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Merge branch 'main' into hilary_dev
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‎.flake8‎

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exclude=
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.git,
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venv,
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tests/test_data,

‎.github/workflows/pytest.yml‎

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runs-on: ubuntu-latest
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strategy:
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matrix:
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python-version: [3.7 ,3.8, 3.9, '3.10', 3.11]
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python-version: [3.8, 3.9, '3.10', 3.11, 3.12, 3.13]
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steps:
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- name: Checkout repository and submodules
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uses: actions/checkout@v1
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with:
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submodules: recursive
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- name: Checkout github repo (+ download lfs dependencies)
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uses: actions/checkout@v2
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with:
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lfs: true
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- name: Checkout LFS objects
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run: git lfs checkout
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- name: Checkout repository
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uses: actions/checkout@v4
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- name: Set up Python ${{ matrix.python-version }}
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uses: actions/setup-python@v1
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uses: actions/setup-python@v5
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with:
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python-version: ${{ matrix.python-version }}
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- name: Install dependencies
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run: |
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eval `ssh-agent -s`
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ssh-add - <<< '${{ secrets.syncropatch_export_key }}'
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python -m pip install --upgrade pip
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python -m pip install -e .[test]
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- name: Lint with flake8
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run: |
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python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
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- name: Import sorting with isort
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run: |
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python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
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- name: Extract test data
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run: |
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wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
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tar xvf tests/test_data.tar.xz -C tests/
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- name: Test with pytest
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run: |
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python -m pip install -e .
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python -m pytest --cov --cov-config=.coveragerc
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- name: Run export with test data
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- name: Install TeX dependencies
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timeout-minutes: 15
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run: |
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sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
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- name: Test running QC
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timeout-minutes: 15
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run: |
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pcpostprocess run_herg_qc tests/test_data/13112023_MW2_FF -w A01 A02 A03
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- uses: codecov/codecov-action@v1
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- uses: codecov/codecov-action@v4
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with:
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token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
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- name: Lint with flake8
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run: |
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python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
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- name: Import sorting with isort
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run: |
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python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
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if: success() && matrix.python-version == 3.13
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‎.gitignore‎

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/tests/test_data
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*.pyc
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/test_output
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*__pycache__*
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*.egg-info
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*.DS_Store
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*__pycache__*

