Wednesday, January 19, 2011

I just got the cdk manager into bsl-runner

Finally some real progress. Today I got the cdk-manager running inside bsl-runner. To call it unstable would be an understatement, but from time to time it is there and when so it is possible to create a molecule and run some cdk manager methods on it. For the future I want to get a nightly build which produces something runnable for the project up and running on I should also start working on a test suite for the project. For the moment it's been along the ways of: "I wonder what is needed to get this running" but now that it actually runs it is time to get some tests covering the functionality up and running to be able to see when I break things. However since the Bioclipse project is nearing next release I will probably have to start spending my time on getting the next version out, and the bsl-runner is not Bioclipse 2.6 stuff. Not nearly...

P. S. Oh if you are crazy enough to want to try and run this, check-out all the HEADLESS branches (I think core and cheminformatics might be enough actually) and start the bsl-runner product find in the bsl-runner repo. The feature is not yet complete so you will have to add all required plugins using the run config dialogs 'Add required' button.

Friday, January 14, 2011

I just thought I should show you...

Hm that title is not quite true actually. It was more along the roads of egonw++ asked me to blog about Bioclipse headless. He told me that I should be friendly to potential early adapters. I told him there isn't really much to blog about yet. Which got him asking: "It compiles, no?", at which point I decided to give up. I did put up some more fighting just for the looks of it but he had me. So what exactly is this all about then?

I have been working on the headless branch lately (actually branches because a lot of our repos now have headless branches). The idea is to make the bioclipse scripting environment know as BSL accesible from the command line. The first step has been to refactor away all gui dependencies from the core bioclipse plugins and I am far from finished with that yet. I have played a little with a command line loop for interactively coding and what exists today is just the JavaScript loop made accessible from the command line. It fires up a lot of Bioclipse stuff in the background and my hopes is that the publication of the very first Bioclipse manager into it is within reach but to all of you early adopters out there (yea my best guess it that means you Egon (but anyone else reading, feel free to prove me wrong) :) the only thing you can expect to see if you manage to get the thing running is just a JavaScript prompt looking something like this: