Merge pull request #4000 from RosettaCommons/frankdt/repair_sewing_benchmark_test Adding sewing back to scientific/data folder

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Merge pull request #3996 from RosettaCommons/vmullig/fix_fastrelax_disk_reads FastRelax repeatedly reads multiple scorefunction weights from disk, making it unusable on large clusters. Fixing this. Recent changes to FastRelax have it repeatedly reading not only its own relax script, but also scorefunction weights from disk. This means that I can't run anything that uses FastRelax or FastDesign on Mira or Theta, or other giant supercomputers. Fixing this again. We really need to implement something that firmly prohibits disk reads that are unmanaged by a central manager.

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Merge pull request #3993 from RosettaCommons/sergey/binder PyRosetta update - updating self-test.py script, adding support for --timeout flag - increasing tests timeout for PyRosetta releases in debug mode - adding pyrosetta.PyMOLRosettaServer module so it could be imported in PyMOL on Conda

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Merge pull request #3974 from RosettaCommons/rfalford12/protonation-task-op Task Operation for including protonation variants during packing This PR adds a new task operation, called pHVariantTaskOperation, which allows sampling of protonated/deprotonated side chain variants during repacking. This is currently set up to enable variants for ASP, GLU, HIS, TYR, and LYS and restore the intended functionality of the -pH_mode flag developed by Krishna here. I've also added a unit test.

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Merge pull request #3992 from RosettaCommons/revert-3991-revert-3984-JackMaguire/CxxExtras Retrying #3984 but with extra guards around the static asserts

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Merge pull request #3995 from RosettaCommons/dimaio/cart_bonded_option Changing user() options to check value instead

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Merge pull request #3987 from RosettaCommons/aloshbau/scientific_1 Aloshbau/scientific 1

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Merge pull request #3991 from RosettaCommons/revert-3984-JackMaguire/CxxExtras Revert "Add extras=cxx14, cxx17, and cxx20" Reverts #3984 Looks like it broke the Mac pyrosetta test. Reverting until it's fixed.

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Merge pull request #3984 from RosettaCommons/JackMaguire/CxxExtras Add extras=cxx14, cxx17, and cxx20 Adding extras for newer c++ versions. This probably won't impact the end users much but it would help developers prototype with newer features or play with external libraries that require newer versions. I also added macros like CXX14_OR_LATER because it seems cleaner than comparing __cplusplus to 201402L

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Merge pull request #3983 from RosettaCommons/JWLabonte/PTMs/CK1 This merge simply adds a new database file for a special consensus sequence for beta-catenin substrates for the CK1 kinase enzyme and one for CK2.

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Merge pull request #3980 from RosettaCommons/JWLabonte/PTMs/cofactors Coenzymes: Adding ATP to the Rosetta database by default This merge adds a `.params` file for ATP so that Rosetta will load structures with ATP correctly. The current parameters it pulls from the PDB have Hs on all the phosphates, and this is silly. Anyone using ATP-bound structures will see changes in their results. All integration test changes are expected; all unit tests pass.

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Fix EnergyMap::operator += (#3977) The convention for increment-and-assign type operators is to return a reference to the object that has just been incremented, thereby facilitating multiple increments in a single statement ``` a += ( b+= c ); ``` The original author* of the EMapVector class (aka EnergyMap) did not realize this and so this class does not return a reference, and instead returns void. This has never been a problem for C++ code as no one has seemingly wanted to chain increment-and-assign operations. PyBind11, however, will take the returned type and assign it to the original object: ``` emap1 += emap2 ``` is interpretted as: ``` emap1 = (emap1 += emap2) ``` so that this code: ``` emap1 += emap2 print("Surpise!", emap1) ``` will print ``` Surprise! None ``` This PR changes the signature of just the EMapVector's operator+= and similar methods, but surely there are other places in the code where operators are not conforming to the C++ conventions. *I am the original author of this code.

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Merge pull request #3972 from RosettaCommons/roccomoretti/more_pdb_loading_fixes Better categorization for PDB Diagnostic scientific tests. Add additional categories to the PDB Diganostic scientific test to knock down the number of "unknown" test failures. Mostly this isn't actually fixing any of the failures, just categorizing them better. (Though there are a few small functional changes.)

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Merge pull request #3978 from RosettaCommons/everyday847/SWM_checkpointing_hotfix Update StepWiseMonteCarlo.cc

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Merge pull request #3959 from RosettaCommons/sergey/binder Updating PyRosetta so it could be build with Python-3.7 on Mac

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Merge pull request #3970 from RosettaCommons/sergey/scientific Adding workaround for shebang line overflow. Minor fixes to scientific test template and already imlemented tests.

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