rosetta_dev_tools 1.1.0

A set of tools to facilitate development of the Rosetta protein design suite.

There are a number of reasons why the edit-compile-test cycle is not as convenient as it could be in Rosetta. One is that the source code, the unit tests, and the pilot app executables are all kept in very different places, which requires you to keep changing directories as changes are made. Another is that a large amount of boilerplate has to be written when adding new classes, and yet another is that incremental compilation times can be quite slow.

This package attempts to address some of these issues, in particular the ease with which code can be compiled and tested. Towards this end, a set of scripts are provided which simplify the process of compiling, testing, and running Rosetta. These scripts are aware of Rosetta’s directory structure, so paths do not need to be specified.

These scripts also use the ninja build system, which is much faster than scons at executing incremental builds. This takes some external work to configure properly, but information is available on the Kortemme lab wiki page.

Installation

These tools are available from PyPI, so you can install them using pip. Be sure to use the pip associated with python3 though, because by default pip is usually associated with python2 and will not work with these tools:

$ pip3 install rosetta_dev_tools

This will install a handful of executable scripts in whichever bin/ directory pip is configured to use. These scripts have pretty long names, so I usually alias them to something shorter to make typing them more convenient. For example, put these lines in ~/.bashrc:

alias rk='rdt_stub'
alias rb='rdt_build debug'
alias rr='rdt_build release'
alias ru='rdt_unit_test'
alias rd='rdt_doxygen'

If you want to install these tools on the QB3 cluster, you have to take a couple extra steps. First, the cluster doesn’t have pip installed, so you have to clone this repository and run setup.py manually. Second, you have to be on an interactive node (e.g. iqint) or git clone won’t work. Third, the cluster doesn’t make python3 available by default, so you have to explicitly enable it using the scl enable python33 command:

$ ssh iqint
$ git clone [e-mail]:Kortemme-Lab/rosetta_dev_tools.git
$ cd rosetta_dev_tools
$ scl enable python33 'python setup.py build'
$ scl enable python33 'python setup.py install --user'

You’ll also have to use the scl enable python33 command every time you want to use any of these tools, so it’s easiest to simply wrap them in functions. For example, put these lines in ~/.bashrc:

function rb {} (
    scl enable python33 'rdt_build debug $*'
}
function rr {} (
    scl enable python33 'rdt_build release $*'
}

Filling in boilerplate

To create all the boilerplate files for a new mover, run the following command:

$ rk mover protocols::moves::MyMover

This command will create new *.fwd.hh, *.hh, *Creator.hh, *.cc, and *.cxxtest.hh files. It will also add the mover to the relevant *.src.settings and *.test.settings files, and it will register the mover in init.MoverCreators.ihh and init.MoverRegistrators.ihh. When the command finishes, your new class will be completely ready to compile.

The first argument specifies what kind of file(s) to make and the second argument specifies the name of the new class. The second argument doesn’t have to be a fully qualified name (i.e. it doesn’t have to include a namespace). If you don’t specify a namespace, one will be automatically inferred from the current working directory. So the above command could be abbreviated like so:

$ cd $rosetta/source/src/protocols/moves
$ rk mover MyMover

This command also has a convenient --dry-run option you can use to look at the stub files being generated before they are actually written to disk.

Compiling rosetta

To build rosetta in debug mode, just run the following alias from anywhere in your checkout of rosetta:

$ rb

To build in release mode, run the following alias instead:

$ rr

These aliases require that either ninja or make be installed. Most systems will have make installed by default, so you shouldn’t have to worry about this. However, ninja is preferred if both build tools are installed because it’s faster and more succinct.

Running unit tests

To compile and run a unit test suite, use the following command as a template:

$ ru protocols MyUnitTest

The first argument is the library that the unit test is part of, which usually is protocols. The second argument is the name of the test suite to run (i.e. the name of the class in your *.cxxtest.hh file). You can also specify a third argument to run just one specific test case (i.e. one test_*() method from that class).

Once you’ve run a unit test using a command like the one above, you can use an abbreviated version of that command to run the same test again:

$ ru

That command will rerun the last unit test that was run. It is also possible to assign names to commonly used tests, so that you can run them in as few keystrokes as possible:

$ ru protocols MyOtherUnitTest -s other
$ ru other

Writing documentation

To generate doxygen documentation for whichever directory you’re currently in, run the following command:

$ rd

This will generate documentation and automatically present it to you in a new firefox window.