journal-formatting

name	journal_formatting
description	Apply journal-specific formatting rules to transform a manuscript from Markdown

Skill: Journal Formatting

Purpose

Apply journal-specific formatting rules to transform a manuscript from Markdown into a submission-ready LaTeX or Word document.

When to Use

• Final formatting before submission
• Converting between journal formats (e.g., rejected → resubmit elsewhere)
• Checking manuscript compliance with journal guidelines

Scope: Journal Papers Only (Not Books)

This skill and the --journal profiles apply only to single-manuscript journal papers built with the paperflow new / draft / format / render pipeline (papers/). The journal latex_class and citation_style metadata drive the paper renderer in tools/paper_renderer.py.

Books are a separate pipeline and do NOT use journal profiles. A book lives under books/<slug>/, is configured by book.yaml (not a journal YAML), and is produced by paperflow book-render --format {pdf|docx|html|epub|odf} via the dedicated tools/book_render_* renderers:

Format	Book renderer	Engine
PDF	book_render_pdf.py	Typst (auto-generated preamble)
Word	book_render_word.py	python-docx
HTML	book_render_html.py	custom HTML template
EPUB	book_render_epub.py	pandoc
ODF	book_render_odf.py	odfpy
JATS/DocBook	book_render_xml.py (via book-render-xml)	pandoc

cmd_book_render never calls load_journal_profile, so --journal, elsarticle/achemso classes, and the compliance checks below are irrelevant to books. Style books through book.yaml and the book_render_* engines instead. The shared building blocks between the two pipelines are bibliography handling (refs.bib, Crossref enrichment) and the equation/figure utilities in tools/math_utils.py — not the journal class machinery.

Supported Journals

Each journal has a YAML profile in journals/. Run python paperflow.py list-journals to print this list with the exact --journal names. Currently supported (10 profiles):

Journal	--journal name	Publisher	LaTeX Class	Citation Style
Fluid Phase Equilibria	fluid_phase_equilibria	Elsevier	elsarticle	numbered
Chemical Engineering Science	chem_eng_sci	Elsevier	elsarticle	numbered
Computers & Chemical Engineering	computers_chem_eng	Elsevier	elsarticle	authoryear
Geoenergy Science and Engineering	geoenergy_sci_eng	Elsevier	elsarticle	numbered
Int. J. of Greenhouse Gas Control	ijggc	Elsevier	elsarticle	numbered
Industrial & Engineering Chemistry Research	iecr	ACS	achemso	numbered_superscript
Journal of Chemical & Engineering Data	jced	ACS	achemso	numbered_superscript
Energy & Fuels	energy_fuels	ACS	achemso	numbered_superscript
AIChE Journal	aiche	Wiley	custom	numbered
SPE Conference Paper	spe	SPE	custom	numbered

The latex_class value drives how the LaTeX renderer (tools/paper_renderer.py, render_latex) emits front matter — see the class-specific sections below. The three supported citation_style values are numbered (square-bracket [1]), numbered_superscript (ACS-style ¹), and authoryear ((Author, Year)).

Elsevier Formatting (elsarticle)

LaTeX Class

\documentclass[review,3p,authoryear]{elsarticle}
% review = double-spaced with line numbers
% 3p = three-column proof style
% authoryear or number for citation style

Front Matter

\begin{frontmatter}

\title{Your Title Here}

\author[inst1]{First Author\corref{cor1}}
\cortext[cor1]{Corresponding author. Tel.: +47-xxx}
\ead{[e-mail]}

\author[inst1]{Second Author}
\author[inst2]{Third Author}

\affiliation[inst1]{organization={Department of Chemistry, NTNU},
                     city={Trondheim},
                     country={Norway}}
\affiliation[inst2]{organization={Equinor ASA},
                     city={Stavanger},
                     country={Norway}}

\begin{abstract}
% Check journal profile for abstract word limit (FPE: 250 words)
\end{abstract}

\begin{keyword}
flash calculation \sep phase equilibrium \sep equation of state \sep
successive substitution \sep Newton-Raphson \sep convergence
\end{keyword}

\begin{highlights}
\item Improved TP flash algorithm with adaptive SS-NR switching
\item Systematic benchmark across 1000+ cases and 6 fluid families
\item 15\% fewer iterations on average for multicomponent systems
\item Enhanced robustness for near-critical conditions
\item Open-source implementation in NeqSim
\end{highlights}

\end{frontmatter}

Reference Style

Elsevier numbered style:

\bibliographystyle{elsarticle-num}
\bibliography{refs}

Figure Inclusion

\begin{figure}[htbp]
\centering
\includegraphics[width=\textwidth]{figures/convergence_map.pdf}
\caption{Convergence success map in temperature-pressure space for
the lean gas family. Green dots indicate successful flash convergence;
red crosses indicate failure. The proposed algorithm (right) reduces
the failure region near the phase boundary.}
\label{fig:convergence_map}
\end{figure}

