Using emzed.spyder¶

The emzed terminal¶

When you open a terminal (IPython console) in emzed.spyder, emzed is automatically available — no import needed:

t = emzed.io.load("mydata.mzML")

A set of emzed_* helper functions is also available directly. Run emzed_help() for a full listing.

Discoverability and completion¶

The emzed API is structured to be browsable via tab completion. Typing emzed. and pressing Tab reveals the top-level namespaces (emzed.io, emzed.ms, emzed.chem, …), and completion continues to work at each level, so you can explore available functions without leaving the terminal.

The emzed_* helper functions follow the same principle — typing emzed_ and pressing Tab lists all available commands. Private and internal names are filtered out of the completion list so only the relevant functions appear.

Variable explorer¶

Table and PeakMap objects appear in Spyder's variable explorer with emzed-aware display:

Column	What is shown
Type	`Table`, `PeakMap`, or `ImmutablePeakMap`
Size	e.g. `42 row x 5 columns` for a Table, `128 spectra` for a PeakMap
Value	Column names (for Tables)

Double-clicking a Table or PeakMap in the variable explorer opens the emzed viewer directly — the data is not copied into Spyder's process. Closed objects are automatically hidden from the explorer.

General commands¶

Function	Description
`emzed_help()`	List all emzed-specific commands
`emzed_edit_config()`	Reopen the configuration dialog
`emzed_update()`	Update `emzed` and `emzed_gui` (see note below)
`emzed_check_versions()`	Show installed vs. latest versions
`emzed_install_ext(name)`	Install an emzed extension (e.g. `"mzmine"`)

Restarting after updates

emzed_update() updates the emzed and emzed_gui packages. After it completes, close the terminal and open a new one to load the updated packages.

emzed_update() does not update emzed.spyder itself. If a newer version of emzed.spyder is available, a notice is shown in the console banner at startup. The banner also shows the active project, the resolved environment path, and the Python version used for the current session, and ends with a reminder to run emzed_help(). If you need to change the base interpreter or projects root later, use emzed_edit_config().

To upgrade, close emzed.spyder first, then install the new version via pip or by running a new installer.

Projects and emzed extensions¶

For isolated environments and developing emzed extensions, see Projects and emzed Extensions.