http://cci.lbl.gov/cctbx_docs/

Obviously these are still pretty sparse - right now most of the formal documentation is clustered here:

libtbx

libtbx.utils

libtbx.phil (mostly re-using Ralf's old documentation)

cctbx.miller

iotbx.pdb (built on Ralf's newsletter article)

mmtbx.command_line

These are a combination of inline docstrings and separate restructured text files in cctbx_project/sphinx.  We have automatically generated rst files for some modules, but others will need to be added manually.  In the end I think we'll want to curate every file, but the current layout will get us started.  To facilitate additional contributions, I've modifed the installation script for base packages to include a --sphinx option.  After setting up CCTBX you can then do this:

cd $BUILD

libtbx.configure sphinx

cd $SRC/cctbx_project/sphinx

make html

and you will get the full documentation built locally.  I am still figuring out how to use Sphinx effectively; it is definitely possible to document Boost.Python extensions but it's not quite as obvious.

I don't expect us to retroactively document several hundred thousand lines of code written over a decade, but if we can get the core parts thoroughly covered that will greatly reduce the barrier for new developers.  Suggestions for particular modules to focus on are appreciated; I am going to try to cover the basic PDB+reflection file functionality.  I encourage anyone doing CCTBX-related development to contribute as you go.  (They don't need to be your own APIs, just modules you're reasonably familiar with.)  Those of you who already have a ton of undocumented code can expect me to harass you periodically about fixing this.

(Note that I've cannibalized at least one newsletter article for this, and continue to do so; we should re-use existing prose descriptions as much as possible without violating copyrights.)

-Nat