.11.11 is my local development version, so it is set as the minimum requirement; if you'd like to use your own Python, ensure the `which python` version meets this requirement so `uv` doesn't automatically download a different interpreter; otherwise, I recommend letting `uv` manage everything, including the Python interpreter.
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After cloning the repository, Linux/macOS users (Windows users: see [below](#windows-mingw-gcc)) can synchronize the dependencies with
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```bash
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uv sync
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```
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or use `uv sync --no-dev` if you only intend to run the core code without development dependencies (like `pytest` for running tests).
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**Notes:**
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> * You can install additional packages as needed using `uv add <package_name>`.
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> * In some environments (like HPC clusters), global Python path can contaminate the project environment. You may need to add the `PYTHONPATH=""` prefix to all `uv` commands to isolate the project.
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> * The current version requires **Cython** (and therefore a working C/C++ compiler), though [a fallback backend](/pyafv/finite_voronoi_fallback.py) (based on early pure-Python release) is also implemented. If the Cython compiled extension is accidentally removed or corrupted (you will see a **RuntimeWarning**), you can reinstall the package with `uv sync --reinstall-package pyafv --inexact` (the `--inexact` flag prevents uv from removing any installed packages).
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> * For the old pure-Python implementation with no C/C++ compiled dependencies, see [v0.1.0](https://github.com/wwang721/pyafv/releases/tag/v0.1.0) (also on [GitLab](https://gitlab.com/wwang721/py-afv/-/releases/v0.1.0)). Alternatively, remove [setup.py](/setup.py) in the root folder before running `uv sync`.
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#### Windows MinGW GCC
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* If you are using **MinGW GCC** (rather than MSVC) on Windows, add a `setup.cfg` at the repository root
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```ini
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# setup.cfg
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[build_ext]
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compiler=mingw32
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```
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It will then work in the same way.
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<!--With this configuration in place, you even no longer need to pass the `--compiler=mingw32` flag when trying to compile with `uv run python setup.py build_ext --inplace`.-->
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## Running tests
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Current CI status of the test suite, run via [GitHub Actions](/.github/workflows/tests.yml) on Python 3.12, is shown in the badge at the top of this file.
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* To run the full test suite locally (located in [`tests`](/tests/)):
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```bash
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uv run pytest
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```
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You can also include coverage options such as `--cov` if desired. If you previously use `uv sync --no-dev`, you will need to run `uv sync` again to install the packages in the *dev* dependency group.
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**Notes:**
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> * A comparison against the MATLAB implementation from Ref. [[1](#huang2023bridging)] is included in [test_core.py](/tests/test_core.py).
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> * Unlike [v0.1.0](https://github.com/wwang721/pyafv/releases/tag/v0.1.0), the current test suite is designed to raise errors if the Cython backend is not available, even though a pure-Python fallback implementation is provided and tested.
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## Usage
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Using `uv run python`, you should be able to import `pyafv` from anywhere within the repository directory.
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The following example demonstrates how to construct a finite-Voronoi diagram:
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```python
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import numpy as np
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import pyafv as afv
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N = 100 # number of cells
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pts = np.random.rand(N, 2) * 10 # initial positions
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params = afv.PhysicalParams() # use default parameter values
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sim = afv.FiniteVoronoiSimulator(pts, params) # initialize the simulator
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sim.plot_2d(show=True) # visualize the Voronoi diagram
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```
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To compute the conservative forces and extract detailed geometric information (e.g., cell areas, vertices, and edges), call:
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```python
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diag = sim.build()
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```
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The returned object `diag` is a Python `dict` containing these quantities.
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#### More example scripts
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To run the example scripts in [`examples`](/examples), you need to install at least one additional dependency, `tqdm`, via `uv add tqdm`. Then you can simply run any script in [`examples`](/examples/) with
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```bash
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uv run <script_name>.py
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```
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You can also install all optional dependencies (e.g., `tqdm`, `jupyter`) via `uv sync --extra examples` or `uv sync --all-extras`.
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* To launch Jupyter Notebook: after `uv` has synced all extra dependencies, start Jupyter with `uv run jupyter notebook`. Do not use your system-level Jupyter, as the Python kernel of the current `uv` environment is not registered there.
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> Jupyter notebooks and media are stored via [**Git LFS**](https://docs.github.com/en/repositories/working-with-files/managing-large-files/about-git-large-file-storage). If you clone the repository without **Git LFS** installed, these files will appear as small text pointers. You can either install Git LFS to fetch them automatically or download the files manually (or download the repository as a ZIP archive) from the GitHub web interface.
