Bootstrap starter template

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

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

branch: rosetta:main 「№62187」
Commited by: Jason C. Klima
GitHub commit link: 「df75a9c48e763e52」
Difference from previous tested commit: code diff
Commit date: 2025-09-03 14:23:30

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

Add cooldown time for PyRosettaCluster unit tests (#512)

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replica_docking

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input_and_output

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

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_sequence_recovery

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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.cif

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

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branch: rosetta:main 「№62186」
Commited by: Rocco Moretti
GitHub commit link: 「58d657c59974c1aa」
Difference from previous tested commit: code diff
Commit date: 2025-08-25 11:10:48

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

Change Gemmi submodule from ssh to https (#500) Issue #492 indicates there's issues with having the Gemmi submodule loaded by SSH. Change that to HTTPS, to match other external submodules.

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Test: icc.icc.build.debug

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replica_docking revold_oas

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input_and_output

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

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Test: ubuntu-24.04.gcc.cxx11thread.serialization.unit

branch: rosetta:main 「№62185」
Commited by: Jason C. Klima
GitHub commit link: 「e842d23e18c6567d」
Difference from previous tested commit: code diff
Commit date: 2025-08-19 14:37:10

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

Add support for filtering results in PyRosettaCluster (#459)

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Test: icc.icc.build.debug

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

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 revold_oas

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input_and_output

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

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

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Test: ubuntu-20.04.clang.python36.scientific.mp_f19_sequence_recovery

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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.protein_data_bank_diagnostic.cif

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

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branch: rosetta:main 「№62184」
Commited by: Andrew Muenks
GitHub commit link: 「50a63df696059188」
Difference from previous tested commit: code diff
Commit date: 2025-08-15 17:00:07

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

Removed unused variable in GALigandDock (#499) An unused variable was causing some builds to crash. This PR removes that variable. Additionally, update some values that needed to be changed during peer review. -- Co-authored-by: Andrew Muenks <amuenks@uw.edu>

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Test: icc.icc.build.debug

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

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

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

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: gcc-9.gcc.unit

branch: rosetta:main 「№62183」
Commited by: Jason C. Klima
GitHub commit link: 「7b35872d6974b902」
Difference from previous tested commit: code diff
Commit date: 2025-08-12 17:23:25

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

Refactor PyRosettaCluster protocol logging from multiple processes (#487)

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

Test: ubuntu.gcc.integration.addsan

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

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

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

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.sb_talaris13_fast_design

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Test: linux.gcc.unit.valgrind

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62182」
Commited by: Jason C. Klima
GitHub commit link: 「a492b89a9e4fe490」
Difference from previous tested commit: code diff
Commit date: 2025-08-11 18:23:02

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

Broaden PyRosetta conda package dependency version requirements for NumPy (#496)

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

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

Test: linux.gcc.cxx11thread.integration.thread

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

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

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Test: ubuntu-20.04.clang.python36.scientific.sb_talaris13_fast_design

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62181」
Commited by: Sergey Lyskov
GitHub commit link: 「452533b21daa7fe9」
Difference from previous tested commit: code diff
Commit date: 2025-07-29 20:27:41

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

Refactor PyRosetta unit tests to always run in fresh venv, temporary disable distributed tests for Python-3.12 builds. (#478)

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

Test: ubuntu.gcc.integration.addsan

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

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

Test: linux.gcc.cxx11thread.integration.thread

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

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input_and_output

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

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

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

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

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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.cif

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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.python312.scripts.pyrosetta

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62180」
Commited by: Jason C. Klima
GitHub commit link: 「389c9b9a2d9623d7」
Difference from previous tested commit: code diff
Commit date: 2025-07-28 16:08:04

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

Set correct scope for automatic protocol detection in PyRosettaCluster reproduction (#484)

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

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

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

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

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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branch: rosetta:main 「№62179」
Commited by: Jason C. Klima
GitHub commit link: 「7eecbf982a05136a」
Difference from previous tested commit: code diff
Commit date: 2025-07-28 14:57:51

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

Add the deterministic_flag option to the ProteinMPNNProbabilitiesMetric SimpleMetric (#485) This PR adds the `deterministic_flag` option to the `ProteinMPNNProbabilitiesMetric` PerResidueProbabilitiesMetric. After some evidence provided in #429, the `ProteinMPNNMover` already has the `deterministic_flag` option set to `false` by default, and therefore due to Torch randomness the `ProteinMPNNProbabilitiesMetric` can return non-deterministic PSSM tables, even with the `-run:constant_seed 1` Rosetta option enabled. This PR just adds some control of the `ProteinMPNNMover` from the `ProteinMPNNProbabilitiesMetric` to enable deterministic mode when calculating per-residue ProteinMPNN probabilities.

