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[BUG] unit-tests started failing on github #1959

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bmccandless opened this issue Oct 31, 2020 · 1 comment
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[BUG] unit-tests started failing on github #1959

bmccandless opened this issue Oct 31, 2020 · 1 comment
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@bmccandless
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Describe the bug

Several tests started failing yesterday.

To Reproduce

This can be reproduced by cloning cellxgene in a new virtual environment, building and running.

Additional context

There a few possible issues. semver and numpy recently upgraded.
and pip may have just changed how it resolves dependency conflict.

So far I'm able to work through the issues with minor code changes.
@bmccandless bmccandless self-assigned this Oct 31, 2020
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Another issue is h5py which just had a major version change yesterday to 3.0.0.
This one got us:

Variable-length UTF-8 strings in datasets are now read as bytes objects instead of str by default, for consistency with other kinds of strings. See Strings in HDF5 for more details.

https://docs.h5py.org/en/latest/whatsnew/3.0.html

bmccandless pushed a commit that referenced this issue Oct 31, 2020
Updates due dependency version changes.
e1f9f62 
h5py recently changes and now values once returned as str are now returned as bytes.
This would have caused a much larger change, so instead the version is restricted to <3.0.0.

This caused the bulk of the testing failues.
A few other changes were needed to make a few other tests pass.

 #1959
@bmccandless bmccandless mentioned this issue Oct 31, 2020
Merged
bmccandless pushed a commit that referenced this issue Nov 1, 2020
Updates due dependency version changes. (#1960)
b9e132a 
* Updates due dependency version changes.

h5py recently changes and now values once returned as str are now returned as bytes.
This would have caused a much larger change, so instead the version is restricted to <3.0.0.

This caused the bulk of the testing failues.
A few other changes were needed to make a few other tests pass.

 #1959
seve added a commit that referenced this issue Nov 5, 2020
@seve
Updates due dependency version changes. (#1960)
f68de84 
* Updates due dependency version changes.

h5py recently changes and now values once returned as str are now returned as bytes.
This would have caused a much larger change, so instead the version is restricted to <3.0.0.

This caused the bulk of the testing failues.
A few other changes were needed to make a few other tests pass.

 #1959
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@maniarathi @bmccandless