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[MRG] subtantial refactoring of CounterGather and related Index code. #2116

Merged
merged 45 commits into from
Jul 16, 2022
Merged

[MRG] subtantial refactoring of CounterGather and related Index code. #2116

merged 45 commits into from
Jul 16, 2022

Commits on Jul 8, 2022

  1. move most CounterGather tests over to index protocol tests

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  2. add LinearIndex wrapper

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  3. getting closer

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  4. fix a bunch of the tests

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  5. Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int… 

    …o refactor/counter_gather_tests
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Commits on Jul 9, 2022

  1. Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int… 

    …o refactor/counter_gather_tests
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  2. fix call to 'peek'

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  3. adjust 'counter.add' call signature

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  4. add CounterGather_LCA

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  5. move CounterGather.calc_threshold into search.py

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  6. minor refactoring

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  7. resolve downsampling for linear index wrapper

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  8. fix downsampling for LCA-based CounterGather

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  9. fix location foo

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  10. fix remaining test

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Commits on Jul 10, 2022

  1. minor cleanup

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  2. add doc

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  3. test multiple identical matches

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  4. adjust LinearIndex implementation to skip identical matches

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Commits on Jul 11, 2022

  1. switch to dictionaries for CounterGather

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  2. cleanup protocol tests

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  3. revert LCA_Database fix

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  4. Merge branch 'latest' into refactor/counter_gather_tests

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  5. Merge branch 'refactor/counter_gather_tests' into update/counter_gather

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  6. restore CounterGather_LCA

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  7. cleanup

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  8. Merge branch 'refactor/counter_gather_tests' of https://github.com/so… 

    …urmash-bio/sourmash into refactor/counter_gather_tests
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  9. Merge branch 'latest' into refactor/counter_gather_tests

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  10. Merge branch 'refactor/counter_gather_tests' into update/counter_gather

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  11. Merge branch 'refactor/counter_gather_tests' into update/counter_gather

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  12. fix or ignore most errors ;)

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Commits on Jul 12, 2022

  1. rename make_gather_query to make_containment_query

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  2. rename Index.gather to Index.best_containment

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  3. consolidate threshold_bp => threshold calc code

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  4. change best_containment to return None or a result object, not a list

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Commits on Jul 13, 2022

  1. add flatten_and_* utility functions

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  2. add .signatures() method to CounterGather class

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  3. change CounterGather to take SourmashSignature instead of Minhash

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  4. fix test_index tests for counter

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  5. Merge branch 'latest' into refactor/counter_gather_tests

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  6. lightly clean up LCA_Database based counter

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  7. Merge branch 'refactor/counter_gather_tests' into update/counter_gather

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Commits on Jul 16, 2022

  1. Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int… 

    …o update/counter_gather
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  2. add comment and test re duplicate signatures, per @bluegenes

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  3. fix typo

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