Hi,
Thanks for your work on what seems to be an amazing tool! I can't wait to try it out once I figure out some small dependencies issues for which I could use some help.
I'm walking through the documentation that you provided ( https://hribo.readthedocs.io/en/latest/source/overview.html#tools ), and I am having some issues related to python dependencies.
It seemed that HRIBO relies on DeepRibo (both for DataParser.py and for DeepRibo.py), which I've cloned via git (from https://github.com/Biobix/DeepRibo ).
The issue that I'm having is that it seems DeepRibo relies on some deprecated type aliases (in particular np.int) from numpy. I've searched and these aliases seem to have been deprecated from numpy 1.20.
I breifly thought about updating these (for instance replacing np.int
by np
), but I was scared of going through the rabbit hole of having to fix more and more things on DeepRibo.
So I thought I'd use numpy in version 1.19.5, but then my python (which is setup from the environment.yaml provided) wasn't compatible with it. I tried to force (in the environment.yml) python to an older version (like 3.7) but I got even more dependencies issues during the execution of the command conda create --file HRIBO/environment.yaml
By the way, it seems the webpage https://hribo.readthedocs.io/en/latest/source/overview.html#tools recommends using python 3.7, but the environment.yaml provided explicitly requests python=3.11.0=he550d4f_1_cpython
Can I please ask which one are you using personally?
I'm wondering if you are still having a runnable version of HRIBO, if you could please export and publish an updated version of your working environment. That would be a great help to avoid the dependency issues.
Just a final question/remark about "conda create" versus "conda env create": the same webpage also recommends to use:
conda create --file HRIBO/environment.yaml
But that fails with the error: conda create: error: one of the arguments -n/--name -p/--prefix is required
So of course I've tried:
conda create --file HRIBO/environment.yaml -n hribo_env
But that fails with the error: CondaValueError: could not parse 'name: hribo_env' in: HRIBO/environment.yaml
I've searched a bit, and it seems (according to conda/conda#6827 but which is a fairly old thread) that "environment.yml doesn't work with conda install --file. You need to use conda env commands with environment.yml."
Therefore in everything I have attempted I have used:
conda env create --file HRIBO/environment.yaml
Is that what you would recommend to do as well?
Any help would be very much appreciated!
Kind regards.