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tests: fix broken tests due to breaking changes in dependencies#2988

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Hugovdberg wants to merge 2 commits intosnakemake:mainfrom
Hugovdberg:fix_numpy_2_in_tests
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tests: fix broken tests due to breaking changes in dependencies#2988
Hugovdberg wants to merge 2 commits intosnakemake:mainfrom
Hugovdberg:fix_numpy_2_in_tests

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@Hugovdberg
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@Hugovdberg Hugovdberg commented Jul 28, 2024

String representation of scalars changed in numpy 2 (https://numpy.org/doc/stable/release/2.0.0-notes.html#representation-of-numpy-scalars-changed), which causes tests to fail. This PR fixes the numpy version in the tests to the last pre-2.0 version for now in order for other PRs to be able to continue.
At a later stage the tests should probably be updated to work on more recent verions of numpy or contain explicit formatting.

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  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

@Hugovdberg
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Also paramiko uses TripleDES from a module that is deprecated in cryptography 43, causing the literal output of some tests to include unexpected deprecation warnings. Until that is fixed limit cryptography to < 43.

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@Hugovdberg
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This requires quite some work, apparently all kinds of dependencies have changed and I don't think just hacking the test environment to some magic combination of packages is the right way to go. @johanneskoester what do you think we should do about this?

@Hugovdberg Hugovdberg changed the title fix: restrict numpy to < 2 for current tests tests: fix broken tests due to breaking changes in dependencies Jul 28, 2024
@johanneskoester
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I have fixed the test instead. But thanks for pointing me to the issue!

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