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Install data_to_paper

Install on your local machine

  1. Install anaconda (follow instructions at Anaconda Installation).

  2. Clone the repo, run git clone https://github.com/Technion-Kishony-lab/data-to-paper.

  3. Create a conda environment, run conda create -n data-to-paper python=3.11.

  4. Activate the newly created environment, run conda activate data-to-paper.

  5. Enter the repo root folder, run cd data-to-paper.

  6. Install the required packages, run pip install -r requirements.txt.

  7. Install the app and further required packages, run pip install -e data_to_paper.

  8. Install pandoc (follow instructions at Pandoc Installation).

  9. Install all the required packages for compiling LaTeX:

    • On Ubuntu: 
      sudo apt-get update && \
sudo apt-get install -y --no-install-recommends \
texlive-latex-base \
texlive-latex-extra \
texlive-fonts-recommended
    • On MacOS:
      • Ensure you have Homebrew installed (see Homebrew Installation).
      • Install MacTeX with the following command: 
        brew install --cask mactex-no-gui
      • After installation, you may need to add the TeX binaries to your PATH!
    • On Windows:
      • Download and install MiKTeX from MiKTeX Download Page.
      • During installation, select 'Yes' when asked to install missing packages on-the-fly.
      • After installation, you may need to add the TeX binaries to your PATH!

Install using Docker

The Docker container is a self-contained environment that includes all the required dependencies to run the app. It is simple to install and run, but we do not recommend using it as it currently does not support the GUI app.

  1. Install Docker (follow instructions at https://docs.docker.com/engine/install/) and make sure docker server runs on your computer
  2. Clone the repo, run git clone https://github.com/Technion-Kishony-lab/data-to-paper
  3. Enter the repo root folder cd data-to-paper
  4. Make sure the docker service is running on the machine by running sudo service docker start
  5. Build the docker container by running docker build --pull --rm -f "Dockerfile" -t datatopaper "."

You now have the container with the repo available for run/dev

Add environment variables for API keys

You need to define the following environment variables in your system:

  • OPENAI_API_KEY
  • SEMANTIC_SCHOLAR_API_KEY
  • DEEPINFRA_API_KEY (optional)

To set up the keys on your system, see openai instructions