diff --git a/.gitattributes b/.gitattributes
deleted file mode 100644
index 847dd9a..0000000
--- a/.gitattributes
+++ /dev/null
@@ -1 +0,0 @@
-tests/test_data.tar.xz filter=lfs diff=lfs merge=lfs -text
diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index 6e54e19..18fee45 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -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
+
diff --git a/.gitignore b/.gitignore
index 576aa7a..f1ff992 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,5 @@
/tests/test_data
-*.pyc
-*.DS_Store
-*__pycache__*
-*.egg_info
+/test_output
*__pycache__*
+*.egg-info
+*.DS_Store
diff --git a/README.md b/README.md
index b93affc..08b4c70 100644
--- a/README.md
+++ b/README.md
@@ -1,20 +1,6 @@
-
-
-
-
-
[](https://github.com//CardiacModelling/syncropatch_export/actions/workflows/pytest.yml)
[](https://codecov.io/gh/CardiacModelling/syncropatch_export)
-
-
-
-
-
-
-
-
-
Table of Contents
@@ -40,37 +26,26 @@
+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
-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.
-(back to top)
+This package is tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11, 3.12, and 3.13.
-
-
## 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 git@github.com:CardiacModelling/syncropatch_export && cd syncropatch_export
+```sh
+git clone git@github.com: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`.
@@ -78,11 +53,13 @@ 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.
@@ -90,69 +67,10 @@ Then you can run the tests.
python3 -m unittest
```
-
-## 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
-
-(back to top)
-
-
## License
-(back to top)
-
+At the moment this is a private repo
-
-
## Contact
Joseph Shuttleworth joseph.shuttleworth@nottingham.ac.uk
-
-Project Link: [https://github.com/CardiacModelling/syncropatch\_export](https://github.com/CardiacModelling/syncropatch_export)
-
-(back to top)
-
-(back to top)
-
-
-
-
-
-[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
diff --git a/test_output/test_trace_class/example_trace.png b/test_output/test_trace_class/example_trace.png
deleted file mode 100644
index 137ab19..0000000
Binary files a/test_output/test_trace_class/example_trace.png and /dev/null differ