commit 36665092fdf1cd840a11153603bd540a2d40e383
Merge: d0c9f30 1effab6
Date:   Sat Oct 19 15:21:32 2019 -0400

    Merge pull request #4291 from RosettaCommons/vmullig/bind_fragmentstore_vartypes_to_python
    
    Bind FragmentStore variables to allow access to Python.  This incorporates changes from Brian Weitzner and Bobby Langan, and suggestions from Sergey Lyskov.

commit d0c9f301fdc65bf947176317fed179eacaac1e16
Merge: d5d2eb5 077e824
Date:   Sat Oct 19 14:28:50 2019 -0400

    Merge pull request #4301 from RosettaCommons/vmullig/clean_up_new_in_header
    
    Removing instances of make_shared in header; moving to cc file.

commit d5d2eb54fc225a1bffe31c5c9856171bd411cd52
Merge: 9fc7493 56905a7
Date:   Sat Oct 19 11:15:44 2019 -0500

    Merge pull request #4300 from RosettaCommons/roccomoretti/pyrosetta_nocrash
    
    Turn off crash reporter for PyRosetta
    
    The crash reporter system isn't really well suited for PyRosetta. I thought I had turned it off, but it turns out the PyRosetta build is getting its settings from somewhere else these days.

commit 9fc74931008157c7a9e880ca90542b26655c82ac
Merge: ede810e 6c6344f
Date:   Fri Oct 18 15:11:49 2019 -0400

    Merge pull request #4307 from RosettaCommons/JackMaguire/missingsemicolon
    
    Fixing bug reported here: https://www.rosettacommons.org/node/10662

commit ede810effc721a6d7064ecd1492264e16d56a849
Merge: 2cfb014 1d67038
Date:   Fri Oct 18 00:11:44 2019 -0400

    Merge pull request #4305 from RosettaCommons/vmullig/explicit_genkic_error
    
    Making a GenKIC error more explicit.

commit 2cfb014197a83bb48d8dd4a64a56999bb587f664
Merge: febd1de 351cd48
Date:   Thu Oct 17 15:22:17 2019 -0700

    Merge pull request #4134 from RosettaCommons/bcov/MaxHBondEnergy2
    
    Change MAX_HB_ENERGY to an option and add to BUNSFilter

commit febd1de7eaa847d3b2fde82590bbdbdaf36fdca1
Merge: e065c00 ea05074
Date:   Thu Oct 17 17:15:47 2019 -0400

    Merge pull request #4302 from RosettaCommons/vmullig/remove_XRW_TEMP_lines_from_codebase
    
    Removing the irritating XRW TEMP lines that are cluttering up the codebase.

commit e065c00d3604be63a8c1185fb7429419bd95d96e
Merge: 3baa0b8 cf5b35e
Date:   Thu Oct 17 14:39:48 2019 -0400

    Merge pull request #4299 from RosettaCommons/vmullig/better_jd2_termination_message
    
    I don't know what "Got some signal... It is: 15" means, and neither should a user.  I'm trying to clarify some of the error messages that JD2 produces on abnormal termination.

commit 3baa0b8a57eaac78fe709aa425c0c5b243c2ed23
Merge: 7489d1c 8b63b77
Date:   Wed Oct 16 17:17:35 2019 -0400

    Merge pull request #4298 from RosettaCommons/vmullig/fix_gcc_9_build
    
    Fixing compilation on gcc 9.1.0 by initializing some uninitialized vectors and matrices.

commit 7489d1c37e0a97d5c21ace797f7230b931cbf617
Merge: d226030 56d5fa7
Date:   Mon Oct 14 12:36:49 2019 -0400

    Merge pull request #4061 from RosettaCommons/jkrys/fragments_picking_test
    
    Jkrys/fragments picking test - Justyna's fragment picking test

commit d226030c7ae196b747d69eaa764c6bcc8005d4f2
Merge: 115fa80 8ffe9c6
Date:   Mon Oct 14 11:27:48 2019 -0400

    Merge pull request #4229 from RosettaCommons/parryc_att3
    
    Parryc att3

commit 115fa80f4976a32f4156ea85b959fb9337826566
Merge: 74f2293 6f5f650
Date:   Sun Oct 13 13:44:51 2019 -0700

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

commit 74f22930f025e330fe54d8b2273b668b17d72a81
Merge: 52692eb 6338c98
Date:   Sun Oct 13 10:29:14 2019 -0700

