paper-tex

name	paper-tex
description	Typeset a working paper or journal submission in house-style LaTeX from Markdown, Word, TeX, ODT, RTF, or HTML. Use to convert drafts, build PDFs, or prepare journal-specific spacing, limits, anonymization, disclosures, and citations.

Paper formatter (LaTeX)

Turn a draft in any common format into a clean, house-style LaTeX paper and build the PDF. The mechanical work runs through a committed driver, scripts/format_paper.py: it detects the input format, converts the body with pandoc, wraps it in the EB Garamond template under assets/, and builds with latexmk. The house-specific finishing — captions with notes, disclosure sections, SI cross-references — is done by hand afterward, and the steps are below.

The house style: 12pt EB Garamond, 1-inch margins, author-date citations (apsr), numbered sections with unnumbered subsections, a single-spaced title block, the introduction on its own page, figures and tables placed where they are written ([H]), and every exhibit carrying a title with an italic Note: beneath it (\figcap).

Paths below are relative to this skill directory — the folder containing this SKILL.md. You know its absolute path from having just read this file; set SKILL to it once:

SKILL=/path/to/.../skills/paper-tex   # the directory this SKILL.md lives in

Step 0 — Ask for the journal specifics first

Formatting is journal-dependent, and the defaults are not always what you want. Before converting, confirm the parameters; ask one concise blocking question only when a value cannot be inferred safely. The ones that change the output:

Parameter	Driver flag	Default	Notes
Target journal / working paper	—	working paper	sets the rest
Body spacing	--spacing single|double	single	single fits tight page limits; do not double-space past a hard limit
Page / word limit	—	none	if a limit binds, prefer single spacing and tighten \bibsep before cutting content
Anonymized for review	--anon	off	blanks the author; keep identifying disclosures on a separate title page
Intro placement	--cover-page	intro on its own page	only pass --cover-page if the venue requires the intro on the title page
Citation style	edit \bibliographystyle in assets/preamble.tex	apsr	swap the .bst per journal
Font	edit \usepackage{ebgaramond}	EB Garamond	swap only if a journal mandates a family
Required disclosures	added by hand	none	data availability, ethics, funding, COI — see house-finishing

A few profiles to start from (confirm against the current author guide):

• Working paper — --spacing double, named author, \today, intro on its own page.
• Journal of Politics (short article) — --spacing single, --anon, 15-page limit, data-availability + ethics in the manuscript, other disclosures on a separate title page.
• Generic double-anonymous submission — --anon, --spacing double, no acknowledgments or funding in the body.

Prerequisites

Verified on macOS with TeX Live 2025 and pandoc 3.8. Required on PATH: pandoc, latexmk + pdflatex (a full TeX distribution), and pdfinfo/pdftoppm (poppler) for page counts and proof renders. The ebgaramond, apsr (texlive harvard collection), calc, booktabs, threeparttable, xr-hyper, and newunicodechar packages must be installed — all ship with a full TeX Live / MacTeX.

# macOS
brew install pandoc poppler        # TeX via MacTeX (basictex users: tlmgr install ebgaramond harvard collection-latexextra)
# Debian/Ubuntu
# apt-get install -y pandoc texlive-full poppler-utils

Run the driver (primary path)

One command converts and builds. These are the exact invocations used to validate the skill:

# Markdown -> single-spaced PDF, intro on its own page. A sibling references.bib
# and any figure the draft references by a relative path are staged automatically.
python3 "$SKILL/scripts/format_paper.py" draft.md --out build \
  --title "Democracy and Nationalism, Reconsidered" \
  --author "Jane Q. Researcher" \
  --abstract "Do citizens who value democracy reject nationalism? ..." \
  --keywords "nationalism; democratic values; national identity; ISSP" \
  --spacing single --build

# Word (.docx) -> same; embedded images are extracted into build/media automatically
python3 "$SKILL/scripts/format_paper.py" draft.docx --out build --title "..." --build

