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[MRG] update to sourmash 4.1.0 #171

Merged
merged 35 commits into from
May 24, 2021
Merged

[MRG] update to sourmash 4.1.0 #171

merged 35 commits into from
May 24, 2021

Commits on May 18, 2021

  1. update to sourmash 4.1.0

    @taylorreiter
    taylorreiter authored May 18, 2021
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  2. Update env-sourmash.yml

    @taylorreiter
    taylorreiter authored May 18, 2021
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  3. Update env-reporting.yml

    @taylorreiter
    taylorreiter authored May 18, 2021
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Commits on May 19, 2021

  1. start switch to 4.1. Prefect, zip of matches, load_file_as_signatures

    @taylorreiter
    taylorreiter committed May 19, 2021
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  2. make gather stop when there aren't any more mh in the sig

    @taylorreiter
    taylorreiter committed May 19, 2021
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  3. rm div 0 in f_major calc, change match sig to zip, fix float point

    @taylorreiter
    taylorreiter committed May 19, 2021
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  4. fix IndexError when empty sigs

    @taylorreiter
    taylorreiter committed May 19, 2021
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  5. change reporting env to >=4.1.0<5

    @taylorreiter
    taylorreiter committed May 19, 2021
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  6. readd reporting file

    @taylorreiter
    taylorreiter committed May 19, 2021
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  7. switch test to load_file_as_signatures

    @taylorreiter
    taylorreiter committed May 19, 2021
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  8. update snakemake test to matches.zip

    @taylorreiter
    taylorreiter committed May 19, 2021
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  9. add 2.fa to matches.zip with sourmash sig cat

    @taylorreiter
    taylorreiter committed May 19, 2021
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  10. tests/test_contigs_search.py

    @taylorreiter
    taylorreiter committed May 19, 2021
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  11. start switching to zip, still needs debug

    @taylorreiter
    taylorreiter committed May 19, 2021
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  12. add test dataset

    @taylorreiter
    taylorreiter committed May 19, 2021
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  13. woops -- only break if len(mh) == 0

    @taylorreiter
    taylorreiter committed May 19, 2021
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  14. replace .get_mins() with .hashes

    @taylorreiter
    taylorreiter committed May 19, 2021
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  15. fix ValueError from threshold-bp

    @taylorreiter
    taylorreiter committed May 19, 2021
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  16. woops rm thresholdbp print statement

    @taylorreiter
    taylorreiter committed May 19, 2021
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Commits on May 20, 2021

  1. update to sourmash 1537 instead of 1537

    @taylorreiter
    taylorreiter committed May 20, 2021
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  2. range for sourmash version

    @taylorreiter
    taylorreiter committed May 20, 2021
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  3. switch from gather to prefetch

    @taylorreiter
    taylorreiter committed May 20, 2021
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  4. add except for assertion error from sourmash assert db on empty sigs

    @taylorreiter
    taylorreiter committed May 20, 2021
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  5. refactor to not have pass block

    @taylorreiter
    taylorreiter committed May 20, 2021
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  6. refactor sum_ident

    @taylorreiter
    taylorreiter committed May 20, 2021
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  7. update threshold bp for prefetch to 3*scaled

    @taylorreiter
    taylorreiter committed May 20, 2021
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Commits on May 21, 2021

  1. fix tests

    @ctb
    ctb committed May 21, 2021
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  2. wups, remove test debugging

    @ctb
    ctb committed May 21, 2021
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  3. remove sourmash 4.1.1 code

    @ctb
    ctb committed May 21, 2021
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  4. remove --no-linear in prefetch bc its default

    @taylorreiter
    taylorreiter committed May 21, 2021
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  5. fix load sig with file handle

    @taylorreiter
    taylorreiter committed May 21, 2021
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  6. simplify while 1

    @taylorreiter
    taylorreiter committed May 21, 2021
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  7. Merge pull request #172 from dib-lab/update/tr_sourmash_by_ctb 

    [MRG] Fix tests for #171
    @taylorreiter
    taylorreiter authored May 21, 2021
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Commits on May 22, 2021

  1. update to sourmash v4.1.1

    @ctb
    ctb committed May 22, 2021
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Commits on May 24, 2021

  1. Merge pull request #176 from dib-lab/ctb/update_sourmash_411 

    [MRG] update to sourmash v4.1.1
    @taylorreiter
    taylorreiter authored May 24, 2021
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