diff --git a/.github/workflows/pytest.yml b/.github/workflows/pytest.yml
index b8a95c6b..7f0d8a29 100644
--- a/.github/workflows/pytest.yml
+++ b/.github/workflows/pytest.yml
@@ -6,47 +6,51 @@ jobs:
runs-on: ubuntu-latest
strategy:
matrix:
- python-version: [3.8, 3.9, '3.10', '3.11', '3.12']
+ 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: ${{ matrix.python-version }}
+
- name: Install dependencies
run: |
- eval `ssh-agent -s`
- ssh-add - <<< '${{ secrets.syncropatch_export_key }}'
python -m pip install --upgrade pip
python -m pip install -e .[test]
+
+ - name: Lint with flake8
+ run: |
+ python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
+
+ - name: Import sorting with isort
+ run: |
+ python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
+
- name: 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
- - name: Run export with test data
+
+ - name: Install TeX dependencies
timeout-minutes: 15
run: |
sudo apt-get install dvipng texlive-latex-extra texlive-fonts-recommended cm-super -y
+
+ - name: Test running QC
+ timeout-minutes: 15
+ run: |
pcpostprocess run_herg_qc tests/test_data/13112023_MW2_FF -w A01 A02 A03
- - uses: codecov/codecov-action@v1
+
+ - uses: codecov/codecov-action@v4
with:
token: ${{ secrets.CODECOV_TOKEN }} # not required for public repos
- - name: Lint with flake8
- run: |
- python -m flake8 pcpostprocess/*.py tests/*.py pcpostprocess/scripts/*.py
- - name: Import sorting with isort
- run: |
- python -m isort --verbose --check-only --diff pcpostprocess tests setup.py
+ if: success() && matrix.python-version == 3.13
+
diff --git a/.gitignore b/.gitignore
index 6ab74846..f1ff992d 100644
--- a/.gitignore
+++ b/.gitignore
@@ -1,6 +1,5 @@
/tests/test_data
/test_output
-*.pyc
-*.DS_Store
*__pycache__*
*.egg-info
+*.DS_Store
diff --git a/README.md b/README.md
index 0787dbdd..35701a58 100644
--- a/README.md
+++ b/README.md
@@ -1,97 +1,47 @@
-
-
-
-
-
[](https://github.com//CardiacModelling/pcpostprocess/actions/workflows/pytest.yml)
[](https://codecov.io/gh/CardiacModelling/pcpostprocess)
+This repository 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.
+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).
-
-
-
-
-
-
-
-
-
- Table of Contents
-
- -
- About The Project
-
-
- -
- Getting Started
-
-
- - Usage
- - Roadmap
- - Contributing
- - License
- - Contact
- - Acknowledgments
-
-
-
-
-
-## About The Project
-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).
-
-(back to top)
-
-
-
-## 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 is tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11, 3.12 and 3.13.
-This package has been tested on Ubuntu with Python 3.8, 3.9, 3.10, 3.11 and 3.12.
-
-### Installation
+## Getting Started
-First clone this repository
+First clone the repository
-```
-git clone git@github.com:CardiacModelling/pcpostprocess && cd pcpostprocess
+```sh
+git clone git@github.com:CardiacModelling/pcpostprocess
+cd pcpostprocess
```
-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`.
-```
+```sh
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)
-```
+```sh
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.
-```
+```sh
python3 -m unittest
```
-
-
## Usage
### Running QC and post-processing
@@ -100,7 +50,7 @@ Quality control (QC) may be run using the criteria outlined in [Rapid Characteri
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.
-```
+```sh
$ pcpostprocess run_herg_qc --help
usage: pcpostprocess run_herg_qc [-h] [-c NO_CPUS]
@@ -130,12 +80,11 @@ options:
--Erev EREV The reversal potential during the experiment
```
-
### Exporting Summary
The `summarise_herg_export` command produces additionally output after `run_herg_qc` has been run.
-```
+```sh
$ pcpostprocess summarise_herg_export --help
usage: pcpostprocess summarise_herg_export [-h] [--cpus CPUS]
@@ -162,70 +111,3 @@ options:
--log_level LOG_LEVEL
```
-
-
-## 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)
-
-
-
-
-## Contact
-
-Joseph Shuttleworth joseph.shuttleworth@nottingham.ac.uk
-
-Project Link: [https://github.com/CardiacModelling/pcpostprocess](https://github.com/CardiacModelling/pcpostprocess)
-
-(back to top)
-
-(back to top)
-
-
-
-
-
-[contributors-shield]: https://img.shields.io/github/contributors/CardiacModelling/pcpostprocess.svg?style=for-the-badge
-[contributors-url]: https://github.com/CardiacModelling/pcpostprocess/graphs/contributors
-[forks-shield]: https://img.shields.io/github/forks/CardiacModelling/pcpostprocess.svg?style=for-the-badge
-[forks-url]: https://github.com/CardiacModelling/pcpostprocess/network/members
-[stars-shield]: https://img.shields.io/github/stars/CardiacModelling/pcpostprocess.svg?style=for-the-badge
-[stars-url]: https://github.com/CardiacModelling/pcpostprocess/stargazers
-[issues-shield]: https://img.shields.io/github/issues/CardiacModelling/pcpostprocess.svg?style=for-the-badge
-[issues-url]: https://github.com/CardiacModelling/pcpostprocess/issues
-[license-shield]: https://img.shields.io/github/license/Cardiac/Modelling/pcpostprocess.svg?style=for-the-badge
-[license-url]: https://github.com/CardiacModelling/pcpostprocess/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/setup.py b/setup.py
index 540ca4e3..081561a0 100644
--- a/setup.py
+++ b/setup.py
@@ -56,7 +56,7 @@
'isort',
'mock>=3.0.5', # For mocking command line args etc.
'codecov>=2.1.3',
- 'syncropatch_export @ git+ssh://git@github.com/CardiacModelling/syncropatch_export@main'
+ 'syncropatch_export @ git+https://github.com/CardiacModelling/syncropatch_export.git'
],
},
entry_points={