# Existing TeX (full document or a body fragment) -> rewrapped in the house template
python3 "$SKILL/scripts/format_paper.py" draft.tex --out build --title "..." --build

# Main text + SI together (SI gets SI-A.. section labels, SI-1.. float numbers,
# and an \externaldocument cross-reference so \ref reaches SI from the main text)
python3 "$SKILL/scripts/format_paper.py" main.md --si si.md --out build --build

Output lands in build/: main.tex, body.tex, preamble.tex (and si.tex/si_body.tex with --si), plus main.pdf when --build is set. The driver prints the page count and the house-finishing checklist. With --si, the SI builds first so \externaldocument{si} resolves SI cross-references on main's first pass.

After a successful build the driver deletes the latexmk/bibtex byproducts (.aux, .log, .bbl, .blg, .fls, .fdb_latexmk, .out, .toc, .synctex.gz, …) so the folder holds only the sources, the staged .bib and figures, and the PDFs. Pass --keep-aux while debugging a failed-then-fixed build; with --si, si.aux is kept because xr-hyper reads it when main.tex is rebuilt by hand.

Full options: python3 "$SKILL/scripts/format_paper.py" --help. Notable flags: --anon, --cover-page, --spacing, --bib NAME, --engine pdflatex|xelatex, --no-here-floats, --keep-aux.

The author block

--author is inserted verbatim into \author{...}, so pass the full LaTeX for multiple authors. The house pattern is \and-separated names, each with its own \thanks footnote — \maketitle spaces the names evenly and assigns sequential markers (*, †, ‡, …). The corresponding author's \thanks carries the institutional email (mailto: link); co-authors carry the affiliation only.

--author 'Steven Denney\thanks{Leiden University. Corresponding author: \href{mailto:[e-mail]}{[e-mail]}.} \and Remco Breuker\thanks{Leiden University.} \and Aron van de Pol\thanks{Leiden University.}'

Keep the affiliation in the footnote, not under the name. Use the institutional email, not a personal one. For --anon, the driver blanks the whole block. (Watch shell quoting: single-quote the value so \thanks and \and survive.)

House-finishing (by hand, after the driver)

The driver gets the structure right; these four steps make it house style. Do them in build/body.tex (and si_body.tex), then rebuild with latexmk -pdf -bibtex main.tex in build/.

1. Captions → \figcap{title}{note}. Replace every plain \caption{...} with a title and a note that makes the exhibit self-contained. Put confidence-interval, N, and source details in the note only — never baked into the figure image, and never stated in both the figure and the note. Example:

   \figcap{Cross-national heterogeneity in the rights--exclusion slope}%
     {Points are country-specific within-country slopes, adjusted for age, gender,
      education, and left--right placement; bars are 95\% confidence intervals.
      Colors denote region-regime group. $n = 43{,}517$ in 29 countries.}
   

2. Disclosures as \section*{} with full sentences — never a bold word and a period. Add what the journal requires:

   \section*{Data availability}
   The ISSP 2023 module (ZA10010) is available from the GESIS Data Archive; replication
   code accompanies the submission and will be deposited on acceptance.
   
   \section*{Ethics}
   This study analyzes secondary, publicly archived, de-identified survey data and did
   not require human-subjects review.
   

   Identifying disclosures (funding, acknowledgments, ORCID, COI) go on a separate, non-anonymous title page for double-anonymous review, not in the body.

3. Thread SI cross-references. With --si, \externaldocument{si} is already set, so plain \ref{} reaches SI labels (the preamble does not load cleveref, so do not write \Cref). Make sure the main text actually points readers to the supplementary tables and figures where they support a claim.

4. Remove bold-period run-in subheaders. Convert \textbf{Multi-group CFA.}-style leads into a real \subsection{} (or spell the point into the sentence). Bold-text-with-period headings are banned house style; the formatter does not auto-catch them.

