NameError: name 'pkg_resources' is not defined

[ChristopheH]

Hello,

I am trying to use bamnostic instead of pysam, but I meet several issues on this line using "pkg_resources".

bamnostic/bamnostic/__init__.py

Line 41 in 3d9157e

import pkg_resources

1. Install with : pip install bamnostic

>>> import bamnostic as bs
 UserWarning:C:\Users\XXX\AppData\Local\miniforge3\envs\bamnostic\Lib\site-packages\bamnostic\__init__.py:41: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html. The pkg_resources package is slated for removal as early as 2025-11-30. Refrain from using this package or pin to Setuptools<81.

2. Install with : conda create -n bamnostic bamnostic

>>> import bamnostic as bs
Traceback (most recent call last):
  File "<python-input-0>", line 1, in <module>
    import bamnostic as bs
  File "C:\Users\XXX\AppData\Local\miniforge3\envs\bamnostic\Lib\site-packages\bamnostic\__init__.py", line 42, in <module>
    example_bam = pkg_resources.resource_filename('bamnostic', 'data/') + 'example.bam'
                  ^^^^^^^^^^^^^
NameError: name 'pkg_resources' is not defined

Workaround
I did replace

import pkg_resources
example_bam = pkg_resources.resource_filename('bamnostic', 'data/') + 'example.bam'

with

import os
example_bam = os.path.join(os.path.dirname(__file__), 'data','example.bam')

Is it the proper way to solve this issue according to you ?

[betteridiot]

I see the issue you are dealing with. This is because bamnostic was built on setuptools and used pkg_resources to bring in local files into the environment. I will have to change the installation setup to correct this issue.

[Mirochill]

This appears to be fixed on current master and included in tag v1.3.0. bamnostic/__init__.py now builds example_bam from os.path.dirname(__file__) and data/example.bam, and I do not see any remaining pkg_resources usage in the repository.

If this was observed with an older package build, upgrading to a release containing v1.3.0 should avoid this import-time warning/error path.