Removing pkg_resources

[rnmitchell]

I keep running into various warnings about package deprecation for pkg_resources. This will remove pkg_resources from lusSTR and replace with importlib_resources.

[rnmitchell]

Alright there's something I'm missing here @standage. I've removed the from pkg_resources import resource_filename from all the code (and replaced with a different package) but I'm still encountering a Warning message:

  /Users/rebecca.mitchell/mambaforge/envs/lusstr/lib/python3.7/site-packages/pkg_resources/__init__.py:2871: DeprecationWarning: Deprecated call to `pkg_resources.declare_namespace('mpl_toolkits')`.
  Implementing implicit namespace packages (as specified in PEP 420) is preferred to `pkg_resources.declare_namespace`. See https://setuptools.pypa.io/en/latest/references/keywords.html#keyword-namespace-packages
    declare_namespace(pkg)

-- Docs: https://docs.pytest.org/en/stable/how-to/capture-warnings.html

What am I missing?

[standage]

I think mpl_toolkits is the key here: is this a MatPlotLib issue? Could upgrading it eliminate the warning message?

[rnmitchell]

I'll look into it. It's weird it's popping up with test_snps.py when there's no plotting with SNPs.

[standage]

I'll look into it. It's weird it's popping up with test_snps.py when there's no plotting with SNPs.

Any luck?

[rnmitchell]

It looks like updating to version 3.8.0 should work- although when I try to do this I run into errors with Python versions and macOS versions?

UnsatisfiableError: The following specifications were found
to be incompatible with the existing python installation in your environment:

Specifications:

  - matplotlib=3.8.0 -> python[version='>=3.10,<3.11.0a0|>=3.11,<3.12.0a0|>=3.9,<3.10.0a0|>=3.12,<3.13.0a0']

Your python: python=3.7

If python is on the left-most side of the chain, that's the version you've asked for.
When python appears to the right, that indicates that the thing on the left is somehow
not available for the python version you are constrained to. Note that conda will not
change your python version to a different minor version unless you explicitly specify
that.

The following specifications were found to be incompatible with your system:

  - feature:/osx-64::__osx==12.6.3=0
  - feature:|@/osx-64::__osx==12.6.3=0
  - matplotlib=3.8.0 -> matplotlib-base[version='>=3.8.0,<3.8.1.0a0'] -> __osx[version='>=10.12|>=10.9']

Your installed version is: 12.6.3

[standage]

If I'm upgrading the Python version in a Conda environment, it's almost always easier to just rebuild the environment from scratch.

[rnmitchell]

Upgrading to python 3.10 and Matplotlib 3.8 seems to get rid of this issue. I'm going to close the PR and open a new one.

[standage]

So...pkg_resources is still deprecated, and is unavailable starting in Python 3.12 (I think). So #66 is great, but I think this PR will still be necessary.

[rnmitchell]

This is probably ready for merging, no?

[standage]

This is unnecessary. The importlib.resources module is part of the Python standard library starting with version 3.7. The importlib_resources package is only required for compatibility with older versions of Python.

[rnmitchell]

I had to conda install it into my current environment with Python 3.10.

[standage]

Everywhere you have import importlib_resources you should replace with import importlib.resources, and then the function calls as well. I missed that in my review.

[rnmitchell]

ahh okay! I will fix that.

[rnmitchell]

All fixed.

[standage]

Not sure it's worth going back at this point, but if you're always using this Path object as a string, you could wrap it with str here instead of every single place you use it in the test suite.

[rnmitchell]

Here or in __init__.py?

[standage]

Oops, wrong function. I meant to comment on the data_file function in test/__init__.py.

[rnmitchell]

I think I'll leave it as is for now. Maybe in the future will change it.

[standage]

This is probably ready for merging, no?

Clicking the [Ready for review] button to remove the draft status is a great way to indicate this!

[rnmitchell]

And of course all this requires the higher Python versions....