commit f1c7e97dda7fb7396c009a0e507f12e970b1a21d
Merge: 22df80e f16e467
Date:   Wed Jan 15 12:26:56 2020 -0700

    Merge pull request #4444 from RosettaCommons/benchmark
    
    Updating testing scrips:
    - updating release tests to use mounts
    - updating benchmark.py to properly handle comparisons
    - updating integration.py path-sanitation procedure to use main path as a root to reflect new directories layout (this will cause most integration tests to fail once when this is merged, - this is expected change)

commit 22df80e64c08dca82a33cface2270911f1e3ecf2
Merge: eb01c90 41dee36
Date:   Mon Jan 13 17:56:55 2020 -0500

    Merge pull request #4438 from RosettaCommons/everyday847/copy_weights
    
    Add symlink to the correct, official RNA weights

commit eb01c900dbab562837e17526bb29c7a6d6de4ea7
Merge: 215977b d9a1ad8
Date:   Mon Jan 13 15:02:50 2020 -0600

    Merge pull request #4363 from RosettaCommons/roccomoretti/clang_tidy_3
    
    Fix issues identified by the misc-* series of clang-tidy tests.
    
    Part of my slow effort to extend the things we test for with clang-tidy.
    
    Most of the changes are due to removal of unused using statements (misc-unused-using-decls) or the conversion of std::string::compare() to std::string::operator== (misc-string-compare -- seriously, there's no reason to use the single-argument version of std::string::compare(). operator== is overloaded for char*, and the semantics of the return value make it hard to read.)
    
    Other issues include converting ad hoc rounding to use the standard library (misc-incorrect-roundings), fixing up some potentially error prone macros (misc-macro-parentheses), fixing redundant expressions in comparisons (misc-redundant-expression -- some potential bugs here), better annotation of C-style string comparison functions (misc-suspicious-string-compare), non-delegating delgating constructors (misc-undelegated-constructor), catch/throw issues (misc-throw-by-value-catch-by-reference), unused objects (misc-unused-raii - there's a bug remaining here), assigning integers to strings (misc-string-integer-assignment - bugs fixed).
    
    It also caught some bad definitions-in-headers (misc-definitions-in-headers) and some really odd assignment operators (misc-unconventional-assign-operator), but those tests are too noisy to leave on permanently.
    
    There are some behavioral changes from putative bug fixes, but hopefully they're a "fixed" approach.

commit 215977b061300b1988e0f12962dbe6955af0a649
Merge: 228943b d14d65e
Date:   Mon Jan 13 15:01:49 2020 -0600

    Merge pull request #4442 from RosettaCommons/roccomoretti/revert_nb_to_working
    
    Revert PyRosetta.notebooks to a working state.
    
    The current PyRosetta.notebooks master isn't actually working yet with respect to the PyRosetta4.notebook test server test. Revert the state of the submodule to a version which was, which should fix those tests in main master.
    
    Hopefully the submodule master will be fixed/updated in the near future.

commit 228943ba6236a6ef01477fd54df77262fa9cdded
Merge: 2572a9b 816fb41
Date:   Fri Jan 10 15:43:29 2020 -0800

    Merge pull request #4391 from RosettaCommons/danpf/identify_by_segid
    
    add segmentID to pdbPoseMap find

commit 2572a9b7963894ba59f92a16c72cea3e20fb5972
Merge: 54b367e cd9445e
Date:   Fri Jan 10 17:32:32 2020 -0600

    Merge pull request #4372 from RosettaCommons/roccomoretti/no_chain_back_and_forth
    
    Defer chain parsing to apply time in ligand docking movers.
    
    Some of the ligand docking movers were doing chain parsing in the parse_my_tag function, versus waiting until apply time. Not only does this cause issues if the structure of the pose changes between parse time and apply time, there was a fair bit of back-and-forth (e.g. chain letter->chain id->chain letter) that can be avoided.

commit 54b367efabcb2111544205eeccbf91f6919b8bfd
Merge: c987770 9f1ed3c
Date:   Fri Jan 10 17:25:05 2020 -0600

    Merge pull request #4440 from RosettaCommons/roccomoretti/fix_scriptvar_test
    
    Don't overwrite log file in job_definition_script_vars integration test
    
    This should fix the valgrind test.

commit c9877700346c5e9de2d3fe874a06eb0002831520
Merge: e56969d 80acdd9
Date:   Thu Jan 9 18:39:54 2020 -0600

    Merge pull request #4412 from RosettaCommons/roccomoretti/submodule_update
    
    Update (merge) the top-level submodules to their most recent master
    
    (These were all fast forward merges.)

commit e56969d9778b6c995e4ae9280b47adee51758c25
Merge: c8508a0 074d92e
Date:   Thu Jan 9 18:36:10 2020 -0600

    Merge pull request #4413 from RosettaCommons/roccomoretti/submodule_update_test
    
    An initial attempt at a submodule up-to-date test.
    
