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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.

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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.

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Pipeline Stages

1

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.
2

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.
3

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.
4

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.
5

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.
6

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.
7

Compilation

LaTeX source is compiled to PDF using revtex4-2. The system verifies: zero undefined references, all figures embedded, correct page count, proper bibliography.
8

Submission Package

The final package includes: PDF, LaTeX source, figures, bibliography, supplementary data, and a cover letter. Ready for arXiv upload.

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LaTeX Compilation

All papers use revtex4-2 (Physical Review D format): 
\documentclass[aps,prd,twocolumn,superscriptaddress,
  showpacs,preprintnumbers,nofootinbib,
  longbibliography,floatfix]{revtex4-2}
Compilation runs on GPU pods with texlive-publishers installed: 
# Compile (run twice for cross-references)
pdflatex -interaction=nonstopmode paper.tex
pdflatex -interaction=nonstopmode paper.tex
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.

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Figure Management

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

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Version History

Every change is versioned: 
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"
...

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Readiness Dashboard

The paper readiness dashboard tracks progress across six dimensions:
DimensionWhat It Measures
ContentPercentage of sections drafted
FiguresFigures generated vs required
BibliographyCitations resolved vs referenced
ClaimsClaims verified vs total
CompilationLaTeX errors (target: 0)
ReviewReview rounds completed

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CLI

# 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