chore: update README

[VsevolodX]

Summary by CodeRabbit

• Documentation
  • Updated setup instructions to use Python's built-in virtual environment workflow
  • Reorganized repository contents documentation with clearer hierarchy and improved navigation
  • Added installation options table to choose specific feature sets (API, Materials Designer, Workflows, Development, or Everything)

[coderabbitai]

Caution

Review failed

Pull request was closed or merged during review

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: 433668a0-5ca1-477e-b118-5ce14aa57771

📥 Commits

Reviewing files that changed from the base of the PR and between 38c1137 and 39eec1d.

📒 Files selected for processing (1)

• README.md

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📝 Walkthrough

Walkthrough

README.md documentation restructured to organize repository contents into functional sections (API Examples, Materials Designer, Simulation Workflows, utilities) and updated setup instructions to use Python's built-in venv instead of virtualenv, with a new extras-selection table for different notebook use cases.

Changes

Documentation Updates

Layer / File(s)	Summary
Repository contents overview README.md	Contents section reorganized from a flat table into structured subsections covering API Examples, Materials Designer notebooks, simulation workflows, and shared utilities, with updated notebook links and descriptions.
Setup instructions README.md	Setup section updated to use python -m venv .venv instead of virtualenv, and installation step replaced with a table mapping notebook subsets (API, Materials Designer, Workflows, Everything, Development) to corresponding pip install -e extras.

Estimated code review effort

🎯 2 (Simple) | ⏱️ ~10 minutes

Suggested reviewers

• timurbazhirov

Poem

A rabbit hopped through the README once,
Rearranged the contents—now it makes sense!
No more virtualenv, venv is the way,
Tables of extras guide users today! 🐰✨

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 inconclusive)

Check name	Status	Explanation	Resolution
Title check	❓ Inconclusive	The title 'chore: update README' is vague and generic, using a non-descriptive term 'update' without indicating the specific nature of the changes made.	Consider using a more specific title that describes the main changes, such as 'chore: restructure README contents and update setup instructions' to better convey the scope of documentation updates.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Docstring Coverage	✅ Passed	No functions found in the changed files to evaluate docstring coverage. Skipping docstring coverage check.
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 chore/update-readme

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