    The way it works is to look at the versions of the submodule for the current commit at the merge point. If there's a regression (that is, if master has submodule commits which the new commit doesn't), then the test will fail with a magenta-failure subtest for that module. (This is special cased for tests on master itself, which looks to make sure we haven't regressed on either of the parent commits of the master merge.)
    
    I've also added a check to see if we're up-to-date with the most recent version of the submodule's master. That's not an error, though, it's just reported in the test log.

commit c8508a049f7bff704352e36602a2be4f489cacd4
Merge: fd726f5 fcadc75
Date:   Tue Jan 7 15:58:50 2020 -0800

    Merge pull request #4320 from RosettaCommons/danpf/make_frags_bm
    
    make_fragments scientific test

commit fd726f53cd4c633fd9e689c3446ffb76b380a875
Merge: e9c9089 ec175f7
Date:   Mon Jan 6 12:24:37 2020 -0800

    Merge pull request #4427 from RosettaCommons/BobbyLangan/rosettamp_bugfix
    
    Change to membrane/util.cc to allow 'center' or 'normal' vectors to parse as floats

commit e9c9089bd37c0170536e1319dcac6536e3de2bdd
Merge: 22ef835 97bff0d
Date:   Mon Jan 6 13:20:33 2020 -0500

    Merge pull request #4428 from RosettaCommons/aleaverfay/jd3_bug_writing_output_if_last_job_fails
    
    Fix bug where jd3::MPIjobdist was not outputting
    
    In particular, if the last job in a particular stage
    did not result in a success, then the job distributor
    wouldn't ask the job queen if there were any jobs to
    output. This is problematic as the job queen waits
    until all jobs for a stage have completed before telling
    the job distributor what jobs should be output.
    Therefore, if the last job fails, the job distributor
    will never get any jobs from the job queen to output!
    
    Thanks Odessa @odaunc for bringing this bug to my attention!
    
    New unit test fails with the old code and works with the new code.

commit 22ef835b4a2647af94fcd6421a85720f07eddf12
Merge: 1785269 29dd958
Date:   Sun Jan 5 17:31:56 2020 -0700

    Merge pull request #4430 from RosettaCommons/benchmark
    
    Testing scripts update. Updating headers and levels tests to use new directory layout. Updating build.clean.* test to use HTTPS instead of SSH for submodule cloning.

commit 17852696da60cbdc09f8d8371140f4880d1e41f3
Merge: fac651c e5f18e3
Date:   Sun Dec 29 14:09:34 2019 -0500

    Merge pull request #4423 from RosettaCommons/JackMaguire/MRSScriptVars
    
    Enabling script_vars for JD3 apps

commit fac651cc7d8fe99d4105812adbc70429e0a27b7e
Merge: 0637973 3a264de
Date:   Wed Dec 18 12:41:35 2019 -0500

    Merge pull request #4422 from RosettaCommons/everyday847/fix_2MA
    
    Fix 2MA parameters

commit 0637973c2d1ecb78f06ebfe3834c6d3168946b1d
Merge: fe0943c 5d1b44f
Date:   Tue Dec 17 18:31:20 2019 -0500

    Merge pull request #4421 from RosettaCommons/everyday847/quick_fixes_farfar_drrafter
    
    argh, sorry build hotfix

commit fe0943cd77d7167891286105ab0f9c331a1d9c77
Merge: 4bb7883 c95cd05
Date:   Tue Dec 17 12:17:22 2019 -0500

    Merge pull request #4420 from RosettaCommons/everyday847/quick_fixes_farfar_drrafter
    
    Hotfixes for DRRAFTER

commit 4bb7883abb1ec658a3a651e6c66110b3b5dfe54c
Merge: afa5dc9 a00511c
Date:   Mon Dec 16 11:40:23 2019 -0800

    Merge pull request #4409 from RosettaCommons/guangfeng/galigdock_genparams
    
    Guangfeng/galigdock genparams

commit afa5dc96f1cdc0885ef67c01ac793e2c9ccd8ee3
Merge: 5836500 227d5b1
Date:   Sun Dec 15 08:20:57 2019 -0800

