MatterViz for JupyterLab

Open crystal structures, MD trajectories, band structures and volumetric data directly from the JupyterLab file browser — double-click a .cif, or right-click → Open With → MatterViz. The counterpart to the MatterViz VS Code extension, for people whose file browser lives inside JupyterHub.

Install

pip install matterviz-jupyterlab

That's it — the wheel ships prebuilt assets, so there is no jupyter labextension install step and no Node.js on the user's machine. Restart JupyterLab and verify with:

jupyter labextension list

Requires JupyterLab 4.

Supported formats

Extensionless VASP names (POSCAR, CONTCAR, XDATCAR and the volumetric ones above) are matched by filename. Every format is also recognized with a .gz suffix. Structure JSON (pymatgen/ASE as_dict() output) is available under Open With without displacing Lab's built-in JSON viewer.

A .dump file opens as a structure showing its first frame only, not as an animated trajectory. .xtc, .trr and .dcd are deliberately not registered — MatterViz has no decoder for them, so claiming them would replace another application's handler with an error message.

Limits

Files above 100 MB refuse to parse (transfer already happened; parse in the kernel instead, e.g. with pymatviz's TrajectoryWidget). Below that, parsing runs in a Web Worker so the Lab UI stays responsive; XYZ/EXTXYZ, XDATCAR and LAMMPS dump trajectories above DEFAULTS.trajectory.index_above_bytes (25 MB) are indexed there and decoded frame by frame on demand (ASE .traj always is), and the worker is terminated when the viewer closes. Worker failures show an error; parsing requires a working Web Worker. No host-side streaming like the VS Code extension, so the 100 MB ceiling is hard. Open viewers also don't auto-refresh on external writes — JupyterLab has no filesystem watcher; use File → Reload from Disk.

Development

pnpm install --ignore-workspace --config.strict-dep-builds=false
pnpm build   # vite build && jupyter labextension build . (needs jupyter on PATH)
uv build --wheel

uv_build packages whatever is already on disk — run pnpm build first or you will ship an empty extension. The install flags are needed because this package is outside the monorepo workspace and @jupyterlab/application depends on fontawesome, whose install script pnpm declines to run unattended and then exits non-zero over.

The process devDependency is not imported by anything here. @jupyterlab/builder's webpack config carries an unconditional ProvidePlugin({ process: 'process/browser' }), which has to resolve from this package under pnpm's strict layout. Don't delete it as unused.

The build runs in two stages, which is load-bearing:

1. Vite compiles src/index.ts plus the MatterViz Svelte component graph into plain ESM under lib/. All @jupyterlab/* and @lumino/* imports stay external so JupyterLab supplies the shared singleton instances — bundling a private copy would produce plugin tokens that never match the ones in the application registry.
2. jupyter labextension build webpacks lib/index.js into a federated module under data/share/jupyter/labextensions/matterviz-jupyterlab/, which uv_build copies into the wheel's data directory so pip unpacks it over {sys.prefix}/share.

Webpack cannot build MatterViz directly: the source relies on Vite-only features (import.meta.glob, .json.gz imports) and Svelte compilation. Feeding it already-compiled ESM sidesteps both. Vite's dynamic-import chunks survive the second pass, so HDF5 support stays a ~4.6 MB chunk fetched only when someone actually opens an .h5 file.

jupyter labextension build emits an asset-size warning for the three-dimensional viewer chunks. That is expected for a bundle carrying three.js.