Comments on: git, github, and bioinformatics software development http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/ Thu, 11 Mar 2010 19:45:05 +0000 http://wordpress.org/?v=2.6.2 By: gioby http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-33689 gioby Tue, 11 Nov 2008 14:34:05 +0000 http://www.bioinformaticszen.com/?p=151#comment-33689 For those who prefer subversion, there is also svnhub: - http://svnhub.com/ :) (please note the smile :) ) For those who prefer subversion, there is also svnhub:
- http://svnhub.com/ :)

(please note the smile :) )

]]> By: gioby http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-30829 gioby Thu, 16 Oct 2008 21:47:16 +0000 http://www.bioinformaticszen.com/?p=151#comment-30829 yeah, but trac is free software, and you can create your own private installation withouth having to pay for an account!! :) extreme programming is still useful for 'lonely' programmers. There are some good rules that it is at least useful to know: for example, write your test unit first, measure project velocity, don't overwork, share your scripts with others, and so on. Moreover, it is not good to make science alone. Research is for groups!! :) Anyway, thank you for the article. yeah, but trac is free software, and you can create your own private installation withouth having to pay for an account!! :)

extreme programming is still useful for ‘lonely’ programmers.
There are some good rules that it is at least useful to know: for example, write your test unit first, measure project velocity, don’t overwork, share your scripts with others, and so on.
Moreover, it is not good to make science alone. Research is for groups!! :)

Anyway, thank you for the article.

]]> By: Mike http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-30338 Mike Sun, 12 Oct 2008 16:04:27 +0000 http://www.bioinformaticszen.com/?p=151#comment-30338 @ Gioby Trac is cool, but my personal opinion is that Git+Github = Disco! As for extreme programming, I'd like to, but I think most (academic) bioinformaticians work solo, and extreme programming is most useful for group programmers. However Matt Wood has an iteresting article on Scrum. http://www.greenisgood.co.uk/pages/show/introduction_to_scrum @ Gioby
Trac is cool, but my personal opinion is that Git+Github = Disco!

As for extreme programming, I’d like to, but I think most (academic) bioinformaticians work solo, and extreme programming is most useful for group programmers. However Matt Wood has an iteresting article on Scrum.

http://www.greenisgood.co.uk/pages/show/introduction_to_scrum

]]> By: gioby http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-29970 gioby Wed, 08 Oct 2008 14:59:08 +0000 http://www.bioinformaticszen.com/?p=151#comment-29970 have a look at trac, too: http://trac.edgewall.org/ It is free software, it integrates a wiki, a subversion/CVS repository, and a lot of things more. Also, are you going to write an article on extreme programming? cheers have a look at trac, too:
http://trac.edgewall.org/

It is free software, it integrates a wiki, a subversion/CVS repository, and a lot of things more.

Also, are you going to write an article on extreme programming?
cheers

]]> By: gioby http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-25845 gioby Tue, 19 Aug 2008 09:20:08 +0000 http://www.bioinformaticszen.com/?p=151#comment-25845 I have also found this website: - http://www.assembla.com/ It seems to offer a svn/git hosting, a bug tracking system, wiki, chat, all for free in the basic version. I have also found this website:
- http://www.assembla.com/

It seems to offer a svn/git hosting, a bug tracking system, wiki, chat, all for free in the basic version.

]]> By: Mike http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-22756 Mike Thu, 17 Jul 2008 15:30:46 +0000 http://www.bioinformaticszen.com/?p=151#comment-22756 @Jan Thanks for all your hard work, I think BioRuby will really benefit from the move to GitHub. As for my use case, I'm currently writing a manuscript which looks at the cost of a protein sequence, and I've a got a load of Ruby libraries to do this. I was planning to package all of them into the appropriate format and add them to the BioRuby library. However we're still focusing on tying up the manuscript first, so it might be a few weeks before this is done. @Jan
Thanks for all your hard work, I think BioRuby will really benefit from the move to GitHub. As for my use case, I’m currently writing a manuscript which looks at the cost of a protein sequence, and I’ve a got a load of Ruby libraries to do this. I was planning to package all of them into the appropriate format and add them to the BioRuby library. However we’re still focusing on tying up the manuscript first, so it might be a few weeks before this is done.

]]> By: gioby http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-21245 gioby Tue, 01 Jul 2008 15:34:45 +0000 http://www.bioinformaticszen.com/?p=151#comment-21245 There is also gitorious: - http://gitorious.org/ It seems to be free, but you can't create private projects. There is also gitorious:
- http://gitorious.org/

It seems to be free, but you can’t create private projects.