    Merge pull request #4419 from RosettaCommons/bcov/FixMaster2
    
    Fixing the clang tidy error in master

commit 5836500739cd5d693cdc91020e91f359ed9a3f82
Merge: f061add 93b4f76
Date:   Sun Dec 15 14:45:48 2019 +0100

    Merge pull request #4312 from RosettaCommons/bazzoli/move-constel
    
    Make "constel" code public

commit f061adda410b42232302ef16d2f6519fd7cde8bb
Merge: b55036b 7934620
Date:   Sat Dec 14 20:18:54 2019 -0800

    Merge pull request #4418 from RosettaCommons/klimaj/maybe_init
    
    Update maybe_init() **kwargs handling

commit b55036be39ae5037e8bec2751599b801c29aaf7c
Merge: a68ac28 f818e8e
Date:   Sat Dec 14 16:53:25 2019 -0800

    Merge pull request #4417 from RosettaCommons/klimaj/pin_package_versions
    
    Pin third-party dependency version numbers for T900_distributed unit tests

commit a68ac283f6d6ee69fea4a758c22f5f43fdc5cee0
Merge: b24d2b8 f64c20a
Date:   Fri Dec 13 20:36:46 2019 -0700

    Merge pull request #4401 from RosettaCommons/jkleman/SciBen_sfxns
    
    renaming relax scientific tests

commit b24d2b8eb3c8c52a0e67aa939dc82c7b1efdc834
Merge: 0d1716f bf0b728
Date:   Fri Dec 13 21:53:55 2019 +0100

    Merge pull request #4378 from RosettaCommons/roccomoretti/more_residue_selector_switch
    
    Convert a bunch of XML object to use ResidueSelectors internally.
    
    Another spinoff of PR#2466, aiming at removing the pose dependence at parse time.
    
    There's a number of objects which use pose in parse_my_tags() which can (and likely should) be converted to using /ResidueIndexDescriptors. (Note that I haven't changed the XML interface, just implemented the internals with ResidueSelectors/ResidueIndexDescriptors.)

commit 0d1716fc665498562b3823c80243d821ac9d3653
Merge: 91b7a94 e421ce2
Date:   Fri Dec 13 21:48:51 2019 +0100

    Merge pull request #4397 from RosettaCommons/roccomoretti/cppcheck_188_fixes
    
    Some fixes for cppcheck 1.88
    
    Sergey is looking to update some backends on the test server. This will involve updating the cppcheck version to 1.88.
    
    That newer version catches more things. To avoid perma-failing on the cppcheck, we should address the new issues. I had already updated the known issues list with existing cppcheck 1.88 issues, but a few new ones have slipped through since. I've either just fixed them, or have updated the cppcheck suppression list to simply ignore a style test which doesn't quite match how we use Rosetta.

commit 91b7a940f06ab065a81d9ce3046b08eef0de0b31
Merge: 09b9214 3f16792
Date:   Thu Dec 12 23:03:24 2019 -0500

    Merge pull request #4087 from RosettaCommons/kkappel1/drrafter_updates
    
    On behalf of @kkappel1: DRRAFTER updates

commit 09b9214e464ebf3a67809c9c32d13bc36d55e0f8
Merge: 973b1b4 64fe669
Date:   Thu Dec 12 23:02:54 2019 -0500

    Merge pull request #4416 from RosettaCommons/everyday847/FARFAR2_demo
    
    Update demos submodule

commit 973b1b43e97c8ebdd0badfb77e89e21fc9fab561
Merge: 885fe07 6419634
Date:   Wed Dec 11 15:04:44 2019 -0800

    Merge pull request #4384 from RosettaCommons/bcov/ArgCationPi
    
    arg_cation_pi guidance score term for arginine cation pi interactions

commit 885fe0750dc3c76a695ee5853ea761727041fac8
Merge: 8ef5837 47d3440
Date:   Wed Dec 11 15:24:19 2019 -0600

    Merge pull request #4411 from RosettaCommons/roccomoretti/fix_release_script
    
    Fix release script
    
    I had changed the interface to generate_version_information() by adding an argument, but I missed an intermediate function. This should correct that (and future proof a bit, too).

commit 8ef5837f2cd19a89d22612f52ddccc007ea99d47
Merge: 9416046 036a410
Date:   Tue Dec 10 13:06:03 2019 -0800

