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[MRG] implement sourmash sketch fromfile #1885

Merged
merged 155 commits into from
Apr 1, 2022
Merged

[MRG] implement sourmash sketch fromfile #1885

merged 155 commits into from
Apr 1, 2022

Commits on Jan 4, 2022

  1. add -d/--debug to various commands

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Commits on Mar 13, 2022

  1. upgrade ComputerParameters with __repr__ and __eq__

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  2. cleanup and refactor

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  3. add tests for new behavior

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  4. finish tests

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  5. initial 'sourmash sketch fromfile' implementation

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  6. add ComputeParameters.to_param_str

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Commits on Mar 14, 2022

  1. add ComputeParameters.to_param_str

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  2. output sourmash commands, hackity hack hack

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  3. fix spelling

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  4. Merge branch 'add/sketchfrom_support' into add/sketch_fromfile

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  5. a fix, and some tests

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  6. add tests for to_param_str

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  7. Merge branch 'add/sketchfrom_support' into add/sketch_fromfile

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

    …o add/sketch_fromfile
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  9. add ComputeParameters.from_manifest_row

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  10. switch to using ComputeParameters.from_manifest_row

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  11. add ComputeParameters.from_manifest_row

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  12. Merge branch 'update/more_sketch_fromfile_support' into add/sketch_fr… 

    …omfile
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  13. moar

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  14. add tests for ComputeParameters.from_manifest_row

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  15. whoops, add param string into sourmash cmd output

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  16. Merge branch 'update/more_sketch_fromfile_support' into add/sketch_fr… 

    …omfile
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Commits on Mar 15, 2022

  1. initial tests

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  2. more tests

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  3. clean up help

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  4. tests and more tests

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  5. enable and test CSV output from fromfile

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Commits on Mar 16, 2022

  1. fix multiple param strs output

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Commits on Mar 19, 2022

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

    …o add/sketch_fromfile
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Commits on Mar 20, 2022

  1. simplify/report on missing

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Commits on Mar 21, 2022

  1. test --already done

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Commits on Mar 22, 2022

  1. initial implementation of StandaloneManifestIndex

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  2. support prefix if not abspath

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Commits on Mar 23, 2022

  1. clean up

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  2. some standalone manifests tests - incl CLI

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  3. iterate over internal locations instead

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  4. switch to picklist API

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  5. aaaaand swap out for load_file_as_index 🎉

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  6. remove unnecessary spaces

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  7. more tests

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  8. more better prefix test

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Commits on Mar 24, 2022

  1. remove unnec space

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  2. remove sourmash sketch command output

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  3. add --output-manifest

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  4. do sketch summarization

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Commits on Mar 25, 2022

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

    …o add/debug
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  2. upgrade output error messages

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  3. Merge branch 'add/debug' into add/manifestindex

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  4. fix SBT subdir loading error

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  5. add message about using --debug

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  6. Merge branch 'add/debug' into add/manifestindex

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  7. Merge branch 'add/test_sbt_load_fail' into add/manifestindex

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  8. doc etc

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  9. rationalize _signatures_with_internal

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  10. test describe and fileinfo on manifests

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  11. think through more manifest stuff

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

    …o add/manifestindex
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  13. fix descr

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  14. rationalize _signatures_with_internal

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  15. Merge branch 'refactor/mf_internal' into add/manifestindex

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  16. fix docstring

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  17. add heading anchors config; fix napoleon package ref

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  18. pin versions for doc building

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  19. fix internal refs

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  20. fix one last ref target

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  21. add docs

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  22. clarify language

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  23. add docs

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  24. add more/better tests for lazy loading

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  25. clarify

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  26. a few more tests

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  27. Merge branch 'add/manifestindex' into add/sketch_fromfile

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  28. fixes

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Commits on Mar 26, 2022

  1. Merge branch 'fix/docs' into add/manifestindex

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  2. update docs

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  3. cleanup and comment on index code

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  4. minor improvements to Index tests

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  5. add explicit test for lazy-loading prefetch on StandaloneManifestIndex

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  6. add explicit test for lazy-loading prefetch on StandaloneManifestIndex

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  7. Merge branch 'fix/docs' into add/sketch_fromfile

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  8. Merge branch 'add/manifestindex' into add/sketch_fromfile

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  9. Merge branch 'cleanup/index' into add/sketch_fromfile

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  10. Merge branch 'cleanup/index_2' into add/sketch_fromfile

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  11. start adding sig check

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  12. add some more tests

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  13. some cleanup and refactor

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  14. cleanup

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  15. write some manifest utility methods

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

    …o add/sketch_fromfile
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  17. updated output messages

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Commits on Mar 27, 2022

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

    …o add/sketch_fromfile
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  2. Merge branch 'latest' of https://github.com/sourmash-bio/sourmash int… 

    …o add/manifestindex
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  3. update comments/docstrings

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  4. Merge branch 'add/manifestindex' into cleanup/index

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  5. Merge branch 'cleanup/index' into cleanup/index_2

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  6. Merge branch 'cleanup/index_2' into add/sketch_fromfile

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  7. get non-standard column names work with sig check -o

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  8. add an exclude test

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  9. fix comments

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  10. test many different coltypes

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Commits on Mar 28, 2022

  1. Update doc/command-line.md 

    Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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  2. update comments/docstrings

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  3. Merge branch 'add/manifestindex' into add/sketch_fromfile

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

    …o cleanup/index
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  5. Merge branch 'cleanup/index' into cleanup/index_2

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  6. Merge branch 'cleanup/index' into add/sketch_fromfile

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  7. Merge branch 'cleanup/index_2' into add/sketch_fromfile

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Commits on Mar 29, 2022

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

    …o cleanup/index_2
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  2. Apply suggestions from code review 

    Co-authored-by: Tessa Pierce Ward <bluegenes@users.noreply.github.com>
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  3. Merge branch 'cleanup/index_2' into add/sketch_fromfile

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

    …o add/sketch_fromfile
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  5. command line docs for sig check

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  6. adjust command line, add usage etc

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  7. copy sig check code over

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  8. Merge branch 'add/sig_check' into add/sketch_fromfile

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  9. add --fail to sig check

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  10. require manifests etc

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  11. test no --picklist

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  12. test nosave manifest

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  13. test __iadd__ for manifests

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  14. remove 'add_to_found'

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  15. revert

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Commits on Mar 30, 2022

  1. simplify per @bluegenes

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  2. Merge branch 'add/sig_check' into add/sketch_fromfile

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

    …o add/sketch_fromfile
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  4. test --force-output

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  5. test --output-manifest-matching

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

    …o add/sketch_fromfile
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  7. add some missing-name tests

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  8. catch/error out on missing names.

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Commits on Mar 31, 2022

  1. seed, license tests

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  2. add some minimal how-to-docs docs

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  3. add docs

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  4. other columns will be ignored

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  5. adjust --check-sequence usage and add initial test

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  6. add tests; still failing

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  7. add more tests, fix bad DNA check

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  8. allow multiple CSVs to fromfile

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  9. consume multiple CSVs; check for dup names

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  10. annotate places for further work/coverage

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  11. test --ignore-missing

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  12. add test of partially done

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  13. adjust comments

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  14. catch empty files/files with no data

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Commits on Apr 1, 2022

  1. tighten code

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  2. test multiple -p

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  3. refactor

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  4. more refactor

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  5. more refactor

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  6. warning messages about missing genomes/proteomes

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  7. some more tidying

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

    …o add/sketch_fromfile
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  9. resolve most of the review issues

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  10. add test for bad ComputeParameters

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