‎README.md‎

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<!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
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<a name="readme-top"></a>
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<!-- PROJECT SHIELDS -->
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[![Unit tests](https://github.com/CardiacModelling/pcpostprocess/actions/workflows/pytest.yml/badge.svg)](https://github.com//CardiacModelling/pcpostprocess/actions/workflows/pytest.yml)
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[![codecov](https://codecov.io/gh/CardiacModelling/pcpostprocess/graph/badge.svg?token=HOL0FrpGqs)](https://codecov.io/gh/CardiacModelling/pcpostprocess)
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This repository contains a python package and scripts for handling time-series data from patch-clamp experiments.
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The package has been tested with data from a SyncroPatch 384, but may be adapted to work with data in other formats.
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It can also be used to perform quality control (QC) as described in [Lei et al. (2019)](https://doi.org/10.1016%2Fj.bpj.2019.07.029).
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<!-- PROJECT LOGO -->
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<!-- <br /> -->
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<!-- <div align="center"> -->
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<!-- <img src="images/logo.png" alt="Logo" width="80" height="80"> -->
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<!-- </a> -->
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<!-- TABLE OF CONTENTS -->
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<details>
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<summary>Table of Contents</summary>
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<ol>
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<li>
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<a href="#about-the-project">About The Project</a>
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<ul>
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<li><a href="#built-with">Built With</a></li>
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</ul>
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</li>
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<li>
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<a href="#getting-started">Getting Started</a>
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<ul>
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<li><a href="#prerequisites">Prerequisites</a></li>
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<li><a href="#installation">Installation</a></li>
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</ul>
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</li>
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<li><a href="#usage">Usage</a></li>
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<li><a href="#roadmap">Roadmap</a></li>
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<li><a href="#contributing">Contributing</a></li>
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<li><a href="#license">License</a></li>
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<li><a href="#contact">Contact</a></li>
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<li><a href="#acknowledgments">Acknowledgments</a></li>
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</ol>
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</details>
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<!-- ABOUT THE PROJECT -->
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## About The Project
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This project contains a python package and scripts for handling time-series data from patch-clamp experiments. The package has been tested with data from a SyncroPatch 384, but may be adapted to work with data in other formats. The package can also be used to perform quality control (QC) as described in [Lei et al. (2019)](https://doi.org/10.1016%2Fj.bpj.2019.07.029).
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<p align="right">(<a href="#readme-top">back to top</a>)</p>
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<!-- GETTING STARTED -->
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## Getting Started
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This is an example of how you may give instructions on setting up your project locally.
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To get a local copy up and running follow these simple example steps.
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### Prerequisites
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This package is tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11, 3.12 and 3.13.
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This package has been tested on Ubuntu with Python 3.7, 3.8, 3.9, 3.10 and 3.11.
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### Installation
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## Getting Started
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First clone this repository
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First clone the repository
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```
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git clone git@github.com:CardiacModelling/pcpostprocess && cd pcpostprocess
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```sh
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git clone git@github.com:CardiacModelling/pcpostprocess
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cd pcpostprocess
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```
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With one of these versions install, create and activate a virtual environment.
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Create and activate a virtual environment.
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```sh
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python3 -m venv .venv && source .venv/bin/activate
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```
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```sh
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python3 -m venv .venv && source .venv/bin/activate
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```
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Then install the package with `pip`.
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```
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```sh
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python3 -m pip install --upgrade pip && python3 -m pip install -e .'[test]'
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```
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To run the tests you must first download some test data. Test data is available at [cardiac.nottingham.ac.uk/syncropatch\_export](https://cardiac.nottingham.ac.uk/syncropatch_export)
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To run the tests you must first download some test data.
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Test data is available at [cardiac.nottingham.ac.uk/syncropatch\_export](https://cardiac.nottingham.ac.uk/syncropatch_export)
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```
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```sh
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wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
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tar xvf tests/test_data.tar.xz -C tests/
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rm tests/test_data.tar.xz
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```
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Then you can run the tests.
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```
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```sh
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python3 -m unittest
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```
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<!-- USAGE -->
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## Usage
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### Running QC and post-processing
