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allow multiple npz key names #90

Merged
merged 2 commits into from Jun 6, 2020
Merged

allow multiple npz key names #90

merged 2 commits into from Jun 6, 2020

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ngreenwald
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Some of the old NPZ files were generated with (raw, annotated) keys. The newer NPZs have been standardized to to (X, y). This PR modifies the toolbox to accept either input so that manual renaming isn't necessary

geneva-miller
geneva-miller reviewed May 28, 2020
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Is this the only util function that may need to load data? Is X ever loaded? This looks good to me, I just want to make sure we're not missing other cases where the array name matters.

@ngreenwald
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Yes, currently this is the only function that loads NPZ files, and currently we don't load the X data from the corrected NPZs, only the y.

@ngreenwald ngreenwald requested a review from willgraf June 4, 2020 17:48
willgraf
willgraf requested changes Jun 4, 2020
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caliban_toolbox/utils/io_utils.py Outdated Show resolved Hide resolved
@ngreenwald ngreenwald requested a review from willgraf June 4, 2020 20:01
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Any idea why coveralls keeps seeing random fluctuations in coverage for the data_loader?

@MekWarrior
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The tests for the data_loader chooses randomly from a list of possible data types/specs (e.g. "all", "None", "HEK293", etc" at multiple levels of the ontology). It's likely that this is the source of the stochasticity - something that could be addressed with better tests.

willgraf
willgraf approved these changes Jun 5, 2020
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👍

@MekWarrior MekWarrior merged commit 9aae72a into master Jun 6, 2020
@MekWarrior MekWarrior deleted the npz_key_name branch June 6, 2020 06:02
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@willgraf willgraf willgraf approved these changes

@geneva-miller geneva-miller geneva-miller approved these changes

@MekWarrior MekWarrior Awaiting requested review from MekWarrior

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4 participants
@ngreenwald @MekWarrior @willgraf @geneva-miller