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Dorado plugin #344
Dorado plugin #344
Commits on Apr 3, 2024
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Introducing a dorado specific plugin which handles the change from on…
…t_pyguppy_client_lib to ont_pybasecaller_client_lib
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Commits on Apr 17, 2024
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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
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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
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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
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Commits on Apr 20, 2024
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Commits on Apr 22, 2024
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Commits on Apr 24, 2024
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Commits on May 7, 2024
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* 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>
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Commits on May 8, 2024
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Commits on May 9, 2024
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