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Installation

cellpy is available on Windows, macOS, and Linux. Prefer conda when you want the scientific stack and awkward native deps handled for you; use pip when you want a lean install and can manage system packages yourself.

After installing, continue to Setup and configuration and Check your installation.

Install by platform

Conda

conda install -c conda-forge cellpy

This pulls in the critical dependencies (and Jupyter, which is handy for the tutorials). Install into a virtual environment if you can.

New to Python? Teaspoon path
  1. Install Miniconda or Anaconda (64-bit, Python 3.11+).
  2. Open Anaconda Prompt and create an environment:
conda create -n cellpy python=3.13
conda activate cellpy
  1. Install cellpy:
conda install -c conda-forge cellpy

Bitness matters for Arbin .res (Access) drivers: match the driver to your Python build (32- vs 64-bit).

Pip

python -m pip install cellpy

On Windows, packages such as tables (HDF5) can be awkward with pip. Prefer conda, or create an env from the repo environment.yml first.

Arbin .res files

.res files are Microsoft Access databases. You need an Access / ACE ODBC driver that matches your Python bitness (Microsoft download). If loading fails, try:

python -m pip install sqlalchemy-access

System packages

For Arbin .res support, cellpy uses mdbtools to export to temporary CSV (there is no Access ODBC path like on Windows). Also install HDF5 libs if you plan to build tables with pip:

brew install mdbtools hdf5 c-blosc

Apple Silicon (Homebrew prefixes) — if tables fails to build under pip:

export HDF5_DIR=/opt/homebrew/opt/hdf5
export BLOSC_DIR=/opt/homebrew/opt/c-blosc
python -m pip install cython tables

Conda

conda install -c conda-forge cellpy

Pip

python -m pip install cellpy

Use a virtual environment (python -m venv .venv or conda env).

System packages

For Arbin .res support, cellpy uses mdbtools to export to temporary CSV (there is no Access ODBC path like on Windows). Ubuntu/Debian example, plus common pip build deps:

sudo apt update
sudo apt-get install -y mdbtools unixodbc-dev libhdf5-serial-dev

Other distros: install the equivalent packages with your package manager.

Conda

conda install -c conda-forge cellpy

Pip

python -m pip install cellpy

Prefer a virtual environment. Without sudo, try the same apt packages in a user/container image, or stick to conda.

Installation from sources

Clone the public repository:

git clone https://github.com/jepegit/cellpy.git
cd cellpy

Recommended for contributors (see CONTRIBUTING.md):

uv sync

Or with conda + editable install:

conda env create -f environment.yml
conda activate cellpy
python -m pip install -e .

Dependencies

Conda and environment.yml / the project lockfile (uv.lock, driven by pyproject.toml) install what you need for normal use. Highlights:

Need Packages / notes
Core science stack numpy, scipy, pandas
cellpy files (HDF5 path) tables (PyTables)
Fitting helpers lmfit
Templates jinja2-time, and git on PATH
Tutorials / notebooks jupyter, seaborn, plotly

Optional extras and plotting backends evolve with the release — prefer the conda-forge package or the repo env file over hand-picking versions.