cenotetaker3 Unable to Locate Installed pyrodigal-gv Package

[F4NG666]

Hi,

I hope this message finds you well.
Although I have correctly installed the pyrodigal-gv package and verified that it is importable within my Python environment, cenotetaker3 still reports that it cannot find pyrodigal-gv.

When running cenotetaker3, I receive the following error message:

(ct3_env) t120554@starvk10-server:~$ /home/data/t120554/miniconda3/envs/ct3_env/bin/cenotetaker3 -c database1/EGVC_100_39910_1000.fa -r test_ct3 -p T
this script dir: /home/data/t120554/miniconda3/envs/ct3_env/lib/python3.12/site-packages/cenote
FASTA checked.
pyrodigal-gv not found in installed python packages. Exiting.

I have confirmed that the pyrodigal-gv package is installed in the environment at /home/data/t120554/miniconda3/envs/ct3_env/lib/python3.12/site-packages and can be successfully imported in Python.

i have attempted the following steps to resolve the issue, but the problem persists:
Verified that the PYTHONPATH environment variable is set correctly.
Reinstalled cenotetaker3 and pyrodigal-gv.

I appreciate your assistance and thank you for your time.

Best regards,
Fang

[mtisza1]

Hmmm. Interesting. This hasn't been a problem for others.

The way I check whether the required pacakges are installed uses pip freeze:

https://github.com/mtisza1/Cenote-Taker3/blob/main/src/cenote/cenotetaker3.py#L395

I seem to have gotten this code from here:

https://pip.pypa.io/en/stable/user_guide/#using-pip-from-your-program

Can you see if an package info is returned when you run this command while the ct3_env is activated:

python3 -m pip freeze | grep "pyrodigal-gv"

There are other ways to check for dependencies, apparently. So, I could change the code if this is a problem for users

[ZihengWu]

Hello, Mike and Fang.

Thank you, Mike, for developing such a useful software—it’s truly amazing! I encountered the same issue, but I was able to resolve it and successfully run Cenote-Taker3 by following these steps:

1. pip uninstall pyrodigal-gv
2. pip install pyrodigal-gv==0.3.1

I hope this is helpful to you.

Best regards,
Ziheng Wu

[mtisza1]

Wow, Ziheng, thank you for this solution!

I'll evaluate if there are some versions of pyrodigal-gv that show up as a slightly different package name. I'll see if there is a more flexible coding solution in the next update of Cenote-Taker 3

I'll leave this issue open for visibility.

Mike