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norns's Issues

Update of norns to 0.1.6 on PyPI

Hi, I saw that you fixed the deprecation error of collections in norns version 0.1.6 here and on bioconda (thank you for maintaining!). Would you be able to update norns to 0.1.6 on PyPI as well? I am a frequent user of gimmemotifs and just ended up in a very specific scenario on python 3.10, where I installed gimmemotifs with pip, but pip then only fetched norns=0.1.5 on install, leading to an error on import. Would be great to still be able to install with pip.

sys is not defined

I was playing around with genomepy and accidentally wiped my config.yaml clean. This gave me the error that sys was not defined:

Traceback (most recent call last):
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/bin/genomepy", line 11, in <module>
    load_entry_point('genomepy==0.5.5', 'console_scripts', 'genomepy')()
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/pkg_resources/__init__.py", line 489, in load_entry_point
    return get_distribution(dist).load_entry_point(group, name)
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2852, in load_entry_point
    return ep.load()
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2443, in load
    return self.resolve()
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/pkg_resources/__init__.py", line 2449, in resolve
    module = __import__(self.module_name, fromlist=['__name__'], level=0)
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/genomepy/__init__.py", line 2, in <module>
    from genomepy.functions import (
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/genomepy/functions.py", line 13, in <module>
    from genomepy.plugin import get_active_plugins, init_plugins, activate
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/genomepy/plugin.py", line 7, in <module>
    config = norns.config("genomepy", default="cfg/default.yaml")
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/norns-0.1.4-py2.7.egg/norns/__init__.py", line 4, in config
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/norns-0.1.4-py2.7.egg/norns/cfg.py", line 58, in __init__
  File "/home/sande/Desktop/snakemake-workflows/workflows/alignment/.snakemake/conda/a8623ecd/lib/python3.6/site-packages/norns-0.1.4-py2.7.egg/norns/cfg.py", line 72, in load
NameError: name 'sys' is not defined

On this line:

norns/norns/cfg.py

Line 72 in 81db000

sys.stderr.write("Warning: config file is empty!\n")

It seems like simply adding import sys would solve this problem.

DeprecationWarning: pkg_resources

Hi,

A deprecated warning appear when using pyfaidx:

================== warnings summary ===================
/tools/python/current/lib/python3.10/site-packages/norns/cfg.py:9: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
    import pkg_resources

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

It seems to be this code location:
https://github.com/simonvh/norns/blob/master/norns/cfg.py#L9

As mentioned in the provided URL:

Use of pkg_resources is deprecated in favor of importlib.resources, importlib.metadata and their backports (importlib_resources, importlib_metadata). Some useful APIs are also provided by packaging (e.g. requirements and version parsing). Users should refrain from new usage of pkg_resources and should work to port to importlib-based solutions.

Python 3.10.12 | packaged by conda-forge | (main, Jun 23 2023, 22:40:32) [GCC 12.3.0] on linux
SetupTools 68.2.2

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