PR: Refactor GraphDB and Update ML Dependency Handling#3

Merged

lllangWV merged 21 commits intomainfrom

graphdb-move-to-parquetdb

May 9, 2025

Commits on May 8, 2025

chore: Moved the generalized GraphDB module to parquetdb package as ParquetGraphDB.
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chore: Update pyproject.toml and README for ML dependencies
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refactor: Consolidate material-related modules into core package
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chore: Update optional dependencies in pyproject.toml
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chore: Reorder optional dependencies in pyproject.toml
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chore: Remove unused optional dependencies from pyproject.toml
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refactor: Replace GraphDB with ParquetGraphDB in test fixture
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refactor: Update imports in Getting Started notebook to core package
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refactor: renamed module from data to builders CrystalGraphBuilder and HeteroGraphBuilder classes
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refactor: Update notebook metadata to prevent execution during build
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refactor: Update load method to use ParquetGraphDB
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refactor: Update GraphBuilder references to HeteroGraphBuilder
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refactor: Update material references in tests and graph loading
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chore: Update .gitignore to include tmp.py and clean data entry
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refactor: Restructure API documentation for materials and nodes
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