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MRG: add generic support for any type of sketch collection as query or database #430

Merged
merged 111 commits into from
Oct 15, 2024
Merged

MRG: add generic support for any type of sketch collection as query or database #430

merged 111 commits into from
Oct 15, 2024

Commits on Aug 17, 2024

  1. refactor & rename & consolidate

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  2. remove 'lower'

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Commits on Aug 18, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc_cleanup
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  2. add cargo doc output for private fn

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  3. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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  4. add a few comments/docs

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  5. switch to dev version of sourmash

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  6. tracking

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  7. cleaner

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  8. cleanup

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  9. load rocksdb natively

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  10. foo

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Commits on Aug 19, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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  2. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc_cleanup
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  3. Merge branch 'ctb_misc_cleanup' into ctb_misc2

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  4. cargo fmt

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Commits on Aug 20, 2024

  1. upd

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  2. upd

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  3. fix fmt

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  4. MRG: create MultiCollection for collections that span multiple files ( 

    #434)

* preliminary victory

* compiles and mostly runs

* cleanup, split to new module

* cleanup and comment

* more cleanup of diff

* cargo fmt

* fix fmt

* restore n_failed

* comment failing test

* cleanup and de-vec

* create module/submodule structure

* comment for later

* get rid of vec

* beg for help

* cleanup and doc
    @ctb
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  5. clippy fixes

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  6. compiling again

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  7. cleanup

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Commits on Aug 21, 2024

  1. bump sourmash to v0.15.1

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  2. Merge branch 'bump_sourmash' into ctb_misc2

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  3. check if is rocksdb

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  4. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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  5. weird error

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  6. use remove_unwrap branch of sourmash

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  7. get index to work with MultiCollection

    @ctb
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  8. old bug now fixed

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  9. clippy, format, and fix

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  10. make names clearer

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  11. ditch MultiCollection for index, at least for now

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  12. testy testy

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  13. getting closer

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Commits on Aug 22, 2024

  1. update sourmash

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  2. mark failing tests

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Commits on Aug 24, 2024

  1. upd

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  2. cargo fmt

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  3. MRG: test exit from pairwise and multisearch if no loaded sketches ( 

    #437)

* upd

* check for appropriate multisearch error exits

* add more tests for pairwise, too

* cargo fmt
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  4. MRG: switch to more efficient use of Collection by removing cloning (… 

    …#438)

* remove unnecessary clones by switch to references in SmallSignature

* switch away from references for collections => avoid clones

* remove MultiCollection::iter
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  5. MRG: add tests for RocksDB/RevIndex, standalone manifests, and flexib… 

    …le pathlists (#436)

* test using rocksdb as source of sketches

* test file lists of zips

* cargo fmt

* hackity hack hack a picklist

* ok that makes more sense

* it works

* comments around future par_iter

* support loading from a .sig.gz for index

* test pairwise loading from rocksdb

* add test for queries from Rocksdb

* decide not to implement lists of manifests :)
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  6. reenable and fix test_fastgather.py::test_indexed_against

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  7. impl Deref for MultiCollection

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  8. clippy

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  9. switch to using load_sketches method

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  10. deref doesn't actually make sense for MultiCollection

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Commits on Aug 27, 2024

  1. update to latest sourmash code

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  2. update to latest sourmash code

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  3. simplify

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  4. update to latest sourmash code

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  5. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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  6. remove unnecessary flag

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Commits on Sep 8, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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Commits on Sep 9, 2024

  1. MRG: support & test loading of standalone manifests within pathlists (#… 

    …450)

* use recursion to load paths into a MultiCollection => mf support

* MRG: clean up index to use `MultiCollection` (#451)

* try making index work with standard code

* kinda working

* fmt

* refactor

* clear up the tests

* refactor/clean up

* cargo fmt

* add tests for index warning & error

* comment
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  2. MRG: documentation updates based on new collection loading (#444) 

    * update docs for #430

* upd documentation

* upd
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  3. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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Commits on Sep 10, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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  2. Update src/lib.rs 

    Co-authored-by: Tessa Pierce Ward <[email protected]>
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  3. switch unwrap to expect

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  4. Merge branch 'ctb_misc2' of github.com:sourmash-bio/sourmash_plugin_b… 

    …ranchwater into ctb_misc2
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  5. move unwrap to expect

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  6. minor cleanup

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Commits on Sep 11, 2024

  1. cargo fmt

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Commits on Sep 15, 2024

  1. provide legacy method to avoid xfail on index loading

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  2. switch to using reference

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  3. update docs to reflect pathlist behavior

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  4. test recursive nature of MultiCollection

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  5. re-enable test that is now passing

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Commits on Sep 16, 2024

  1. update to latest sourmash

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  2. upd sourmash

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  3. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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Commits on Sep 17, 2024

  1. update sourmash

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Commits on Sep 18, 2024

  1. mut MultiCollection

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  2. cleanup

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Commits on Sep 21, 2024

  1. update after merge of sourmash-bio/sourmash#3305

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Commits on Sep 22, 2024

  1. fix contains_revindex

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  2. add trace commands for tracing loading

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Commits on Sep 25, 2024

  1. use released version of sourmash

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Commits on Oct 2, 2024

  1. add support for ignoring abundance

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  2. cargo fmt

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Commits on Oct 4, 2024

  1. avoid downsampling until we know there is overlap

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Commits on Oct 5, 2024

  1. change downsample to true; add panic assertion

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  2. move downsampling side guard

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  3. eliminate redundant overlap check

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  4. move calc_abund_stats

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  5. extract abundance code into own function; avoid downsampling if poss

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  6. cleanup

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  7. Merge branch 'toggle_manysearch_abund' into ctb_misc2

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  8. fmt

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Commits on Oct 6, 2024

  1. Merge branch 'toggle_manysearch_abund' into ctb_misc2

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Commits on Oct 9, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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Commits on Oct 11, 2024

  1. update to next sourmash release

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  2. cargo fmt

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  3. upd sourmash

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  4. correct numbers

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Commits on Oct 12, 2024

  1. upd sourmash

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  2. upd sourmash

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  3. Merge branch 'update_sourmash_latest' into ctb_misc2

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  4. upd sourmash

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Commits on Oct 13, 2024

  1. upd sourmash

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  2. use new try_into() and eliminate several clone()s

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  3. Merge branch 'update_sourmash_latest' into ctb_misc2

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  4. refactor a bit more

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  5. deallocate collection?

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  6. upd sourmash

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  7. cargo fmt

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    ctb committed Oct 13, 2024
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  8. fix merge foo

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    ctb committed Oct 13, 2024
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Commits on Oct 14, 2024

  1. Merge branch 'main' of github.com:sourmash-bio/sourmash_plugin_branch… 

    …water into ctb_misc2
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    ctb committed Oct 14, 2024
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Commits on Oct 15, 2024

  1. merge

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