]]> By: jan. http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-21144 jan. Mon, 30 Jun 2008 13:19:50 +0000 http://www.bioinformaticszen.com/?p=151#comment-21144 Just to update you guys: bioruby now *is* available on github: http://github.com/bioruby/bioruby. Toshiaki and Naohisa are look(ing into it at the moment and I'm expecting a phase out of CVS in the next couple of weeks. When that happens we'll send out an official notice to the mailing list as well.) So go ahead and fork/clone! @Mike: can you tell me what additions to bioruby you worked on during your own analysis? (See the "use case" in your post) Just to update you guys: bioruby now *is* available on github: http://github.com/bioruby/bioruby. Toshiaki and Naohisa are look(ing into it at the moment and I’m expecting a phase out of CVS in the next couple of weeks. When that happens we’ll send out an official notice to the mailing list as well.)
So go ahead and fork/clone!

@Mike: can you tell me what additions to bioruby you worked on during your own analysis? (See the “use case” in your post)

]]> By: Using Github, Lighthouse, and Twitter in my research | michael barton http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-18820 Using Github, Lighthouse, and Twitter in my research | michael barton Wed, 04 Jun 2008 17:03:01 +0000 http://www.bioinformaticszen.com/?p=151#comment-18820 [...] think git is great, and I now use this git instead of subversion to version my research. Github is the natural place [...] [...] think git is great, and I now use this git instead of subversion to version my research. Github is the natural place [...]

]]> By: Software Development http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-16086 Software Development Tue, 29 Apr 2008 06:25:17 +0000 http://www.bioinformaticszen.com/?p=151#comment-16086 Sing up for git, git and github is now coming up with wonderful opportunities for bioinformatics software development. Hey ! there is a free option too.......... Sing up for git, git and github is now coming up with wonderful opportunities for bioinformatics software development. Hey ! there is a free option too……….

]]> By: Around the web - April 19, 2008 : business|bytes|genes|molecules http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15648 Around the web - April 19, 2008 : business|bytes|genes|molecules Sun, 20 Apr 2008 07:21:42 +0000 http://www.bioinformaticszen.com/?p=151#comment-15648 [...] Michael Barton riffs on Git and Github (and yes I have an account) [...] [...] Michael Barton riffs on Git and Github (and yes I have an account) [...]

]]> By: Craig http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15485 Craig Thu, 17 Apr 2008 15:27:34 +0000 http://www.bioinformaticszen.com/?p=151#comment-15485 Immensely agree. I can't tell you how much this would help BioRuby. Mercurial is an excellent piece of software, no doubt, but in this case BioRuby really needs github since there's so many different directions people want to take it. Git and github could really inject some life into it. I'm "meh" on Lighthouse, but it would certainly be better than the present situation. svn isn't even worth considering at this point - too little too late. Video introductions to git: http://www.youtube.com/watch?v=4XpnKHJAok8 http://video.google.com/videoplay?docid=-3999952944619245780 Immensely agree. I can’t tell you how much this would help BioRuby.

Mercurial is an excellent piece of software, no doubt, but in this case BioRuby really needs github since there’s so many different directions people want to take it. Git and github could really inject some life into it.

I’m “meh” on Lighthouse, but it would certainly be better than the present situation. svn isn’t even worth considering at this point - too little too late.

Video introductions to git:
http://www.youtube.com/watch?v=4XpnKHJAok8
http://video.google.com/videoplay?docid=-3999952944619245780

]]> By: Mike http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15474 Mike Thu, 17 Apr 2008 13:24:52 +0000 http://www.bioinformaticszen.com/?p=151#comment-15474 Ruby on Rails has moved onto github recently, and when they did so they froze the existing repository. I think this is important for two reasons, two different repositories are difficult to maintain, and second how would a developer know which repository to update. There a ways to make git work over the top of SVN, but I think that keeping it simple is always better. I will email the BioRuby mailing list to make the suggestion. @ Charles Thanks for the discussion of forking. I'll be the first to admit I don't completely understand git's capabilities and but there are some interesting features that look like exploring in more detail. For example git rebase --interactive is <a href="http://tomayko.com/writings/the-thing-about-git" rel="nofollow">looks interesting</a> @Jan I saw your post on BioRuby participation and agree that widening participation can only benefit. In my case I want to contribute more, it's just that it is difficult for me to find the time, think the more simpler it is to contribute the better and the more likely people will contribute @Sebastian Yes, Mercurial is also worth looking at. I wrote about git after seeing that Rails and many other Ruby based projects were moving over. That's not to say that Mercurial wouldn't be worth a try too, the more options the better. Ruby on Rails has moved onto github recently, and when they did so they froze the existing repository. I think this is important for two reasons, two different repositories are difficult to maintain, and second how would a developer know which repository to update. There a ways to make git work over the top of SVN, but I think that keeping it simple is always better.