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Quality control (QC) may be run using the criteria outlined in [Rapid Characterization of hERG Channel Kinetics I](https://doi.org/10.1016/j.bpj.2019.07.030) and [Evaluating the predictive accuracy of ion channel models using data from multiple experimental designs](https://doi.org/10.1101/2024.08.16.608289). These criteria assume the use of the `staircase` protocol for quality control, which should be the first and last protocol performed. We also assume the presence of repeats after the addition of an IKr blocker (such as dofetilide).
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Quality control (QC) may be run using the criteria outlined in [Rapid Characterization of hERG Channel Kinetics I](https://doi.org/10.1016/j.bpj.2019.07.029) and [Evaluating the predictive accuracy of ion channel models using data from multiple experimental designs](https://doi.org/10.1101/2024.08.16.608289). These criteria assume the use of the `staircase` protocol for quality control, which should be the first and last protocol performed. We also assume the presence of repeats after the addition of an IKr blocker (such as dofetilide).
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Prior to performing QC and exporting, an `export_config.py` file should be added to the root of the data directory. This file (see `example_config.py`) contains a Python `dict` (`Q2S_DC`) specifying the filenames of the protocols used for QC, and names they should be outputted with, as well as a Python `dict` (`D2S`) listing the other protocols and names to be used for their output. Additionally, the `saveID` field specifies the name of the expeirment which appears in the output file names.
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```
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```sh
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$ pcpostprocess run_herg_qc --help
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usage: pcpostprocess run_herg_qc [-h] [-c NO_CPUS]
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--Erev EREV The reversal potential during the experiment
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```
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### Exporting Summary
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The `summarise_herg_export` command produces additionally output after `run_herg_qc` has been run.
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```
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```sh
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$ pcpostprocess summarise_herg_export --help
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usage: pcpostprocess summarise_herg_export [-h] [--cpus CPUS]
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--log_level LOG_LEVEL
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```
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<!-- CONTRIBUTING -->
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## Contributing
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Any contributions you make are **greatly appreciated**.
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If you have a suggestion that would make this better, please fork the repo and create a pull request. You can also simply open an issue with the tag "enhancement".
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1. Fork the Project
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2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
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3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
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4. Push to the Branch (`git push origin feature/AmazingFeature`)
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5. Open a Pull Request
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<p align="right">(<a href="#readme-top">back to top</a>)</p>
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<!-- LICENSE -->
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## License
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<p align="right">(<a href="#readme-top">back to top</a>)</p>
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<!-- CONTACT -->
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## Contact
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Joseph Shuttleworth joseph.shuttleworth@nottingham.ac.uk
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Project Link: [https://github.com/CardiacModelling/pcpostprocess](https://github.com/CardiacModelling/pcpostprocess)
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<p align="right">(<a href="#readme-top">back to top</a>)</p>
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<p align="right">(<a href="#readme-top">back to top</a>)</p>
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<!-- MARKDOWN LINKS & IMAGES -->
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<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
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[contributors-shield]: https://img.shields.io/github/contributors/CardiacModelling/pcpostprocess.svg?style=for-the-badge
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[contributors-url]: https://github.com/CardiacModelling/pcpostprocess/graphs/contributors
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[forks-shield]: https://img.shields.io/github/forks/CardiacModelling/pcpostprocess.svg?style=for-the-badge
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[forks-url]: https://github.com/CardiacModelling/pcpostprocess/network/members
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[stars-shield]: https://img.shields.io/github/stars/CardiacModelling/pcpostprocess.svg?style=for-the-badge
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[stars-url]: https://github.com/CardiacModelling/pcpostprocess/stargazers
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[issues-shield]: https://img.shields.io/github/issues/CardiacModelling/pcpostprocess.svg?style=for-the-badge
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[issues-url]: https://github.com/CardiacModelling/pcpostprocess/issues
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[license-shield]: https://img.shields.io/github/license/Cardiac/Modelling/pcpostprocess.svg?style=for-the-badge
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[license-url]: https://github.com/CardiacModelling/pcpostprocess/blob/master/LICENSE.txt
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[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555
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[linkedin-url]: https://linkedin.com/in/linkedin_username
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[product-screenshot]: images/screenshot.png
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[Next.js]: https://img.shields.io/badge/next.js-000000?style=for-the-badge&logo=nextdotjs&logoColor=white
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[Next-url]: https://nextjs.org/
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[React.js]: https://img.shields.io/badge/React-20232A?style=for-the-badge&logo=react&logoColor=61DAFB
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[React-url]: https://reactjs.org/
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[Vue.js]: https://img.shields.io/badge/Vue.js-35495E?style=for-the-badge&logo=vuedotjs&logoColor=4FC08D
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[Vue-url]: https://vuejs.org/
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[Angular.io]: https://img.shields.io/badge/Angular-DD0031?style=for-the-badge&logo=angular&logoColor=white
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[Angular-url]: https://angular.io/
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[Svelte.dev]: https://img.shields.io/badge/Svelte-4A4A55?style=for-the-badge&logo=svelte&logoColor=FF3E00
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[Svelte-url]: https://svelte.dev/
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[Laravel.com]: https://img.shields.io/badge/Laravel-FF2D20?style=for-the-badge&logo=laravel&logoColor=white
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[Laravel-url]: https://laravel.com
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[Bootstrap.com]: https://img.shields.io/badge/Bootstrap-563D7C?style=for-the-badge&logo=bootstrap&logoColor=white
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[Bootstrap-url]: https://getbootstrap.com
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[JQuery-url]: https://jquery.com

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