For example, Dmitry made this commit in his branch, having the URL https://github.com/dmak/cdk/commit/9b0478d50c7b5ca10f77fb01d89329db5fe80625. The patch for this commit can then be downloaded at this URL https://github.com/dmak/cdk/commit/9b0478d50c7b5ca10f77fb01d89329db5fe80625.patch.

Click on the images to get a higher resolution version.

Step 1: find the class you want to review

Use the GitHub web interface to browse your way towards the source code of the class you want to review. For example, the SmartsMatchingHelper.java:

Step 2: identify something you like to comment on

Next step is to perform some code reviewing. For example, we might want to ask something about how parseProperty() works:

Now, this page on GitHub does not provide the means to leave comments; instead, you comment on commits.

Step 3: find the last commit that touched the line you like to comment on

Git has a blame option (also called annotate) which will show you for each line who last changed that line. The GitHub web page makes this functionality available with the ‘blame’ link just above the first line of the source code:

This link will lead us to a page with a new column on the left side showing commit hashes, name of the commit author, and the first few characters of the commit message. For example, the web page bits relevant to code we want to comment on, looks like:

This shows us that commit 3ce78ba5 is the one we are interested in:

Step 4: Look up the line again and add a comment

In the web page with the appropriate commit looked in the previous step, you scroll down to the line you want to comment on. If you hover over that line, a blue comment bubble will show up on the left side:

Clicking that blue comment icon, you get a dialog where you can enter your comment:

The ‘Add Line Note’ button confirms and saves your comment:

Step 5: inform the commiter about your review

The next step would be to inform the commit author. GitHub actually helps here, and should send a message, like this one:

But it would certainly not hurt of you filed a bug report or sent an email.

Now, I should only convert this into a screencast…

BTW, this screenshot is for a paper I am writing about the use of blogs and source code repositories in chem- and bioinformatics education.

I was wondering how I could bring my fork synchronized with Ola’s version again, and found the answer in this guide on GitHub. It turns out all I have to do is, though this is locally:

$ git remote add olas git://github.com/olas/bioclipse.qsar.git
$ git pull olas master

This gets me into the following state:

This gitk output show that my local master branch is identical to Ola’s master branch on GitHub, while both are three commits ahead of my current master branch at GitHub.

Right after this, I updated my fork at GitHub with a simple git push, resulting in this gitk output:

We decided to split up the repositories, and have one benevolent dictator, or dr. Who , for each repository who will maintain the plugins defined in the repository and coordinate development:

• bioclipse.core
• bioclipse.statistics
• bioclipse.ds
• bioclipse.qsar
• bioclipse.cheminformatics
• bioclipse.rdf
• bioclipse.bioinformatics

Several plugins are still in the SVN world, but a good deal is now Git-ready. BTW, this move also adds several new accounts to watch on GitHub (see Rich’ 17 GitHub accounts to watch on Cheminformatics ).

GitHub turns out to be our big friend here, not SourceForge, which only supports one Git repository. GitHub recently must have added hooks recently, but I am really happy to see those. The above Bioclipse repositories have hooks turned on for CIA (so that commit messages end up on our #bioclipse IRC channel) and email (as indicated by the green color):

The splitting up, was rather interesting indeed. We wanted to keep the complete commit history, but still reduce the git repositories considerably. This means removing history of the plugins which should not end up in the repository. Git allows this! Git rules! This time, git filter-branch is our friend and there are basically two options: constructive and destructive. The first copied bit by bit plugins from the old to the new repository. The second one does the opposite, and removed bit by bit stuff you do not want. Depending on the ratio of plugins you want to keep and those you want to remove, either solution is more appropriate. I have summarized the git commands I used in detail on this Bioclipse wiki page.

Now, what was missing until today, was easy access to gists in Bioclipse itself. No gist.load(33421) yet. There still is not, but I uploaded earlier today a Wizard for it. (The manager will follow later). Right click on an open Project, select New -> Other, and pick Download Gist:

and click Next:

Then, just type the number of the Gist you want to open in Bioclipse, for example 18315 (see Bioclipse2 Scripting #1: from SMILES to a UFF optimized structure in Jmol ), and click another Next to select a file name and location:

The current code does require you to know the Gist number, so you’ll need a web browser to look it up, but we do have search facilities in mind. Also, while the code attempts so, the resulting Gist is not automatically openend in an editor (a bug). Another idea is to just install the egit plugin in Bioclipse :)

So, the other day, when I blogged about Bioclipse2 scripts , I should have embedded the script like this:

dimethylether = cdk.fromSMILES( "COC" );
cdk.addExplicitHydrogens( dimethylether );
cdk.generate3dCoordinates( dimethylether );

// save as CML
cdk.saveCML( dimethylether, "/Virtual/dimethylether.cml" );
ui.open( "/Virtual/dimethylether.cml" ); // this should open a JmolEditor

jmol.minimize();

You can see four of my favorite cheminformatics tools integrated: CDK is used to convert a SMILES into connection table with add explicit hydrogens, and to create initial 3D coordinates (with the code from Christian Hoppe, and thanx to Stefan for fixing that code in the CDK 1.1.x branch!). Then, CMLDOM is used to create and save a CML document, which is then opened into a Jmol editor in Bioclipse.

A variation of this script is visible in the following screenshot:

This and other Bioclipse2 scripts I will post in Gist, a sort of pastebin supporting version history, and I’ll tag them with bioclipse gist on delicious, so that you can always browse them, comment on them, or add your own gists at http://delicious.com/tag/bioclipse+gist.