Metadata-Version: 2.2
Name: cellects
Version: 0.1.0
Summary: Cell Expansion Computer Tracking Software.
Author: Aurèle Boussard
Project-URL: Homepage, https://github.com/Aurele-B/Cellects
Project-URL: Issues, https://github.com/Aurele-B/Cellects/issues
Classifier: Programming Language :: Python :: 3
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Operating System :: OS Independent
Requires-Python: <3.13,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE.odt
Requires-Dist: coloredlogs
Requires-Dist: exif
Requires-Dist: ExifRead
Requires-Dist: numba
Requires-Dist: opencv-python
Requires-Dist: pandas
Requires-Dist: psutil
Requires-Dist: PySide6>=6.5
Requires-Dist: scipy
Requires-Dist: screeninfo
Requires-Dist: numpy>=1.26
Requires-Dist: scikit-image
Requires-Dist: tqdm
Requires-Dist: h5py
Requires-Dist: matplotlib
Requires-Dist: natsort
Provides-Extra: test
Requires-Dist: pytest; extra == "test"
Requires-Dist: pytest-env; extra == "test"
Requires-Dist: pytest-cov; extra == "test"
Provides-Extra: doc
Requires-Dist: mkdocs; extra == "doc"
Requires-Dist: mkdocs-material; extra == "doc"
Requires-Dist: pymdown-extensions; extra == "doc"

Cellects: Cell Expansion Computer Tracking Software
===================================================

Description
-----------

Cellects is a tracking software for organisms whose shape and size change over time. 
Cellects’ main strengths are its broad scope of action, 
automated computation of a variety of geometrical descriptors, easy installation and user-friendly interface.


---

## Quick Start


⚠️ **Note:** At this stage, Cellects is available **only from source**.  
You will need **Miniconda3** and **git** installed on your system.

- Install [Miniconda3](https://docs.conda.io/en/latest/miniconda.html)  
  (choose the installer for your operating system).  
- Install [git](https://git-scm.com/downloads)  
  (also available through package managers like `apt`, `brew`, or `choco`).

Once these prerequisites are installed, you can set up Cellects as follows:

```bash
# Clone the repository
git clone https://github.com/Aurele-B/Cellects.git
cd Cellects

# Create and activate the environment
conda env create -f conda/env.yml
conda activate cellects-dev

# Install the package in editable mode
pip install -e .
```

Launch the application:
```bash
Cellects
```

---

## Developer Guide

### Run Tests
Cellects uses `pytest` + `pytest-cov`.  
Install test dependencies:

```bash
pip install -e ".[test]"
```

Run the test suite (with coverage enabled by default via `pyproject.toml`):

```bash
pytest
```

You can access the coverage report with `coverage html` and open `htmlcov/index.html` in your browser.

```bash
open htmlcov/index.html        # macOS
xdg-open htmlcov/index.html    # Linux
start htmlcov\index.html       # Windows (PowerShell)
```

Or explicitly:
```bash
pytest --cov=src/cellects --cov-report=term-missing
```

### Build Documentation
Install doc dependencies:

```bash
pip install -e ".[doc]"
```

Serve the docs locally:
```bash
mkdocs serve
```

Open [http://127.0.0.1:8000](http://127.0.0.1:8000) in your browser.

---

## Resources
- [User manual](https://github.com/Aurele-B/Cellects/blob/main/_old_doc/UserManual.md)  
- [Usage example (video)](https://www.youtube.com/watch?v=N-k4p_aSPC0)
