Today’s #OpenScience Rant: Version Control via Git will never go mainstream in Ecology.

…unless it is made more accessible to the vast majority of us.

I just spent two days trying to figure out why I couldn’t push commits from Rstudio to one of my GitHub repos. I know RStudio’s latest version doesn’t play well with GitHub when you try to link to a Repo with HTTPS, so I headed to twitter and as usual The Twitterverse came quickly to my aid:

Uh oh…I’m already scared since I’m a git amateur and working from the shell, but ok I’m willing to give it a go. And then I got this:

OK first, of all, Hadley Wickham is helping me on twitter! But once I got past that, “…if you can figure out how to open it” isn’t exactly inspiring. So after I tried and failed to fix from the shell I decided to cheat, delete the RStudio Project, and start over with a new one linked via SSH. Do some coding, save, Commit, Push, and….   No luck.   Back to twitter:

And Karthik was right.  I found this helpful post on this by Ben Best that told me what I needed to do, but I couldn’t even do the basic test drive from the shell that would tell me if it was indeed my problem. Plus I also started getting another message:

Screen Shot 2015-02-24 at 8.15.57 AM

…for which Karthik provided a detailed, above-the-call of duty explanation and solution via email.  I tried that for a while, think I correctly implemented the fix and then…no luck.  The authentication problem again (I think).

It’s been two days. It’s 1 am. Fuck it.

I deleted the R studio project, reinstalled git, and followed the great instructions on the BurnedPixel Blog to set up everything from scratch. Created a new RStudio project, linked via SSH, Pull, Edit, Commit, Push and:



My point?  I was stupid for dedicating as much time and effort to this as I did…I should have just folded and moved on – trying to figure this out cost me valuable research time, to say nothing of the fact I ignored the other million things I had on my plate. Of course, I realize that 1) had I had some formal training in Git I probably could have solved it in 10 minutes, 2) If Karthik were next door it could have been solved in 10 minutes, 3) maybe the use of a Git GUI would have helped.

All of those are true, but I would bet that most graduate students still don’t get training in this stuff, and those of us who are comfortable with programming but not in the Premier League…well, I think this kind of frustration and time loss and not distrust of getting scooped or philosophical divergence about the importance of Open Science are the reason why most people don’t commit to using version control as part of their daily routine for their programming.  It’s because the learning curve is too steep.

I was willing to stick with it for days, but most ecologists won’t, and shouldn’t — the effort is better placed elsewhere. There HAS to be a simpler way or this will never become mainstream in our field. 

Rant over.

P.S. Is there a good Git GUI out there?

Edit 10:23 am: Suggestions already rolling in.

8 thoughts on “Today’s #OpenScience Rant: Version Control via Git will never go mainstream in Ecology.

  1. Alexander Shenkin

    sourcetree for mac, sourcetree or tortoisegit for windows. i don’t bother with rstudio’s git stuff.

  2. Pingback: My first experience with GitHub for sharing data and code | Dynamic Ecology

    1. Emilio M. Bruna Post author

      Cool Post! One quick addendum to the “frustration-rant-post” of mine you linked too. That wasn’t actually my first experience with GitHub – I’d already been using it for a while to store and version-control my code (though not much beyond that). I do this mainly within RStudio, and for some reason I couldn’t push anymore, and couldn’t figure out why even with help. THAT’S what frustrated me over the edge. As soon as the advice became “got to the command line and type “complicated git statements” I think many, many users will drop out. But some will go and learn how to use Sourcetree, which is on my to-do list for the summer.

      Don’t forget to add to the list of Git Resources for n00bs!

  3. Bryce Mecum

    Thanks for taking the time to write this up! When I teach biologists how to use git I’m often left wondering whether I’ve doomed them a whole heap of frustration.

    Re: RStudio’s git interface, it will get better but for now you have to pop out to the shell to do common tasks. Hopefully that will change. If you’re on Windows I recommend SourceTree and also learning the shell commands themselves.

    1. Emilio M. Bruna Post author

      Thanks! That’s the suggestion most people have. I’m still just using it mainly for version control of my own code rather than any forking etc., so RStudio does what i need. But soon….will have to move beyond.

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