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🏥 trec24-biogen

Webis at TREC 2024 BioGen.

Installation

  1. Install Python 3.11.

  2. Create and activate a virtual environment:

    python3.11 -m venv venv/
source venv/bin/activate

  3. Install project dependencies:

    pip install -e .

Usage

Run the CLI with:

trec-biogen --help

Index PubMed

TODO

Fetch PubMed full texts

ray job submit --runtime-env ray-runtime-env.yml --no-wait -- python -m trec_biogen index-pubmed-full-texts --sample 0.01

Development

Refer to the general installation instructions to set up the development environment and install the dependencies. Then, also install the test dependencies:

pip install -e .[tests]

After having implemented a new feature, please check the code format, inspect common LINT errors, and run all unit tests with the following commands:

ruff check .                   # Code format and LINT
mypy .                         # Static typing
bandit -c pyproject.toml -r .  # Security
pytest .                       # Unit tests

Contribute

If you have found an important feature missing from our tool, please suggest it by creating an issue. We also gratefully accept pull requests!

If you are unsure about anything, post an issue or contact us:

We are happy to help!

License

This repository is released under the MIT license. Files in the data/ directory are exempt from this license.