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MRG: use core Collection and Select for sig loading #197

Merged
merged 58 commits into from
Feb 13, 2024
Merged

MRG: use core Collection and Select for sig loading #197

merged 58 commits into from
Feb 13, 2024

Commits on Sep 27, 2023

  1. init changes

    @bluegenes
    bluegenes committed Sep 27, 2023
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  2. compiling code using newer mastiff branch

    @bluegenes
    bluegenes committed Sep 27, 2023
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Commits on Oct 2, 2023

  1. use selection

    @bluegenes
    bluegenes committed Oct 2, 2023
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Commits on Nov 5, 2023

  1. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes committed Nov 5, 2023
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  2. rustfmt

    @bluegenes
    bluegenes committed Nov 5, 2023
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Commits on Nov 17, 2023

  1. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes authored Nov 17, 2023
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Commits on Nov 22, 2023

  1. update deps

    @luizirber
    luizirber committed Nov 22, 2023
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  2. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes committed Nov 22, 2023
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Commits on Dec 1, 2023

  1. update to sourmash 0.12.0

    @luizirber
    luizirber committed Dec 1, 2023
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  2. fix index

    @luizirber
    luizirber committed Dec 1, 2023
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Commits on Dec 2, 2023

  1. rm reporting line checks not in smash core idx

    @bluegenes
    bluegenes committed Dec 2, 2023
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Commits on Dec 7, 2023

  1. use selection instead of template

    @bluegenes
    bluegenes committed Dec 7, 2023
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Commits on Jan 23, 2024

  1. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes committed Jan 23, 2024
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  2. rustfmt

    @bluegenes
    bluegenes committed Jan 23, 2024
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  3. fix query file no exist errs

    @bluegenes
    bluegenes committed Jan 23, 2024
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  4. update mastiff_manygather

    @bluegenes
    bluegenes committed Jan 23, 2024
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  5. rustfmt

    @bluegenes
    bluegenes committed Jan 23, 2024
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  6. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes committed Jan 23, 2024
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  7. add cargo lock

    @bluegenes
    bluegenes committed Jan 23, 2024
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Commits on Jan 24, 2024

  1. switch to commit in latest br

    @bluegenes
    bluegenes committed Jan 24, 2024
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  2. cleanup unused imports and code

    @bluegenes
    bluegenes committed Jan 24, 2024
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Commits on Jan 25, 2024

  1. init use collection for query loading

    @bluegenes
    bluegenes committed Jan 25, 2024
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Commits on Jan 26, 2024

  1. ...collection loading in progress

    @bluegenes
    bluegenes committed Jan 26, 2024
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  2. fix fastgather

    @bluegenes
    bluegenes committed Jan 26, 2024
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  3. re-enable more permissive pathlist loading

    @bluegenes
    bluegenes committed Jan 26, 2024
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  4. clean up ms

    @bluegenes
    bluegenes committed Jan 26, 2024
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  5. harmonize errors

    @bluegenes
    bluegenes committed Jan 26, 2024
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Commits on Jan 27, 2024

  1. harmonize error text and output filenames

    @bluegenes
    bluegenes committed Jan 27, 2024
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Commits on Jan 30, 2024

  1. Merge branch 'main' into upd-smash-core

    @bluegenes
    bluegenes authored Jan 30, 2024
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  2. re-allow load from sig; upd manysearch

    @bluegenes
    bluegenes committed Jan 30, 2024
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Commits on Jan 31, 2024

  1. fix all except moltype selection

    @bluegenes
    bluegenes committed Jan 31, 2024
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  2. update fastgather and multisearch

    @bluegenes
    bluegenes committed Jan 31, 2024
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  3. Merge branch 'upd-smash-core' into use-core-more-broadly

    @bluegenes
    bluegenes authored Jan 31, 2024
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  4. update pairwise

    @bluegenes
    bluegenes committed Jan 31, 2024
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  5. clean up a little

    @bluegenes
    bluegenes committed Jan 31, 2024
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Commits on Feb 1, 2024

  1. clean up; unify sketch loading for pairwise/multisearch

    @bluegenes
    bluegenes committed Feb 1, 2024
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Commits on Feb 2, 2024

  1. ...cleaner

    @bluegenes
    bluegenes committed Feb 2, 2024
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  2. unify more code

    @bluegenes
    bluegenes committed Feb 2, 2024
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  3. rm unused save_paths option

    @bluegenes
    bluegenes committed Feb 2, 2024
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  4. use updated mh loading

    @bluegenes
    bluegenes committed Feb 2, 2024
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  5. standardize indexed writing using local struct for now

    @bluegenes
    bluegenes committed Feb 2, 2024
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  6. clean up sketch loading and file opening/writing

    @bluegenes
    bluegenes committed Feb 2, 2024
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  7. apply clippy suggestions

    @bluegenes
    bluegenes committed Feb 2, 2024
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  8. add back SmallSignature and use

    @bluegenes
    bluegenes committed Feb 2, 2024
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  9. rename fn back to load_sketches

    @bluegenes
    bluegenes committed Feb 2, 2024
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  10. use serde serialize for writing instead of custom traits

    @bluegenes
    bluegenes committed Feb 2, 2024
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Commits on Feb 10, 2024

  1. upd to 0.12.1 sourmash core; clean up index tests

    @bluegenes
    bluegenes committed Feb 10, 2024
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  2. Merge branch 'main' into use-core-more-broadly

    @bluegenes
    bluegenes authored Feb 10, 2024
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  3. Merge branch 'main' into use-core-more-broadly

    @bluegenes
    bluegenes authored Feb 10, 2024
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  4. fix issues from merge conflicts

    @bluegenes
    bluegenes committed Feb 10, 2024
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  5. clean up tests

    @bluegenes
    bluegenes committed Feb 10, 2024
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  6. rustfmt

    @bluegenes
    bluegenes committed Feb 10, 2024
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Commits on Feb 12, 2024

  1. Merge branch 'main' into use-core-more-broadly

    @ctb
    ctb authored Feb 12, 2024
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Commits on Feb 13, 2024

  1. make fmg output filenaming robust to spaces in signame

    @bluegenes
    bluegenes committed Feb 13, 2024
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  2. Merge branch 'use-core-more-broadly' of github.com:sourmash-bio/sourm… 

    …ash_plugin_branchwater into use-core-more-broadly
    @bluegenes
    bluegenes committed Feb 13, 2024
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  3. minor doc updates

    @bluegenes
    bluegenes committed Feb 13, 2024
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  4. disable rocksdb for fastgather

    @bluegenes
    bluegenes committed Feb 13, 2024
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  5. instead, disable rocksdb reading within load_collection

    @bluegenes
    bluegenes committed Feb 13, 2024
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