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ConorFWild / pandda_2_gemmi

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Help message is out of date #30

Open ConorFWild opened 2 years ago

ConorFWild commented 2 years ago
  • -h message incorrect: doesn't contain "=" in arguments ... or maybe that is not needed anyway?

  • What does

    --structure_factors STRUCTURE_FACTORS A string which gives the structure factors to use. It should be of the form 'FWT,PHWT'.

    mean? --structure_factors='2FOFCWT,PH2FOFCWT' doesn't seem to work: I get at some point

    StructureFactors(f='2', phi='F')

<- needs fixing in message and also internally

  • The explanations to --local_processing are very opaque and technical. What should one use if sitting on a multi-core box? Maybe --local_processing=multiprocessing_spawn and --global_processing=serial? Furthermore, the default reported (local_processing=ray) is not even explained.

    Why is --local_cpus defaulting to 6 on a 32 thread machine? And why does it say memory_availability=low as a default? I would expect the default to be "run only on local machine, using all available threads" - anything finetuned towards cluster systems, DLS or other environment should require special arguments (and not defaults). Or maybe provide settings files (similar to our macros) that could hold specific collections of settings that could be loaded via a command-line flag.

<- needs clearer readme and an option internally

ConorFWild commented 2 years ago

  • How can one limit the resolution of the data analysed? The explanation given

    --high_res_upper_limit HIGH_RES_UPPER_LIMIT A float that gives the highest resolution datasets to conside for processing. --high_res_lower_limit HIGH_RES_LOWER_LIMIT A float that gives the lowest resolution datasets to consider processing

    is not very clear. How can a float define a "resolution datasets"? And: I can't see where that parameter would be used anywhere anyway ... confused ...

Also needs clarrification