Journal formatting

Journal Formatting

Look up and apply journal-specific formatting requirements to manuscripts. references/journal-database.md carries 16 publisher and journal profiles (Elsevier, Springer, Nature family, IEEE, ACM, Wiley, Taylor and Francis, PLOS ONE, Science, MDPI, and more); anything not in it is looked up from the publisher's author guidelines via web search.

Supported Publishers and Document Classes

Publisher	Document Class	Notes
Elsevier	elsarticle	Supports 1p, 3p, 5p column layouts
Springer	svjour3	Also svmono, svmult for books
IEEE	IEEEtran	Conference and journal variants
ACM	acmart	sigconf, sigplan, sigchi, tog formats
Wiley	wiley	Uses custom .cls per journal
Taylor & Francis	interact	NLM-style markup
PLOS	plos	Single LaTeX class for all PLOS journals
Nature	Custom	Requires Nature .cls and .bst
Science	Custom	AAAS submission template
MDPI	mdpi	Open-access multidisciplinary journals

Journal Requirement Categories

Document Structure

• Required sections (e.g., Data Availability, Ethics Statement, CRediT Author Statement)
• Section ordering constraints
• Abstract structure (structured vs unstructured)
• Abstract word limit
• Keyword count and format

Length Limits

• Total word count (e.g., 8000 words for full article)
• Per-section word guidance
• Maximum number of figures and tables
• Maximum number of references
• Page limits for camera-ready versions

Figure Requirements

• Minimum resolution (typically 300 DPI for print, 150 DPI for web)
• Accepted file formats (EPS, PDF, TIFF, PNG, JPEG)
• Color mode (CMYK for print, RGB for online)
• Maximum figure file size
• Figure width specifications (single-column: 84mm, double-column: 174mm)
• Naming convention (e.g., Fig1.eps, Figure_1.tiff)

Figure Style Presets

Map the target journal's publisher family to a figure style preset before generating figures:

• Nature portfolio (Nature, Nature Communications, Scientific Reports, and sibling journals): use the nature preset
• IEEE (journal or conference IEEEtran targets): use the ieee preset
• Everything else (Elsevier, Springer, ACM, Wiley, Taylor and Francis, PLOS, Science, MDPI, and any journal not otherwise matched): use the default preset

Presets (fonts, color palettes, line weights, sizing) are defined in references/figure-styles.md.

Reference Format

• Citation style (APA, IEEE, Vancouver, Chicago, numbered, author-year)
• BibTeX style file (.bst) to use
• Maximum number of references
• DOI requirement (mandatory or optional)
• URL formatting rules

Supplementary Material

• Allowed supplementary formats
• Naming conventions
• Separate file or appendix
• Maximum file sizes

Requirement Lookup Workflow

1. User specifies target journal name
2. Check references/journal-database.md for cached requirements
3. Or search that same file from the command line with scripts/journal-lookup.py "<journal name>". The database is its only data source and it makes no web requests, so it can only return a journal already listed there
4. Read the result honestly. The script exits 0 only on a real hit: an exact profile name, or a query and a profile name that contain one another. A profile that merely shares words with the query is a guess, not a hit, and is never presented as one: text output lists such profiles by name under Closest matches (not exact database entries), --format json puts them under a separate suggestions key (real hits go under matches), and a query with no real hit exits 1. Never apply a suggested profile's requirements to the queried journal
5. If there is no hit, use web search to locate the journal's author guidelines
6. Parse and structure requirements into standard format
7. Cache results in references/journal-database.md for future use

Formatting Application

LaTeX Formatting

1. Read current main.tex document class and packages
2. Switch document class to journal-required class (e.g., \documentclass[review]{elsarticle})
3. Update preamble: add required packages, remove conflicting ones
4. Restructure sections to match journal ordering
5. Apply bibliography style (\bibliographystyle{journal-style})
6. Set figure and table formatting to journal specifications
7. Add required boilerplate sections (data availability, conflicts, etc.)

Word Formatting

1. Download journal Word template if available
2. Apply template styles to existing DOCX
3. Adjust margins, fonts, spacing per requirements
4. Ensure heading styles match template definitions

Compliance Validation

Run a pre-submission checklist that verifies:

Check	Rule
Word count	Under journal maximum
Abstract length	Under journal limit
Figure count	Under journal maximum
Figure resolution	Meets minimum DPI
Figure format	Accepted file type
Reference count	Under journal limit
Reference format	Matches required style
Required sections	All present
Author information	Complete (affiliations, ORCID, corresponding author)
Keywords	Correct count and format
Title length	Under character/word limit if specified
Line numbering	Enabled if required for review
Double spacing	Applied if required for review

Validation Output

# Submission Compliance Report: [Journal Name]

## Status: PASS / FAIL (N issues)

### Passed Checks
- [x] Word count: 7,234 / 8,000 max
- [x] Abstract: 248 / 250 words
- [x] Figures: 5 / 8 max
...

### Failed Checks
- [ ] Missing section: Data Availability Statement
- [ ] Figure 3: resolution 150 DPI (minimum 300 DPI required)
...

### Warnings
- Reference count 48 / 50 max (close to limit)
...

Workflow

1. User provides target journal name (or it is read from manuscript/config.yaml)
2. Look up journal requirements via database, script, or web search
3. Display requirements summary for user confirmation
4. Apply formatting changes to manuscript files
5. Run compliance validation
6. Report pass/fail with specific issues to fix
7. Re-validate after user addresses issues

Integrity constraints

• Never fabricate citations: every reference must come from an actual retrieval (API, MCP, or user-provided source). If a citation cannot be verified, flag it: never invent a DOI, author list, venue, or year.
• Never invent data: only user-provided or actually computed numbers may appear as results. Anything illustrative must be labeled "(synthetic, for demonstration)".
• Refuse to present as valid output: a likely-fabricated or unresolvable citation, a data claim with no traceable source, or a retracted source (unless the user explicitly cites it as retracted).
• Compile-check all LaTeX by running scripts/latex-compile.py (or latex-compile.sh on POSIX) before delivery: it uses whichever TeX engine is installed (tectonic recommended, or latexmk / pdflatex from TeX Live, MiKTeX, or MacTeX).

Canonical copy: references/integrity-constraints.md.