Fix broken math notation, editor notes, and contradictory guidance in documentation

[Copilot]

The PDF book documentation had rendering issues with math symbols, visible editor notes, and contradictory technical guidance.

Math notation fixes (chapter10)

• Converted Unicode subscripts to ASCII underscore notation to prevent parameter vanishing in PDF
• Before: λᵢ = 1 - ∏ⱼ (1 - β)^(Aᵢⱼ · Iⱼ) → After: λ_i = 1 - ∏_j (1 - β)^(A_ij · I_j)
• Added explicit parameter names and ranges: β (beta): transmission probability per contact (0 ≤ β ≤ 1)

Editor artifacts removed

• Deleted bracketed instruction [Keep this section SHORT—no long speculative lists] from chapter11

Dependency consistency (chapter16)

• Unified requirements.txt example to use exact pins (==) instead of mixing with version ranges (>=)
• Removed networkx version contradiction (was showing both >=3.0 and >=2.8)

Color palette clarity (chapter06)

• Made colorblind_safe the explicit default instead of claiming "colorblind-safe by default" while showing rainbow
• Added accessibility warning: rainbow not recommended for publications
• Added citation: Wong, B. (2011). Nature Methods, 8(6), 441

FastAPI docker consistency (appendix_b)

• Changed FLASK_ENV=production to ENV=production (GUI uses FastAPI, not Flask)
• Updated port from 5000 to 8000

GUI deployment messaging (chapter17, appendix_b)

• Renamed "Production Deployment" → "Controlled Environment Deployment"
• Added explicit warning that GUI is experimental and not suitable for public internet deployment
• Clarified that hardening instructions are for trusted networks only (lab LANs, behind VPN)

Warning

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I tried to connect to the following addresses, but was blocked by firewall rules:

• docs.python.org
  • Triggering command: /home/REDACTED/.local/bin/sphinx-build sphinx-build -M html . _build (dns block)
• networkx.org
  • Triggering command: /home/REDACTED/.local/bin/sphinx-build sphinx-build -M html . _build (dns block)
• numpy.org
  • Triggering command: /home/REDACTED/.local/bin/sphinx-build sphinx-build -M html . _build (dns block)

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Original prompt

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This section details on the original issue you should resolve

<issue_title>docs</issue_title>
<issue_description>pdf book
The math is literally broken on the page. Key symbols/parameters vanish in multiple places (e.g., SIS/SIR update rules, parameter definitions, and even the expressions). You end up with nonsense like “probability = 1 − (1 − )^(A·I)” and blank parameter bullets.

It ships with visible “editor notes,” i.e., you published the draft brain. The bracketed instruction “[Keep this section SHORT—no long speculative lists]” is still in the body text. That’s not a typo; it’s a process failure.

There are copy/paste + encoding artifacts that scream “uncurated generation.” Example: “under active devel�opment.”

Dependency guidance contradicts itself in the same chapter. It recommends networkx>=3.0 in one “requirements.in” example, then later shows “networkx>=2.8” in an “example requirements.txt structure,” right after preaching “exact pins.”

Misleading/contradictory guidance (the “don’t trust this manual” category)

“Colorblind-safe by default” followed immediately by “Automatic rainbow colors.” Rainbow palettes are the opposite of colorblind-safe, and presenting them as the default undermines the claim.

GUI messaging conflicts with its own deployment chapter. The GUI is described as “experimental… local use only… not hardened for public internet deployment,” yet later you include a “Production Deployment” section with nginx/TLS/auth hardening guidance that reads like you do expect public deployment.

Tech stack inconsistency: it says the GUI is “FastAPI + SvelteKit,” but the docker-compose snippet sets FLASK_ENV=production (why is Flask here?).

Writing/structure problems

Way too much generic “software engineering advice” padding (Docker/Git/seeds/checklists) relative to py3plex-specific insight. It reads like a template manual that occasionally mentions py3plex.

Big claims with little grounding. Example: “Wong palette (scientifically validated)” is asserted without any citation or explanation of what validation means.

What’s actually good (credit where due)

The explanation of node–layer pairs and why tuples play nicely with NetworkX is clear and useful.

The multilayer vs. multiplex distinction is presented in a way that will genuinely help users avoid modeling mistakes.

Explicitly marking stable vs experimental features is a strong idea (you just need the rest of the book to reach that level of rigor).
</issue_description>

Comments on the Issue (you are @copilot in this section)

• Fixes docs #907

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