    Merge pull request #4271 from RosettaCommons/danpf/crossover_bug_fix
    
    fix bug in baseEtableEnergy get_count_pair_function_trie

commit 9416046d30b05f6d927d5f7eb0f3b24345520ff2
Merge: 7f2bd01 f57c836
Date:   Tue Dec 10 10:45:47 2019 -0600

    Merge pull request #4410 from RosettaCommons/roccomoretti/pre_talaris_HOH
    
    Remove HOH from pre-talaris exclude_pdb_components_list\
    
    The pre-talaris residue type set doesn't have an HOH type. As such, it shouldn't list the type in the exclude_pdb_component_list.txt file.

commit 7f2bd0108df8569443fde0c4e75002e83fdfc3a5
Merge: 4e9b337 ec96b83
Date:   Mon Dec 9 15:31:20 2019 -0600

    Merge pull request #4402 from RosettaCommons/roccomoretti/release_indication_in_version
    
    Add backtrace to console output for developers
    
    A desire was recently expressed to return the backtrace information to the console/tracer output for developers.
    
    In order to provide this info for developers (for whom it may be useful) but not for users-at-large (for whom it probably isn't), this PR adds an additional version info feature for being a "public release". This will be true for the Academic and Commercial downloads of Rosetta, but will be false for any version of Rosetta directly compiled from Git. While the recently added -run:crash_to_console flag will control things if given, if the option is omitted, the behavior will be print the results on the console for git/developer releases, and to leave it out for the public releases.
    
    In all cases, the ROSETTA_CRASH.log file is still generated.

commit 4e9b337b554a80e74a44037ca5b2e40fe2eef0e2
Merge: a280003 593bdfe
Date:   Mon Dec 9 15:30:29 2019 -0600

    Merge pull request #4406 from RosettaCommons/roccomoretti/fix_tests
    
    Fix some broken-in-master tests.
    
    This fixes some tests which are currently broken in master. (Except for those issues already addressed by #4404) In particular, it fixes the clang_tidy tests, as well as the glycan_anomers test.

commit a280003bbdf28fb885d2e6306db833b9c0957bc1
Merge: 3f906cc d81f864
Date:   Fri Dec 6 11:46:24 2019 -0800

    Merge pull request #4405 from RosettaCommons/dimaio/clang11_build
    
    Fix build on clang11 on OSX

commit 3f906ccf518b80b52fec1cb0c9ac033eb6141ead
Merge: 20fce0f d99796b
Date:   Fri Dec 6 12:10:03 2019 -0700

    Merge pull request #4231 from RosettaCommons/sergey/submodules
    
    Adding tools, demos and documentation as submodules to main repository and fixing most of known scripts path to point to a new location. Rest of the scripts (and particularly all release scripts and clone scripts) will be fixed in a follow up PR.

commit 20fce0fd08c79195b2b1d9bbb50777028d733e7a
Merge: f8f5427 2db9510
Date:   Fri Dec 6 10:03:52 2019 -0800

    Merge pull request #4404 from RosettaCommons/bcov/FixMaster
    
    Fix gcc9 compile warning

commit f8f5427db5cbe4034071a560c5356a7061aeafba
Merge: 0d6dc32 0bb5d95
Date:   Fri Dec 6 09:25:06 2019 -0500

    Merge pull request #4403 from RosettaCommons/JackMaguire/KillAtoPolarDesign
    
    Renaming KillA2019 to PolarDesign2019
    
    @Haddox found that KillA2019 doesn't actually Kill Alanines. In fact, it results in more alanines than MonomerDesign2019 (though nothing creates more alanines than "legacy", our old default until 8/2019). It also results in more polar residues, so the new name is PolarDesign2019.
    
    This PR updates the database and integration tests to have the new name. Additionally, there is a check in FastRelax that will switch database queries for "KillA2019" with "PolarDesign2019". This protects us against poor advertising about the name change and allows users to keep the more fun name if they want (I probably will).

commit 0d6dc321777f2451275c9b37bf7e2fb99e870f8f
Merge: 00b619f 1b7d715
Date:   Thu Dec 5 09:00:56 2019 -0600

    Merge pull request #4367 from RosettaCommons/jadolfbr/thread_safe_sugar_bb
    
    Make SugarBB Threadsafe
    
    This PR addresses #2441 in association with @vmullig 's Scoring Threadsafety issue #4358 .
    
