Merge pull request #13 from CardiacModelling/readme-and-gitignore

Readme and gitignore

Author: MichaelClerx

.gitattributes

@@ -6,41 +6,40 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        python-version: [3.7 ,3.8, 3.9, '3.10', 3.11]
+        python-version: [3.8, 3.9, '3.10', 3.11, 3.12, 3.13]
     steps:
-    - name: Checkout repository and submodules
+    - name: Checkout repository
       uses: actions/checkout@v4
-      with:
-        submodules: recursive
-    - name: Checkout github repo (+ download lfs dependencies)
-      uses: actions/checkout@v4
-      with:
-        lfs: true
-    - name: Checkout LFS objects
-      run: git lfs checkout
 
     - name: Set up Python ${{ matrix.python-version }}
       uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
+
     - name: Install dependencies
       run: |
-        python -m pip install --upgrade pip
         python -m pip install .[test]
+
+    - name: Lint with flake8
+      run: |
+        python -m flake8 syncropatch_export/*.py tests/*.py
+
+    - name: Import sorting with isort
+      run: |
+        python -m isort --verbose --check-only --diff syncropatch_export tests setup.py
+
     - name: Download and extract test data
       run: |
         wget https://cardiac.nottingham.ac.uk/syncropatch_export/test_data.tar.xz -P tests/
         tar xvf tests/test_data.tar.xz -C tests/
+
     - name: Test with pytest
       run: |
         python -m pip install -e .
         python -m pytest --cov --cov-config=.coveragerc
+
     - uses: codecov/codecov-action@v4
       with:
         token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
-    - name: Lint with flake8
-      run: |
-        python -m flake8 syncropatch_export/*.py tests/*.py
-    - name: Import sorting with isort
-      run: |
-        python -m isort --verbose --check-only --diff syncropatch_export tests setup.py
+      if: matrix.python-version == 3.13
+

.github/workflows/pytest.yml

@@ -1,6 +1,5 @@
 /tests/test_data
-*.pyc
-*.DS_Store
-*__pycache__*
-*.egg_info
+/test_output
 *__pycache__*
+*.egg-info
+*.DS_Store

.gitignore

@@ -1,20 +1,6 @@
-
-<!-- Improved compatibility of back to top link: See: https://github.com/othneildrew/Best-README-Template/pull/73 -->
-<a name="readme-top"></a>
-
-<!-- PROJECT SHIELDS -->
 [![Unit tests](https://github.com/CardiacModelling/syncropatch_export/actions/workflows/pytest.yml/badge.svg)](https://github.com//CardiacModelling/syncropatch_export/actions/workflows/pytest.yml)
 [![codecov](https://codecov.io/gh/CardiacModelling/syncropatch_export/graph/badge.svg?token=HOL0FrpGqs)](https://codecov.io/gh/CardiacModelling/syncropatch_export)
 
-
-<!-- PROJECT LOGO -->
-<!-- <br /> -->
-<!-- <div align="center"> -->
-<!--     <img src="images/logo.png" alt="Logo" width="80" height="80"> -->
-<!--   </a> -->
-
-
-<!-- TABLE OF CONTENTS -->
 <details>
   <summary>Table of Contents</summary>
   <ol>
@@ -40,119 +26,51 @@
   </ol>
 </details>
 
+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.
 
-<!-- ABOUT THE PROJECT -->
-## About The Project
-This project 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 also.
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
+This package is tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11, 3.12, and 3.13.
 
-
-<!-- GETTING STARTED -->
 ## Getting Started
 
-This is an example of how you may give instructions on setting up your project locally.
-To get a local copy up and running follow these simple example steps.
-
-### Prerequisites
-
-This package has been tested on Ubuntu with Python 3.7, 3.8, 3.9, 3.10 and 3.11.
-
-### Installation
-
 First clone this repository
 
-```
-git clone [email protected]:CardiacModelling/syncropatch_export && cd syncropatch_export
+```sh
+git clone [email protected]:CardiacModelling/syncropatch_export 
+cd syncropatch_export
 ```
 
-With one of these versions install, create and activate a virtual environment.
+Create and activate a virtual environment.
 
