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EXP: try out lower level pyo3 API#552

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ctb wants to merge 116 commits intomainsourmash-bio/sourmash_plugin_branchwater:mainfrom branch_api_2sourmash-bio/sourmash_plugin_branchwater:branch_api_2Copy head branch name to clipboard

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Commits

Commits on Dec 21, 2024

• steal code from branch_api

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  fcb699f

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• bring in latest main

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Commits on Dec 30, 2024

• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into branch_api_2

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• compiles

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• re-enable

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• better error

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• attempt

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• it's aliiiiive

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• w00t

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• w00t

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• w00t**2

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• more granular

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• ...compiles

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• w00t**4

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Commits on Jan 2, 2025

• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into branch_api_2

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• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into branch_api_2

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Commits on Jan 3, 2025

• stub test for diff ksize in multigather

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• cargo fmt

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• Rename test file

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• refactor CSV output for fastgather/fastmultigather to use mpsc

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• cargo fmt

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• tests mostly pass

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• update API

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• update for revised API

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Commits on Jan 4, 2025

• fix skipmer test

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• upd comment

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• Merge branch 'fix_skip_test' into refactor_gather_csv

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• black

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• Merge branch 'fix_skip_test' into refactor_gather_csv

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• switch to min_max_scaled for rocksdb

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• black

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• comment

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• ensure overlap is > 0

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• rm comment

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• rm print

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• rm print

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• cleanup

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• fix clippy messages about too-complex returns

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• implement to_collection for BranchRevIndex

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• cargo fmt

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• Merge branch 'refactor_gather_csv' into branch_api_2

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• rename BranchCollection to BranchMultiCollection

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Commits on Jan 5, 2025

• combine/collapse

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• add loaded_sketches

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• foo

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• start implementing in Python

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• upgrade x rocksdb

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• more

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• fix scaled

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• punt

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• refactor out to obj fn

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• start making 'index'

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• update error handling, add function & test

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• refactor manysearch out into manysearch_obj

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• better refactor

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• cargo fmt

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• refactor manysearch_rocksdb

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• refactor multisearch

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• cargo fmt and black

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• disable pyexample stuff

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• cargo fmt and black

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• add manysearch x rocksdb

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• separate out Rust API changes from #552

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• rm obsolete code

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• upd overlap

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• Merge branch 'refactor_gather_csv' into factor_out_rust_api

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• fix

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• fix

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• fix

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• remove remaining Box/error stuff

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• remove remaining join => Err

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• remove remaining Box/error stuff

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• remove remaining join => Err

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• add multisearch_against

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• add pairwise

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• add basic pairwise and multisearch tests

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• fmt

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• clean up error handling a bit

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• Merge branch 'factor_out_rust_api' into branch_api_2

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Commits on Jan 6, 2025

• upd fastmultigather

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• refactor out loading of sketches

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• fix tests

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• update docs

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• upd

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Commits on Jan 7, 2025

• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into fix_skip_test

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• break test again

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• do heinous dev stuff

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• fix fix comment

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• Merge branch 'fix_skip_test' into refactor_gather_csv

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• upd

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• upd

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• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into refactor_gather_csv

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• do not require -o after all

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• Merge branch 'refactor_gather_csv' into factor_out_rust_api

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• fix for crate_empty_results

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• fmt

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• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into factor_out_rust_api

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• remove @ctb notes

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• Revert "remove @ctb notes"

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• fix fix

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• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into factor_out_rust_api

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• remove obligatory clone from Rust layer

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• Merge branch 'factor_out_rust_api' into branch_api_2

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• fix

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• Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branchwater into branch_api_2

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