    The changes include removal of step size option for the sampling data, and setup of the sampling data on construction of both the CHIEnergyFunction and OmegaPreferences functions - this is needed to keep threadsafety as Vikram pointed out in 2017 that we can't make either global object with the `safely_create_load_once_object_by_OP` if there are two+ versions that could be created.

commit 00b619fe6821d46b0e7e3d31caf51d03f27578e5
Merge: 18cd90a 65aa201
Date:   Thu Dec 5 08:20:47 2019 -0600

    Merge pull request #4399 from RosettaCommons/jadolfbr/fix_rmsd_metric
    
    Fix bug in RMSDMetric different residue types in pose vs ref_pose
    
    The code would fail if robust was set to true and side chains are being used for to create the atom_id_map of different residues.
    
    Identified and originally fixed by Hope - @woodsh17

commit 18cd90af994cb8129bb3ef996dce4043a4abc9b1
Merge: b429082 a98e9a7
Date:   Wed Dec 4 17:44:50 2019 -0800

    Merge pull request #4357 from RosettaCommons/bcov/SliceResidueSelector
    
    SliceResidueSelector for selecting from selections

commit b42908209dc2bf09a5db3e1e3ae039d7dba9b9d1
Merge: 7dba969 efff158
Date:   Wed Dec 4 17:34:27 2019 -0800

    Merge pull request #4379 from RosettaCommons/bcov/StructProfileAgain
    
    Restore some default behavior in StructProfileMover and MotifGraft

commit 7dba969cf84bae304f90503971295af68f2ca96b
Merge: ce09ef7 2aaeef0
Date:   Tue Dec 3 09:45:20 2019 -0800

    Merge pull request #4351 from RosettaCommons/dimaio/glycan_chiral_volume
    
    Fixes to the glycan chirality constraints in cart_bonded.
    
    - Previous code was special-cased for only a couple sugars and required manual curation of params files
    - this version has automatic logic to set chirality constraints
    - constraints have been tuned to match molprobity's chiral volume check
    
    Note on integration test changes:
    - Most due to an informational message on # of cart_bonded parameters
    - Carbohydrate integration test failures expected

commit ce09ef7f55fd6fb35fcaefab0b3e884971b9f699
Merge: 1893832 5896c64
Date:   Mon Dec 2 17:59:25 2019 -0600

    Merge pull request #4388 from RosettaCommons/roccomoretti/backtrace_tracer_option
    
    Add an option to display the backtrace on the console.
    
    Right now, when Rosetta crashes it only prints the backtrace to the ROSETTA_CRASH.log file.
    This PR adds a (currently default false) option -run:crash_to_console which will cause the crash reporter system to also print the backtrace to the console.

commit 18938325f2431c7d929a6e0e4ebe4a9660ef5db7
Merge: ade43d2 d70586f
Date:   Mon Dec 2 12:02:30 2019 -0800

    Merge pull request #4392 from RosettaCommons/dimaio/update_symmdef_script
    
    A collection of updates for make_symmdef_file.pl. The major change is to add support for apolar helical symmetries (that is, those that include 2-fold symmetry axes perpendicular to the helical axis)

commit ade43d22a1a5b8909f638d332daaf44bfc9da606
Merge: aef4a23 adaea43
Date:   Fri Nov 29 15:39:47 2019 -0500

    Merge pull request #4393 from RosettaCommons/vmullig/add_tsan_tests
    
    Add support for thread sanitizer

commit aef4a23c9b3439d584016b2170cfc54597ee67d8
Merge: f383d57 6494cac
Date:   Fri Nov 29 15:34:32 2019 -0500

    Merge pull request #4395 from RosettaCommons/vmullig/fix_clang_tidy
    
    Switching "virtual" to "override" to fix clang-tidy test.

commit f383d57b5c2d9fc9959353d0413810c71ceaa271
Merge: 57bd79b 0dfd3a9
Date:   Wed Nov 27 13:20:35 2019 -0700

    Merge pull request #4386 from RosettaCommons/benchmark
    
    Updating Benchmark scripts and Rosetta to fix unit tests under GCC-9

commit 57bd79b3ac3c47e23850105f28f3f4704caf3135
Merge: 6de4253 6c6f126
Date:   Tue Nov 26 13:08:38 2019 -0500

    Merge pull request #4389 from RosettaCommons/mlnance/compile_fix_unused_variable
    
    Compilation fix by commenting out unused variable in SilentStruct

commit 6de42530dd26d5248496aabc0854abbeee60182d
Date:   Sat Nov 23 01:28:48 2019 -0500

    beautifying

commit 26178a18f667ab29589a6f3f6a5006de5ab37d31
Merge: f82d28a 772738b
Date:   Fri Nov 22 16:41:26 2019 -0500

    Merge pull request #4383 from RosettaCommons/vmullig/fix_gcc_9_unit_tests
    
    Fix gcc 9 unit tests.
    
