Extract minimum assembly pathways as directed acyclic graphs of fragments - #153

Merged

Garrett-Pz merged 21 commits into

mainfrom

extract-pathways

Aug 12, 2026

Commits on Jun 20, 2026

feat: Add CLI argument controlling assembly pathway reconstruction
jdaymude
committed
87c5045
feat: Implement assembly pathway reconstruction with debug output
jdaymude
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5ecba3f

Commits on Jun 24, 2026

feat: Package assembly pathways as petgraph DAGs with DOT string outputs
jdaymude
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d7aead8
feat: Make DOT-formatted assembly pathways accessible from Python
jdaymude
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ec0dc39

Commits on Jul 28, 2026

feat: Rework the pathway DAG node/edge labels as fragment BitSets
jdaymude
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b09d68e

Commits on Jul 29, 2026

docs: Add pathway example to assembly::index_search docs
jdaymude
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1dabeed
docs: Align index_search docs and examples across Rust/Python
jdaymude
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3767b0b
feat: Rework CLI output based on verbosity, pathways, and timeout
jdaymude
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c0924e2
test: Update Python tests for pathway reconstruction
jdaymude
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9518804
chore: Clippy lints
jdaymude
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9654829
test: Add benchmark for search with match removal order collection
jdaymude
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98ddd1e
perf: Filter and dedup match removal order collection per search state
jdaymude
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1a12aae
docs: Minor docs updates in the benchmarks
jdaymude
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6d9b670
docs: Add better nondeterminism warnings to the CLI and index_search docs
jdaymude
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1bbc7ad

Commits on Jul 30, 2026

docs: Add estimated pathway reconstruction overhead to docs
jdaymude
committed
06e6582

Commits on Aug 10, 2026

Small fixes and clippy lints
Garrett-Pz
committed
d34f361