cellects 0.1.0

Cell Expansion Computer Tracking Software.

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.

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Quick Start

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

• Install Miniconda3
  (choose the installer for your operating system).
• Install git
  (also available through package managers like apt, brew, or choco).

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

# 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:

Cellects

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Developer Guide

Run Tests

Cellects uses pytest + pytest-cov.
Install test dependencies:

pip install -e ".[test]"

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

pytest

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

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

Or explicitly:

pytest --cov=src/cellects --cov-report=term-missing

Build Documentation

Install doc dependencies:

pip install -e ".[doc]"

Serve the docs locally:

mkdocs serve

Open http://127.0.0.1:8000 in your browser.

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Resources

• User manual
• Usage example (video)