pip install not working

[BjornFJohansson]

I think it is the 2to3 option in setup.py.
Is 2to3 still needed?

Collecting CAI Using cached CAI-1.0.3.tar.gz (6.0 kB) ERROR: Command errored out with exit status 1: command: /home/bjorn/anaconda3/envs/new39/bin/python3.9 -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-y9phjkp9/cai_8c869096cf864cb8934fa27a731d3393/setup.py'"'"'; __file__='"'"'/tmp/pip-install-y9phjkp9/cai_8c869096cf864cb8934fa27a731d3393/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-52f8wm2g cwd: /tmp/pip-install-y9phjkp9/cai_8c869096cf864cb8934fa27a731d3393/ Complete output (1 lines): error in CAI setup command: use_2to3 is invalid.

[BjornFJohansson]

Hi @Benjamin-Lee

Are you interested in maintaining CAI in the future? If not, I can make a friendly fork and update so that
it remains useable.

cheers,
Björn

[Benjamin-Lee]

I'm definitely still interested, just super swamped. Making you an admin on the repo so we don't need to fork

[BjornFJohansson]

I'm definitely still interested, just super swamped. Making you an admin on the repo so we don't need to fork

Hi, missed the invite, could you resend it ?

[Benjamin-Lee]

Resent! Here's the link if it doesn't show up: https://github.com/Benjamin-Lee/CodonAdaptationIndex/invitations

[Benjamin-Lee]

PS I'm fine dropping support for Python 2. It's EOL and not needed at all.

[BjornFJohansson]

Hi, I added a new branch called sharp with some changes:

• versioning with setuptools_scm
• an additional test based on the Sharp 1987 paper
• GH workflow for testing
• GH workflow for building a setuptools package (https://test.pypi.org/project/CAI/)
• GH workflow and conda package
• changed to a src layout to facilitate testing of installed files
• restricted python to >=3.7 (same as biopython)

If you make me co-owner of the pypi repo, I can point the setuptools upload there instead of
testpypi. With this setup, making a new github release will automatically trigger builds.

[Benjamin-Lee]

Awesome, let me work on that now

Scratch that. Since I got a new phone, my 2FA codes never transferred. I'll have to recharge the old phone to sign in but will get on it. Sorry!

[Benjamin-Lee]

Are we good to PR sharp into master?

[BjornFJohansson]

I think so, it passes all the tests and I have successfully installed the resulting setuptools package in a fresh environment on my machine.

[Benjamin-Lee]

Could you share your PyPI username? I tried to add BjornFJohansson but no luck

[BjornFJohansson]

This is me: https://pypi.org/user/bjorn

[crockeraw]

For me, pip install is still not working for this repo, even though it looks like there was a merge intended to fix this. I was able to install BjornFJohansson's branch "sharp", however. I did not dig any deeper into the issue, but used the following to install CAI:
pip install git+https://github.com/BjornFJohansson/CodonAdaptationIndex.git

[BjornFJohansson]

For me, pip install is still not working for this repo, even though it looks like there was a merge intended to fix this. I was able to install BjornFJohansson's branch "sharp", however. I did not dig any deeper into the issue, but used the following to install CAI: pip install git+https://github.com/BjornFJohansson/CodonAdaptationIndex.git

Hi, I think 2to3 is the culprit here. I simply removed it in the sharp branch.
I could try to make a new release, but right now I am pressed for time.

[BjornFJohansson]

@crockeraw did you solve your problem? You could install the sharp branch using pip/git.

[SouradiptoC]

Hi @BjornFJohansson, I had been building a python package for analyzing codon usage. While building with readthedocs I get the following error

Collecting CAI~=1.0.3
Downloading CAI-1.0.3.tar.gz (6.0 kB)
Preparing metadata (setup.py): started
Preparing metadata (setup.py): finished with status 'error'
error: subprocess-exited-with-error

× python setup.py egg_info did not run successfully.
│ exit code: 1
╰─> [1 lines of output]
error in CAI setup command: use_2to3 is invalid.
[end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.
error: metadata-generation-failed

× Encountered error while generating package metadata.
╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.
hint: See above for details.

Please look into it

[BjornFJohansson]

@SouradiptoC

Please use cai2: https://pypi.org/project/cai2/

[YouCook21]

@BjornFJohansson would it be possible to distribute cai2 as a conda package and further install as conda install cai2 ?