cellects 0.1.4

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

1. With Cellects_installer.exe (windows)

• Download Cellects_installer.exe

• Double-click on the Cellects_installer.exe file to start installation Note 1: Windows may warn you that it's unsafe; that's normal, because we are not a registered developer. Click "More info" and "Run Anyway". Note 2: For the same reason, some antivirus software can prevent installation.

• To run Cellects, explore the newly created folder to find and execute Cellects.exe

2. Using pip (Mac, Windows or Linux)

• Install python 3.13

• Best practice(optional): create and activate a python environment Use a terminal to create the environment:

cd path/toward/an/existing/folder/
python -m venv ./cellects_env

Activation on Windows:

cellects_env\Scripts\activate

Activation on Unix or MacOS:

source cellects_env/bin/activate

• Installation:

pip install cellects

• Run Cellects:

Cellects

To uninstall, use:

pip uninstall cellects

Note: creating a python environment avoids compatibilities issues with other python scripts. However, the user have to activate this environment every time before running Cellects.

3. To access the source code (Mac, Windows or Linux)

• Install python 3.13
• Install git
• On Mac: also install brew
• Choose a place to install Cellects and use a terminal to write:

cd path/toward/an/existing/folder/

Note: The repository will be cloned to that folder; if updating an existing project, use a different folder name and rename it after verifying the new version.

• Clone Cellects repository in terminal (or any IDE) with:

git clone https://github.com/Aurele-B/Cellects.git
cd ./Cellects
pip install --upgrade pip
python -m venv ./cellects_env

On Windows, run:

cellects_env\Scripts\activate

On Unix or MacOS, run:

source cellects_env/bin/activate

Install Cellects dependencies in editable mode:

pip install -e .

Run Cellects:

Cellects

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.

Create windows executable

When installing Cellects dependencies, do not use editable mode:

python -m venv ./cellects_env
deactivate
cellects_env\Scripts\activate
pip install .
pip install pyinstaller
cd cellects_env/Lib/site-packages/cellects
pyinstaller __main__.py

Then, compress the dist folder into Cellects.zip and us NSIS to generate the installer

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Resources

• User manual
• Usage example (video)