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https://github.com/cardiacmodelling/syncropatch_export

A Python package to export SynroPatch 384 data.

https://github.com/cardiacmodelling/syncropatch_export

Science Score: 26.0%

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    CITATION.cff file
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    Scientific vocabulary similarity
    Low similarity (14.0%) to scientific vocabulary
Last synced: 10 months ago · JSON representation

Repository

A Python package to export SynroPatch 384 data.

Basic Info
  • Host: GitHub
  • Owner: CardiacModelling
  • License: bsd-3-clause
  • Language: Python
  • Default Branch: main
  • Homepage:
  • Size: 203 KB
Statistics
  • Stars: 3
  • Watchers: 2
  • Forks: 0
  • Open Issues: 18
  • Releases: 0
Created over 2 years ago · Last pushed 12 months ago
Metadata Files
Readme License

README.md

Unit tests codecov

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

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

Create and activate a virtual environment.

sh 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

Owner

  • Name: Cardiac Modelling
  • Login: CardiacModelling
  • Kind: organization
  • Location: United Kingdom

Codes and Resources from the University of Nottingham's cardiac modelling team

GitHub Events

Total
  • Issues event: 12
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 8
  • Push event: 12
  • Pull request review event: 1
  • Pull request review comment event: 2
  • Pull request event: 2
Last Year
  • Issues event: 12
  • Watch event: 1
  • Delete event: 1
  • Issue comment event: 8
  • Push event: 12
  • Pull request review event: 1
  • Pull request review comment event: 2
  • Pull request event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 9
  • Total pull requests: 2
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 14 minutes
  • Total issue authors: 3
  • Total pull request authors: 1
  • Average comments per issue: 0.33
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 4
  • Bot pull requests: 0
Past Year
  • Issues: 8
  • Pull requests: 2
  • Average time to close issues: 8 minutes
  • Average time to close pull requests: 14 minutes
  • Issue authors: 3
  • Pull request authors: 1
  • Average comments per issue: 0.0
  • Average comments per pull request: 0.0
  • Merged pull requests: 1
  • Bot issues: 4
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • github-actions[bot] (4)
  • MichaelClerx (3)
  • mirams (3)
Pull Request Authors
  • MichaelClerx (2)
Top Labels
Issue Labels
todo (4)
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Dependencies

.github/workflows/pytest.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • codecov/codecov-action v4 composite
.github/workflows/todo.yml actions
  • actions/checkout v4 composite
  • alstr/todo-to-issue-action v4 composite
setup.py pypi
  • matplotlib >=3.4
  • numpy >=1.21
  • pandas >=1.3
  • regex >=2023.12.25
  • scipy >=1.7