jamescasbon
error in PyVCF setup command: use_2to3 is invalid
when i run command as : $ pip3 install PyVCF==0.6.8 Collecting PyVCF==0.6.8 Using cached PyVCF-0.6.8.tar.gz (34 kB) Preparing metadata (setup.py) ... error ERROR: Command errored out with exit status 1: command: /data/b01/user/chenming/prog/installed/python3.6/bin/python3.6 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-a038wp5_/pyvcf_e119330b1d0c4c109a16e1b494de7db1/setup.py'"'"'; file='"'"'/tmp/pip-install-a038wp5_/pyvcf_e119330b1d0c4c109a16e1b494de7db1/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(file) if os.path.exists(file) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, file, '"'"'exec'"'"'))' egg_info --egg-base /tmp/pip-pip-egg-info-0mlgtl_c cwd: /tmp/pip-install-a038wp5_/pyvcf_e119330b1d0c4c109a16e1b494de7db1/ Complete output (1 lines): error in PyVCF setup command: use_2to3 is invalid.
WARNING: Discarding https://files.pythonhosted.org/packages/20/b6/36bfb1760f6983788d916096193fc14c83cce512c7787c93380e09458c09/PyVCF-0.6.8.tar.gz#sha256=e9d872513d179d229ab61da47a33f42726e9613784d1cb2bac3f8e2642f6f9d9 (from https://pypi.org/simple/pyvcf/). Command errored out with exit status 1: python setup.py egg_info Check the logs for full command output. ERROR: Could not find a version that satisfies the requirement PyVCF==0.6.8 (from versions: 0.6.8.linux-x86_64, 0.0.0, 0.1, 0.2, 0.2.1, 0.3.0, 0.4.0, 0.4.1, 0.4.2, 0.4.3, 0.4.4, 0.4.5, 0.4.6, 0.5.0, 0.6.0, 0.6.1, 0.6.2, 0.6.3, 0.6.4, 0.6.5, 0.6.6, 0.6.7, 0.6.8) ERROR: No matching distribution found for PyVCF==0.6.8
I hit this as well. I just installed the (new) November 2021 Anaconda release on linux-64bit (CentOS 7) and hit this issue as well when I attempted $ pip install PyVCF
I can't imagine why PyVCF is support Python2 in 2021. I would recommend dropping that, if that is the issue.
Setuptools, understandably since Version 58.0.0, has dropped support for 2to3 (if I am reading my google correctly)
On latest Anaconda distro, we are at 58.0.4
$ python Python 3.9.7 (default, Sep 16 2021, 13:09:58) [GCC 7.5.0] :: Anaconda, Inc. on linux Type "help", "copyright", "credits" or "license" for more information.
import setuptools setuptools.version '58.0.4'
I will also file a ticket at Anaconda.
It seems fairly trivial to manually run 2to3 inside the new Anaconda environment and update the PyCVF *.py files... in a hard-coded directory. But yes, it would be preferable to have PyVCF maintained as a Python3 library, and integrated into the "pip" approach.
I think it is urgent to fix this issue. Someone to contact the author to take over the project?
Many have tried to contact the author, apparently. I had no problems just adding the few source files to my own development work, after running 2to3 and adjusting a few lines of code. I don't have time to "maintain a new repo" - but it should be a trivial task for someone with a little bit of bandwidth.
It is a command line tool that takes python2 source files as input, and returns python3 files.... that are mostly ready for python3.
https://stackoverflow.com/questions/20458011/how-to-use-2to3-properly-for-python
At this moment, my web server is down, but please remind me on Monday, and I'll post the library that I created using 2to3 as a downloaded .tar file. I don't have time to be responsible for all the python platform integrations around the planet, but the conversion process to get everything working again was very little work.
Hey @ChrisMoth I am running into the exact same issue, did you end up posting the library you created using 2to3?
For me, I only needed this much of the library - here is what I am using now under Python 3.9 - latest Anaconda release
https://github.com/CapraLab/pdbmap/tree/master/vcf [https://opengraph.githubassets.com/c8bd1dfe09781d6b672067c7175c2ccab4fe27d95330a8f466b5e70f906214f3/CapraLab/pdbmap]https://github.com/CapraLab/pdbmap/tree/master/vcf pdbmap/vcf at master · CapraLab/pdbmaphttps://github.com/CapraLab/pdbmap/tree/master/vcf Contribute to CapraLab/pdbmap development by creating an account on GitHub. github.com I believe this "pdbmap" library is public, and you can grab the needed vcf directory and 5 or so .py files easily.
From: esavage111 @.> Sent: Friday, February 11, 2022 10:44 AM To: jamescasbon/PyVCF @.> Cc: Moth, Christopher W @.>; Mention @.> Subject: Re: [jamescasbon/PyVCF] error in PyVCF setup command: use_2to3 is invalid (Issue #334)
Hey @ChrisMothhttps://nam04.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2FChrisMoth&data=04%7C01%7Cchris.moth%40vanderbilt.edu%7C0d99b2319f834fb7ccb308d9ed7dc3d6%7Cba5a7f39e3be4ab3b45067fa80faecad%7C0%7C0%7C637801946691924256%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=CZ%2By%2F%2FttZ1zbMVDhbirsXRfE7j0xC3W7Sj%2FamXPIGC8%3D&reserved=0 I am running into the exact same issue, did you end up posting the library you created using 2to3?
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In case someone else really needs to use PyVCF from here, you can get the install to work on Python 3.10 with the following:
pip install pip==23 setuptools==57
pip install pyvcf
