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INSTALL.md

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Install data-to-paper

Install for users

  1. pip install the package, run pip install data-to-paper.
  2. Install dependencies (see below).
  3. Add environment variables for API keys (see below).
  4. Check dependencies and keys (see below).
  5. Run the app, run data-to-paper.

Install for developers

  1. Clone the repo, run git clone https://github.com/Technion-Kishony-lab/data-to-paper.
  2. Create a conda environment, run conda create -n data-to-paper python=3.11.
  3. Activate the newly created environment, run conda activate data-to-paper.
  4. Enter the repo root folder, run cd data-to-paper.
  5. Install the app and further required packages, run pip install -e ..
  6. Install dependencies (see below).
  7. Add environment variables for API keys (see below).
  8. Check dependencies and keys (see below).

Install dependencies

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

  2. Install all the required packages for compiling LaTeX:

    • On debian-based systems: 
      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!

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

Check dependencies and keys

To test installation of dependencies and check the API keys, run the following command:

data-to-paper-chkres