narrative review: LaTeX submission package

[neuromechanist]

Summary

Single-file LaTeX submission package via manuscript:manuscript-formatting. Closes #14.

What was produced

File	Purpose
main.tex	Single LaTeX source with all sections inlined (no \input{} references) — 220 lines, ~42KB
main.pdf	Compiled output — 28 pages, 1.5MB
Makefile	Build target (make) running pdflatex -> bibtex -> pdflatex -> pdflatex
.gitignore	LaTeX build artifacts (.aux, .bbl, .log, etc.) excluded
refs.bib	Patched: removed @key substring from comment (BibTeX was interpreting it as an entry start)

Document class + style

• \documentclass[preprint,12pt]{elsarticle} (Elsevier / Cell Press family; correct for TiCS)
• \bibliographystyle{elsarticle-num} (numeric citations, Cell Press house style)
• natbib for \cite{} resolution
• tcolorbox for the Box 1 (yellow), Trends Box (blue), Outstanding Questions Box (green) coloured callouts
• hyperref for clickable DOI / URL links in the bibliography

Document structure (28 pages)

Page	Content
1	Highlights (frontmatter, elsarticle convention)
2	Title + author + abstract + Section 1 starts
3-12	Sections 1-7 with inline numbered citations
13	Box 1 + Trends Box + Outstanding Questions Box
14-15	Glossary (15 defined terms in description list)
16	Figures section + Figure 1 + References starts
17-28	Figures 2-4 + remaining References (82 entries)

Conversion path

# 1. Build per-section LaTeX from per-section Markdown:
#    - Strip <!-- comments -->, demote # H1 -> [removed; top-level is \section]
#    - [Key1; Key2] -> \cite{key1,key2}
#    - **bold** -> \textbf{}, *italic* -> \textit{}, `code` -> \texttt{}
#    - Escape & % _ outside cite/code blocks
#    - Convert markdown bullets to itemize/enumerate
#    - Convert markdown ## H2 -> \subsection{}
# 2. Wrap in elsarticle template with title/author/affiliation from YAML frontmatter
# 3. Append \bibliography{refs}

Issues caught and fixed

1. \texttt{clean_rawdata} had unescaped underscore (LaTeX math-mode). Fixed by escaping underscores inside texttt blocks after the markdown conversion.
2. refs.bib had @key literal inside a comment line. BibTeX interpreted it as an entry start. Patched to key.
3. Affiliation showed trailing comma. Added country={USA} to complete the affiliation block.
4. Figures were initially placed mid-references because LaTeX float placement defaulted. Added \clearpage + \section*{Figures} to group them after the Glossary and before References.

Compile commands

# Using the Makefile:
make

# Manually:
pdflatex -interaction=nonstopmode main.tex
bibtex main
pdflatex -interaction=nonstopmode main.tex
pdflatex -interaction=nonstopmode main.tex

# Output: main.pdf (28 pages, 1.5MB)

Final compile: Output written on main.pdf (28 pages, 1580441 bytes), 0 undefined references, 0 fatal errors.

Test plan

• pdflatex + bibtex + pdflatex + pdflatex cycle produces main.pdf with 0 undefined citations
• All 82 cited refs resolved via natbib
• All 4 figures embedded via \includegraphics
• Highlights appear in elsarticle frontmatter (page 1)
• Abstract appears in elsarticle frontmatter (page 2)
• 7 numbered sections + 3 callout boxes (Box 1, Trends, Outstanding Questions) + Glossary + Figures + References all present
• Pre-commit (markdownlint, typos, .gitignore) passes
• Build artifacts (.aux/.log/.bbl/.blg/.out) excluded via .gitignore
• Makefile for future rebuilds