[Biopython-dev] "Developing on Github" wiki amendment

Eric Talevich eric.talevich at gmail.com
Fri Jul 1 15:47:09 UTC 2011

On Fri, Jul 1, 2011 at 6:37 AM, Brandon Invergo <b.invergo at gmail.com> wrote:

> Hi everyone,
> Based on my own experiences working with Github, I suggest a minor addition
> to the wiki tutorial on using it. I'm working behind an HTTP proxy at my
> university, which doesn't pose big problems with cloning or pushing, which
> use the git http_proxy setting without problem. However, git-pull for
> whatever reason doesn't seem to use that setting but instead relies on the
> GitProxy setting. I haven't been able to get this to play nicely, so I had
> trouble pulling upstream changes to my repository for a while. In the end,
> the easiest solution was to just change my upstream master to
> https://github.com/biopython/**biopython.git<https://github.com/biopython/biopython.git>rather than git:// so that the git https_proxy is used.
> The only problem is that I couldn't find a git command to change the
> upstream master (didn't search very deeply, admittedly), so I did it by
> manually editing the .git/config file in my repository. Does anyone know if
> there is one?

I think the "git remote" command can do what you need, but editing
.git/config is fine too. The config file is meant to be useful to

So, if it's ok with everyone, I would write a small addition of a sentence
> or two offering this as a work-around for people having problems pulling
> upstream changes from behind a proxy.

You mean the http://biopython.org/wiki/GitUsage ? Sure, go right ahead, it's
a wiki :)

> Before I do so, perhaps it would be prudent to ask if there are any
> problems about using https:// rather than git:// for pulling.
If you're a committer, then the public https:// option won't let you push
changes back upstream (from the command line); the repo is read-only. For
pulling, it should be perfectly fine.


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