Merge pull request #2438 from RosettaCommons/roccomoretti/release_mode_fix Address release system issues * Remove Werror from the releases * Make release mode default in releases * Add path searching as default in site.settings * Remove pilot directories more broadly.

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Merge pull request #2425 from RosettaCommons/roccomoretti/test_fixes Some fixes to uninitialized variables found by the best-effort tests (valgrind, addsan, ubsan).

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Merge pull request #2454 from RosettaCommons/atom-moyer/pyrosetta-poses_from_silent Atom moyer/pyrosetta poses from silent

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Merge pull request #2424 from RosettaCommons/rhiju/new_scorefxn_tags new best stepwise scorefunction: rna_res_level_energy7beta • only tests that change appear cosmetic (due to new hbondoption; or to small differences in JD3 to legacy stepwise job distributor)

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Merge pull request #2458 from RosettaCommons/jklai/hydrate Fixing remaining failed tests for the Hydrate/SPaDES application. PR #2418 broke multiple tests, which were subsequently fixed with commit 5441c8635ed5f646 and some changes by Andy Watkins. The changes in this PR fixes the remaining two failed integration tests: "thread_local_tracers_check" and "app_exception_handling," which were identified by the test server and in a comment by Rocco Moretti.

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Merge pull request #2456 from RosettaCommons/everyday847/fix_branch_conn Fix farfar_mrna by fixing branch connection energies

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fixing problem with cleanAlignment integration test

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Merge pull request #2452 from RosettaCommons/bcov/XmlObjects XmlObjects: Importing your xml scripts into C++/PyRosetta Ever since I moved to PyRosetta/C++ from RosettaScripts, I've had a desire to import my RosettaScript into xml and use the components. Well now it's possible! Consider the following code snippets: objs = protocols.rosetta_scripts.XmlObjects.create_from_file("script.xml") my_fully_configured_mover = objs.get_mover("best_mover") my_fully_configured_mover.apply(pose) the_wholel_xml_protocol = objs.get_mover("ParsedProtocol") objs = protocols.rosetta_scripts.XmlObjects.create_from_string(""" <RESIDUE_SELECTORS> <Chain name="chainA" chains="A" /> <Neighborhood name="neighborhood" distance="7" selector="chainA" /> </RESIDUE_SELECTORS> """) neighborhood = objs.get_residue_selector("neighborhood") neighborhood.set_distance(9) neighborhood.apply(pose) task_op = protocols.rosetta_scripts.XmlObjects.static_get_task_operation("<PreventRepacking />") These all work which I think opens up all sorts of possibilities. If you've worked hard on an xml and you want to use its parts in PyRosetta, now you can! I can even see large xml libraries being prepared so that one can load pre-configured movers into PyRosetta. If you want to use this in C++, you'll need to get cozy with std::dynamic_pointer_cast< >.

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Merge pull request #2449 from RosettaCommons/everyday847/start_stop_size FoldTree edges should start and stop on Sizes

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Beautifying master.

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Fixed build

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Fixing a test that _someone else_ had broken, woo.

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weights files

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remove references in performance benchmark to unimplemented fa_plane

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Merge pull request #2435 from RosettaCommons/JWLabonte/sugars/docking Carbohydrates: Moving dock_glycans.cc to public This work is published, so it should be in public. dock_glycans integration test changes expected.

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Merge pull request #2448 from RosettaCommons/everyday847/comment_faplane comment out unimplemented fa_plane

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