The second patches the init file as above. It also adds an argument
extraroot which adds to the include search path and the lib path (and to
the runtime link path since it is needed to make the boost tests pass
currently).
I can't apply this patch because it would break builds for everything
except gcc and Python 2.5 on Linux. But I can certainly put in an
equivalent feature which works everywhere if you can briefly explain the
use case.
Also, as a general point, the SConscript files
which build things should all be changed to add the local include and
lib paths to the front so that local headers mask globally installed
headers.
I'm 95% sure the include path search order is compiler-dependent, so
this probably would only have the desired effect for gcc, but I agree
that it's a good statement of intent if nothing else.
The fifth adds set_particles to the the list restraint I added before
(this is independent of anything else).
Wouldn't compile for me:
kernel/include/IMP/restraints/SingletonListRestraint.h:41: error: no
members matching 'using IMP::Restraint::set_particles' in 'class
IMP::Restraint'
As regards the nonbonded list, we cannot include CGAL in the kernel
since it restricts the use of IMP to that of the QPL license. I
certainly agree that CGAL has some useful features which we may want to
use in IMP - but it cannot go in the kernel. Thus, it should go in an
extension module. This appears to preclude use of the current patch,
since Algorithm is an enum - I guess either Algorithm needs to become a
class, or a CGAL_NBL class (in a module) can derive from a base NBL
class (in the kernel). At the Python level it is easy to fall back from
CGAL_NBL to regular NBL at runtime if the extension module is not
available - just wrap the import in a try block.