Metadata-Version: 2.4
Name: cr_mech_coli
Version: 0.5.3
Classifier: Programming Language :: Rust
Classifier: Programming Language :: Python :: Implementation :: CPython
Classifier: Programming Language :: Python :: Implementation :: PyPy
Requires-Dist: pyvista>=0.42
Requires-Dist: numpy==2
Requires-Dist: opencv-python
Requires-Dist: tqdm>=4.60
Requires-Dist: scikit-image>=0.24
Requires-Dist: pytest>=8
Requires-Dist: matplotlib
License-File: LICENSE
Requires-Python: >=3.10
Description-Content-Type: text/markdown; charset=UTF-8; variant=GFM

        The cellular_raza logo

# cr_mech_coli
[![License: GPL 2.0](https://img.shields.io/github/license/jonaspleyer/cr_mech_coli?style=flat-square)](https://opensource.org/license/gpl-2-0/)
[![Test](https://img.shields.io/github/actions/workflow/status/jonaspleyer/cr_mech_coli/test.yml?label=Test&style=flat-square)](https://github.com/jonaspleyer/cr_mech_coli/actions)
[![CI](https://img.shields.io/github/actions/workflow/status/jonaspleyer/cr_mech_coli/CI.yml?label=CI&style=flat-square)](https://github.com/jonaspleyer/cr_mech_coli/actions)
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[![PyPI - Version](https://img.shields.io/pypi/v/cr_mech_coli?style=flat-square)]()

Find the documentation of this package under
[jonaspleyer.github.io/cr_mech_coli/](https://jonaspleyer.github.io/cr_mech_coli/).

## Example

```python
import cr_mech_coli as crm

# Contains settings regarding simulation domain, time increments etc.
config = crm.Configuration()

# Use predefined values for agents
agent_settings = crm.AgentSettings()

# Automatically generate agents
agents = crm.generate_agents(
    4,
    agent_settings,
    config
)

# Run simulation and return container
cell_container = crm.run_simulation_with_agents(agents, config)

# Plot individual results
crm.store_all_images(cell_container, config.domain_size)
```

The generated images will be stored (by default) in `out`.
```text
out
├── images
│   ├── 000000100.png
│   ...
│   └── 000001000.png
├── masks
│   ├── 000000100.png
│   ...
│   └── 000001000.png
```

## Installation
Use [maturin](https://github.com/PyO3/maturin) to build the project.
The following instructions are for nix-like operating systems.
Please use the resources at [python.org](https://python.org/) to adjust them for your needs.
First we create a virtual environment and activate it.

```
python3 -m venv .venv
source .venv/bin/activate
```

If you have not yet used maturin, install it.
We recommend that you use the [uv](https://github.com/astral-sh/uv) package manager for dependency
management.

```
uv pip install maturin
maturin develop -r --uv
```

Now you are ready to use `cr_mech_coli`.
If you modify the source code, you have rerun the last command in order to install the updated
version.