    The gcc 9 unit tests revealed a silly float-float comparison that could fail stochastically. Fixing.

commit f82d28a98d8d025c5a1159f10240db4479c4119c
Merge: 2138e5c 15d4727
Date:   Fri Nov 22 14:14:54 2019 -0500

    Merge pull request #4197 from RosettaCommons/vmullig/add_options_to_simple_cycpep_predict
    
    Adding a few features to simple_cycpep_predict and helical_bundle_predict.
    
    This pull request adds:
    - The ability to automatically calculate RMSD to the lowest-energy structure encountered to `simple_cycpep_predict` and `helical_bundle_predict`.
    - The ability to calculate various metrics related to solubility and membrane permeability for each sample, and to compute the Boltzmann-weighted ensemble average for these metrics.
    - Support for sampling bond lengths and angles.
    
    I'll flesh this out more as I go along.
    
    <u>TODO:</u>
    - [x] Pull request #4216 should be merged before this one.
    - ~~Pull request #4220 should be merged before this one.~~ --> Merged into this one and closed that one, since this one fixes some bugs that persist in that one.
    - [x] Add the options.
    - [x] Register them as relevant to `simple_cycpep_predict`.
    - [x] Register them as relevant to `helical_bundle_predict`.
    - [x] Write the ensemble lowest-energy RMSD calculator.
         - [x] Output.
         - [x] Integration test.
         - [x] Add to scientific test.
         - [x] Document new flag.
    - [x] Write the ensemble SASA calculator.
         - [x] Total, polar, and hydrophobic SASA.
         - [x] Compute ensemble average.
         - [x] Output.
         - [x] Integration test.
         - [x] Add to scientific test.
         - [x] Document new flag.
    - [x] Add support for sampling bond lengths and angles.
         - [x] Add options.
         - [ ] Document new options.
         - [x] Add GenKIC bond angle and bond length perturbers.
         - [ ] Document new GenKIC features.
         - [x] Register with `simple_cycpep_predict` (but _not_ `helical_bundle_predict`).
         - [x] Have the options do something.
         - [x] Integration test.
    - [x] Check scientific test with new features: queued here (https://b3.graylab.jhu.edu/revision/commits/14270).
    - [x] Beautify.

commit 2138e5c9e5a37d7dbd8340b7472977a6dececa11
Merge: 64dae26 82dcce9
Date:   Fri Nov 22 00:07:16 2019 -0500

    Merge pull request #4381 from RosettaCommons/everyday847/everyday847/accelerate_test
    
    Shorten test for general polymer sampler

commit 64dae26f31e6b62cec936d57aae85c1da1eaf933
Merge: 5ce1d01 86331d3
Date:   Thu Nov 21 17:35:41 2019 -0500

    Merge pull request #4380 from RosettaCommons/JackMaguire/quietTF
    
    Reducing Noise in TF Tests
    
    The tensorflow integration tests are noisy when comparing output from different processors.
    
    This is an example from PR 4359's merge with master:
    ```diff
    < [DATESTAMP]: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 FMA
    ---
    > [DATESTAMP]: I tensorflow/core/platform/cpu_feature_guard.cc:141] Your CPU supports instructions that this TensorFlow binary was not compiled to use: SSE4.1 SSE4.2 AVX AVX2 AVX512F FMA
    ```
    
    This PR simply adds that line to the `ignore_list`

commit 5ce1d0151fc3b6803e5227a1d4d44135049f4e70
Merge: b67bf8c ceb6b0a
Date:   Thu Nov 21 16:34:13 2019 -0500

    Merge pull request #4382 from RosettaCommons/JackMaguire/fixsubmodule
    
    Updating scientific tests submodule
    
    I've been tripping over submodules recently and accidentally merged in a change to tests/scientific/data. This PR reverts that change.

commit b67bf8ccf699fe79f9a03f6fe221c45834dd2b8f
Merge: 3d995b1 a6e8ce1
Date:   Thu Nov 21 15:56:39 2019 -0500

    Merge pull request #4260 from RosettaCommons/JackMaguire/BetterAnnealer
    
    Expanding user interface to the SequenceSymmetricAnnealer
    
    We're having a discussion on Slack about how the SequenceSymmetricAnnealer I added in #4117 could be used for a wider set of design cases. My goal in this PR is to provide a residue selector interface to the annealer so that the user can define regions that need to be sequence-symmetric.