Pushed Revisions

branch: master 「№60984」
Commited by: Christopher Parry
GitHub commit link: 「d226030c7ae196b7」「№4229」
Difference from previous tested commit: code diff
Commit date: 2019-10-14 11:27:48

branch: master 「№60983」
Commited by: Frank DiMaio
GitHub commit link: 「115fa80f4976a32f」「№4292」
Difference from previous tested commit: code diff
Commit date: 2019-10-13 16:44:51

Merge pull request #4292 from RosettaCommons/dimaio/glycan_fixes_3 Fix typo in N4-acetylation patch

branch: master 「№60982」
Commited by: Jason C. Klima
GitHub commit link: 「74f22930f025e330」「№4293」
Difference from previous tested commit: code diff
Commit date: 2019-10-13 13:29:14

Merge pull request #4293 from RosettaCommons/klimaj/viewer_docs Update documentation of pyrosetta.distributed.viewer

branch: master 「№60981」
Commited by: Vikram K. Mulligan
GitHub commit link: 「52692eb4e4d55995」「№4276」
Difference from previous tested commit: code diff
Commit date: 2019-10-11 19:42:48

Merge pull request #4276 from RosettaCommons/vmullig/fix_pose_from_sfr_builder Fix a bug in the PoseFromSFRBuilder The -in:Ctermini and -in:Ntermini options aren't working as expected. This ensures that, if the user uses these, they properly apply termini only to those chains that are listed. This also adds a unit test for the desired functionality.

branch: master 「№60980」
Commited by: Daniel Farrell
GitHub commit link: 「94f6040c83f5106f」「№4267」
Difference from previous tested commit: code diff
Commit date: 2019-10-11 19:34:08

Merge pull request #4267 from RosettaCommons/danpf/denovo_dump_pdb make debug denovo_density dump pdb not text

branch: master 「№60979」
Commited by: Vikram K. Mulligan
GitHub commit link: 「8609e6b76dd3af30」「№4285」
Difference from previous tested commit: code diff
Commit date: 2019-10-11 18:32:30

Merge pull request #4285 from RosettaCommons/vmullig/fix_rollmover_again Trying to fix Rollmover ubsan test. I think the problem is that the Rollmover doesn't initialize all of its variables in both constructors. This creates problems on copying, when, for example, a boolean variable is initialized with a non-binary value.

branch: master 「№60978」
Commited by: Jason C. Klima
GitHub commit link: 「c539e482f684c2c1」「№4279」
Difference from previous tested commit: code diff
Commit date: 2019-10-11 16:41:18

Merge pull request #4279 from RosettaCommons/klimaj/update_notebooks Update PyRosetta.notebooks submodule, and add serialization build and external packages

branch: master 「№60977」
Commited by: Julia Koehler Leman
GitHub commit link: 「4d45638c4b09c264」「№4284」
Difference from previous tested commit: code diff
Commit date: 2019-10-11 13:34:28

Merge pull request #4284 from RosettaCommons/jkleman/SciBen_fixes_and_cutoffs Jkleman/sci ben fixes and cutoffs Fixing a bunch of small things in various scientific tests. For instance, some cutoffs to make them pass. * mp_symdock still needs to be fixed, this is a bigger issue next on my list * dock_glycans requires some fixes and thresholds adjusted still, next on my list

branch: master 「№60976」
Commited by: Vikram K. Mulligan
GitHub commit link: 「3955550348d10c0b」「№4288」
Difference from previous tested commit: code diff
Commit date: 2019-10-10 19:50:58

Merge pull request #4288 from RosettaCommons/vmullig/add_pnear_for_sci_tests Adding PNear calculator to quality_measures.py in the scientific tests

branch: master 「№60975」
Commited by: Rocco Moretti
GitHub commit link: 「9f9005b67cd2faed」「№4281」
Difference from previous tested commit: code diff
Commit date: 2019-10-10 16:21:03

Merge pull request #4281 from RosettaCommons/roccomoretti/clang_tidy_test_fixes Fixes for clang-tidy issues This merge both adds a new test server test which runs clang-tidy on the Rosetta code base, as well as fixing a number of issues which the default clang-tidy settings identify. (Mostly using virtual functions in constructors and destructors, but a smattering of other issues.) There are a couple of places where the current (C++ standard-mandated) behavior probably isn't what is intended, but I've added comments to those, so hopefully people looking at it in the future can figure out if they want/need to change things.

branch: master 「№60974」
Commited by: Frank DiMaio
GitHub commit link: 「89351902936639bf」「№4282」
Difference from previous tested commit: code diff
Commit date: 2019-10-10 15:16:38

Merge pull request #4282 from RosettaCommons/dimaio/glycan_cartrefine_fixes_2 More fixes for glycans: - fix amide H generation for N acetylation patches - fix bug with symmetrization of poses containing free glycans

branch: master 「№60973」
Commited by: Julia Koehler Leman
GitHub commit link: 「9b408312222ba9d1」「№3858」
Difference from previous tested commit: code diff
Commit date: 2019-10-10 11:17:28

Merge pull request #3858 from RosettaCommons/JWLabonte/sugars/scientific_benchmarking Carbohydrates: Adding scientific benchmark for dock_glycans protocol tests still failing, cutoffs will be adjusted after talking with Labonte

branch: master 「№60972」
Commited by: Julia Koehler Leman
GitHub commit link: 「733259da8aef42ce」「№4280」
Difference from previous tested commit: code diff
Commit date: 2019-10-09 13:11:50

Merge pull request #4280 from RosettaCommons/everyday847/fix_scientific_tests Fix scientific test thresholds for RNA tests- Thanks Andy!

branch: master 「№60971」
Commited by: Sergey Lyskov
GitHub commit link: 「aeda51ea830d1d31」「№4269」
Difference from previous tested commit: code diff
Commit date: 2019-10-07 19:21:58

Merge pull request #4269 from RosettaCommons/sergey/binder PyRosetta update: - Updating Binder submodule - fixing RotamerSets → RotamerSetsBase conversion issue - adding inheritance test - adding core.RotamerSets test

branch: master 「№60970」
Commited by: Julia Koehler Leman
GitHub commit link: 「f05cf97f6f457801」「№4227」
Difference from previous tested commit: code diff
Commit date: 2019-10-07 15:57:54

Merge pull request #4227 from RosettaCommons/rfalford12/fix-mp-docking-tests Rebecca's fix to mp_dock and mp_symdock - I thought this was merged weeks ago but in fact, I missed it. Thanks Rebecca!!!

branch: master 「№60969」
Commited by: Sergey Lyskov
GitHub commit link: 「d5cc5b88fe14ada4」「№4272」
Difference from previous tested commit: code diff
Commit date: 2019-10-07 12:36:05

Merge pull request #4272 from RosettaCommons/sergey/notebook Updating `PyRosetta4.notebook` test: - adding DEBUG environment variable - refactoring execution to run in parallel - switching to use iPython during execution - adding matplotlib and biopython packages

Legend:

queued	Queued Test
queued for comparison	Test finished running but not yet compared
running	Test is Running right now
comparing	Test results is now comparing with previous results
finished	Test is finished without errors
failed	Test failed
build Failed	Test could not be run because build failed
script failed	Test results is unknow because test-script failed
canceled	Test was canceled