Table Style (Three-Line)

\begin{table}[htbp]
\centering
\caption{Benchmark results summary across all fluid families.
$N$ is the number of test cases, Conv.\ is the convergence rate,
Med.\ Iter.\ is the median iteration count for converged cases.}
\label{tab:results}
\begin{tabular}{lrcccc}
\toprule
Family & $N$ & \multicolumn{2}{c}{Conv.\ (\%)} & \multicolumn{2}{c}{Med.\ Iter.} \\
\cmidrule(lr){3-4} \cmidrule(lr){5-6}
       &     & Base & Cand. & Base & Cand. \\
\midrule
Lean gas       & 200  & 100.0 & 100.0 & 6  & 5  \\
Rich gas       & 200  & 99.0  & 99.5  & 8  & 7  \\
Gas condensate & 200  & 95.0  & 98.0  & 14 & 11 \\
CO2-rich       & 200  & 97.5  & 98.5  & 10 & 9  \\
Wide-boiling   & 100  & 93.0  & 96.0  & 18 & 14 \\
Near-critical  & 100  & 85.0  & 92.0  & 22 & 16 \\
\midrule
\textbf{All}   & \textbf{1000} & \textbf{95.8} & \textbf{98.2} & \textbf{10} & \textbf{8} \\
\bottomrule
\end{tabular}
\end{table}

ACS Formatting (achemso)

ACS journals (iecr, jced, energy_fuels) use the achemso document class. Unlike elsarticle, achemso declares authors, affiliations, and the title in the preamble — before \begin{document} — and has no frontmatter or highlights environment. The renderer emits this automatically based on latex_class: achemso.

LaTeX Class

\documentclass{achemso}
% achemso auto-detects the journal style from \journal{} when set; the
% journal profiles deliberately set `latex_options: null` so no class options
% are injected (the renderer omits the [] brackets entirely).

Preamble (before \begin{document})

\author{First Author}
\affiliation{Department of Chemistry, NTNU, Trondheim, Norway}
\author{Second Author}
\affiliation{Equinor ASA, Stavanger, Norway}
\email{[e-mail]}   % only for the corresponding author
\title{Your Title Here}

\begin{document}

Body front matter (after \begin{document})

\begin{abstract}
% Check journal profile for the abstract word limit
\end{abstract}

\keywords{flash calculation; phase equilibrium; equation of state}

Citations and References

ACS journals use superscript numbered citations (citation_style: numbered_superscript):

\bibliographystyle{achemso}
\bibliography{refs}

Highlights: achemso has no highlights environment. When a profile sets highlights_required: true, the renderer preserves the highlight text as a LaTeX comment block so no content is lost, but it does not appear in the compiled PDF. Move highlight content into the abstract for ACS submissions.

Custom / Generic Formatting (custom)

aiche (Wiley) and spe (SPE) set latex_class: custom because the publisher supplies its own class file. The renderer falls back to a generic \maketitle front matter that compiles with the standard article class as a preview, then you drop in the publisher template for the real submission.

\documentclass{custom}      % swap for the publisher-provided class

\begin{document}

\title{Your Title Here}
\author{First Author \and Second Author}
\maketitle

\begin{abstract}
% ...
\end{abstract}

\noindent\textbf{Keywords:} keyword one, keyword two, keyword three

Both custom journals use citation_style: numbered. Replace the generic preamble with the publisher's macros (Wiley \corraddress, SPE template fields) before final submission.

Compliance Checklist Generator

def check_compliance(manuscript, journal_profile):
    """Check manuscript against journal requirements."""
    checks = []

    # Abstract length
    abstract = extract_abstract(manuscript)
    word_count = len(abstract.split())
    max_words = journal_profile["abstract_words_max"]
    checks.append({
        "check": "Abstract length",
        "status": "PASS" if word_count <= max_words else "FAIL",
        "detail": f"{word_count}/{max_words} words"
    })

    # Keywords
    keywords = extract_keywords(manuscript)
    max_kw = journal_profile["keywords_max"]
    checks.append({
        "check": "Keywords count",
        "status": "PASS" if len(keywords) <= max_kw else "FAIL",
        "detail": f"{len(keywords)}/{max_kw} keywords"
    })

    # Highlights
    if journal_profile.get("highlights_required"):
        highlights = extract_highlights(manuscript)
        checks.append({
            "check": "Highlights present",
            "status": "PASS" if highlights else "FAIL",
            "detail": f"{(highlights)} highlights"
        })
         i, h  (highlights):
            max_chars = journal_profile[]
            checks.append({
                : ,
                :   (h) <= max_chars  ,
                : 
            })

    
     journal_profile.get():
        has_da =   manuscript.lower()
        checks.append({
            : ,
            :   has_da  
        })

     checks

Cross-Journal Conversion

When a paper is rejected and needs to be resubmitted elsewhere:

1. Read the new journal's YAML profile
2. Adjust section order if different
3. Change citation style
4. Update abstract length if needed
5. Add/remove highlights
6. Update LaTeX class and options
7. Re-run compliance check

Common Gotchas

Issue	Solution
Abstract too long for target journal	Shorten, keep key numbers
Wrong citation style	Change \bibliographystyle{}
Double spacing not applied	Add \usepackage{setspace}\doublespacing
Line numbers missing	Add \usepackage{lineno}\linenumbers
Figures wrong format	Convert PNG → PDF/EPS
Highlights missing	Extract from abstract/conclusions
CRediT statement missing	Add to acknowledgements

Word Document Generation

Overview

The word_renderer.py tool in tools/ generates publication-quality Word documents from paper.md. It is called automatically by paperflow format.

