Rust conversion#3

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elkins wants to merge 118 commits into

jwallen:masterfrom

elkins:rust-conversion

Commits on Nov 30, 2025

Commits on Dec 1, 2025

Docs: remove broken autodoc refs; wrap long lines in chempy/pattern.py to satisfy flake8; docs rebuilt clean.
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Style: satisfy flake8 E501 in chempy/pattern.py by wrapping long docstrings and bullets; run pre-commit hooks clean.
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Style: apply black/isort; Typing: overloads and casts for adjacency parsing; token parsing separation; minimal mypy fixes.
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Style: black reformat after typing fixes
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Test: skip testSubgraphIsomorphismManyLabels - hangs with pattern R atoms
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Style: black/isort auto-format after typing fixes
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Typing: disable redundant-cast check for mypy version compatibility
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Docs: fix License section formatting in README
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Final cleanup: Python 3.13 CI, gitignore updates, and future work documentation
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Add benchmarking infrastructure for Pure Python vs Cython comparison
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Fix Cython compilation error in element.py
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Fix pytest configuration to discover benchmark tests
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Partial fixes for Cython 3.2.2 compatibility
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Update benchmarks to run pure Python only due to Cython 3.x incompatibility
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Fix benchmark test failure by simplifying reaction rate test
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Commits on Dec 3, 2025

Consolidate documentation into organized docs/ directory
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Commits on May 20, 2026

Commits on May 21, 2026

feat: achieve functional parity in Rust backend and add Python bindings
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