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independent km caches for distinct cases; clear the Aesara cache if it's large #1127

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merged 5 commits into from
Jul 27, 2021

Commits on Jul 22, 2021

  1. independent km caches for distinct cases

    Put a checksum into the `KmcountsCached` cache filename so different cases get independent cache files, e.g. when switching git branches, Parca options during parameter optimization, or mono/polycistronic operons.
    
    This renames the cache file from `fixtures/endo_km/km3.cPickle` to `parca-km-1918837868.cPickle`, for instance.
    
    Q. Does anyone prefer the "fixtures" directory name?
    
    The cache files `cache/parca-km-*.cPickle` will accumulate until `make clean`.
    
    Does this succeed in distinguishing current cases?
    
    We could make this more sensitive by checksumming more inputs or less picky by rounding `Kmcounts.astype(np.float16)`.
    
    See #1123
    1fish2 committed Jul 22, 2021
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  2. Fix #1120: clear the Aesara cache if it's large

    This `make clean` will clear the current Aesara cache if it's larger than a threshold. 30MB seems fair the cache is 11MB locally and 350 MB in `~tahorst` on Sherlock.
    
    Aesara's cache management is not straightforward, partly to handle multiple processes and NFS.
    1fish2 committed Jul 22, 2021
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Commits on Jul 25, 2021

  1. checksum Kmcounts, isEndoRnase, alpha

    1/2 of code review feedback: add isEndoRnase and alpha to the cache checksum calculation to account for all the loss function's inputs.
    1fish2 committed Jul 25, 2021
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Commits on Jul 27, 2021

  1. Fix #996

    This should fix #996 by putting more cross-checks in the Km counts cache, but I don't have a test case for that.
    
    Ideally we'd factor out this part of the very long `setKmCooperativeEndoRNonLinearRNAdecay()` function and add test cases for it.
    
    Q. Should `arrays_differ()` set the absolute and/or relative tolerances?
    
    Adding to the cache file grew it from 37K to 110K. That should be fine but
    1fish2 committed Jul 27, 2021
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  2. fix a refactoring step typo

    ... which affects the cache file content so it's esp. good to fix before merging into master.
    1fish2 committed Jul 27, 2021
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