Native OMML Equations (Primary Pipeline)

Word documents use native Office Math (OMML) equations — the same editing experience as typing in Word's equation editor. The pipeline is:

LaTeX string → latex2mathml → MathML XML → XSLT (MML2OMML.XSL) → OMML element → Word paragraph

Requirements:

• Python packages: latex2mathml, lxml, python-docx
• XSL file: MML2OMML.XSL (ships with Microsoft Office 2013+, typically at %ProgramFiles%\Microsoft Office\root\Office16\MML2OMML.XSL)

Fallback: If OMML pipeline is unavailable, equations render as Unicode text (Greek letters, operators) — readable but not editable as math objects.

Reusable Helpers for Per-Paper build_word.py

Per-paper build_word.py scripts MUST reuse the shared helpers in tools/math_utils.py rather than flattening LaTeX to plain text (which renders poorly in Word — literal ^, _, and (a)/(b) fractions):

import sys
from pathlib import Path
sys.path.insert(0, str(Path(__file__).resolve().parents[2] / "tools"))
import math_utils

# Display equation ($$...$$): centered native OMML, Unicode fallback
p = math_utils.add_display_equation(doc, eq_text, size=11)

# Inline math ($...$): native OMML appended to an existing paragraph
math_utils.append_inline_math(paragraph, latex, size=10.5)

Both helpers automatically fall back to a Unicode text run when the OMML toolchain (latex2mathml + MML2OMML.XSL) is unavailable, so builds stay robust on CI and machines without Microsoft Office.

Word Rendering Features

Feature	Implementation
Inline math $...$	OMML elements embedded in paragraph runs
Display equations $$...$$	Centered OMML with sequential (N) numbering
Tables	Booktabs style: top/bottom 1.5pt borders, thin inside-H, blue header fill, no vertical rules
Figures	Embedded PNG with numbered "Figure N." caption
Citations \cite{key}	Resolved to [N] from refs.bib (alphabetical order)
Code blocks	Shaded single-cell table in Consolas 8.5pt
Bold/italic/code	Inline formatting via **, *, backtick
Page numbers	Footer field (auto-incrementing PAGE)
Highlights	Bulleted list with filled circles
Abstract	Slightly indented, 1.5× line spacing
References	Hanging indent [N] Author (year). Title. Journal.

Journal Profile Integration

The Word renderer reads journal profile YAML values:

# In journals/computers_chem_eng.yaml
double_spacing_required: true
line_spacing: 2.0

These override the renderer defaults (font sizes, margins, spacing).

API Usage

from word_renderer import render_word_document

# Basic usage
render_word_document("papers/my_paper/")

# With journal profile
import yaml
with open("journals/computers_chem_eng.yaml") as f:
    profile = yaml.safe_load(f)
render_word_document("papers/my_paper/", journal_profile=profile)

# Custom output directory
render_word_document("papers/my_paper/", output_dir="output/")

How It Works Internally

1. Setup: Creates Word document with page layout, styles, footer
2. Parse: Splits paper.md into sections by # headings
3. Front matter: Title → Author placeholder → Highlights → Abstract → Keywords
4. Body: For each section:
   • Display equations ($$...$$) → centered OMML + equation number
   • Tables (pipe syntax) → booktabs-style Word table
   • Images (![alt](path)) → embedded figure with caption
   • Code blocks → shaded table cell
   • Lists → bulleted or numbered paragraphs
   • Text → paragraph with inline math/bold/italic/code
5. References: Parsed from refs.bib, numbered alphabetically
6. Save: Writes to submission/paper.docx (uses timestamped name if locked)

Limitations

• Does not support line numbering (Word limitation in python-docx)
• No automatic cross-references (\ref{fig:X} not resolved)
• BibTeX parsing is regex-based (covers standard entry types)
• Complex nested LaTeX (e.g., \frac{\frac{a}{b}}{c}) may need manual cleanup

Pre-Submission Quality Tools

Run these CLI commands before generating submission files:

# Validate figures meet journal requirements (DPI, format, size)
python paperflow.py validate-figures papers/<slug>/ --journal <journal_name>

# Validate bibliography completeness and cross-references
python paperflow.py validate-bib papers/<slug>/

# Check prose readability, passive voice, hedging language
python paperflow.py check-prose papers/<slug>/

# Discover missing highly-cited references
python paperflow.py suggest-refs papers/<slug>/ --max 10

# After revision: generate visual diff for reviewer response
python paperflow.py diff papers/<slug>/

All [!!] (fail) items from validate-figures and validate-bib must be resolved before formatting. check-prose and suggest-refs are advisory.