5. Leave the folder clean. Hand rebuilds recreate the latexmk byproducts the driver cleaned. When the PDF is final, remove them (this is mandatory — a working-paper folder must hold only sources, staged assets, and PDFs):

   python3 "$SKILL/scripts/format_paper.py" --clean --out build
   

   This deletes .aux/.bbl/.blg/.fdb_latexmk///// and friends, and never touches sources or PDFs. If you rebuild again later with an SI, build first so finds a fresh .

Two more house rules the formatter cannot enforce for you: tables get a title and note beneath them (use \figcap inside threeparttable/table, booktabs rules, no vertical lines), and case or country names that carry the argument are written plainly — not bolded or otherwise over-emphasized — even when they do special work.

What the template encodes (reference)

assets/preamble.tex and assets/main.template.tex already set: EB Garamond + T1; 1-inch margins; setspace; \setcounter{secnumdepth}{1}; \captionsetup{labelfont=bf, labelsep=colon, ...}; the \figcap macro; float for [H]; natbib + apsr; xr-hyper; a single-spaced {\singlespacing \maketitle ... abstract ... keywords} block followed by \newpage; and pandoc-compatibility shims (\tightlist, \real, a working \pandocbounded, calc, newunicodechar) so converted bodies build without hand-patching. To retarget a journal, edit the font and \bibliographystyle lines in the preamble; leave the body alone.

Gotchas (learned building this)

• Figures from pandoc overflow the margin unless \pandocbounded is real. Pandoc emits width-less \includegraphics wrapped in \pandocbounded and, for a body fragment, does not emit the macro's definition. The preamble defines the genuine scaling version; a no-op \providecommand{\pandocbounded}[1]{#1} lets wide figures run off the page.
• .docx tables need calc. Word tables carry explicit column widths, so pandoc writes p{(\columnwidth - ...) * \real{0.5}}. Without \usepackage{calc} this throws ! Missing number, treated as zero. The preamble loads it.
• Extracted media must be out-relative. The driver runs pandoc with cwd=build/ and --extract-media=media, so the image path is media/... and resolves at build time. Running pandoc elsewhere writes a path that breaks when latexmk runs from build/.
• Stage assets before building. --build needs the bibliography and any local figures in build/. The driver auto-copies a sibling references.bib and any figure referenced by a relative path; supply --bib NAME if the file is named differently, and copy figures in by hand if they live elsewhere.
• EB Garamond builds with pdflatex — no xelatex required. Use --engine xelatex only if you switch to an OpenType font or need CJK (below).
• apsr.bst lives in the texlive harvard collection (bibtex/bst/harvard/apsr.bst); basictex users install it with tlmgr.
• apsr.bst emits URLs through \harvardurl, which is undefined by default and tokenizes its argument with normal catcodes, so a URL with _ or ~ throws ! Missing $ inserted. Alias it with \let (not a wrapper) so \url rescans verbatim: \AtBeginDocument{\let\harvardurl\url}. And never put a literal % in a bib url/doi field — it starts a comment mid-.bbl and produces a runaway ; truncate the URL to its directory or drop the query string instead.

Troubleshooting

Symptom	Fix
! Missing number, treated as zero. after a table	a Word/HTML table needs calc — it is in the preamble; confirm \input{preamble} is present
Figure runs past the right margin	\pandocbounded is a no-op — use the preamble's real definition
File 'media/...png' not found	run via the driver (it sets pandoc's cwd) rather than calling pandoc by hand
Citation 'x' undefined after build	the .bib was not staged — pass --bib NAME or copy it into build/; the driver auto-copies a sibling references.bib
Over a hard page limit	switch to --spacing single, then add \setlength{\bibsep}{4pt} before cutting content
Author name leaks in a double-anonymous build	pass --anon; move funding/acknowledgments/ORCID to a separate title page
SI cross-references print ?? in main.pdf	si.aux is missing — build si.tex before main.tex (the driver does this)
Folder cluttered with .log/.fls/.blg/.aux files	the driver cleans these after its own builds; after hand latexmk runs, format_paper.py --clean --out build (house-finishing step 5)