> ## Documentation Index
> Fetch the complete documentation index at: https://hubify.com/docs/llms.txt
> Use this file to discover all available pages before exploring further.

# Paper Pipeline

> End-to-end workflow from experiment results to arXiv-ready PDF, drafting, review, LaTeX compilation, and submission.

# Paper Pipeline

The paper pipeline is a structured workflow that takes raw experiment results and produces publication-ready manuscripts. Every step is assisted by agents, reviewed across models, and tracked with full version history.

## Pipeline Stages

<Steps>
  <Step title="Evidence Collection">
    As experiments complete, their results are tagged for inclusion in specific paper sections. The system maintains a mapping from experiment IDs to paper sections.
  </Step>

  <Step title="Claims Lock">
    Before drafting begins, the Paper Lead produces a **claims table**, every scientific assertion the paper will make, linked to its supporting evidence. No claim can exist without an experiment or derivation backing it.
  </Step>

  <Step title="Outline">
    An outline is generated from the claims table. Each section gets a scope: what claims it contains, what figures it needs, and what prior work it must cite.
  </Step>

  <Step title="Drafting">
    Agents draft sections in parallel. The Research Lead writes methods and results. The Paper Lead handles introduction and discussion. Workers generate tables and format equations.
  </Step>

  <Step title="Cross-Model Review">
    The full manuscript is reviewed by AI models from at least two different providers. Reviews are structured: accuracy, completeness, clarity, overclaiming, missing citations.
  </Step>

  <Step title="Revision">
    Based on review feedback, agents revise the manuscript. Each revision round produces a diff showing what changed and why. The revision tracker logs every round.
  </Step>

  <Step title="Compilation">
    LaTeX source is compiled to PDF using `revtex4-2`. The system verifies: zero undefined references, all figures embedded, correct page count, proper bibliography.
  </Step>

  <Step title="Submission Package">
    The final package includes: PDF, LaTeX source, figures, bibliography, supplementary data, and a cover letter. Ready for arXiv upload.
  </Step>
</Steps>

## LaTeX Compilation

All papers use `revtex4-2` (Physical Review D format):

```latex theme={null}
\documentclass[aps,prd,twocolumn,superscriptaddress,
  showpacs,preprintnumbers,nofootinbib,
  longbibliography,floatfix]{revtex4-2}
```

Compilation runs on GPU pods with `texlive-publishers` installed:

```bash theme={null}
# Compile (run twice for cross-references)
pdflatex -interaction=nonstopmode paper.tex
pdflatex -interaction=nonstopmode paper.tex
```

<Warning>
  Common pitfalls: Do not use `aastex631`. Do not use `\citep`/`\citet` (use `\cite{}`). Do not use `deluxetable` (use `ruledtabular`). Figures must be in the same directory as the `.tex` file.
</Warning>

## Figure Management

Figures are auto-generated from experiment outputs and linked to papers:

```bash theme={null}
# List figures available for a paper
hubify paper figures paper-1

# Add a figure
hubify paper add-figure paper-1 \
  --experiment EXP-054 \
  --file posterior_w0wa.png \
  --caption "Joint posterior distribution of w0 and wa"

# Regenerate all figures
hubify paper regenerate-figures paper-1
```

## Version History

Every change is versioned:

```bash theme={null}
hubify paper history paper-1
```

```
v2.2.0  2026-03-15  "Focused version, 24 pages, 63 references"
v2.1.0  2026-02-28  "Added quintom MCMC results"
v2.0.0  2026-02-01  "Major restructure: bounce-model agnostic"
v1.5.0  2026-01-15  "Added anomaly sweep results"
...
```

## Readiness Dashboard

The paper readiness dashboard tracks progress across six dimensions:

| Dimension        | What It Measures                 |
| ---------------- | -------------------------------- |
| **Content**      | Percentage of sections drafted   |
| **Figures**      | Figures generated vs required    |
| **Bibliography** | Citations resolved vs referenced |
| **Claims**       | Claims verified vs total         |
| **Compilation**  | LaTeX errors (target: 0)         |
| **Review**       | Review rounds completed          |

## CLI

```bash theme={null}
# Create a paper
hubify paper create --title "Bounce Cosmology Constraints" --template prd

# Compile to PDF
hubify paper compile paper-1

# Run peer review
hubify paper review paper-1

# Package for arXiv
hubify paper package paper-1 --output submission.tar.gz
```