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Implement improved & consistent argument parsing #785

Merged
merged 34 commits into from
Jan 8, 2020
Merged

Implement improved & consistent argument parsing #785

merged 34 commits into from
Jan 8, 2020

Commits on Jan 8, 2020

  1. Add CLI demo

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  2. Extend ArgumentParser subclass

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  3. Reorg

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  4. More CLI work

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  5. Moving things aroundl implement "sourmash compare" CLI completely

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  6. Do the compute command

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  7. Clean it up with argument groups

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  8. Gather command

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  9. sourmash info and plot

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  10. sourmash search

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  11. All "sourmash lca" subcommands

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  12. All "sourmash sbt" subcommands

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  13. All "sourmash signature" subcommands

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  14. CLI complete, 1 command and 1 subcommand are functional

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  15. Weirdness to support "import" subcommand

    @standage @luizirber
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  16. Support both old and new interface

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  17. implementation for the new CLI PR (#811) 

    * implementation for the cli branch
* watch
* multigather, two test fixes, raise SystemError 1 instead of 0
* add test to make sure help is printed when cmd is called without subcmd
* add import_csv
* init ksize properly in lca index
    @luizirber
    luizirber committed Jan 8, 2020
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  18. sigh, py27...

    @luizirber
    luizirber committed Jan 8, 2020
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  19. remove unused imports

    @luizirber
    luizirber committed Jan 8, 2020
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  20. use new main methods for lca and sig

    @luizirber
    luizirber committed Jan 8, 2020
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  21. remove unused import

    @luizirber
    luizirber committed Jan 8, 2020
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  22. Reformat usage

    @standage @luizirber
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  23. More concise "sourmash --help" output

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  24. Clean up usage statements

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  25. Marked some subcommands as expert

    @standage @luizirber
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  26. Make multigather elitist, drop alt_subparsers

    @standage @luizirber
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  27. Sigh

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  28. fix test behavior for py27

    @luizirber
    luizirber committed Jan 8, 2020
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  29. Print citation

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  30. Add module docstrings, fix descriptors

    @standage @luizirber
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  31. Add module docstrings

    @standage @luizirber
    standage authored and luizirber committed Jan 8, 2020
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  32. Module docstrings

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    standage authored and luizirber committed Jan 8, 2020
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  33. add docstrings to cli modules and some of the commands

    @ctb @luizirber
    ctb authored and luizirber committed Jan 8, 2020
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  34. print citation only once

    @luizirber
    luizirber committed Jan 8, 2020
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