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Journal templates

Pick the template that matches your target journal and add it to the yaml header of your markdown:

journal:
    template: ametsoc          # template name, see table below
    draft: false               # optional — switch to the publication-ready layout
    # options: twocol          # optional, per-template raw class options — see the docs page

Article-class templates (single PDF, any journal):

template covers example docs
copernicus (aliases cp, esd, ...) Copernicus / EGU: ACP, BG, CP, ESD, HESS, NHESS, TC, ... PDF docs
science AAAS Science, Science Advances PDF docs
ametsoc (aliases jclim, jas, mwr, bams, ...) AMS: J. Climate, JAS, MWR, BAMS, ... PDF docs
arxiv (alias preprint) arXiv preprint, generic article-class PDF docs
elsarticle (alias elsevier) Elsevier: QSR, EPSL, GPC, Earth-Science Reviews, Cell, Lancet, ... PDF docs
agujournal (aliases agu, jgr, grl, james, wrr, ...) AGU: JGR family, GRL, Earth's Future, JAMES, ... PDF docs
springernature (aliases nature, naturecomms, natclimchange, natgeoscience, scirep) Springer Nature: Nature, Nature Communications, Nature Climate Change, Nature Geoscience, Scientific Reports, ... PDF docs
pnas PNAS PDF docs

Book-family templates (theses, monographs, multi-chapter documents):

template document class structure docs
book \documentclass{book} \frontmatter / \mainmatter / \backmatter docs
report \documentclass{report} No front/main/back matter macros docs
memoir \documentclass{memoir} \frontmatter / \mainmatter / \backmatter; configurable chapter styles docs
classicthesis \documentclass{scrreprt} + bundled classicthesis.sty Bringhurst-inspired typography; no front/main/back matter macros docs

Presentation templates (Beamer slide decks):

template aliases covers docs
beamer slides, presentation Lecture slides, conference presentations, seminar talks docs

Book-family templates support \include{...} for chapters (enabling --only for selective recompilation), front-matter YAML keys (dedication:, list_of_figures:, etc.), and bibliography_per_chapter: true for per-chapter biblatex bibliographies.

Submission vs publication-ready layout

Every article-class template defaults to the publisher's submission layout (the 1.5-/double-spaced, usually single-column style journals want for peer review). Set journal.draft: false to switch that one template to its publication-ready typeset layout (2-column journal look) for a preview of how the article will appear in print:

template draft: true (default, submission) draft: false (publication-ready)
copernicus [short, manuscript] one-column [short] two-column production
ametsoc no options — 1.5-spaced one-column twocol two-column journal style
elsarticle preprint, 12pt 1.5-spaced final, 5p, times typeset 2-column
agujournal draft double-spaced, line numbers final single-spaced production
springernature …, referee double-spaced one-column …, iicol two-column production
pnas always 2-column + DRAFT watermark always 2-column, watermark removed
science, arxiv single-column preprint (no production variant — flag is a no-op)

journal.draft is the unified, template-independent switch. For finer control, set journal.options to raw class options — that overrides the flag and is passed to the document class verbatim. The per-journal docs pages list each class's full option set.

Partial support only

Before submitting, you will likely need to hand-edit the final LaTeX — appendix structure, special sections (Methods Online, Extended Data, Significance, …) and journal-specific cross-reference macros are not all wired up automatically. Use the example PDF to confirm the layout looks reasonable, then run texmark --tex out.tex and finish the manuscript in LaTeX directly.

See the YAML reference for the common front-matter fields shared by all templates.