nimh-dsst / osm

OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.

OpenSciMetrics

OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.

How to setup and run the application

• After cloning the repo, navigate into the project's root directory by running cd osm

• Run python -m venv venv to create a Virtual Environment

• Depending on your system, run the approriate command to Activate the Virtual Environment Windows: venv\Scripts\activate
  macOS and Linux: source venv/bin/activate

• Next, run pip install -e . to install the package with its dependencies.

• Finally, run osm pdf-xml "path_to_file_name.pdf" file_id

How to run tests of the application

Run tox

How to run the unit tests

• Navigate to the project's root directory and run pytest

Using pre-commit for commit checks

Pre-commit will run all of its hooks on every commit you make. To install pre-commit and its hooks, run the following commands:

pip install pre-commit
pre-commit install