Marcus D. Hanwell's Blog

I just made a few commits using my trusty git svn dcommit (I am still really loving git and it looks like the bug I reported may be fixed in it now too). Then I saw the commit numbers - we just hit commit 1000. Development has really been accelerating recently and I haven't had time to write about as much as I wish I could.

Hopefully I will get a chance to take some screenshots and show off some of the latest stuff. I have coded a QGraphicsView based periodic table I am pretty happy with. It is compact, allows elements to be chosen, shows our colour scheme and even displays a little extra information on the selected element. Then there is the ribbon engine which is coming along but needs some loving attention from some bio people.

I am very pleased with the new quick rendering stuff we have added. It still has its issues. I had fixed some but some of Benoit's recent commits seem to have reintroduced the cache problem upon engine changes. Tim has added a new hydrogen bond engine which looks great thanks to some stipple line stuff from Geoff. There is some great stuff in the properties dialogs too along with lots of improvements to our force fields.

There is certainly lots more for us to do. The biggest thing I still haven't gotten in yet is surface support! I really want to get that sorted as I think it will be both useful and should look great. Along with some extra dialogs for graphics export, POV-Ray rendering etc.

At the start of October I began my first postdoctoral position, at the University of Pittsburgh in the Chemistry Department working in the newly formed Hutchison Group for Geoffrey Hutchison. Life has been so hectic these last few months finishing my doctorate and preparing for my biggest move ever.

Louise and I arrived on the 27th of September and had less than a week to find a suitable apartment out here ready for me to start work. I am now a legal non-resident alien (I think - someone correct me if I got it wrong). I am very excited to be starting this new job, the move has been really tough but the research looks very interesting and I am sure that my time here will be very productive.

I have already been to quite a few interesting talks in the department and am making the transition from physics to chemistry. It is OK though as I get to do lots of physics and programming along with some more chemistry. Exciting times and I am sure I will talk more about my work in future. I have already posted a tutorial article on installing Sun Grid Engine on a Mac OS X cluster.

Dax made it out here and we are both enjoying the recent snow. This entry sat in drafts for about a month or so as I have been so busy sorting things out, coding, reading and going to physio for my high ankle sprain which I am told is both unusual and the worst kind of sprain...

It seems I have read quite a few posts in the last half a year or so on the virtues on decentralised version control and how good git it. Before my laptop died I had installed git and was using it for development. Unfortunately that was pretty short lived due to the failure of my laptop. Now all of my development is taking place on Apple Mac machines using Leopard (I used Tiger for a while too).

Recently I built git from source on the laptop I am using and checked out the full Avogadro subversion repository using the following commands.

git svn init -t tags -b branches -T trunk https://avogadro.svn.sourceforge.net/svnroot/avogadro
git svn fetch

Then I went and grabbed a coffee while it imported over 800 commits which is pretty small compared to many of the other repositories I have heard about being imported. It didn't take too long, but I would happily make my git repository available should anyone want a copy.

I have found git to be very fast which is absolutely great. There are some things which I have found a little confusing while getting to grips with git and its interaction with the subversion repository.

For my day to day work I need very few commands. git svn rebase synchronises with the subversion repository. I really like this way of updating too as it displays the diffs for the commits and the log messages. git commit -a commits all local changes to the local repository. git status shows the current status of the repository, git show shows local changes already committed and git svn dcommit pushes my local changes to the subversion repository.

It is this last feature I think I like the most. I can queue up multiple change sets which might actually break Avogadro, giving nice bite size commits as I make progress, but only committing them once I am done and everything is working (at least reasonably well). Then there is the potential for doing this when off line which is also great.

One of the most confusing things I found was how to nuke local changes if I didn't want to keep them. Deleting the file and updating doesn't work as it does with subversion. Also revert didn't do what I was after. I finally found git checkout which was not what I was expecting. Issuing the command with no arguments resets the repository to the last committed state. Adding filenames as arguments reverts just those files.

Another one I haven't found the answer to is files reappearing that we long since deleted. The avogadro.pro file is the main one left but a set of directories also reappeared. They are not there when checking out using just subversion. If anyone has the answer I would love to know. If I git rm the file the commit to subversion does nothing and it loops round.

Other than that I am really happy with git. It can be a little too easy to use the wrong commands and wipe out changes so I am moving quite gingerly at times but I think it is well worth the trade off. A few guides such as this one, this one and of course this have helped me along the way.

UPDATE: Just to note that I was using the git 1.5.3 release compiled from source.