Bootstrap starter template

Failed sub-tests (click for more details):
src/protocols/drug_design/DrugPolishMover.cc src/protocols/drug_design/ReactionFragment.cc src/protocols/drug_design/ReactionGrow.cc src/protocols/drug_design/ReactionMultiTransform.cc src/protocols/drug_design/SubstituentReplace.cc src/protocols/drug_design/SubstructureReplace.cc src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer cyclization

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

branch: rosetta:main 「№62158」
Commited by: Rocco Moretti
GitHub commit link: 「ed695263dca1bd3d」
Difference from previous tested commit: code diff
Commit date: 2025-04-30 14:50:28

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Monte Carlo Drug Design, base code. (#282) This is code from the long-running drug design branch (PR 1036 in the old repo), and consists of everything which hasn't already been merged and is probably worth still merging. This is being merged at this time primarily as Tracy Tang has based her work on this branch, and is getting ready to merge & publish her stuff. The changes are primarily Movers, Filters and and Chemistries added to src/protocols/drug_design/ Other changes of notes are additions of the src/protocols/rotamer_gen/ directory, which contains two Chemistry objects, one which adds RDKit rotamers, and one which adds BCL rotamers (and requires the extras=bcl build).

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Failed sub-tests (click for more details):
database_md5 replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cyclization database_md5 output_schema

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
database_md5

Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):
database_md5

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
database_md5 output_schema

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branch: rosetta:main 「№62157」
Commited by: Claiborne Tydings
GitHub commit link: 「fabfc12491cff4c3」
Difference from previous tested commit: code diff
Commit date: 2025-04-25 17:39:18

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Unfolded state tlc bugfix (#336) This changes two lines that were preventing mpi rosetta from compiling. It seems that two mentions of slave_data_vector should actually be slave_tlc_vector. The comments imply that this is the case and changing the mentions enables rosetta with mpi to compile again.

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Failed sub-tests (click for more details):
src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: ubuntu-20.04.gcc.cxx11thread.mpi.serialization.python36.scientific.peptide_pnear_vs_ic50

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branch: rosetta:main 「№62156」
Commited by: Rocco Moretti
GitHub commit link: 「a7b0eeecf9acff94」
Difference from previous tested commit: code diff
Commit date: 2025-04-25 13:46:00

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Update load_ligand.py (#375) Fix issues with `import pyrosetta.toolbox.load_ligand` -- This won't fix things for people who use the functions in question, but it will allow for use of the other functions in this module.

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cyclization

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax revold

branch: rosetta:main 「№62155」
Commited by: Sergey Lyskov
GitHub commit link: 「356248d2035a0749」
Difference from previous tested commit: code diff
Commit date: 2025-04-17 23:51:51

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

trigger clean rebuild

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Test: linux.clang.code_quality.clang_analysis

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Failed sub-tests (click for more details):
src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cyclization

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax revold

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Test: ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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Test: ubuntu-20.04.gcc.cxx11thread.mpi.serialization.python36.scientific.peptide_pnear_vs_ic50.debug

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Test: ubuntu-20.04.clang.python36.scientific.protein_data_bank_diagnostic.full

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Test: ubuntu-20.04.clang.python36.scientific.rna_denovo_favorites

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branch: rosetta:main 「№62154」
Commited by: Paul Eisenhuth
GitHub commit link: 「729367d2066d37ea」
Difference from previous tested commit: code diff
Commit date: 2025-04-14 17:28:27

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

fix clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug build (#392)

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Failed sub-tests (click for more details):
src/core/scoring/etable/etrie/TrieCountPair1BC3.cc src/core/scoring/etable/etrie/TrieCountPair1BC4.cc src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager

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branch: rosetta:main 「№62153」
Commited by: Sergey Lyskov
GitHub commit link: 「9da7ff1cb6113a3c」
Difference from previous tested commit: code diff
Commit date: 2025-04-11 23:24:03

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Fix PyRosetta on build on Python-3.11 to Apple Silicon Mac's (#393)

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Test: ubuntu.clang.cxx11thread.serialization.python38.PyRosetta.unit

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Test: clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug

