Reference¶

Look-up material. For "how do I do X", see the how-to guides; for "why is it built this way", the concepts.

Data format ¶

The complete info file specification and the layout of every data file a project can contain. This is what you need to build a project.

Keyboard and mouse ¶

Every shortcut, grouped by where it applies.

Widgets ¶

Every panel, tab and window, control by control.

Menus ¶

The menu bar, item by item, with shortcuts.

Command line ¶

bigclust2 flags and what they do, plus the update command for refreshing a project's meta data without opening the app.

Annotation backends ¶

Clio, neuPrint, FlyTable and CSV — configuration fields, what each can write, and the side effects.

Changelog ¶

What changed in each release, newest first.

Conventions in this documentation¶

Keyboard shortcuts are written with the macOS modifier names, since that is where most of BigClust's development happens. On Linux and Windows:

Written	macOS	Elsewhere
`Cmd`	⌘ Command	`Ctrl` Control
`Ctrl`	⌃ Control	`Ctrl` Control
`Alt`	⌥ Option	`Alt` Alt

Where the two platforms genuinely differ — and there are a couple of places — it is called out on the page.

Names of user-interface elements are written in bold and quoted exactly as they appear in the app, so you can search for them. Column names, file names and values are written in code.

Not documented here¶

There is no API reference. BigClust is an application, and its internal modules are not a supported interface — they change without notice. If you want to build a project directory programmatically, write the files described in the data format with pandas or pyarrow; that format is the stable contract.