error in PyVCF setup command: use_2to3 is invalid #334
Comments
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I hit this as well. 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
I will also file a ticket at Anaconda. |
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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. |
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I think it is urgent to fix this issue. Someone to contact the author to take over the project? |
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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. |
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So, let's fork the repository and create PyVCF2 ? |
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By the way, could you detail how you fix with use_2to3 ? |
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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. |
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Hey @ChrisMoth I am running into the exact same issue, did you end up posting the library you created using 2to3? |
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check pyvcf3 |
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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 |
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
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