Installation

Anaconda 2025.12 or newer is required.

  1. Create a new conda environment

conda create -n ciclope python=3.10

  1. Activate the environment

conda activate ciclope

  1. Install IPyKernel and register the ciclope kernel to be seen by the main Jupyter installation

conda install ipykernel

  1. For mesh generation, ciclope requires pygalmesh, a Python frontend to CGAL. Pygalmesh installed via (ana)conda from conda-forge channel already ships with a CGAL binary installation.

conda install -c conda-forge pygalmesh

  1. Install Ciclope

pip install ciclope[all]

Basic installation (voxelFE only)

A minimal version of ciclope (voxelFE pipelines only) can be installed without CGAL, Eigen, and pygalmesh with:

micromamba create -n ciclope ipython python==3.11.11 jupyter numpy pymcubes scipy scikit-image meshio h5py -c conda-forge
git clone https://github.com/ciclope-microFE/ciclope.git
cd ciclope
pip3 install .

Testing

To verify your installation checkout this repository and run the tests with the command:

cd test
python -m unittest -v test_ciclope.run_tests

How to contribute

If you want to contribute to ciclope follow the installation steps below:

Create and activate a virtual environment for development:

conda env create -n ciclope
conda activate ciclope

Clone (or fork and clone) the git repository:

git clone https://github.com/gianthk/ciclope.git

Navigate to the repo folder and install the package using pip:

cd ciclope
pip install .

Or install the package locally for development with Flit:

flit install --symlink

Build instructions

Build package:

python -m build

Upload to pypi:

python -m twine upload --repository pypi dist/*

Uninstall the existing build:

python -m pip uninstall ciclope