feat: add scoped material bridge helpers

[VsevolodX]

Summary

• add generic Pyodide host data sending with a JupyterLite-compatible fallback
• add scoped material synchronization for Python REPL sessions
• add package-owned material preamble and unit coverage

Validation

• 26 Python unit tests passed
• Ruff, Black, isort, mypy, and repository pre-commit checks passed

Related

• feat: add python REPL [AI-written] cove#96
• feature/SOF-7961 Feat: Material REPL [AI-written] materials-designer#279

Summary by CodeRabbit

• New Features
  • Added automatic synchronization of materials created in interactive Python notebooks.
  • Added support for sending notebook data through Pyodide and JupyterLite environments.
  • Added a ready-to-use material setup for interactive Python sessions, including material types, defect and nanoparticle options, and coordinate utilities.
• Bug Fixes
  • Improved data delivery across supported notebook environments, including fallback handling when direct browser communication is unavailable.

[coderabbitai]

No actionable comments were generated in the recent review. 🎉

ℹ️ Recent review info

⚙️ Run configuration

Configuration used: defaults

Review profile: CHILL

Plan: Pro Plus

Run ID: 08abdea6-bba2-4ece-8c64-f3720ecdd74b

📥 Commits

Reviewing files that changed from the base of the PR and between fd8fc52 and 786bb15.

📒 Files selected for processing (7)

• src/py/mat3ra/notebooks_utils/core/entity/material/io.py
• src/py/mat3ra/notebooks_utils/io.py
• src/py/mat3ra/notebooks_utils/preamble/__init__.py
• src/py/mat3ra/notebooks_utils/preamble/material.py
• src/py/mat3ra/notebooks_utils/pyodide/io.py
• tests/py/unit/core/entity/test_material_io.py
• tests/py/unit/test_pyodide_io.py

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📝 Walkthrough

Walkthrough

Changes

Material synchronization

Layer / File(s)	Summary
Pyodide payload transport src/py/mat3ra/notebooks_utils/io.py, src/py/mat3ra/notebooks_utils/pyodide/io.py, tests/py/unit/test_pyodide_io.py	Adds the public send_data wrapper and Pyodide transport. The transport uses the JavaScript bridge when available and a lazy-loaded display fallback otherwise.
Material collection and REPL preamble src/py/mat3ra/notebooks_utils/core/entity/material/io.py, src/py/mat3ra/notebooks_utils/preamble/*, tests/py/unit/core/entity/test_material_io.py	Adds sync_materials, which collects public direct and one-level nested Material values, excludes reserved bindings, and sends scoped entities. Adds material preamble exports and tests.

Estimated code review effort: 3 (Moderate) | ~20 minutes

Sequence Diagram(s)

sequenceDiagram
  participant Notebook as Notebook code
  participant Sync as sync_materials
  participant PublicIO as send_data
  participant PyodideIO as send_data_pyodide
  participant Bridge as JavaScript bridge
  Notebook->>Sync: provide globals_dict
  Sync->>Sync: collect and serialize Material values
  Sync->>PublicIO: send synchronization payload
  PublicIO->>PyodideIO: forward payload in Pyodide
  PyodideIO->>Bridge: send serialized payload

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Possibly related PRs

• mat3ra/api-examples#310: Introduced the material and Pyodide I/O utilities extended by this change.

Suggested reviewers: timurbazhirov

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

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.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the addition of scoped material synchronization and bridge helper functionality.
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.

✨ Finishing Touches 💡 1

📝 Generate docstrings 💡

• Create stacked PR
• Commit on current branch

🧪 Generate unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch fix/solid-solution

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[VsevolodX]

Superseded by #355, opened from the correct feature/SOF-7961 branch. The commit and file contents are unchanged.