Handle NumPy 1.14 API changes #2935
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There seems to be a lot of issues with the recent numpy release besides the ones fixed via this PR: These are mostly due to the new pretty printing of ndarrays. |
soupault
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As a stop gap measure one can use |
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Nah, I think that is a half measure. @scikit-image/packaging do you foresee any issues if we update the docstrings in accordance with the new standard? Is |
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@jarrodmillman What was your solution for this in NetworkX? |
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@soupault what do you mean? skimage gets tested with minimal requirements in our CI... The real solution would be to fix doctest to detect equivalences, but that seems improbable. I personally do favour printing in legacy mode until we no longer depend on NumPy <1.14. |
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@jni ah, indeed, we have one
Would it imply adding a config line to each of the mentioned docstrings? |
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FYI, here is what we did for nx: |
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@jarrodmillman 2818 is super depressing LOL. @soupault I really hope that there is an option in pytest to run specific code before each doctest. i don't know if that's true. If not then let's just give up on life. =P Because we have a lot more docstrings depending on numpy than NX does. |
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@oleksandr-pavlyk I think there are several more to address. For example, |
…ith np.issubdtype(dt, np.floating)
soupault
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This PR looks good.
There are couple of warning related to np.issubdtype (see https://travis-ci.org/scikit-image/scikit-image/jobs/329168966), but they will be addressed within #2888.
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It is not clear whether match.py#L57 needs replacing It was probably meant as An instance where turning on the deprecation warning likely caught a genuine bug. |
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Just in case you didn't find it, you can apply the legacy printing package-wide with this in your It will only apply to the pytest run because pytest imports |
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@oleksandr-pavlyk it seems that it does not pass for all Travis configurations... |
soupault
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their stale review
I'm going to finalize the solution within this PR
…_), since the former is interpreted as issubdtype(dt, np.generic) per deprecation warning, clearly unintended here
… per deperecation warning
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Two travis jobs failed with unrelated issues, and 4 passed. XCode build is pending. |
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| # List of files that pytest should ignore | ||
| # Use legacy numpy printing. This fix is made to keep doctests functional. | ||
| # For more info, see https://github.com/scikit-image/scikit-image/pull/2935 . | ||
| # TODO: remove this workaround once minimal required numpy is set to 1.14.0 |
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Please add this to TODO.txt, then we're ready to go.
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@Borda tried twice (including Travis cache removal). There seems to be some issues with the pre-release versions of the dependencies. |
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@soupault do you mean you suggest to merge anyway, despite the problems with Travis? |
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@emmanuelle yes, that's correct. |
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I do not feel happy about merging without full pas on Travis, but on the other hand, it is much better to have this mostly fix then nothing... shall we also create a new PR for the rest of required changes? |
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@Borda what remains to be done? (in a separate PR) |
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It seems there is an Shinx issue |
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How do I find out what is different between invoking the build with no set environment, and with I created /pull/2947, hoping to see if the phenomenon is specific to changes made in this commit, but errors this PR resolves muddle the picture. Suggestions? |
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@oleksandr-pavlyk With |
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Thank you @soupault . Inspecting outputs of
Here is the full list. |
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The change in Sphinx 1.7 removed support for configuration variable I was only able to find a commented out reference in |
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In Sphinx 1.7 sources, a plugin for The issue needs to be fixed there. Going to raise an issue. This PR should be merged please. The sooner the better. |
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In it goes; thanks! |
Borda
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Borda
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@oleksandr-pavlyk @stefanv @soupault
I found an issue in this correction such that any version lover that 1.10 pass throw the condition and crash for unsupported legacy parameter... rather use this
# parse the numpy versions
np_version = [int(i) for i in np.version.full_version.split('.')]
# comparing strings does not work for version lower 1.10
if np_version >= [1, 14]:
np.set_printoptions(legacy='1.13')
| # TODO: remove this workaround once minimal required numpy is set to 1.14.0 | ||
| import numpy as np | ||
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| if np.version.full_version >= '1.14.0': |
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fails for version lower than 1.10
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although I see requirements that says minimal 1.11 :) |
Yes, that was exactly my thinking. :) |
* fixed NumPy 1.14 deprecation warning * replaced remaining instances of deprecated np.issubdtype(dt, float) with np.issubdtype(dt, np.floating) * repacing issubdtype(dt, np.bool) with intended issubdtype(dt, np.bool_), since the former is interpreted as issubdtype(dt, np.generic) per deprecation warning, clearly unintended here * issubdtype(dt, 'half') replaced with issubdtype(dt, np.half) per deprecation warning * replaced issubdtype(dt, np.int) with issubdtype(dt, np.signedinteger) per deperecation warning * Attempt at replacing use of np.subtract with use of np.logical_xor for arrays of boolean type per NumPy deprecation warning * Use legacy numpy printing in pytest * fixed incorrect replacement of np.issubdtype(dt, 'half') with np.issubdtype(dt, np.half). NumPy 1.13 was interperting that as np.issubdtype(dt, np.floating) * Use view to convert arrays of type np.bool into np.uint8 when passing them to scipy.ndimage functions to work around deprecation warnings in NumPy 1.14 on arithmetic with np.bool arrays * Added reminedr on pytest doctest workaround to TODO
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A number of test errors result when testing scikit-image with just released NumPy 1.14. The following change fixes the following errors:
The fix is the same as was applied to scikit-learn.