cellPACK documentation

Welcome to cellPACK! This documentation provides an overview of the cellPACK package, its modules, and how to contribute.

cellPACK

Continuous Integration Documentation Code Coverage

An algorithm to pack molecular recipes

Installation

[!NOTE] These are the basic installation steps. However, our recommendation for developers is to install using uv. See advanced installation instructions here.

  1. Install Python 3.11 and git. Update pip at least to 24.0.0.

  2. Clone this git repository.

git clone git@github.com:mesoscope/cellpack.git
cd cellpack

  1. Create a new virtual environment and activate it.

python -m venv .venv
source .venv/bin/activate

  1. Install the required packages for your operating system. Replace linux with macos or windows as appropriate.

pip install --upgrade pip
pip install -r requirements/linux/requirements.txt
pip install -e .

Pack example recipes

  1. v1: pack -r examples/recipes/v1/NM_Analysis_FigureB1.0.json -c examples/packing-configs/run.json

  2. v2: pack -r examples/recipes/v2/one_sphere.json -c examples/packing-configs/run.json

  3. Pack from remote server: pack -r  github:recipes/NM_Analysis_FigureB1.0.json  -c examples/packing-configs/run.json

Stable Release: pip install cellpack
Development Head: pip install git+https://github.com/mesoscope/cellpack.git

Documentation

For full package documentation please visit mesoscope.github.io/cellpack.

Development

See CONTRIBUTING.md for information related to developing the code.

Remote databases

cellPACK uses AWS and Firebase Firestore as remote databases to store packing results and recipes. Follow setup instructions for access.

Docker

cellPACK can be run in Docker containers for both AWS ECS and AWS Batch. Follow the instructions to set up the Docker environment.

MIT license