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Fix scikit-image dependency specification #675

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merged 2 commits into from
Jul 14, 2023

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@rossbar rossbar commented Jul 13, 2023

What

There have been several deprecations and expirations of deprecations in scikit-image as of v0.18 that have affected the codebase. We caught most of these usages in vanvalenlab/deepcell-toolbox#131. Unfortunately, due to internal usage of functools.wraps, the stacklevel of some of the calls containing deprecated kwargs had changed, which prevented the DeprecationWarnings from being visible within deepcell-tf itself. This leads to all-out failures if scikit-image v0.21 is installed.

This PR fixes the situation by:

Additional context

This should fix the situation for those who are just installing deepcell. Things get more complicated if e.g. a user has installed deepcell-toolbox separately. There will likely need to be changes along the lines of `vanvalenlab/deepcell-toolbox#136 as well for better coverage of different installation orders, etc.

Why

Without the lower-bound pin, it is possible to install deepcell with a non-functional environment (i.e. if scikit-image is installed as a transitive dependency by some other package in the environment).

@rossbar rossbar added bug Something isn't working dependencies Pull requests that update a dependency file chore Maintenance labels Jul 13, 2023
@rossbar rossbar merged commit 35ee983 into vanvalenlab:master Jul 14, 2023
@rossbar rossbar deleted the fix-gh-655 branch July 14, 2023 11:40
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h_maxima() got an unexpected keyword argument 'footprint' Problems with latest scikit-image v0.20.0
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