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Failed sub-tests (click for more details):
src/core/scoring/etable/etrie/TrieCountPair1BC4.cc src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer

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Test: ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release

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Test: gcc-10.gcc.unit

Failed sub-tests (click for more details):
protocols:MoverFactoryTests:test_MoverFactory_all_Mover_all_attributes_have_descriptions protocols:MoverFactoryTests:test_MoverFactory_all_Mover_complexTypes_have_descriptions protocols:MoverFactoryTests:test_all_movers_define_valid_xsds

branch: rosetta:main 「№62152」
Commited by: Sergey Lyskov
GitHub commit link: 「85949a986e33c0ce」
Difference from previous tested commit: code diff
Commit date: 2025-04-10 14:18:47

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

fix Mac RC release packages (#388)

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Test: clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug

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Failed sub-tests (click for more details):
src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

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Test: m1.clang.python311.release.PyRosetta.MinSizeRel

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Test: m1.clang.python311.release.PyRosetta.Release

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branch: rosetta:main 「№62151」
Commited by: Rocco Moretti
GitHub commit link: 「695b0f21aed8ace8」
Difference from previous tested commit: code diff
Commit date: 2025-03-27 10:24:21

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Fix for the maintenance.documentation test (#374) With the new open repository, direct committing to the repos don't really work anymore. Instead, we can have the test simply test for changes, and provide a patch file that can be applied to the documentation repository. This PR also updates the documentation repo to pull in all the changes made through the wiki interface since the last update.

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Test: clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug

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Failed sub-tests (click for more details):
src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

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Test: m1.clang.python311.release.PyRosetta.MinSizeRel

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Test: m1.clang.python311.release.PyRosetta.Release

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Test: ubuntu.clang.python36.scientific.antibody_grafting

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_tilt_angle

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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Test: ubuntu-20.04.clang.python36.scientific.protein_data_bank_diagnostic.full

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branch: rosetta:main 「№62150」
Commited by: Paul Eisenhuth
GitHub commit link: 「80dd00bc09d2543c」
Difference from previous tested commit: code diff
Commit date: 2025-03-27 09:32:50

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Rosetta Evolutionary Ligand (REvoLd) (#303) This PR aims to include the newly developed application REvoLd into Rosetta. REvoLd preprint: https://arxiv.org/abs/2404.17329 The algorithm optimizes small molecule ligands within combinatorial libraries like Enamine REAL. Most code changes are self enclosed and do not affect any functionality outside of the application. The only exception are changes to cmake compile directives for mpi which were broken. A guide on how to run REvoLd is available here: https://docs.rosettacommons.org/docs/wiki/revold Unit and integration test run locally and passed all. --------- Co-authored-by: Paul Eisenhuth <eisenhuth@informatik.uni-leipzig.de>

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Test: clang-10.clang.cxx11thread.mpi.serialization.tensorflow.build.debug

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Failed sub-tests (click for more details):
src/core/scoring/etable/etrie/TrieCountPair1BC3.cc src/core/scoring/etable/etrie/TrieCountPair1BC4.cc src/protocols/ligand_evolution/FragmentLibrary.cc

Failed sub-tests (click for more details):
replica_docking revold

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cmaes_minimizer features revold

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
tensorflow_manager

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
revold

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Test: m1.clang.python311.release.PyRosetta.MinSizeRel

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Test: m1.clang.python311.release.PyRosetta.Release

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Test: linux.clang.release.source

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_tilt_angle

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branch: rosetta:main 「№62149」
Commited by: Sergey Lyskov
GitHub commit link: 「74f819c4dd581428」
Difference from previous tested commit: code diff
Commit date: 2025-03-24 15:18:17

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

change numpy.alltrue to alltrue.all to improve compatibility with Numpy-2+ (#370)

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Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
cyclization

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax

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branch: rosetta:main 「№62148」
Commited by: Rocco Moretti
GitHub commit link: 「05ba3ce142c657de」
Difference from previous tested commit: code diff
Commit date: 2025-03-17 10:39:16

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Better debugging on CIF file read in. (#356) Issue #355 indicates that errors in mmCIF parsing are not well handled. This commit attempts to fix that in two ways. The first is to add a 'from extension' fallback if the from-contents parser doesn't like it. We assume that if you're naming it xyz.pdb, you want it parsed as a PDB. The second is to print the diagnostics report for mmCIF files to the tracer -- this is what's being used to autodetect mmCIF format, so better transparency of what the failure issue is would be warranted.