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

Test: linux.clang.integration.release_debug_no_symbols

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

Test: mac.clang.python39.integration

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

branch: rosetta:main 「№62178」
Commited by: Jason C. Klima
GitHub commit link: 「ac33e63d6cac6784」
Difference from previous tested commit: code diff
Commit date: 2025-07-28 14:54:43

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

Initial commit (#483) If using the local `OptionsCollection` in the `ProtocolSettingsMetric` CompositeStringMetric, the `get_script_vars` and `get_user_options` arguments are swapped relative to the `parse_options` signature. These options are both `true` by default, so this bug has likely gone unnoticed, but would only have an effect when `get_script_vars` and `get_user_options` have different values.

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

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
control_flow_rs protocol_metric simple_metrics_in_protocols

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
control_flow_rs protocol_metric simple_metrics_in_protocols

branch: rosetta:main 「№62177」
Commited by: Jason C. Klima
GitHub commit link: 「fce88fc4bd527d5f」
Difference from previous tested commit: code diff
Commit date: 2025-07-21 07:05:21

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

Support yielding PackedPose objects in memory from PyRosettaCluster (#452) * Initial commit * Refactor * Fix import * Fix import * Update typing * Update unit tests * Support str inputs * Update typing and docstrings * Clean up * Refactor yield_results * Refactor __call__ method * Add warning and update docstring * Update docstring * Enable runtime tests for evaluation * Update logging in runtime tests * Set logging stream handler * Disable runtime tests

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

Test: ubuntu.gcc.integration.addsan

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

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

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

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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.ligand_scoring_ranking

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

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

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Test: linux.gcc.python310.unit

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Test: linux.gcc.python38.unit

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Test: linux.gcc.python39.unit

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62176」
Commited by: Jason C. Klima
GitHub commit link: 「c07e51cae6c8448b」
Difference from previous tested commit: code diff
Commit date: 2025-07-11 11:50:06

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

Enable Pose.scores dictionary to store arbitrary python objects (#430) * Fix KeyError for string objects * Serialize and deserialize values in pose scores dictionary * Update TypeError message * Maybe deserialize ScoreMap.get_arbitrary_string_data_from_pose data * Test PyJobDistributor with arbitrary scoretypes * Test SimpleMetric implementation * Fix NotImplementedError * Update unit tests that assert that float values are rounded upon score set/get round trips * Add warnings for setPoseExtraScore float value precision change, type casting, and possible UnicodeDecodeError * Update import * Update reserved scoretypes * Add rounding difference to warning message * Update imports * Initial refactor of pose.cache dictionary * Add pose.cache unit tests * Remove numpy dependency for non-serialization builds * Change pose.scores to pose.cache * Move pose.cache into modules for comprehensibility * Use pose.cache instead of packed_pose.update_scores * Set clobber warnings in pose.scores * Add deprecation warning to pose.scores * Add warning if key in immutable SimpleMetrics data exists * Clean up * Setting PackedPose.scores to Pose.cache * Set cache with packed_pose.update_scores * Fix warning * Reserve pose.cache keys * Update warning messages * Update warning message * Update PackedPose.scores dictionary with pose.cache * Update logging message test * Update reserve_scores decorator to be using pose.cache * Add update_scores in reserve_scores * Update version * Add syntax warning for setting PackedPose.scores items * Test saving detached scores in the PackedPose.scores dictionary * Improve docstring example * Update docstrings * Clean up * Split into separate warnings when deleting reserved scoretypes * Return nested MappingProxyType read-only data by pose.cache.all_scores * Update docstrings * Minor tweaks to docstrings * Clean up applying SimpleMetrics to the pose * Validate strict base64

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

Test: ubuntu.gcc.integration.addsan

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

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

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

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

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62175」
Commited by: Rocco Moretti
GitHub commit link: 「8b147f0d79aeb0e1」
Difference from previous tested commit: code diff
Commit date: 2025-07-10 16:33:45

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

Add RosettaLigand docking scores to the Pose when JD2 is not active. (#456) People running RosettaLigand jobs under PyRosetta keep having problems that the computed docking scores don't show up. This is because the current RosettaLigand code was written for RosettaScripts and assumes the use of JD2. The scores get stuck in a JD2 job, which is hard to access when you're not running a command line JD2 job. We can change the code to stick the scores into the pose instead of (in addition to) the job when not running under JD2 (e.g. PyRosetta) Hopefully this should make the access easier.

