update: handle plotting in pyodide

[VsevolodX]

Summary by CodeRabbit

• Refactor
  • Improved plot rendering consistency by consolidating visualization display logic across scatter plots, RDF distributions, and series plots through a unified rendering system, ensuring better compatibility and reliability across different notebook environments.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: 0c801187-c2c9-47b2-a3ce-689f8110fe8d

📥 Commits

Reviewing files that changed from the base of the PR and between d090615 and 9818f3a.

📒 Files selected for processing (1)

• utils/plot.py

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📝 Walkthrough

Walkthrough

Consolidated plotting display logic in utils/plot.py by replacing direct Matplotlib and IPython display calls with a centralized render_figure() function. Removed Pyodide-specific backend handling from plot_rdf and updated multiple plotting functions to standardize their display approach.

Changes

Cohort / File(s)	Summary
Plot Display Consolidation utils/plot.py	Refactored four plotting functions (plot_strain_vs_area, plot_twisted_interface_solutions, plot_rdf, plot_series) to use centralized render_figure() instead of direct fig.show() and IPython display calls. Removed Pyodide-specific matplotlib backend switching and buffer-based PNG rendering from plot_rdf. Updated imports to include render_figure and removed io, sys, and IPython.display.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Possibly related PRs

• Fix/rdf plot (SOF-7807) #264 — Also modifies utils/plot.py plotting/display logic and Pyodide handling but implements opposing approaches to the current changes.

Suggested reviewers

• timurbazhirov

Poem

🐰 The plots once showed in tangled ways,
With Pyodide quirks and display delays,
Now render_figure keeps things neat,
One function makes the cleanup complete! 🎨✨

🚥 Pre-merge checks | ✅ 3

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title directly and specifically describes the main change: refactoring plot functions to use a unified render_figure() handler instead of direct display calls, which enables proper Pyodide support.
Docstring Coverage	✅ Passed	Docstring coverage is 100.00% which is sufficient. The required threshold is 80.00%.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/SOF-7887

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