Export documents

Export#

The Export button in the status bar, or Alt+E, opens a dialog with two independent choices: the file format (PDF, Word, HTML) and the journal style.

• Every format saves where you choose, defaulting to the project’s exports/ folder. The suggested file name follows the format you pick, so switching to Word suggests a .docx name; a name you typed yourself is kept.
• Word and journal-styled PDF run through Quarto. The dialog says so when Quarto isn’t installed; see PDF dependencies and Installation.
• A long render shows its progress and can be cancelled.
• Figure renders, captions and panel references are resolved during export. A failure appears as a notification that names what to fix.

Journal styles#

Choosing a journal — Nature, say — makes the exported file follow that journal’s house style: how figure and panel references read (Fig. 1a,b), how citations are marked (superscript numerals, before the punctuation), how reference entries are built (all authors up to five, then et al.), what order the sections appear in, and the submission formatting a manuscript needs (12pt Times, double-spaced, line-numbered).

Your writing never changes. The editor keeps Flux’s own conventions no matter which journal is selected — chips, figure references and caption leads look the same whether you are aiming at Nature or nowhere. Only the exported file and the preview follow the journal, so switching journals is instant, and switching back loses nothing. Nothing is rewritten in your manuscript on disk: a journal style is a lens on the way out, not an edit.

Selecting a style is remembered per project, and agents can use the same one from the terminal with flux compile --to docx --style nature.

Journal Check#

Alt+J opens Journal Check, which reads your manuscript against the selected journal’s rulebook: title and summary-paragraph length, headings the journal doesn’t print (Nature uses neither “Introduction” nor “Results”), missing sections like Data availability, word budgets, display-item and reference caps, and typed-out figure references that don’t match house style. Click any item to jump to it.

It is advice, and never blocks an export — Nature itself says style and length won’t influence consideration at first submission. Switch the panel to Accepted / final and the sections a journal requires at acceptance become warnings rather than notes.

One deliberate limit: Flux formats references it owns — the ones you insert as figure references — and only points at figure references you typed by hand. It cannot tell your “Figure 2, panel D” from a mention of someone else’s Figure 2D, so it never rewrites your prose.

PDF dependencies#

Flux’s built-in PDF export needs neither Quarto nor TeX. Word and journal-styled exports use Quarto; Quarto PDF also needs TeX. Set up Flux can install Quarto and TinyTeX.

Journal styles may need additional TeX packages and an SVG converter. Install the packages for your TeX distribution.

With TinyTeX:

tlmgr install lineno setspace

With MacTeX:

sudo tlmgr install lineno setspace

With TeX Live on Debian or Ubuntu:

sudo apt install texlive-latex-recommended \
  texlive-humanities texlive-luatex \
  texlive-fonts-recommended

Install rsvg-convert through librsvg on Homebrew or Arch, or librsvg2-bin on Debian/Ubuntu. Check the converter, and confirm that TeX can find the packages:

rsvg-convert --version
kpsewhich lineno.sty setspace.sty

TinyTeX’s own commands may need its bin folder on your shell’s PATH: ~/Library/TinyTeX/bin/universal-darwin on macOS or ~/.TinyTeX/bin/x86_64-linux on Linux. Flux and Quarto can find TinyTeX without that shell change. These dependencies do not affect Word export.