beautifying

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Merge pull request #2608 from RosettaCommons/sergey/binder Updating PyRosetta so it uses Binder compatible with Pybind11-2.2

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Merge pull request #2618 from RosettaCommons/sergey/f Updating PyRosetta build script (was broken on some Mac's)

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Explicitly specify for which branch we setting upstream

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Updating `beautify` test so it explicitly set upstream for beautifying branch

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Merge pull request #2614 from RosettaCommons/egurapha/remodel_cutpoint_fix Remodel: fixing broken cutpoint assignment

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beautifying

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Merge pull request #2575 from RosettaCommons/aleaverfay/jd3_output_structure_naming JD3: output indices change The JobOutputIndex is a 4-tuple of integers representing a primary- and a secondary-index as well as an upper bound on the number of primary- and secondary-indices. The interface to the PoseOutputters changes slightly. Derived job queens of the SJQ may override the assign_output_index method to give the just-about-to-be-output Poses different indices if she wants. This is particularly necessary for multi-stage jobs, where there might be more than one InnerLarvalJob (and so the nstruct index is not unique!). This pull request is a launch point for PR #2613 which further changes the way the JobQueen interacts with generating output. The changes in this PR are not overridden by PR #2613, but if you are writing a new JQ and this PR is disruptive, then you will possibly find the next one disruptive too. Please email me if this affects you.

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Merge pull request #2606 from RosettaCommons/everyday847/fmi_segid Full segment ID support in RNA applications

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Merge pull request #2601 from RosettaCommons/jadolfbr/glycan_fixes Jadolfbr/glycan fixes This PR has a bunch of bug fixes, mainly in `GlycanTreeRelax's` quench mode found during benchmarking. I'll list them below. - Fix `GlycanTreeRelax` issues if not modeling all glycans in the PDB. Improve the logic of `ResidueSelector` masking for quench mode. - Add logic to exit if `GlycanTreeRelax` has no glycans to work on. Set mover failure, which can be picked up and passed through the JD machinery. Makes us waste less time benchmarking something that does not need to be benchmarked (for example short glycans where the layer size is equivalent to the number of glycans being modeled - this then is just basic `GlycanRelax`. - Make some 'Error' output be 'Debug' in carbohydrate util functions as they are not actually errors if you are checking the return values. - `Fix GlycanTreeRelax quench mode logic` - __Fix `GlycanRelaxMover` where the MonteCarlo object was being set at the wrong place. This potentially caused input models to be output as final models and was not seen earlier, as up until this point we have been primarily building glycans from scratch and modeling them or loading very low-res models that have huge potential for improvement. __ - Add `min_rings` and `cartmin` options to `GlycanTreeRelax`

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beautifying

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Updating beautify test so beautification for master beautify all files regardless of origin of changes.

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One more minor fix.

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Minor fix for build test failures.

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Merge pull request #2610 from RosettaCommons/klimaj/backrub_disulfidize_monte_carlo Merging: Adding my first RosettaScript to the rosetta_scripts_scripts repository

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Fixed linux build settings for the BOINC graphics build.

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