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Failed sub-tests (click for more details):
src/apps/public/motif_ligand_discovery/remove_duplicate_motifs.cc

Test: ubuntu.gcc.integration.addsan

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

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

Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
features ligand_dock_cholesterol ligand_dock_script_jd3 output_schema revold_oas

Test: mac.clang.python39.integration

Failed sub-tests (click for more details):
ligand_dock_cholesterol ligand_dock_script_jd3 output_schema revold_oas

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

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62174」
Commited by: Rocco Moretti
GitHub commit link: 「d5c0879478ad1543」
Difference from previous tested commit: code diff
Commit date: 2025-07-09 18:11:15

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

Update mmCIF parsing (#450) It's been noted that Rosetta's mmCIF parsing doesn't work with a number of structures. (Critically, with the mmCIF files output by AlphaFold3). One big limitation is that we're using an old CIFPARSE-OBJ library. This was reasonable at the time, as it was the official C++ library from the RCSB. However, the RCSB has since moved to Python-level processing, and CIFPARSE-OBJ has had no maintenance since before we incorporated it. We've also been consistently bumping up against issues with how it functions. The Gemmi library has been integrated into Foldit, and that seemed to work well. This is an actively maintained, open source(*) header only (at least for CIF parsing) library. The interface is slightly different from CIFPARSE-OBJ, but not terribly difficult to translate. This PR removes CIFPARSE-OBJ and replaces it with Gemmi. (Version v0.7.1) Additionally, I included some changes to the ciffile readers and writers to make them more compatible. ChimeraX is still complaining a bit about Rosetta-produced cif files, but I think that's mainly cosmetic. One possible complication is that Gemmi is nominally C++14 (versus our current C++11). It looks like we're actually okay with the bits we're using (no C++14 issues), but even if we do have to bump the C++ version, given the increasing importance of mmCIF files (e.g. supporting AlphaFold3 output), I think that's a decent reason to do it. *) Gemmi is under the Mozilla Public License Version 2.0. This has "share alike" provisions, but only at the file level. Provided we keep Gemmi-provided code in the external/ directory, this should be compatible with the Rosetta license. (CoMotion has confirmed that MPL is acceptable.)

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Test: icc.icc.build.debug

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Test: ubuntu-24.04.clang.build.debug

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.debug

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Test: ubuntu-24.04.clang.build.release

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Test: ubuntu-24.04.clang.cxx11thread.serialization.build.release

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Failed sub-tests (click for more details):
InterfaceAnalyzer_ligand features jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO ligand_motif_identification mmtfIO_score_test pymol_cif restype_converter simple_grafting_movers simple_metrics_b_factor simple_metrics_per_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):
InterfaceAnalyzer_ligand jd2test_PDBin_mmCIFout jd2test_PDBin_mmCIFout_extra_data_separate jd2test_mmCIFIO ligand_motif_identification mmtfIO_score_test mp_f19_relax pymol_cif restype_converter simple_grafting_movers simple_metrics_b_factor simple_metrics_per_residue

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

Test: mac.clang.python39.integration

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Test: linux.clang.performance

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

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

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Test: ubuntu-24.04.clang.cxx11thread.serialization.unit

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Test: ubuntu-24.04.clang.unit

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branch: rosetta:main 「№62173」
Commited by: Rocco Moretti
GitHub commit link: 「4af227b4a532553b」
Difference from previous tested commit: code diff
Commit date: 2025-07-09 16:27:17

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

Add option to control intermediate dumping in BackrubProtocol (#372) Especially with XML (where the Backrub protocol is part of a more extensive protocol), you don't necessarily want an unconditional dumping of the last & low results from the Backrub stage. This commit adds an XML option which will allow the dumping of the poses (old behavior), but turns it off by default. This only changes XML usage -- I didn't change how the backrub application behaves. Changes to the backrub_interface_ddG integration test is expected.

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