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

commit 52692eb4e4d559958744a1d890acadc53b630a64
Merge: 94f6040 b92726e
Date:   Fri Oct 11 19:42:48 2019 -0400

    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.

commit 94f6040c83f5106fd0476510c763efea213987bf
Merge: 8609e6b 5c042f7
Date:   Fri Oct 11 16:34:08 2019 -0700

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

commit 8609e6b76dd3af30aee46a807936985ac1bdff5a
Merge: c539e48 de2cecd
Date:   Fri Oct 11 18:32:30 2019 -0400

    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.

commit c539e482f684c2c1319f99193cc03b51fad0dab8
Merge: 4d45638 c35ca8f
Date:   Fri Oct 11 13:41:18 2019 -0700

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

commit 4d45638c4b09c264a65b7af3ee0acfa9585063f1
Merge: 3955550 af72ee2
Date:   Fri Oct 11 13:34:28 2019 -0400

    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

commit 3955550348d10c0b8456b7facfed1b46d6142ece
Merge: 9f9005b d9b1faf
Date:   Thu Oct 10 19:50:58 2019 -0400

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

commit 9f9005b67cd2faed24aef294f2d60939bd0efe29
Merge: 8935190 dd3c749
Date:   Thu Oct 10 15:21:03 2019 -0500

    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.

commit 89351902936639bf5098d0db3bf4ff02a5e5852d
Merge: 9b40831 c8fa3e4
Date:   Thu Oct 10 12:16:38 2019 -0700

    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

commit 9b408312222ba9d113da7aeafaebdf709533660a
Merge: 733259d b095818
Date:   Thu Oct 10 11:17:28 2019 -0400

    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

commit 733259da8aef42ce0a2e778fb5046d3a3a6b47f8
Merge: aeda51e 53dadb8
Date:   Wed Oct 9 13:11:50 2019 -0400

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

commit aeda51ea830d1d315912d2563a754cb38d9e49b8
Merge: f05cf97 824bd5f
Date:   Mon Oct 7 17:21:58 2019 -0600

    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

commit f05cf97f6f4578019e0f35299af16ced09c66773
Merge: d5cc5b8 366b92f
Date:   Mon Oct 7 15:57:54 2019 -0400

    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!!!

commit d5cc5b88fe14ada49bf2ac1ca1c8305e75c954f7
Merge: 2df5261 b325ccd
Date:   Mon Oct 7 10:36:05 2019 -0600

    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

commit 2df5261739aafedd031ebe9fb394deecf4cc0ed9
Date:   Sun Oct 6 18:27:33 2019 -0400

    RosettaAI: Setting rosetta_scripts_scripts submodule to latest origin/master version.

commit c4c324751f5a3ce5a53936790378072e8302b7c9
Merge: df27cea 5493a3c
Date:   Sun Oct 6 15:42:24 2019 -0400

    Merge pull request #4275 from RosettaCommons/vmullig/fix_macos_compilation
    
    Comment out unused variable in RollMover.
    
    This was preventing compilation on my Mac with Clang 11.0.0.  (Note that Clang 9 is used on the test server for the MacOS compilation test.)

commit df27ceab8379f26801cbde91f9df00fb1192f4ed
Merge: 952a6f5 26f061b
Date:   Sat Oct 5 15:44:57 2019 -0400

    Merge pull request #4273 from RosettaCommons/vmullig/fix_clang_analysis_test
    
    Commenting out an unread variable flagged by clang analysis.

commit 952a6f58c6b13d3d04018751c23ba81a3c31af0b
Merge: d1662a3 1ff0a5f
Date:   Fri Oct 4 14:42:32 2019 -0700

    Merge pull request #4263 from RosettaCommons/klimaj/viewer_bug_fixes
    
    Minor bug fixes in pyrosetta.distributed.viewer

commit d1662a3fa1f5739728efa9a22e5cbf2f81fb7cbc
Merge: 513cc22 38ff56c
Date:   Fri Oct 4 16:10:14 2019 -0400

    Merge pull request #4265 from RosettaCommons/vmullig/clean_up_parameters_hh
    
    Clean up Parameters.hh and Parameter.hh a bit to reduce transclusions.
    
    This is part of Andrew Leaver-Fay's attempt to improve compilation efficiency by reducing unnecessary inclusions. Some of my parametric code puts too much in header files, necessitating inclusion of headers like Residue.hh (which themselves include a lot of other stuff). I can clean this up.