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* Below are representative simulation snapshots generated using the code:
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| Model illustration | Periodic boundary conditions[*](/examples/jupyter/periodic_plotting.ipynb) |
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|-----------------|-----------------|
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| <img src="./assets/model_illustration.png" height="373"> | <img src="./assets/pbc.png" height="385">|
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| Initial configuration | After relaxation | Active dynamics enabled |
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|-----------------------|-----------------------|-----------------------|
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| <img src="./assets/initial_configuration.png" height="300"> | <img src="./assets/relaxed_configuration.png" height="300"> | <img src="./assets/active_FV.png" height="300"> |
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## More information
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See important [**issues**](https://github.com/wwang721/pyafv/issues?q=is%3Aissue%20state%3Aclosed) for additional context, such as:
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* [QhullError when 3+ points are collinear #1](https://github.com/wwang721/pyafv/issues/1) [Closed - see [comments](https://github.com/wwang721/pyafv/issues/1#issuecomment-3701355742)]
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* [Add customized plotting to examples illustrating access to vertices and edges #5](https://github.com/wwang721/pyafv/issues/5) [Completed in PR [#7](https://github.com/wwang721/pyafv/pull/7)]
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* [Time step dependence of intercellular adhesion in simulations #8](https://github.com/wwang721/pyafv/issues/8) [Closed in PR [#9](https://github.com/wwang721/pyafv/pull/9)]
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## Zenodo
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The releases of this repository is cross-listed on [Zenodo](https://doi.org/10.5281/zenodo.18091659).
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## License
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This project is licensed under the [MIT License](/LICENSE), which permits free use, modification, and distribution of the code for nearly any purpose.
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## References
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<table>
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<tr>
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<td id="huang2023bridging" valign="top">[1]</td>
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<td>
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J. Huang, H. Levine, and D. Bi, <em>Bridging the gap between collective motility and epithelial-mesenchymal transitions through the active finite Voronoi model</em>, <a href="https://doi.org/10.1039/D3SM00327B">Soft Matter <strong>19</strong>, 9389 (2023)</a>.
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</td>
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</tr>
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<tr>
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<td id="teomy2018confluent" valign="top">[2]</td>
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<td>
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E. Teomy, D. A. Kessler, and H. Levine, <em>Confluent and nonconfluent phases in a model of cell tissue</em>, <a href="https://doi.org/10.1103/PhysRevE.98.042418">Phys. Rev. E <strong>98</strong>, 042418 (2018)</a>.
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</td>
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<td id="wang2026divergence" valign="top">[3]</td>
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<td>
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W. Wang (汪巍) and B. A. Camley, <em>Divergence of detachment forces in the finite-Voronoi model</em>, manuscript in preparation (2026).
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</td>
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</tr>
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</table>
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<!--[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml?query=branch:main)-->
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[](https://github.com/wwang721/pyafv/actions/workflows/tests.yml)
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[](https://codecov.io/github/wwang721/pyafv/tree/main)
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[](https://doi.org/10.5281/zenodo.18091659)
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Python code that implements the **active-finite-Voronoi (AFV) model**.
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The AFV framework was introduced and developed in, for example, Refs. [[1](#huang2023bridging)–[3](#wang2026divergence)].
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## More information
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GitHub: [https://github.com/wwang721/pyafv](https://github.com/wwang721/pyafv)
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See important [**issues**](https://github.com/wwang721/pyafv/issues?q=is%3Aissue%20state%3Aclosed) for additional context, such as:
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* [QhullError when 3+ points are collinear #1](https://github.com/wwang721/pyafv/issues/1) [Closed - see [comments](https://github.com/wwang721/pyafv/issues/1#issuecomment-3701355742)]
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* [Add customized plotting to examples illustrating access to vertices and edges #5](https://github.com/wwang721/pyafv/issues/5) [Completed in PR [#7](https://github.com/wwang721/pyafv/pull/7)]
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* [Time step dependence of intercellular adhesion in simulations #8](https://github.com/wwang721/pyafv/issues/8) [Closed in PR [#9](https://github.com/wwang721/pyafv/pull/9)]
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## References
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<table>
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<tr>
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<td id="huang2023bridging" valign="top">[1]</td>
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<td>
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26
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J. Huang, H. Levine, and D. Bi, <em>Bridging the gap between collective motility and epithelial-mesenchymal transitions through the active finite Voronoi model</em>, <a href="https://doi.org/10.1039/D3SM00327B">Soft Matter <strong>19</strong>, 9389 (2023)</a>.
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</td>
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</tr>
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<tr>
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<td id="teomy2018confluent" valign="top">[2]</td>
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<td>
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E. Teomy, D. A. Kessler, and H. Levine, <em>Confluent and nonconfluent phases in a model of cell tissue</em>, <a href="https://doi.org/10.1103/PhysRevE.98.042418">Phys. Rev. E <strong>98</strong>, 042418 (2018)</a>.
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</td>
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</tr>
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<tr>
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<td id="wang2026divergence" valign="top">[3]</td>
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<td>
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W. Wang (汪巍) and B. A. Camley, <em>Divergence of detachment forces in the finite-Voronoi model</em>, manuscript in preparation (2026).
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</td>
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</tr>
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</table>
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# chooses fast vs fallback implementation
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try:
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from . import finite_voronoi_fast as _impl
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_BACKEND_NAME = "cython"
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except ImportError: # pragma: no cover
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_BACKEND_NAME = "python"
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from . import finite_voronoi_fallback as _impl
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# ---- for explicit API ----
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backend_simulator = _impl.FiniteVoronoiSimulator
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__all__ = [
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"backend_simulator",
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"_BACKEND_NAME",
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]
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