-  ```sh
-  python3 -m venv .venv && source .venv/bin/activate
-  ```
+```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](https://cardiac.nottingham.ac.uk/syncropatch_export)
+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)
 
 ```
 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
 ```
 
-<!-- CONTRIBUTING -->
-## Contributing
-
-Any contributions you make are **greatly appreciated**.
-
-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".
-
-1. Fork the Project
-2. Create your Feature Branch (`git checkout -b feature/AmazingFeature`)
-3. Commit your Changes (`git commit -m 'Add some AmazingFeature'`)
-4. Push to the Branch (`git push origin feature/AmazingFeature`)
-5. Open a Pull Request
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-<!-- LICENSE -->
 ## License
 
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
+At the moment this is a private repo
 
-
-<!-- CONTACT -->
 ## Contact
 
 Joseph Shuttleworth [email protected]
-
-Project Link: [https://github.com/CardiacModelling/syncropatch\_export](https://github.com/CardiacModelling/syncropatch_export)
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-<p align="right">(<a href="#readme-top">back to top</a>)</p>
-
-
-
-<!-- MARKDOWN LINKS & IMAGES -->
-<!-- https://www.markdownguide.org/basic-syntax/#reference-style-links -->
-[contributors-shield]: https://img.shields.io/github/contributors/CardiacModelling/syncropatch_export.svg?style=for-the-badge
-[contributors-url]: https://github.com/CardiacModelling/syncropatch_export/graphs/contributors
-[forks-shield]: https://img.shields.io/github/forks/CardiacModelling/syncropatch_export.svg?style=for-the-badge
-[forks-url]: https://github.com/CardiacModelling/syncropatch_export/network/members
-[stars-shield]: https://img.shields.io/github/stars/CardiacModelling/syncropatch_export.svg?style=for-the-badge
-[stars-url]: https://github.com/CardiacModelling/syncropatch_export/stargazers
-[issues-shield]: https://img.shields.io/github/issues/CardiacModelling/syncropatch_export.svg?style=for-the-badge
-[issues-url]: https://github.com/CardiacModelling/syncropatch_export/issues
-[license-shield]: https://img.shields.io/github/license/Cardiac/Modelling/syncropatch_export.svg?style=for-the-badge
-[license-url]: https://github.com/CardiacModelling/syncropatch_export/blob/master/LICENSE.txt
-[linkedin-shield]: https://img.shields.io/badge/-LinkedIn-black.svg?style=for-the-badge&logo=linkedin&colorB=555
-[linkedin-url]: https://linkedin.com/in/linkedin_username
-[product-screenshot]: images/screenshot.png
-[Next.js]: https://img.shields.io/badge/next.js-000000?style=for-the-badge&logo=nextdotjs&logoColor=white
-[Next-url]: https://nextjs.org/
-[React.js]: https://img.shields.io/badge/React-20232A?style=for-the-badge&logo=react&logoColor=61DAFB
-[React-url]: https://reactjs.org/
-[Vue.js]: https://img.shields.io/badge/Vue.js-35495E?style=for-the-badge&logo=vuedotjs&logoColor=4FC08D
-[Vue-url]: https://vuejs.org/
-[Angular.io]: https://img.shields.io/badge/Angular-DD0031?style=for-the-badge&logo=angular&logoColor=white
-[Angular-url]: https://angular.io/
-[Svelte.dev]: https://img.shields.io/badge/Svelte-4A4A55?style=for-the-badge&logo=svelte&logoColor=FF3E00
-[Svelte-url]: https://svelte.dev/
-[Laravel.com]: https://img.shields.io/badge/Laravel-FF2D20?style=for-the-badge&logo=laravel&logoColor=white
-[Laravel-url]: https://laravel.com
-[Bootstrap.com]: https://img.shields.io/badge/Bootstrap-563D7C?style=for-the-badge&logo=bootstrap&logoColor=white
-[Bootstrap-url]: https://getbootstrap.com
-[JQuery.com]: https://img.shields.io/badge/jQuery-0769AD?style=for-the-badge&logo=jquery&logoColor=white
-[JQuery-url]: https://jquery.com