- The model io code as moved into the kernel so it is now IMP::write_model() and IMP::read_model()
- Remove the version_info argument from the implementation macros. Instead, just pick up the module version info automatically.
- Add a function Object::get_type_name() and Object::get_module() to get the respective bits of information about each object.
- Change Object::show() to be a non-virtual wrapper which prints the object name and other info before passing control off to Object::do_show().
- The containers were moved to IMP.container. See that module page for a full list of what moved. In the process, the backwards compatability functions were removed from IMP::container::PairsRestraint and kin.
- IMP.atom.create_protein() now returns the created protein
- the simplify functions have been moved from IMP.helper. They are now IMP.atom.create_simplified_along_backbone().
- IMP.helper.clone() has been renamed to IMP.atom.create_clone()
- IMP.misc.ConnectingPairContainer has been moved to IMP.core.ConnectingPairContainer
- The locations for pixels in IMP::em::DensityMap have been moved to the center of the corresponding voxel from the lower left corner.
- IMP::em::get_transformed(), IMP::em::get_resampled() and IMP::em::get_density() have been added.
- The documentation has been majorly cleaned up and simplified. Please look around and see if you like it. There are now two main pages, the introduction and the developers guide, rather than the previous plethora of pages.
- IMP::algebra::Cone3D::get_bounding_sphere() has been removed since it was not of general use, not returning the bounding sphere you would expect and was trivial to implement.
- IMP::algebra::projection() was removed since it didn't actually project onto the segment and the name didn't follow the normal conventions. And it wasn't used.
- Most geometry now has namespace methods IMP::algebra::get_bounding_box(), IMP::algebra::get_surface_area(), IMP::algebra::get_volume().