Comments (16)
Please use cai2: https://pypi.org/project/cai2/
from codonadaptationindex.
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
from codonadaptationindex.
I'm definitely still interested, just super swamped. Making you an admin on the repo so we don't need to fork
from codonadaptationindex.
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 ?
from codonadaptationindex.
Resent! Here's the link if it doesn't show up: https://github.com/Benjamin-Lee/CodonAdaptationIndex/invitations
from codonadaptationindex.
PS I'm fine dropping support for Python 2. It's EOL and not needed at all.
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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.
from codonadaptationindex.
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!
from codonadaptationindex.
Are we good to PR sharp
into master
?
from codonadaptationindex.
I think so, it passes all the tests and I have successfully installed the resulting setuptools package in a fresh environment on my machine.
from codonadaptationindex.
Could you share your PyPI username? I tried to add BjornFJohansson
but no luck
from codonadaptationindex.
This is me: https://pypi.org/user/bjorn
from codonadaptationindex.
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
from codonadaptationindex.
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.
from codonadaptationindex.
@crockeraw did you solve your problem? You could install the sharp branch using pip/git.
from codonadaptationindex.
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
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Related Issues (11)
- Add a jupyter notebook to docs or tests HOT 3
- Conda package
- Some test input files would be useful for newcomers.
- More guidance on contributing / filing issues.
- Locale issues installing from pip HOT 2
- Dependabot can't evaluate your Python dependency files
- Bug report HOT 1
- Bug with sequence length HOT 1
- Documentation Request for Using RSCU param with `python_codon_tables`
- Small performance improvement
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