docs: add Windows setup guide and fix for 'tree' and 'pdbfixer' import errors (resolves #1047) #1080
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This PR resolves #1047, where users encounter:
ModuleNotFoundError: No module named 'tree'
This is caused by the dm-tree package not being properly installed or recognized on some Windows environments.
✅ What I Did
Installed dm-tree manually using "" pip install --force-reinstall --no-cache-dir dm-tree "" to resolve the tree module error.
Resolved a follow-up ModuleNotFoundError for pdbfixer by installing it via GitHub:
pip install git+https://github.com/openmm/pdbfixer.git
Verified both test cases in run_alphafold_test.py passed successfully on Windows 10 with Python 3.12.6.
Added a step-by-step Windows installation guide to README.md to help other users avoid this issue.