Pushed Revisions

branch: master 「№59220」
Commited by: Rhiju Das
GitHub commit link: 「150d7a9187717af4」「№1942」
Difference from previous tested commit: code diff
Commit date: 2017-01-13 19:39:01

Merge pull request #1942 from RosettaCommons/rhiju/recces_info RECCES TODO + single-nt-bulge updates Some integration tests change due to an update in how fold_tree is setup inside fixed domains. connections between end of one chain & beginning of next chain are preferred (this matches the behavior of figure_out_reasonable_rna_fold_tree). In some swm protein/rna tests, this produces very very tiny floating point errors (1e-7) that accumulate.

branch: master 「№59219」
Commited by: Frank DiMaio
GitHub commit link: 「41bbcf4dc237dc84」「№1951」
Difference from previous tested commit: code diff
Commit date: 2017-01-13 13:01:47

Merge pull request #1951 from RosettaCommons/dimaio/lkball_threadsafe Dimaio/lkball threadsafe

branch: master 「№59218」
Commited by: Vikram K. Mulligan
GitHub commit link: 「96a063ec865acca1」「№1950」
Difference from previous tested commit: code diff
Commit date: 2017-01-12 20:41:58

Merge pull request #1950 from RosettaCommons/vmullig/fix_pepalign_mover Fixing a few parsing errors in SymmetricCycpepAlign.cc. I had a few mistakes in the parse_my_tag function that caused issues in certain usage cases.

branch: master 「№59217」
Commited by: Ryan Pavlovicz
GitHub commit link: 「ad3f4ebee1b716ba」「№1952」
Difference from previous tested commit: code diff
Commit date: 2017-01-12 18:42:30

Merge pull request #1952 from RosettaCommons/rpavlovicz/beta_nov16_simplefix fix flag issue with lk_ball_water_donor

branch: master 「№59216」
Commited by: Rocco Moretti
GitHub commit link: 「610256f6161e58cb」「№1948」
Difference from previous tested commit: code diff
Commit date: 2017-01-12 16:48:36

Merge pull request #1948 from RosettaCommons/roccomoretti/ClangSA_debug_assert Fix issue with null pointer dereference in Clang Analysis The way we had debug_assert() set up, Clang static analysis wasn't realizing that execution stops when the condition is false. This pull request fixes that, so that spurious ClangSA issues no longer occur.

branch: master 「№59215」
Commited by: Rocco Moretti
GitHub commit link: 「8736d7cc31d1cef6」「№1945」
Difference from previous tested commit: code diff
Commit date: 2017-01-12 16:44:24

Merge pull request #1945 from RosettaCommons/roccomoretti/xml_addsan Fix various issues with Addsan server tests The major fix here was to close a memory leak in XMLSchemaValidation.cc. There were also some issues with how sqlite was being used. (You can't bind a return-by-value vector1 into a query - the temporary vector gets deleted before the query actually gets run, resulting in an memory access issue.) These fixes now turn the integration.addsan test green on the test server. The unit.addsan still has issues with the crashing DynamicAggregateFunctionTests, and differential results with AntibodyTaskOps tests

branch: master 「№59214」
Commited by: Sergey Lyskov
GitHub commit link: 「2fc5a79d7b595be1」「№1940」
Difference from previous tested commit: code diff
Commit date: 2017-01-12 14:50:37

Merge pull request #1940 from RosettaCommons/sergey/binder Adding binding (as __str__) for types with template operator<<. Cleaning up some of Evan Baugh toolbox code. Porting pose_from_rcsb to Python-3.

branch: master 「№59213」
Commited by: Andrew Watkins
GitHub commit link: 「6bdc2e52312ae6b3」「№1949」
Difference from previous tested commit: code diff
Commit date: 2017-01-11 15:34:14

branch: master 「№59212」
Commited by: Andrew Watkins
GitHub commit link: 「64c3ddf6544116df」「№1946」
Difference from previous tested commit: code diff
Commit date: 2017-01-11 02:04:20

Merge pull request #1946 from RosettaCommons/everyday847/build_full_model_farfar Build full model with fragment assembly refinement

branch: master 「№59211」
Commited by: Vikram K. Mulligan
GitHub commit link: 「e2ec8f145672049a」「№1941」
Difference from previous tested commit: code diff
Commit date: 2017-01-10 21:20:18

Merge pull request #1941 from RosettaCommons/vmullig/nmethyl_valgrind_issue Fix an uninitialized variable issue flagged by Valgrind in the N-methylation unit tests. This was caused by some uninitialized local vars in LK_BallEnergy.cc that were being used to set other things.

branch: master 「№59210」
Commited by: Gerard Daniel
GitHub commit link: 「0343a52f046fb425」「№1947」
Difference from previous tested commit: code diff
Commit date: 2017-01-10 19:44:53

Merge pull request #1947 from RosettaCommons/GerardDaniel/nbrhdResSelc_custNbrAtm fixing potential serialization issues

branch: master 「№59209」
Commited by: Gerard Daniel
GitHub commit link: 「ffb45508bebdefd5」「№1944」
Difference from previous tested commit: code diff
Commit date: 2017-01-10 02:23:04

Merge pull request #1944 from RosettaCommons/GerardDaniel/nbrhdResSelc_custNbrAtm Fixing serialization test issues

branch: master 「№59208」
Commited by: Vikram K. Mulligan
GitHub commit link: 「2fa862826ee493cf」
Difference from previous tested commit: code diff
Commit date: 2017-01-09 19:18:01

branch: master 「№59207」
Commited by: Rhiju Das
GitHub commit link: 「ffbe5cedfe3d6f3c」「№1935」
Difference from previous tested commit: code diff
Commit date: 2017-01-06 15:07:42

Merge pull request #1935 from RosettaCommons/rhiju/refactor_recces Rhiju/refactor recces + only integration tests that really change are thermal_sampler and recces, and those changes are cosmetic text diffs. Numerical trajectories are exactly the same.

Rocco Moretti 8 years
Looks like this commit may have introduced an uninitialized variable issue with Valgrind and the thermal_sampler integration test: http://benchmark.graylab.jhu.edu/sub_test/53709003

branch: master 「№59206」
Commited by: Gerard Daniel
GitHub commit link: 「e4488bd8b537f76a」「№1936」
Difference from previous tested commit: code diff
Commit date: 2017-01-06 00:34:20

Merge pull request #1936 from RosettaCommons/GerardDaniel/nbrhdResSelc_custNbrAtm Added the ability to take in and use custom atoms per residue for defining neighbor selection

branch: master 「№59205」
Commited by: Sergey Lyskov
GitHub commit link: 「ba961939e2a8d549」「№1937」
Difference from previous tested commit: code diff
Commit date: 2017-01-04 23:46:19

Merge pull request #1937 from RosettaCommons/sergey/binder Fixing PyRosetta release scripts which got broken during PyMOL mover refactoring

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queued	Queued Test
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