Argparse defaults #37
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Co-authored-by: M Bernt <[email protected]>
Co-authored-by: M Bernt <[email protected]>
needed because of the specifics of the Galaxy tool generator
needed because of the specifics of the Galaxy tool generator
Co-authored-by: M Bernt <[email protected]>
Co-authored-by: M Bernt <[email protected]>
- unified handling of --configFile - specify default values only in the parsing, nowhere else (but only for "train" and "predict", for the other modes, this still needs to be done) - put modes into separate files (train, predict, trainggn, predictgnn, interpretgnn, convert) - parse JSON configs just like CLI args (this will give the user feedback concerning syntax errors etc in the JSON, just like with CLI args) - removed jsonpickle dependency - removed py/object from JSON configs (not needed anymore) - removed aeOptimizer argument (wasn't being used) - added parsing for --fnnType - split train/predict Options into three classes (common, train, predict) - added todo's regarding some confusing parts
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This primarily fixes the order in which values/defaults are loaded.
--configFiletrainandpredict, for the other modes, this still needs to be done)train,predict,trainggn,predictgnn,interpretgnn,convert)jsonpickledependencypy/objectfrom JSON configs (not needed anymore)aeOptimizerargument (wasn't being used)--fnnTypeI first focussed on getting
trainandpredictrunning, the other modes (trainggn,predictgnn,interpretgnn,convert) still need some work.Also, the tests (
run_*.py) need some work.I will make further commits onto this branch until this PR is ready to be merged.