Add generic plot widgets and demos (#341)

* Add generic plot widgets and demos

- add ScatterPlotWidget, BarPlotWidget, and HistogramWidget with shared series normalization
- wire new widgets into exports and anywidget frontend mapping, plus notebook/marimo/vscode demos
- harden trajectory dict validation for empty species lists and extend widget tests

* Fix marimo widget rendering and improve demo notebooks

Marimo serializes cell outputs independently with a ~10 MB limit,
causing widgets embedding ~10 MB of inline JS to fail. anywidget
also only treats _esm values starting with http(s):// as URLs.

- Serve ESM via marimo's virtual-file system with absolute URL
  resolution so anywidget imports it as a URL (not inline source)
- Keep CSS inline (~166 KB) to avoid stylesheet loading edge cases
- Add _in_marimo_runtime, _marimo_esm_url, _init_marimo_assets with
  27 tests including mutation-verified coverage
- Fix marimo demo cell dependency wiring (_struct, _phonon_doc,
  _band_data, _dos_data), broken markdown cells, and ruff noqa
- Add marimo check --strict pre-commit hook
- Fix RUF005 in bar_plot.py, TRY300 in matterviz.py

* Update widget demos with realistic fixture data and clearer narratives

Replace synthetic band/DOS demo payloads with phonon test fixtures and add concise explanatory headings across notebook, marimo, and VSCode interactive demos.

* Guard against marimo VS Code extension kernel crash

- Skip js() virtual file call when virtual_files_supported=False to
  prevent ~14 MB base64 data URL allocations that crash the kernel
- Fall back to relative ./@file/ URL when request context is unavailable
- Set resolved ESM URL on class (not per-instance) to avoid N copies
- Use display() from IPython for plot widgets that shadow the method
- Document VS Code extension limitation in MatterVizWidget docstring

* Simplify marimo ESM caching in MatterVizWidget

Use dedicated class-level marimo URL cache fields instead of overloading the generic asset tuple cache, and keep test cache cleanup aligned with the new cache state.

* Auto-discover to_dict fields from synced traitlets and reorganize tests

Replace manual state_fields tuples with automatic discovery via
self.traits(sync=True) in MatterVizWidget.to_dict(). This fixes
serialization for ScatterPlotWidget and HistogramWidget which were
missing their state_fields definitions, and eliminates the need for
every subclass to maintain a redundant field list.

Also simplify production code (DRY numpy conversion in normalize_plot_json,
loop-ify lattice params, remove narrating comments in trajectory.py) and
split test_new_widgets.py into test_normalize.py, test_widget_construction.py,
and test_mime.py organized by domain rather than chronology.

* Rename display() to show(), add configure_assets(), fix marimo cell deps

- Rename MatterVizWidget.display() to show() to avoid shadowing the
  'display' traitlet on ScatterPlot/BarPlot/HistogramWidget which made
  widget.display() raise TypeError: 'dict' object is not callable
- Add configure_assets(version=, esm_src=, css_src=) for global asset
  override via version tags, HTTP URLs, or local file paths
- Fix marimo demo: cells now properly return and declare dependencies
  for _struct, _band_data, _phonon_doc, _dos_data
- Simplify matterviz.py: flatten _marimo_esm_url resolution, trim docstrings,
  merge isinstance checks in normalize_plot_json

* Add CI job to execute widget demos

Runs all three widget demos (vscode, marimo, jupyter) in a single
consolidated step to catch runtime errors in demo scripts.

Author: janosh

.github/workflows/test.yml

@@ -42,6 +42,30 @@ jobs:
       test-cmd: pytest --durations 20 --cov-branch --cov-report=xml --cov pymatviz --splits 4 --group ${{ matrix.split }} --splitting-algorithm least_duration
       upload-coverage: strict
 
+  run-widget-demos:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Check out repository
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+
+      - name: Setup uv
+        uses: astral-sh/setup-uv@v6
+
+      - name: Build widget assets, install deps, run all demos
+        run: |
+          curl -fsSL https://deno.land/install.sh | sh
+          export PATH="$HOME/.deno/bin:$PATH"
+          cd pymatviz/widgets/web && deno task build && cd ../../..
+          uv pip install -e '.[test]' marimo nbconvert --system
+          python examples/widgets/vscode_interactive_demo.py
+          marimo export script examples/widgets/marimo_demo.py -o /tmp/marimo_flat.py && python /tmp/marimo_flat.py
+          jupyter nbconvert --to notebook --execute --ExecutePreprocessor.timeout=120 examples/widgets/jupyter_demo.ipynb --output /tmp/jupyter_out.ipynb
+
   find-example-scripts:
     runs-on: ubuntu-latest
     outputs:

.pre-commit-config.yaml

@@ -26,6 +26,15 @@ repos:
         files: ^(readme\.md|pymatviz/.*\.py)$
         pass_filenames: false
 
+  - repo: local
+    hooks:
+      - id: marimo-check
+        name: marimo check
+        entry: marimo check --strict
+        language: python
+        files: examples/widgets/marimo_demo\.py$
+        additional_dependencies: [marimo]
+
   - repo: https://github.com/janosh/format-ipy-cells
     rev: v0.1.11
     hooks: