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PoonLab / OpenRDP

An open-source re-implementation of the RDP4 recombination detection program
GNU General Public License v3.0
45 stars 9 forks source link

DeprecationWarning with simple run #79

Closed ArtPoon closed 3 weeks ago

ArtPoon commented 3 months ago 
(venv) art@Wernstrom OpenRDP % openrdp tests/short.fasta
/Users/art/venv/bin/openrdp:4: DeprecationWarning: pkg_resources is deprecated as an API. See https://setuptools.pypa.io/en/latest/pkg_resources.html
  __import__('pkg_resources').run_script('OpenRDP==0.1.0', 'openrdp')
Loading configuration from /Users/art/venv/lib/python3.11/site-packages/OpenRDP-0.1.0-py3.11.egg/openrdp/default.ini
Starting 3Seq Analysis

This system is using macOS 14.3.1 and Python 3.11.5 with commit faae2dcfb2893bf85605c21fe35d42627758e8a2

GopiGugan commented 2 months ago

Additional DeprecationWarnings when running python3 setup install:

/usr/local/lib/python3.11/site-packages/setuptools/command/install.py:34: SetuptoolsDeprecationWarning: setup.py install is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/setuptools/command/easy_install.py:144: EasyInstallDeprecationWarning: easy_install command is deprecated. Use build and pip and other standards-based tools.
  warnings.warn(
/usr/local/lib/python3.11/site-packages/pkg_resources/__init__.py:123: PkgResourcesDeprecationWarning:  is an invalid version and will not be supported in a future release

Following documentation, I was able to get around these warnings by installing using python3 -m pip install .

ArtPoon commented 1 month ago

We need to update installation instructions

ArtPoon commented 3 weeks ago

Close on merging PR