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Failed sub-tests (click for more details):
helical_bundle_predict helical_bundle_predict_psipred helical_bundle_predict_psipred_with_helix_globals helical_bundle_predict_sequence helical_bundle_predict_skipping_residues recon_design_mpi replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Test: linux.clang.tensorflow.integration.tensorflow

Failed sub-tests (click for more details):
PTMPrediction abinitio_with_trRosetta esm_model_perplexity smart_annealer trRosettaProtocolMover

Test: linux.gcc.cxx11thread.integration.thread

Failed sub-tests (click for more details):
fragment_picker multithreaded_fastdesign multithreaded_fixbb multithreaded_packrotamersmover

Test: mac.clang.python39.integration

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Test: m1.clang.python310.release.PyRosetta.Release

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Test: linux.clang.release.source

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Test: ubuntu-20.04.clang.python36.scientific.FlexPepDock

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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Test: ubuntu-20.04.clang.python36.scientific.protein_data_bank_diagnostic.full

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branch: rosetta:main 「№62147」
Commited by: David Johnson
GitHub commit link: 「029c6a159b896477」
Difference from previous tested commit: code diff
Commit date: 2025-02-04 16:14:13

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

Bugfix for RosettaCM and branched glycans (#221) RosettaCM, with a branched glycan ligand, was segfaulting. In 2 locations, the "previous residue" of the given polymer entity was selected by choosing the position prior to the one in question, which is not appropriate for a branched glycan. The fix was to set a conditional for carbohydrates that uses conformation::carbohydrates::find_seqpos_of_saccharides_parent_residue to find the previous residue.

...

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
cyclization ddG_of_mutation mp_f19_relax

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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Test: ubuntu-20.04.gcc.cxx11thread.mpi.serialization.python36.scientific.peptide_pnear_vs_ic50.debug

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Test: ubuntu-20.04.clang.python36.scientific.protein_data_bank_diagnostic.full

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Test: ubuntu-20.04.clang.python36.scientific.sb_talaris13_relax_fast

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branch: rosetta:main 「№62146」
Commited by: Sergey Lyskov
GitHub commit link: 「e5e4b278bef53bc7」
Difference from previous tested commit: code diff
Commit date: 2025-01-23 20:15:53

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

fix Conda release procedure (#306)

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Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
ddG_of_mutation

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax

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Test: ubuntu-20.04.clang.python36.scientific.FlexPepDock

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Test: ubuntu-20.04.clang.python36.scientific.mp_lipid_acc

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Test: ubuntu-20.04.clang.python36.scientific.protein_data_bank_diagnostic.full

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branch: rosetta:main 「№62145」
Commited by: Sergey Lyskov
GitHub commit link: 「8ef4ef1eaaf65967」
Difference from previous tested commit: code diff
Commit date: 2025-01-21 17:59:35

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

trigger clean rebuild

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Failed sub-tests (click for more details):
replica_docking

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
mp_f19_relax

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Test: ubuntu.clang.cxx11thread.serialization.python38.release.PyRosetta.conda.Release

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Test: ubuntu-20.04.clang.python36.scientific.FlexPepDock

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branch: rosetta:main 「№62144」
Commited by: Rocco Moretti
GitHub commit link: 「c4410d087fd76508」
Difference from previous tested commit: code diff
Commit date: 2025-01-17 18:39:15

	linux.clang	linux.gcc	linux.srlz	mac.clang
debug
release
unit

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.

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Test: ubuntu.gcc.integration.addsan

Failed sub-tests (click for more details):
ligand_dock_ensemble mp_f19_relax

Failed sub-tests (click for more details):
replica_docking

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
code_template_tests_src features output_schema replica_docking

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
code_template_tests_src output_schema replica_docking