experiment/sevennet

[timurbazhirov]

• experiment: support for uma
• chore: update uma logic
• chore: antlr package
• chore: git attributes
• chore: f16 pt file
• chore: update notebook
• chore: update notebook
• chore: int8 pt file
• Revert "chore: update notebook"
• Revert "chore: update notebook"
• chore: update notebook
• poc: use playwright for notebook tests
• experiment: dequantization to save space/memory
• feature: mattersim poc added
• feature: sevennet poc added

Summary by CodeRabbit

Release Notes

• New Features

  • Added three new interactive notebooks for material structure relaxation using MatterSim, SevenNet, and UMA interatomic potentials in JupyterLite.
  • Extended notebook environment configuration to support additional machine learning models and dependencies.

• Tests

  • Added Playwright-based end-to-end tests for notebook execution and validation.

• Chores

  • Updated Git configuration for model artifact management.
  • Added Playwright dependency for automated testing.

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📝 Walkthrough

Walkthrough

This PR adds three new JupyterLite notebook demonstrations for crystal structure relaxation using different interatomic potentials (FAIRChem UMA, MatterSim, and SevenNet), along with the necessary Pyodide/WebAssembly infrastructure, configuration, and validation tests.

Changes

Structural Relaxation Notebooks with Pyodide Support

Layer / File(s)	Summary
Artifact & Configuration Setup .gitattributes, .gitignore, config.yml, packages/antlr4_python3_runtime-4.9.3-py3-none-any.whl, packages/models/uma-s-1p1-f16.pt, packages/models/uma-s-1p1-int8.pt, tests/playwright/package.json	Git LFS rules for *.pt model files, Pyodide package lists for three notebooks (uma, mattersim, sevennet) with core dependencies and stubbed packages, ANTLR and UMA model artifact pointers, and Playwright test dependency.
Pyodide PyTorch Patching Infrastructure src/py/mat3ra/notebooks_utils/pyodide/packages/torch.py	Enhanced patch_torch_linalg() with NumPy interop for tensor conversion and indexing; new patch_torch_compiler(), patch_torch_distributed(), patch_fairchem_deps(), patch_mattersim_deps(), and patch_sevennet_deps() functions; parameterized apply_all_patches(include_fairchem, include_mattersim, include_sevennet) to conditionally enable stubs for each framework.
FAIRChem UMA Structural Relaxation Notebook other/experiments/jupyterlite/relax_structure_with_uma.ipynb	Sets input parameters (structure name, relaxation FMAX, UMA task/model path), installs packages and applies FAIRChem patches, loads structure from uploads or materials registry, constructs UMA calculator, runs BFGS optimization with Plotly energy tracking, and reports original vs. relaxed interlayer distances.
MatterSim Structural Relaxation Notebook other/experiments/jupyterlite/relax_structure_with_mattersim.ipynb	Configures MatterSim checkpoint path and relaxation parameters, installs dependencies and enables MatterSim patches, loads structure with fallback, creates MatterSimCalculator, executes BFGS relaxation with live energy updates, visualizes original and relaxed structures, and computes interlayer distance changes.
SevenNet Structural Relaxation Notebook other/experiments/jupyterlite/relax_structure_with_sevennet.ipynb	Defines structure loading and FMAX configuration, installs packages and applies SevenNet patches, loads pretrained SevenNet model, converts structure to ASE, runs BFGS relaxation with real-time Plotly chart updates (with FigureWidget fallback), and outputs before/after interlayer distances.
Playwright Notebook Validation Tests tests/playwright/debug_cell8.mjs, tests/playwright/debug_sevennet.mjs, tests/playwright/debug_sevennet_cell7.mjs, tests/playwright/test-results/.last-run.json, tests/playwright/test_mattersim_notebook.mjs, tests/playwright/test_notebook.mjs, tests/playwright/test_sevennet_notebook.mjs	Playwright automation scripts that launch Chrome, navigate to JupyterLite notebooks, wait for kernel idle, trigger "Restart & Run All", poll execution progress via DOM inspection, collect per-cell outputs, detect failures via Traceback text, report results with exit codes, and close browser. Includes both general and model-specific test scripts.

Estimated code review effort

🎯 3 (Moderate) | ⏱️ ~25 minutes

Poem

🐰 Three potentials dance in JupyterLite's embrace,
UMA, MatterSim, SevenNet in WebAssembly's space,
With patches and with patches, the heavy models play,
Relaxing crystal structures in your browser, every day! ✨

🚥 Pre-merge checks | ✅ 3 | ❌ 2

❌ Failed checks (2 warnings)

Check name	Status	Explanation	Resolution
Title check	⚠️ Warning	The PR title 'experiment/sevennet' refers to a real and significant part of the changeset (SevenNet notebook and dependencies), but it is incomplete and does not capture the main scope of the PR, which includes UMA, MatterSim, PyTorch model files, Playwright tests, and configuration updates.	Consider a more comprehensive title that reflects the primary objectives, such as 'Add experimental support for UMA, MatterSim, and SevenNet with PyTorch patches and notebook tests' or 'Add foundation model experiments and JupyterLite notebook tooling'.
Docstring Coverage	⚠️ Warning	Docstring coverage is 11.36% which is insufficient. The required threshold is 80.00%.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ 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 unit tests (beta)

• Create PR with unit tests
• Commit unit tests in branch experiment/sevennet

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