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Modularize top-down algorithm components#89

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jdaymude merged 15 commits intomainfrom
modularize
Jul 18, 2025
Merged

Modularize top-down algorithm components#89
jdaymude merged 15 commits intomainfrom
modularize

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@jdaymude jdaymude commented Jul 17, 2025 •
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Resolves #86.

  • Exposes a modular CLI for all variations of the top-down recursive algorithm
  • Moves enumeration, canonization, kernelization, and bounds each to their own modules
  • Strips dead and redundant code from assembly and molecule
  • Aligns the Python interface with the current Rust interface, including exposing assembly::index
  • Many documentation/doctest updates and cleanup

@jdaymude jdaymude requested a review from AgentElement July 17, 2025 22:53
jdaymude and others added 14 commits July 17, 2025 16:12
@jdaymude
proto: Add all CLI options, but leave interface unchanged for now
014debd
@jdaymude
refactor: Move bounds to their own module
f958702
@jdaymude
refactor: Remove naive search and expose assembly depth as a CLI flag
ccae263
@jdaymude
refactor: Avoid CLI enum duplication for bounds::Bound
eda66e4
@jdaymude
refactor: Move enumerate, canonize, parallel, and kernel modes
71ea749
@jdaymude
refactor: Strip dead code from Molecule, update documentation
afbf553
@jdaymude
refactor: Split out enumerate and canonize, consolidate index_search
15cdba2
@jdaymude
feat: Expose default index calculation to the python interface
b6396b8
@jdaymude
feat: Connect --kernel and --memoize CLI options to index_search
1babe40
@jdaymude
refactor: Renamed variables in index_search for clarity
01fb65f
@AgentElement @jdaymude
feat: canonize::canonize returns a Labeling enum
52d2b2b
@jdaymude
data: Add ma-index.csv to data/stress (ignores b12.mol)
2122e10
@jdaymude
chore: Run cargo fmt and clippy
80cd924
@jdaymude
chore: clippy wants two-space indents, not actual indents
9d7db73
@jdaymude jdaymude marked this pull request as ready for review July 17, 2025 23:15
AgentElement
AgentElement reviewed Jul 18, 2025
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jdaymude commented Jul 18, 2025

Self-approval, with @AgentElement's permission.

@jdaymude jdaymude merged commit fa4d3a8 into main Jul 18, 2025
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@jdaymude jdaymude deleted the modularize branch July 18, 2025 02:13
@jdaymude jdaymude mentioned this pull request Jul 23, 2025
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Modularize top-down algorithm components

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@jdaymude @AgentElement