PEPbench - The python package for automated pre-ejection period (PEP) extraction algorithms.

pepbench presents a framework for the automated extraction of the pre-ejection period (PEP) from electrocardiogram (ECG) and impedance cardiography (ICG) signals. The package includes a variety of algorithms for PEP extraction, as well as tools for the evaluation of these algorithms.

• 💻 3 Q-peak and 10 B-point Detection Algorithms from the literature
• 📚 Extensive documentation
• 📝 Build to be easily extendable
• 📁 2 manually annotated reference datasets for evaluation
• 📊 Evaluation tools for PEP extraction algorithms

Documentation: pepbench.readthedocs.io

Installation

pepbench can easily be installed via pip:

pip install pepbench

Installing from GitHub

If you want to install the latest version from GitHub, you can use the following command:

pip install "git+https://github.com/empkins/pepbench.git"

Note: We don't guarantee that the latest version on GitHub is stable.

Contributing

We want to hear from you (and we want your algorithms)!

👍 We are always happy to receive feedback and contributions. If you run into any issues or have any questions, please open an issue on GitHub or start a discussions thread.

📚 If you are using pepbench in your research or project, we would love to hear about it and link your work here!

💻 And most importantly, we want your algorithms! If you have an algorithm that you think would be a good fit for pepbench, open an issue, and we can discuss how to integrate it. We are happy to help you with the integration process. Even if you are not confident in your Python skills, we can discuss ways to get your algorithm into pepbench.

License

pepbench (and biopsykit, which contains the core algorithm implementations) are published under a MIT license. This is a permissive license, which allows you to use the code in nearly any way you want, as long as you include the original license in you modified version.

For Developers

Install Python >=3.10 and uv. Then run the commands below to install poethepoet, get the latest source, and install the dependencies:

git clone https://github.com/empkins/pepbench.git
uv tool install poethepoet
uv sync --all-extras --dev

All dependencies are specified in the main pyproject.toml when running uv sync.

To run any of the tools required for the development workflow, use the poe commands:

uv run poe
...
CONFIGURED TASKS
  format            Format all files with black.
  lint              Lint all files with ruff.
  check             Check all potential format and linting issues.
  test              Run Pytest with coverage.
  docs              Build the html docs using Sphinx.
  conf_jupyter      Register the pepbench environment as a Jupyter kernel for testing.
  version           Bump version in all relevant places.

Format and Linting

To ensure consistent code structure this project uses black and ruff to automatically check (and fix) the code format.

poe format  # runs ruff format and ruff lint with the autofix flag
poe lint # runs ruff without autofix (will show issues that can not automatically be fixed)

If you want to check if all code follows the code guidelines, run poe ci_check. This can be useful in the CI context.

Tests

All tests are located in the tests folder and can be executed by using poe test.