PaperPlumber

Paper Plumber is a Python package that employs large language models to scan, understand, and extract key data points from scientific papers, streamlining research and data analysis. Currently the project is a CLI application. It's built on top of the findpapers package. You can find more information about findpapers at https://github.com/jonatasgrosman/findpapers.

Installation

You install the package by cloning the repository and installing the dependencies.

git clone https://github.com/OxfordSchmidtAIFellows/paper-plumber.git
cd paper-plumber
pip install .

Usage

After the package is installed, you can run paperplumber with different commands and options. Here is a quick overview of the commands available.

Commands

• download - Download full-text papers using the search results.
• list - List the available papers in the local directory, after searching. You can control the command logging verbosity by the -v (or --verbose) argument.
• parse - Parse the available papers in the local directory, after searching. You can control the command logging verbosity by the -v (or --verbose) argument.
• refine - Refine the search results by selecting/classifying the papers.
• search - Search for papers metadata using a query.
• version - Show the current version.

Each command has its own set of options which can be found in the --help information for each command.

For instance, the parse command usage is as follows:

paperplumber parse [OPTIONS] PATH TARGET

This command is used to parse the available papers in the local directory, after searching.

Arguments

• path - A valid path for the search result and full-text papers files. This argument is required.
• target - The value to extract from the papers. This argument is also required.

Options

• --verbose, -v - Use this option if you want verbose mode logging.
• --filter-with-embedding-search, -f - Use this option if you want to filter pages based on similarity to target. By default, it is set to True.

If you need help, you can use the --help option after any command to get more information about that command.

Full example

The following command search papers that contains quantum computing and two-qubit gate error, download them and extract the values of two-qubit error in these pdfs.

paperplumber search -q  "[quantum computing] AND [two-qubit gate error]" `pwd`
paperplumber download `pwd`
paperplumber parse `pwd` "two-qubit gate error"

License

This project is licensed under the MIT License.

Support

If you have any questions or run into any trouble, please open an issue on the GitHub repository.