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use new load_file_as_signatures function more broadly #1059

Merged
merged 57 commits into from
Jul 2, 2020
Merged

use new load_file_as_signatures function more broadly #1059

merged 57 commits into from
Jul 2, 2020

Commits on Jun 28, 2020

  1. deploy new load_signatures API a bit more broadly

    @ctb
    ctb committed Jun 28, 2020
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  2. pay attention to do_raise properly in load_signatures

    @ctb
    ctb committed Jun 28, 2020
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  3. explicitly test new sig rename behavior of failing on non-existent files

    @ctb
    ctb committed Jun 28, 2020
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  4. refactor sourmash_args.load_dbs_and_sigs

    @ctb
    ctb committed Jun 28, 2020
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  5. refactor traverse into load_database code

    @ctb
    ctb committed Jun 28, 2020
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  6. cleanup & simplify

    @ctb
    ctb committed Jun 28, 2020
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  7. comment strange code

    @ctb
    ctb committed Jun 28, 2020
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  8. replace load_signatures with new load fn in load_query_signatures

    @ctb
    ctb committed Jun 28, 2020
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  9. add query signature loading from databases for search, gather

    @ctb
    ctb committed Jun 28, 2020
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  10. add to compare

    @ctb
    ctb committed Jun 28, 2020
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  11. change sourmash index to use new loading function

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    ctb committed Jun 28, 2020
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  12. change sourmash lca index to use new loading function

    @ctb
    ctb committed Jun 28, 2020
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  13. special case stdin sig loading

    @ctb
    ctb committed Jun 28, 2020
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  14. amend lca classify and summarize to use new load_file_as_signatures

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

  1. add --from-file to sourmash index

    @ctb
    ctb committed Jun 29, 2020
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  2. adjust cli for index to fix tests

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    ctb committed Jun 29, 2020
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  3. add --query-from-file to lca classify

    @ctb
    ctb committed Jun 29, 2020
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  4. add --query-from-file to lca summarize

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    ctb committed Jun 29, 2020
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  5. add --from-file to lca index

    @ctb
    ctb committed Jun 29, 2020
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  6. upgrade multigather with --query-from-file

    @ctb
    ctb committed Jun 29, 2020
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  7. add comments to categorize

    @ctb
    ctb committed Jun 29, 2020
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  8. add top-level fn load_file_as_index

    @ctb
    ctb committed Jun 29, 2020
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  9. more properly test Index.select method on SBTs and LCAs

    @ctb
    ctb committed Jun 29, 2020
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  10. Merge branch 'master' of github.com:dib-lab/sourmash into update_load… 

    …_sigs
    @ctb
    ctb committed Jun 29, 2020
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  11. make _load_database an internal function, remove error/sys.exit output

    @ctb
    ctb committed Jun 29, 2020
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  12. update sig export to allow --md5

    @ctb
    ctb committed Jun 29, 2020
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  13. rename some things to make activity of traverse_find_sigs clearer

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    ctb committed Jun 29, 2020
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  14. fix typo in sourmash_args; add test for index --from-file

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

  1. add tests for lca summarize --query-from-file

    @ctb
    ctb committed Jun 30, 2020
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  2. add tests for lca classify --query-from-file

    @ctb
    ctb committed Jun 30, 2020
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  3. rename test functions to remove traverse

    @ctb
    ctb committed Jun 30, 2020
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  4. trap certain errors

    @ctb
    ctb committed Jun 30, 2020
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  5. reset traverse_yield_all to false by default

    @ctb
    ctb committed Jun 30, 2020
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  6. add tests for --from-file and --force to lca index

    @ctb
    ctb committed Jun 30, 2020
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  7. test & fix --traverse-directories for lca summarize

    @ctb
    ctb committed Jun 30, 2020
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  8. fix index --traverse-dir -f

    @ctb
    ctb committed Jun 30, 2020
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  9. add multigather tests for --query-from-file

    @ctb
    ctb committed Jun 30, 2020
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  10. add --from-file to compare + tests

    @ctb
    ctb committed Jun 30, 2020
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  11. add test for compare --traverse-dir -f

    @ctb
    ctb committed Jun 30, 2020
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  12. fix and test bad ksize for lca db load

    @ctb
    ctb committed Jun 30, 2020
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  13. check failed gather load

    @ctb
    ctb committed Jun 30, 2020
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  14. add explicit test for no-such-file in load_file_as_index

    @ctb
    ctb committed Jun 30, 2020
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  15. add tests for sourmash sig describe on SBT, LCA, and dir

    @ctb
    ctb committed Jun 30, 2020
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  16. add a test for sig describe on stdin

    @ctb
    ctb committed Jun 30, 2020
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  17. remove errant comment

    @ctb
    ctb committed Jun 30, 2020
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  18. add load_file_as_signatures at top-level sourmash

    @ctb
    ctb committed Jun 30, 2020
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  19. whups, remove leftover test setup stuff

    @ctb
    ctb committed Jun 30, 2020
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  20. fix IOError vs OSError by choosing OSError

    @ctb
    ctb committed Jun 30, 2020
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  21. fix quotes expected in error message

    @ctb
    ctb committed Jun 30, 2020
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  22. detect file-like fp with 'read' as well

    @ctb
    ctb committed Jun 30, 2020
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  23. update command line docs

    @ctb
    ctb committed Jun 30, 2020
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Commits on Jul 1, 2020

  1. update documentation a bit

    @ctb
    ctb committed Jul 1, 2020
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  2. Merge branch 'master' into update_load_sigs

    @ctb
    ctb authored Jul 1, 2020
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  3. improve docstrings, defaults

    @ctb
    ctb committed Jul 1, 2020
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  4. Merge branch 'update_load_sigs' of github.com:dib-lab/sourmash into u… 

    …pdate_load_sigs
    @ctb
    ctb committed Jul 1, 2020
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  5. make sure md5 selector is unique in collection

    @ctb
    ctb committed Jul 1, 2020
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Commits on Jul 2, 2020

  1. Merge branch 'master' into update_load_sigs

    @luizirber
    luizirber authored Jul 2, 2020
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