Quickstart

This walkthrough takes a manuscript from a directory of files to a filled-out submission portal. The example targets bioRxiv, but the same five steps work for any supported venue.

For a real, end-to-end transcript of this flow (targeting Bioinformatics), see Example session.

The five-step workflow

  1. Create a submission template

    paperpush subfile biorxiv

    This writes biorxiv.sub — a commented, YAML-like template listing every field bioRxiv requires, with the allowed options for each choice field. See paperpush subfile.

  2. Fill it in. You have three options:

    1. Edit biorxiv.sub by hand.

    2. Ask an AI agent to fill it (the Claude skill /paperpush-autofill, or any agent following AGENTS.md).

    3. Use an LLM API:

      paperpush autofill -d MANUSCRIPT_DIR --engine api biorxiv.sub

    See paperpush autofill.

  3. Validate

    paperpush validate biorxiv.sub

    Checks for missing required fields, files that don’t exist, and values that aren’t valid options. See paperpush validate.

  4. Log in and store your credentials for the venue:

    paperpush login biorxiv

    Credentials are stored in your OS keyring. See paperpush login.

  5. Submit — open the portal and fill it out:

    paperpush submit biorxiv.sub

    PaperPush drives the venue’s submission portal in a browser. It stops before the final submit click so you can review everything. See paperpush submit.

Run the whole pipeline at once

scripts/paperpush_pipeline.py runs subfile → autofill → validate → login → submit in sequence, taking you from a manuscript directory to a filled portal in one command:

python scripts/paperpush_pipeline.py -d /PATH/TO/MANUSCRIPT/DIRECTORY --engine api biorxiv

Run it with --help for the full set of options, grouped by step.

Using PaperPush with an AI agent

If you use Claude Code, the simplest entry point is a single natural-language request:

Prepare my manuscript in PATH/TO/MANUSCRIPT/DIRECTORY for submission to
VENUE with PaperPush.

The /paperpush-prepare-submission skill drives the full pipeline, and /paperpush-autofill handles just the field extraction. Both encode the same contract described in AGENTS.md.