README.md

This repository contains a python package and scripts for processing data outputted from Nanion SynroPatch 384.

With this package you can export each sweep of each protocol for each well as individual files (.csv). Meta-data describing the protocol, and variables such as membrance capacitance (Cm), Rseries and Rseal can be exported.

This package is tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11, 3.12, and 3.13 and is distributed under a BSD 3-Clause License.

Getting Started

First clone this repository

git clone git@github.com:CardiacModelling/syncropatch_export 
cd syncropatch_export

Create and activate a virtual environment.

python3 -m venv .venv && source .venv/bin/activate

Then install the package with pip.

python3 -m pip install --upgrade pip && python3 -m pip install -e .'[test]'

To run the tests you must first download some test data. Test data is available at cardiac.nottingham.ac.uk/syncropatch_export

wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
tar xvf tests/test_data.tar.xz -C tests/
rm tests/test_data.tar.xz

Then you can run the tests.

python3 -m unittest

Usage example

...TODO

Development

Commits should be merged in via pull requests.

Tests are written using the standard unittest framework.

Online testing, style-checking, and coverage testing is set up using GitHub actions. Coverage testing is handled via Codecov.

Style testing is done with flake8. For example, to test with 4 subprocesses use

flake8 -j4

Import sorting can be checked with isort:

isort --verbose --check-only --diff syncropatch_export tests setup.py

Documentation is implemented using Sphinx. To compile locally, first install the required dependencies

pip install -e .'[docs]'

and then use Make

cd docs
make html