How to contribute documentation to COBRApy?

[natJimenez]

I don't know if this should be posted here since I already solved my issue, but I think it could be added to the documentation to prevent other people having the same problem.

I tried to install cobrapy using pip directly into my computer (macOS Sierra) without virtualenv and I found that since the OS X capitan upgrade there have been some issues using pip (For more details see How to use pip after the OS X El Capitan upgrade?)

I manage to install cobrapy only for my user which is not a problem since I'm the only user on this computer, using pip install --user cobra

Also I wanted to ask if there is a more direct way to contribute to your documentation?

Thanks!

[Midnighter]

Also I wanted to ask if there is a more direct way to contribute to your documentation?

Any and all contributions to the documentation are very welcome! It depends a little if you want to change the general documentation or function documentation since the latter is auto-generated. So the way forward is to follow the first part of the contributing instructions on forking the repository. Then change the specific .rst file in documentation_builder or modify the function docstrings directly. When you're satisfied you issue a pull request to cobrapy's devel branch.

Let me know about your questions here and we'll be happy to help.

[pstjohn]

To your specific problem, I'd discourage you from doing too much development using the system python that ships with your mac. (this page has more details on why)

homebrew and anaconda (or miniconda) would probably give you fewer problems in the future 😄

[cdiener]

I agree that the install instructions are not easy to find. For instance right now they are inside https://github.com/opencobra/cobrapy/blob/devel/INSTALL.rst which for some reason is not part of the docs. A troubleshooting guide might be a good idea as well since we receive a lot of install problem questions on the mailing list as well...

[Midnighter]

Good idea. Additionally, we want to focus cobrapy development in the next sprint which hopefully means we can release cobrapy without the old solvers and thus end up with a vastly simplified installation, i.e., pure Python.

[natJimenez]

To your specific problem, I'd discourage you from doing too much development using the system python that ships with your mac.

I usually don't do it but I needed to quickly install cobrapy to work while being completely disconnected from the outside world. I knew I was not suppose to do so but I didn't know why, so thanks for the link.

A troubleshooting guide might be a good idea as well since we receive a lot of install problem questions on the mailing list as well...

Maybe we should add that to the install.rst in github? How is that connected to the "official documentation"?

[cdiener]

Maybe we should add that to the install.rst in github? How is that connected to the "official documentation"?

Yes definitely. I think is should be moved there.