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Dorado plugin #344

Merged
merged 19 commits into from
May 9, 2024
Merged

Dorado plugin #344

merged 19 commits into from
May 9, 2024

Commits on Apr 3, 2024

  1. Introducing a dorado specific plugin which handles the change from on…

    …t_pyguppy_client_lib to ont_pybasecaller_client_lib
    mattloose committed Apr 3, 2024
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  2. minor code reformat

    mattloose committed Apr 3, 2024
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Commits on Apr 17, 2024

  1. Bump version

    Adoni5 committed Apr 17, 2024
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  2. Update Changelog

    Adoni5 committed Apr 17, 2024
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  4. fix typo

    Adoni5 committed Apr 17, 2024
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  5. Add try/except on import helper functions and pyclient for basecaller

    This is so pytest collections (The only time both are imported into the same interperter runtime) doesn't crash.
    This requires all tests to only test one, so I've moved all tests to test dorado
    Adoni5 committed Apr 17, 2024
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  6. Move tests to test dorado rather than guppy plugin when validating

    This is due to the fact that pytest imports all files, the only time that pyguppy-client-lib and pybasecall-client-lib are imported at the same time
    In a real experiment, the plugin choice for base-caller imports the correct module and leaves the other one out of the interpreter runtime
    Adoni5 committed Apr 17, 2024
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  7. Remove dorado, guppy and _read_until_client from coverage reporting a…

    …s we can't really cover them
    
    They require things link a read_until_api or live base caller to properly test
    Adoni5 committed Apr 17, 2024
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Commits on Apr 20, 2024

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Commits on Apr 22, 2024

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  2. Clean trailing whitespace

    mattloose committed Apr 22, 2024
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Commits on Apr 24, 2024

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Commits on May 7, 2024

  1. Feature/check minknow (#351)

    * Initial validation of minknow version and guppy dorado versions
    
    * MinKNOW compatibility check function
    Base-caller compatibiity check
    
    * Compatibility checks
    
    * Remove rogue comment
    
    * edit insanely long string multiline string example of sub tags
    
    * Local updates
    
    * Error checking and minor corrections to address compatibility. We no longer raise RuntimeException when a version issue is encountered. This means that readfish will continue to function with future versions of minKNOW if compatible.
    
    * Add default when popping `sample_rate` from guppy params
    Prevents `KeyError` from being raised if `sample_rate`isn't listed as a `kwarg`
    
    * Remove unused basecaller compatibilty function
    We now just check in `dorado.py` and warn if there is a mismatch
    
    * Correct docstring, add doctests
    
    * Add more complete docstring to `DIRECTION` enum
    Only return Enum variant from `check_compatibility`, not tuple of (bool, variant)
    
    * Suggest opening an issue if a suitable version of readfish doesn't exist
    
    ---------
    
    Co-authored-by: Adoni5 <roryjmunro1@gmail.com>
    mattloose and Adoni5 authored May 7, 2024
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Commits on May 8, 2024

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Commits on May 9, 2024

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