feature/SOF 7894 4

[VsevolodX]

• update: fix of imports
• update: fix of imports 2

Summary by CodeRabbit

• Chores

  • Updated example notebooks to use revised package install/import targets and adjusted plotting import paths for compatibility.
  • Reorganized plotting utilities to expose a clearer public API.

• New Features

  • Automatic matplotlib renderer configuration for non-interactive environments (improves plotting in browser/Pyodide).
  • Notebooks now explicitly import helper for downloading remote outputs before post-processing.

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⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

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Run ID: e1fa7bef-4c48-408b-ab57-d8c224431548

📥 Commits

Reviewing files that changed from the base of the PR and between f845ddc and 973a881.

📒 Files selected for processing (5)

• examples/workflow/qe_scf_calculation.ipynb
• other/materials_designer/workflows/valence_band_offset.ipynb
• src/py/mat3ra/notebooks_utils/ipython/plot/_matplotlib.py
• src/py/mat3ra/notebooks_utils/ipython/plot/_plotly.py
• src/py/mat3ra/notebooks_utils/plot.py

💤 Files with no reviewable changes (1)

• src/py/mat3ra/notebooks_utils/ipython/plot/_plotly.py

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📝 Walkthrough

Walkthrough

Centralizes plotting exports and pyodide-aware Matplotlib backend configuration into mat3ra.notebooks_utils.plot and updates several notebooks to import utilities and install api_examples where previously they referenced older/internal paths.

Changes

Notebooks utilities API restructuring and import consolidation

Layer / File(s)	Summary
Plot module public API and renderer configuration src/py/mat3ra/notebooks_utils/ipython/plot/_matplotlib.py, src/py/mat3ra/notebooks_utils/plot.py, src/py/mat3ra/notebooks_utils/ipython/plot/_plotly.py	Adds configure_matplotlib_renderer() (Pyodide-aware backend switch), re-exports plotting helpers from ipython submodules in plot.py, invokes renderer configuration on import, and defines __all__ to control public exports.
Notebook imports updated to new module paths examples/workflow/qe_scf_calculation.ipynb, examples/job/run-simulations-and-extract-properties.ipynb, other/materials_designer/workflows/convergence.ipynb, other/materials_designer/workflows/total_energy_convergence.ipynb, other/materials_designer/workflows/valence_band_offset.ipynb	Notebooks: switch dependency install spec to `api_examples

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~20 minutes

Possibly related PRs

• Exabyte-io/api-examples#310: Related plotting-module restructuring and notebooks rendering helpers.
• Exabyte-io/api-examples#292: Related additions to convergence-series retrieval utilities used by updated notebooks.
• Exabyte-io/api-examples#285: Overlaps with updates to total_energy_convergence notebook imports and flow.

Suggested reviewers

• pranabdas
• timurbazhirov

Poem

🐰 I hopped through imports, neat and spry,
I nudged the backend so plots won't cry,
Re-exports bundled, paths made right,
Notebooks now import with delight,
A rabbit's hop — clean code in sight.

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (1 warning, 1 inconclusive)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 0.00% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.
Title check	❓ Inconclusive	The title 'feature/SOF 7894 4' is vague and does not clearly describe the actual changes made in the PR.	Use a descriptive title that summarizes the main change, such as 'Refactor imports: reorganize plotting and API utilities' or 'Update notebook imports and consolidate plotting API'.

✅ Passed checks (3 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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✨ Finishing Touches

📝 Generate docstrings

• Create stacked PR
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🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch feature/SOF-7894-4

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Actionable comments posted: 1

🤖 Prompt for all review comments with AI agents

Verify each finding against current code. Fix only still-valid issues, skip the
rest with a brief reason, keep changes minimal, and validate.

Inline comments:
In `@src/py/mat3ra/notebooks_utils/plot.py`:
- Around line 21-30: The __all__ list in the module is unsorted and triggers
Ruff RUF022; reorder the entries in the __all__ assignment (the __all__ variable
containing "display_matplotlib_figure", "plot_distribution_function",
"plot_series", "create_scatter_plot_2d", "create_realtime_plot",
"create_update_callback", "plot_2d_heatmap", "plot_3d_surface") into
lexicographical order and commit the updated sorted list so the linter warning
is resolved.

🪄 Autofix (Beta)

Fix all unresolved CodeRabbit comments on this PR:

• Push a commit to this branch (recommended)
• Create a new PR with the fixes

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ℹ️ Review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro

Run ID: f363dd8e-a736-42bc-af92-8e11f007899a

📥 Commits

Reviewing files that changed from the base of the PR and between 438f16c and f845ddc.

📒 Files selected for processing (5)

• examples/job/run-simulations-and-extract-properties.ipynb
• examples/workflow/qe_scf_calculation.ipynb
• other/materials_designer/workflows/convergence.ipynb
• other/materials_designer/workflows/total_energy_convergence.ipynb
• src/py/mat3ra/notebooks_utils/plot.py