I will email the BioRuby mailing list to make the suggestion.

@ Charles
Thanks for the discussion of forking. I’ll be the first to admit I don’t completely understand git’s capabilities and but there are some interesting features that look like exploring in more detail. For example git rebase –interactive is looks interesting

@Jan
I saw your post on BioRuby participation and agree that widening participation can only benefit. In my case I want to contribute more, it’s just that it is difficult for me to find the time, think the more simpler it is to contribute the better and the more likely people will contribute

@Sebastian
Yes, Mercurial is also worth looking at. I wrote about git after seeing that Rails and many other Ruby based projects were moving over. That’s not to say that Mercurial wouldn’t be worth a try too, the more options the better.

]]> By: Sebastian http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15473 Sebastian Thu, 17 Apr 2008 12:44:48 +0000 http://www.bioinformaticszen.com/?p=151#comment-15473 You should also have a look at Mercurial (http://www.selenic.com/mercurial/wiki/). There are also a lot of comparisons between git and Mercurial out there. I found it straight forward and easy to use, even though I just use it for simple stuff. You should also have a look at Mercurial (http://www.selenic.com/mercurial/wiki/). There are also a lot of comparisons between git and Mercurial out there. I found it straight forward and easy to use, even though I just use it for simple stuff.

]]> By: jan. http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15467 jan. Thu, 17 Apr 2008 09:42:20 +0000 http://www.bioinformaticszen.com/?p=151#comment-15467 Hi Mike and Charles. During the last hackathon in Japan, we decided to - over time - move bioruby from CVS to SVN together with the move to open-bio and when Toshiaki would have some time to do that. Purely by coincidence, I mailed him not more than an hour ago about having a look at git instead of SVN. My reasons being exactly the ones pinpointed by you two here. It'd be helpful if you (both?) could start a discussing on the bioruby mailing list about that. I've posted a while back on the state of bioruby on my own blog arguing that it would gain immensely from a more active community. I believe git can make that work. Toshiaki could still maintain the "main" repository that everyone trusts and can pull from, but people can trust other developers as well who they can pull directly from. Hi Mike and Charles.

During the last hackathon in Japan, we decided to - over time - move bioruby from CVS to SVN together with the move to open-bio and when Toshiaki would have some time to do that. Purely by coincidence, I mailed him not more than an hour ago about having a look at git instead of SVN. My reasons being exactly the ones pinpointed by you two here. It’d be helpful if you (both?) could start a discussing on the bioruby mailing list about that. I’ve posted a while back on the state of bioruby on my own blog arguing that it would gain immensely from a more active community. I believe git can make that work. Toshiaki could still maintain the “main” repository that everyone trusts and can pull from, but people can trust other developers as well who they can pull directly from.

]]> By: Charles Comstock http://www.bioinformaticszen.com/2008/04/git-github-and-bioinformatics-software-development/#comment-15422 Charles Comstock Wed, 16 Apr 2008 17:01:17 +0000 http://www.bioinformaticszen.com/?p=151#comment-15422 I have been giving git a lot of thought recently concerning last minute change that could break existing functionality in order to make the code work for a specific project. If I had been using git, I could have made a topic branch, and committed each group of change seperately, then I could have cherry picked which changes should actually be pushed to the head, and leave the rest as modifications that require further work before moving them back to HEAD. I wonder if we could contact the bioruby people, and see if they would be amenable to a fork of BioRuby into github with the understanding that the release versions still go through CVS. It seems like it would open up the playing field for more patches, and then at a later date they could determine if they wanted to include them, but it would not preclude others from using those patches in the meantime. I have been giving git a lot of thought recently concerning last minute change that could break existing functionality in order to make the code work for a specific project. If I had been using git, I could have made a topic branch, and committed each group of change seperately, then I could have cherry picked which changes should actually be pushed to the head, and leave the rest as modifications that require further work before moving them back to HEAD.

I wonder if we could contact the bioruby people, and see if they would be amenable to a fork of BioRuby into github with the understanding that the release versions still go through CVS. It seems like it would open up the playing field for more patches, and then at a later date they could determine if they wanted to include them, but it would not preclude others from using those patches in the meantime.

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