Merge pull request #324 from RosettaCommons/roccomoretti/braaaiiins
File-level dead code removal
Remove files that aren't compiled or used by any of the standard processes (regular build, unit test, PyRosetta) This includes both .cc files and header files. Only the main library directories (basic, utility, numeric, core, protocols) have been cleaned. "External" libraries (I include ObjexxFCL in this) weren't touched. I also didn't touch the unit test directory (I want to make it easy to re-enable those tests which aren't running currently), nor the apps or devel directory (as I didn't want to penalize people who sped up compilation by turning off their devel work). -- Though if we're sunsetting the devel directory, a cleanup there may be warranted.
If I deleted something you needed, feel free to add it back (remember it's still available in git's history), but: 1) make sure you put the .cc file in the appropriate .src.settings file 2) make (and enable) a unit test for the functionality
No test changes expected, as the removed code shouldn't be used.
Merge pull request #256 from RosettaCommons/kalekundert/fix_integration_tests
Fix the instability in the loop_creation integration test. I decided to do this because I already spent a day figuring out how to run valgrind for my own unstable integration test, and it turned out to be a really easy process. So I thought I might as well fix the other unstable test while I still remembered how.
The problem in this case was related to the prevent_nonloop_modifications_ variable being declared in the parent class and the child class, but only defined in the child class. I fixed this by removing the child class declaration and forcing everything through the parent class.
Merge pull request #154 from RosettaCommons/koepnick/envsmooth_zero_negatives
Updated envsmooth energy to read data from database, and added a new option.
Merge pull request #127 from RosettaCommons/dougrenfrew/fix_app_exception_itest
Fix the app_integration_handeling itest by adding a return -1 to couple_moves
Updated all Splice integration tests. Changes include adding the default ignore list to all command files and limiting the residues that are designed to reduce the run time
Splice mover is also updated. "add_dihedral_constraints" was changed to solve problem with n-ter tails.