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popgenmethods / pyrho

Fast inference of fine-scale recombination rates based on fused-LASSO
MIT License
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warning deprecation ABC.collections #7

Closed kullrich closed 4 years ago

kullrich commented 4 years ago

Dear pyrho developers, I get the following warnings when running the tests.py:

pyrho-env) [root@citrin biosoftware]# python -m pytest pyrho/tests/tests.py ================================================================================================ test session starts ================================================================================================= platform linux -- Python 3.7.5, pytest-5.3.1, py-1.8.0, pluggy-0.13.1 rootdir: /share/apps/biosoftware/pyrho collected 20 items

pyrho/tests/tests.py .................... [100%]

================================================================================================== warnings summary ================================================================================================== /share/apps/anaconda3/envs/pyrho-env/lib/python3.7/site-packages/nose/importer.py:12 /share/apps/anaconda3/envs/pyrho-env/lib/python3.7/site-packages/nose/importer.py:12: DeprecationWarning: the imp module is deprecated in favour of importlib; see the module's documentation for alternative uses from imp import find_module, load_module, acquire_lock, release_lock

/share/apps/anaconda3/envs/pyrho-env/lib/python3.7/site-packages/numba/types/containers.py:3 /share/apps/anaconda3/envs/pyrho-env/lib/python3.7/site-packages/numba/types/containers.py:3: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working from collections import Iterable

-- Docs: https://docs.pytest.org/en/latest/warnings.html ========================================================================================== 20 passed, 2 warnings in 22.74s ===========================================================================================

jeffspence commented 4 years ago

Thanks for this. Everything should run fine until python3.9, but I will incorporate some checks in the next version of pyrho to get ready for this.

jeffspence commented 4 years ago

This seems like it's actually an upstream issue with nose and numba. The dependency on nose was minimal, and everything could be replaced by pytest, so I've removed the dependency on nose entirely.

The deprecation warning in numba has been fixed in numba version 0.46.0. Upgrading numba to the latest version (pip install --upgrade numba) should clear that warning. Would you mind pulling the latest commit of pyrho (8398212766d3c6536dca0af15269a942241f7c9c), reinstalling, and then rerunning the tests?

jeffspence commented 4 years ago

Okay, I checked with python 3.7.4 and was able to replicate. The new commit gets rid of the nose warning, but the numba warning looks like it will persist until numba version 0.47.0: https://github.com/numba/numba/issues/4733

I'll keep this issue open until numba 0.47.0 gets released.

As I said before, everything else in pyrho should work fine as is.

jeffspence commented 4 years ago

Okay, numba 0.47.0 is now available on PyPI, and I've updated setup.py in cdf15aceb98e41ec8edb228f44bdac63ba4d9d7e to require it. This gets rid of the warning for me so I'll close this. Please let me know if you encounter any further issues.