refactor: migrate to pixi + marimo + nxviz plotly backend#477
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- Move all Python deps into [project] dependencies (pypi via editable install) - Add marimo>=0.14, nxviz>=0.9.0, plotly>=5.0 to project deps - Switch all nxviz calls to use backend='plotly' - Remove inline script metadata from all notebooks (pixi handles deps) - Add pixi task 'notebook' -> marimo edit --no-token notebooks/ - Remove render_html from nams.functions, update solutions modules - Update setup instructions to use pixi instead of uv - Update [tool.pixi.project] -> [tool.pixi.workspace] - Remove jupyter/ipykernel conda deps (no longer needed)
…bottom - Move marimo import to a single cell that returns mo, all other cells reference it via marimo's reactive dependency system - Wrap intentional G.edges[15,16] KeyError in try/except in 02-networkx-intro - Delete empty cell in 02-networkx-intro - Cosmetic reformatting from marimo auto-save in 01-setup
…-save - Standardize mo.md() call formatting (single-line vs multi-line) - Add __generated_with version marker - Remove backend='plotly' from some nxviz calls in 01-hubs - Return nv from nxviz import cell for downstream use
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Summary
Rearchitects the tutorial to use pixi for dependency management with marimo notebooks and nxviz plotly backend.
Changes
pyproject.toml
[project](installed via pypi editable):marimo>=0.14,nxviz>=0.9.0,plotly>=5.0, etc.pixi run notebooktask →marimo edit --no-token notebooks/[tool.pixi.project]→[tool.pixi.workspace](newer pixi format)nams package
render_html()fromnams/functions.py(no longer needed)paths,structures,bipartite) to return/print plain strings insteadAll 16 notebooks
# /// scriptinline metadata (pixi handles deps)backend="plotly"to allnxvizcalls (nv.circos,nv.arc,nv.matrix,nv.hive,nv.geo)annotate.*calls andplt.show()after nxviz (plotly handles rendering)plt.show()for pure matplotlib (nx.draw,plt.hist,plt.scatter)Usage
Verification
All 16 notebooks pass
marimo check(0 errors, markdown indentation warnings only).