mhcnuggets
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KarchinLab
Feature request: add continuous integration
Dear MHCnuggets maintainer,
MHCnuggets appears awesome to me!
But without any form of continuous integration, one cannot verify if indeed everything (still) works. Also, a CI install script shows all steps needed to install and run any repo, which I find always helpful.
I would enjoy any form of continuous integration added and a juicy build badge to show everything works.
I volunteer to do so.
Hi Richel,
Thank you for your question. I see a couple potential solutions here.
- It seems like your python is not recognizing your mhcnuggets's installation, that's why it is errorring out on the first step. You should probably check whether your "./bashrc" file has point your export paths to the right libraries or how your python environments are set up. For example, if you are calling one python2 environment, but mhcnuggets is installed under your python3 environment, you won't be able to call that package. You could find out more with this link here: https://stackoverflow.com/questions/53952214/how-can-i-find-out-which-python-virtual-environment-i-am-using.
- We built MHCnuggets mostly on python2 instead of python3. Although we built it to be indifferent to python versions, it could be one aspect of your problem (probably not the main issue here).
Hope my answer helps you.
Melody
Sounds great. Let us know what you need to get started.
On Monday, May 25, 2020, Richel Bilderbeek [email protected] wrote:
Dear MHCnuggets maintainer,
MHCnuggets appears awesome to me!
But without any form of continuous integration, one cannot verify if indeed everything (still) works. Also, a CI install script shows all steps needed to install and run any repo, which I find always helpful.
I would enjoy any form of continuous integration added and a juicy build badge to show everything works.
I volunteer to do so.
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-- Rachel Karchin, Ph.D. Professor of Biomedical Engineering, Oncology and Computer Science The William R. Brody Faculty Scholar Institute for Computational Medicine Johns Hopkins University 217A Hackerman Hall. 3400 N. Charles St. Baltimore, MD 21218
Hi @XiaoshanShao: thanks for your suggestions, let's see if I can fix it now :+1:
@RachelKarchin: thanks for allowing me to make MHCnuggets even more awesome! I need nothing to get started, but I will ask to activate Travis CI (free, can login with GitHub account) when I am done. Maybe today, probably tomorrow...
Created a Pull Request (#13). It's a beginning, as there are no tests yet, which I suggest to be added in the future (#14)
@RachelKarchin I previously added continuous integration (Travis CI) to some of my repositories (e.g., https://github.com/KarchinLab/probabilistic2020). So I believe once it is setup for mhcnuggets, then we just need to toggle it on the Travis CI website.
@ctokheim what you did there looks great! I guess that can just be copied :slightly_smiling_face:
I submitted a stub Pull Request already that allows one to see if Travis CI is activated (#13). From that moment on, or earlier, I hope Collin works his magic :+1:
@ctokheim Thanks for activating Travis CI!
I will try to copy the .travis.yml from another one of your examples to the richel branch. If it takes me too long (say, 60 minutes), could I ask you for help?
I know in some of my projects, those things only take minutes if you are into them :+1: