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[MRG] MinHash class refactoring #1128

Merged
merged 59 commits into from
Aug 5, 2020
Merged

[MRG] MinHash class refactoring #1128

merged 59 commits into from
Aug 5, 2020

Commits on Jul 25, 2020

  1. move sourmash._minhash to sourmash.minhash

    @ctb
    ctb committed Jul 25, 2020
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  2. deprecate max_hash throughout

    @ctb
    ctb committed Jul 25, 2020
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  3. change MinHash.add(...) to MinHash.add_kmer(...)

    @ctb
    ctb committed Jul 25, 2020
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  4. remove update and is_molecule_type from MinHash

    @ctb
    ctb committed Jul 25, 2020
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  5. remove subtract_mins

    @ctb
    ctb committed Jul 25, 2020
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  6. rename downsample_n to downsample_num

    @ctb
    ctb committed Jul 25, 2020
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  7. switch to hashes property instead of using get_mins()

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    ctb committed Jul 25, 2020
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  8. replace get_mins(...) with hashes thruout

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    ctb committed Jul 25, 2020
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Commits on Jul 26, 2020

  1. change deprecated 'compare' usage to 'similarity' in test_jaccard

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    ctb committed Jul 26, 2020
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  2. elminate most of the deprecation warnings in test__minhash by switchi… 

    …ng compare to similarity
    @ctb
    ctb committed Jul 26, 2020
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  3. fix remaining tests in test__minhash

    @ctb
    ctb committed Jul 26, 2020
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  4. fix compat message

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    ctb committed Jul 26, 2020
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  5. Merge branch 'master' of github.com:dib-lab/sourmash into remove_comp… 

    …are_from_tests
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    ctb committed Jul 26, 2020
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Commits on Jul 27, 2020

  1. Merge branch 'master' of github.com:dib-lab/sourmash into minhash_cla… 

    …ss_munge
    @ctb
    ctb committed Jul 27, 2020
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  2. restore removed functions, sigh :)

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    ctb committed Jul 27, 2020
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  3. minor upd

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    ctb committed Jul 27, 2020
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Commits on Jul 28, 2020

  1. add deprecations

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    ctb committed Jul 28, 2020
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  2. Merge branch 'master' into remove_compare_from_tests

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  3. Merge branch 'remove_compare_from_tests' of github.com:dib-lab/sourma… 

    …sh into minhash_class_munge
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  4. Merge branch 'master' of github.com:dib-lab/sourmash into minhash_cla… 

    …ss_munge
    @ctb
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  5. use a wrapper object for .hashes and make it read-only

    @ctb
    ctb committed Jul 28, 2020
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  6. refactor to use downsample(num/scaled=

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    ctb committed Jul 28, 2020
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Commits on Jul 29, 2020

  1. refactor to use downsample(scaled=...)

    @ctb
    ctb committed Jul 29, 2020
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  2. return two deleted tests

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    ctb committed Jul 29, 2020
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  3. fixed test that was masked by another test

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    ctb committed Jul 29, 2020
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  4. add explicit check for length of kmer in add_kmer

    @ctb
    ctb committed Jul 29, 2020
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  5. fix ordering in hash retrieval

    @ctb
    ctb committed Jul 29, 2020
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  6. fix more tests for py2 <khaaaaaaaaaan>

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    ctb committed Jul 29, 2020
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Commits on Jul 30, 2020

  1. add 'flatten' method to MinHash

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    ctb committed Jul 30, 2020
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  2. add test for MinHash.flatten

    @ctb
    ctb committed Jul 30, 2020
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  3. add tests for add and add_kmer

    @ctb
    ctb committed Jul 30, 2020
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  4. remove nonsense test

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    ctb committed Jul 30, 2020
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  5. test the (now deprecated) get_mins function

    @ctb
    ctb committed Jul 30, 2020
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  6. test (deprecated) get_hashes

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    ctb committed Jul 30, 2020
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  7. add tests for downsample and is_molecule_type

    @ctb
    ctb committed Jul 30, 2020
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  8. test moltype properties more explicitly

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    ctb committed Jul 30, 2020
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  9. fix py27

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    ctb committed Jul 30, 2020
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Commits on Aug 1, 2020

  1. move translate_codon to module level

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    ctb committed Aug 1, 2020
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Commits on Aug 2, 2020

  1. put a stub in place of _minhash with a FutureWarning

    @ctb
    ctb committed Aug 2, 2020
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  2. adjust import req

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    ctb committed Aug 2, 2020
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Commits on Aug 3, 2020

  1. Merge branch 'master' of github.com:dib-lab/sourmash into minhash_cla… 

    …ss_munge
    @ctb
    ctb committed Aug 3, 2020
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Commits on Aug 4, 2020

  1. remove __future__ imports

    @ctb
    ctb committed Aug 4, 2020
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  2. remove sys.version checks for py 2

    @ctb
    ctb committed Aug 4, 2020
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  3. remove requirement for enum34

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    ctb committed Aug 4, 2020
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  4. remove __reduce__ from MinHash class (#1144)

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    ctb committed Aug 4, 2020
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  5. remove __reduce__ again, here :)

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    ctb committed Aug 4, 2020
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Commits on Aug 5, 2020

  1. avoid the DeprecationWarning

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    ctb committed Aug 5, 2020
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  2. update docs: only python 3.7 and 3.8

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    ctb committed Aug 5, 2020
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  3. remove 2.7 from travis

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    ctb committed Aug 5, 2020
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  4. remove _compat from signature.py

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    ctb committed Aug 5, 2020
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  5. remove _compat from exceptions.py

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    ctb committed Aug 5, 2020
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  6. remove _compat from index and sbt_storage

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  7. remove _compat from nodegraph

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  8. remove _compat completely

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  9. Merge branch 'remove_py2' into minhash_class_munge

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  10. make signature -> sig in CLI using py3 'aliases'

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  11. put back assert that didn't work in py2

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  12. Merge branch 'remove_py2' into minhash_class_munge

    @ctb
    ctb committed Aug 5, 2020
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  13. Update sourmash/minhash.py 

    Co-authored-by: Luiz Irber <luizirber@users.noreply.github.com>
    @ctb @luizirber
    ctb and luizirber committed Aug 5, 2020
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