Merge pull request #4044 from RosettaCommons/revert-4004-vmullig/threadsafe_options_system Revert "Make the options system threadsafe" Reverts #4004 @lyskov found that there were problems with the PyRosetta tests with this PR. I need to fix them and remerge. Please be aware that the options system is not threadsafe in the meantime.

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Merge pull request #4041 from RosettaCommons/sergey/binder PyRosetta update. Fixing `show` function output so they could be used in Jupyter notebooks.

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Merge pull request #4027 from RosettaCommons/danpf/add_more_spline_fn Add convenience functions to splines

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Merge pull request #3285 from RosettaCommons/danpf/mmtf mmtf IO v1

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Merge pull request #4028 from RosettaCommons/JWLabonte/PTMs/DYRK1A PTMs: adding new enzyme

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Merge pull request #4006 from RosettaCommons/roccomoretti/tag_self_weak_fix Remove the string constructor from utility::tag::Tag It's a nice idea, but unfortunately when read() adds subtags, it uses the shared_from_this functionality. shared_from_this isn't valid in constructors (or for that matter, anytime the object isn't already in an OP). The way Tag is structured, you really do need to do a construct-then-read two-step.

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Merge pull request #4030 from RosettaCommons/jadolfbr/user1 Fix use of .user() up through core.scoring (Part 1)

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Merge pull request #3957 from RosettaCommons/sergey/f3 updating integration test script, adding support for `thread` suffix

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Merge pull request #4016 from RosettaCommons/jadolfbr/sc_to_public Make two pilot apps used in a paper public. (sc, and report_hbonds_for_plugin)

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Merge pull request #4021 from RosettaCommons/sergey/scientific Updating scientific tests API. Adding `build_and_install_pyrosetta`, updating `_template_` scientific test, cherrypicking HPC driver updates from other branches.

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Merge pull request #4025 from RosettaCommons/JackMaguire/ClangCxx14 Correcting extras=cxx... flags for clang #3992 added options to compile with std=c++1y and later versions of c++. To do this, I needed to remove std=c++1x from those builds but failed to notice that clang uses std=c++11 instead. This PR simply corrects the flag being removed. Thanks for the review Sergey!

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Merge pull request #4007 from RosettaCommons/JWLabonte/PTMs/options EnzymaticMovers: Adding command-line option for controlling enzyme efficiency

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beautifying

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Merge pull request #4020 from RosettaCommons/vmullig/fix_settorsion_perturb Minor bugfix for perturbing arbitrary dihedrals with the SetTorsion mover. Adding missing conversion from radians to degrees.

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Merge pull request #4023 from RosettaCommons/vmullig/fix_cadmium Attempting to fix GasteigerAtomTyperTests. Apologies -- merged too quickly.

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Merge pull request #4014 from RosettaCommons/jaumebonet/nubinitio_updates added ability to provide sse and alternative filter to NubInitioMover

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