Development

Installation

For package development, the installation procedure is more complex than the one for the end user

Getting plinder

For development you need a clone of the official GitHub repository.

$ git clone https://github.com/plinder-org/plinder.git

Creating the Conda environment

The data generation pipeline (plinder.data) and evaluation require a few tools that are only available via Conda (mmseqs2, foldseek, OpenStructure). If you have not Conda installed yet, we recommend its installation via miniforge.

$ mamba env create -f environment.yml
$ mamba activate plinder

Installing plinder

All Python dependencies are declared in pyproject.toml. With uv, install plinder in editable mode with the complete dev dependency group (all extras used in CI, including CPU-only pytorch on Linux and the git-only pipeline packages) into the active Conda environment:

$ UV_PROJECT_ENVIRONMENT="$CONDA_PREFIX" uv sync --inexact

CI runs the same command. Without the Conda environment, a plain uv sync installs into .venv; tests that need the Conda-only tools will then fail.

With pip, the base install covers data generation and the core library:

$ pip install -e ".[dev]"

Evaluation scoring (optional)

plinder.eval runs the OpenStructure command-line actions for ligand and protein-interface evaluation. OpenStructure 2.12.0 or newer is installed from Bioconda by the repository’s environment.yml; it is not a PyPI dependency. Install the optional evaluation dependencies with:

$ pip install -e ".[eval]"

Note

The eval extra installs PoseBusters. OpenStructure is Conda-only and is installed by mamba env create -f environment.yml above. Data generation (plinder.data) does not require OpenStructure and works with numpy 2.

The full data pipeline also needs the git-only packages in the dev dependency group, which only uv sync installs.

Enabling Pre-commit hooks

Please install pre-commit hooks, that will run the same code quality checks as the CI:

$ pre-commit install

Testing and linting

plinder uses tox for running tests, type checks and code linting (with ruff).

$ tox -e test
$ tox -e type
$ tox -e lint

See tox.ini and .pre-commit-config.yaml for details.

Debugging

In order to change log levels in plinder, please set:

export PLINDER_LOG_LEVEL=10