Attempt to fix failing tests in main. (#299) This PR attempts to address (in part) the following failures: * code_template_tests_src integration -- Update test (and script documentation) for the new scheme * unit valgrind -- fix for Python3 * clang tidy -- update NULL/nullptr * mp_f19_tilt_angle scientific -- Make more robust, and remove unneeded (for the scientific test) repacking step added with RosettaCommons/main#5551 * protein_data_bank_diagnostic scientific -- Errors are due to running out of pseudotty handles, attempt to recognize that situation and use a fall-back approach. * glycan_structure_prediction scientific -- Adjust number of processors and runtime to run on single node. I've also made some changes to better support the GCC 11 & Rocky9 build I'm now doing locally. I've also attempted to fix the replica_docking MPI integration test timeout, but there some additional issues which mean it's not quite working correctly.

• Summary
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.rosetta.conda.release
• ubuntu.clang.cxx11thread.serialization.python312.release.rosetta.conda.release

removing "defaults" Conda channel in favor of "conda-forge" (#241) Conda recently changed the licensing terms for they "defaults" channel so let use conda-forge instead.

• Summary
• mac.clang.cxx11thread.serialization.python310.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python311.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python39.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python312.release.rosetta.conda.release

Fix issue related to PackerTask usage in homodimer_design. (#115) With a -pack_min_runs of 2 or greater, there's a chance that the sequence of the structure changes. This is a problem for a fixed PackerTask run, as `task_is_valid( pose )` fails if the base residue types don't match up properly. This is an issue found in Discussion #112 The fix is simple -- just use the TaskFactory which we already have lying around instead of manually generating the packer task. (The PackRotamersMover will properly re-apply the TaskFactory.) We can also make the interface of PackRotamersMover a bit nicer.

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trigger test run

• Summary
• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.Release
• m1.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• mac.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release
• ubuntu.clang.cxx11thread.serialization.python313.release.PyRosetta.conda.Release

rename pytorch → torch extras and defines (#170)

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Update README.md, add Conda install instructions. (#151)

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add bindings for vector1<WaterBuilder> and test script (#131)

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fix PyRosetta builds (#69)

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set a prefix for util files (#57) The prefix is the argument passed via class_name. It is added in the description of --class_name.

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Crosslinker Mover lanthionine (#24) This is the code to enable lanthipeptide modeling in Rosetta. Crosslinker updated to include lanthionine and methyllanthionine connections. -This includes D/L ALA steriochem for lanthionine and D/L and 3 R/S steriochem for methylanthionine (B(L/D)(R/S)) Dehydrated amino acid patches for DBU and DHU were updated/added The AmbiguouosNMRDistanceConstraints were updated to work for NCAA (hardcoding was generalized) Additionally, I noticed that the thioether lariat in simple cyc pep predict only samples cis omega bonds for the N terminal residue. I changed this to trans, which should be energetically preferred.

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Fix pre-compile script calls on Windows build (#58) The windows build test on the test server doesn't seem to be updating options appropriately. It looks like the issue is that the *.sh files aren't being properly called -- adding "bash" to the front of them allows them to run properly.

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Update SCons for compilation with Python 3.12 (#54) Python 3.12 removed the imp module, which means our current SCons 3.0.4 doesn't work with it. Upgrading to SCons 4 will fix this. However, this removes support for building with Python 2.7 -- I think at this point this is acceptable, as anyone compiling Rosetta will likely have a Python3 version installed for RFDiffusion, etc. anyway. Additionally, the error message printed is relatively user friendly: ``` scons: *** SCons version 4.2.0 does not run under Python version 2.7. Python >= 3.5 is required. ``` SCons 4.2.0 was selected as it's the last version which supports Python 3.5 -- I don't know how many people that will actually help, but we don't need to be bleeding edge. Some additional files were changed to address warning messages with a Python 3.12 build. (Note that the current external/scons-local directory was deleted and then re-created from the official download. No manual changes were made, save for deleting some unnecessary documentation files.)

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Update benchmark scripts for Python3.12. (#51) Python 3.12 gets rid of the imp module. Moreover, it gets rid of imp.load_source() altogether. We thus need to change around how we do the magic 'import from parent directory' statement. There are also a few other things which were popping up warnings when I ran things locally.

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• linux.gcc.unit 「6」

QOL update to the PerResidueEsmProbabilitiesMetric (#26) This short PR: * Adds the proper citation for ESM * Adds some checks for NaNs/Infs to the Perplexity/softmax calculation * fixes a typo in MIFST.cc * Prevents an error in SampleSequenceFromProbabilities when calling the SimpleThreadingMover without mutations * Fixes const behavior in SampleSequenceFromProbabilities --------- Co-authored-by: moritzertelt <moritz.ertelt@gmail.com>

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fix PyRosetta build on Ubuntu-22.04 (#45)

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rename torch extras and defines (#43) * rename torch extras and defines * fix integration tests

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