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19fc50f
Initial commit
klimaj Mar 17, 2026
ade55e8
git pull origin main
klimaj Mar 17, 2026
a3e893e
git pull origin main
klimaj Mar 17, 2026
8232678
Clean up commented main blocks
klimaj Mar 17, 2026
c978619
Add validator for max_task_replicas keyword argument
klimaj Mar 17, 2026
0d9117c
Pop max_task_replicas and task_registry
klimaj Mar 17, 2026
ad2b572
Assert that full simulation records do not save the 'max_task_replica…
klimaj Mar 17, 2026
d3a6bbf
Clean up new line
klimaj Mar 17, 2026
3467761
Refactor setup_worker_logging wrapper positional-or-keyword parameters
klimaj Mar 17, 2026
b180497
Refactor user_spawn_thread positional-or-keyword parameters
klimaj Mar 17, 2026
7174109
Disable verbose
klimaj Mar 17, 2026
fa0febd
Supporting max_task_replicas and task_registry keyword arguments
klimaj Mar 17, 2026
96b9ad9
Clarify docstrings
klimaj Mar 17, 2026
af183d1
Fix line lengths
klimaj Mar 17, 2026
ec45062
Clarify docstrings and exceptions
klimaj Mar 18, 2026
2fe6b90
Raise exception if task resubmission failed for consistency with lega…
klimaj Mar 18, 2026
8ff4344
Loosen validation to allow a started AMM but disabled ReduceReplicas …
klimaj Mar 18, 2026
f0c8f10
Update docstring
klimaj Mar 18, 2026
8bf1852
Update PrioritiesTest test case to reflect different user_spawn_threa…
klimaj Mar 18, 2026
599a109
Update relevant exception messages in RetriesTest test case
klimaj Mar 18, 2026
e6d17d0
Raise TaskCancelledError during CancelledError exception handling
klimaj Mar 18, 2026
bb51d39
Clarify logging messages
klimaj Mar 18, 2026
a14182e
Clean up comments in WorkerPreemptionTest
klimaj Mar 18, 2026
ca63e4a
Validate 'tasks' attribute
klimaj Mar 20, 2026
c718c79
Add tests for 'tasks' attribute validation
klimaj Mar 20, 2026
9379df1
git rebase --onto origin/main preempt validate_tasks
klimaj Mar 20, 2026
cf64034
Validate keys of 'tasks' attribute
klimaj Mar 20, 2026
f6c6b7b
Add tests for 'tasks' attribute key validation
klimaj Mar 20, 2026
ecf4aca
Update typing
klimaj Mar 22, 2026
c0ec735
Split tasks validator function to validate an individual task
klimaj Mar 22, 2026
b388dfe
Validate tasks produced by user-provided PyRosetta protocols
klimaj Mar 22, 2026
5b0749f
Test that logging warnings are emitted when attempting to return keys…
klimaj Mar 22, 2026
18c9e6c
Test that keys starting with reserved key prefix are ignored
klimaj Mar 22, 2026
c5deb75
Validate input task dictionaries are equal after roundtrip JSON-seria…
klimaj Mar 22, 2026
f0b2cec
Add TestReproducibilityTaskUpdates test case
klimaj Mar 22, 2026
c7e83bb
Clean up TestReproducibilityTaskUpdates
klimaj Mar 22, 2026
be8c51c
Update version
klimaj Mar 22, 2026
1abe62a
Add TestReproducibilityRemodelTaskUpdates.test_reproduce_remodel_task…
klimaj Mar 23, 2026
5bf197a
Only normalize task options on the first PyRosetta protocol
klimaj Mar 23, 2026
5e72882
Wrap score_function_is_available with staticmethod
klimaj Mar 23, 2026
f862b94
Define PackedPoseHasher to hash Pose geometry, scores, and comments
klimaj Mar 23, 2026
e144d1b
git pull origin main
klimaj Mar 23, 2026
c383d4c
Make task JSON-serializable in SmokeTestMulti.test_smoke_multi; also …
klimaj Mar 23, 2026
4093ec7
Test normalized packing option group values
klimaj Mar 23, 2026
49b24eb
git pull origin main
klimaj Mar 23, 2026
901deac
Update version
klimaj Mar 23, 2026
458e041
Update docstrings and exceptions for clarity
klimaj Mar 23, 2026
a8d0b61
Reformat usage examples in docstrings for Sphinx
klimaj Mar 23, 2026
20b906e
Reformat docstrings for Sphinx
klimaj Mar 23, 2026
b52193d
Make tasks JSON serializable in ScoresTest.test_secure_packages_billi…
klimaj Mar 23, 2026
d7f1ff9
Clarifying module docstring
klimaj Mar 23, 2026
57244de
Partially reformat docstring
klimaj Mar 24, 2026
580a6e9
Enabling verbose
klimaj Mar 24, 2026
7f35612
Disable some tests to debug
klimaj Mar 24, 2026
ed00c99
Partially reformat docstring
klimaj Mar 24, 2026
133aabf
Fix output directories; Set max_workers and add cooldown_time
klimaj Mar 24, 2026
663ce5b
Disable a scorefunction
klimaj Mar 24, 2026
ae52b4f
Clear energies before return
klimaj Mar 24, 2026
ebcfd7a
Partially reformat docstring
klimaj Mar 24, 2026
399d6b5
Set init=False for 'task_registry_dir' attribute
klimaj Mar 24, 2026
a5ce7d4
Disable a test
klimaj Mar 24, 2026
758233b
Disable scorefunctions
klimaj Mar 24, 2026
44d9144
Partially reformat docstring
klimaj Mar 25, 2026
aaedb03
Partially reformat docstring
klimaj Mar 25, 2026
1d261b8
Reorder docstring keyword arguments based on keyword parameters
klimaj Mar 25, 2026
e29c5d2
Change available scorefunctions
klimaj Mar 25, 2026
f70a795
Testing a scorefunction
klimaj Mar 25, 2026
182a348
Re-enable unit tests
klimaj Mar 25, 2026
b4a0f18
Clean up; add comments
klimaj Mar 25, 2026
ad8a6af
Update docstrings
klimaj Mar 25, 2026
4eee094
Fix validator
klimaj Mar 25, 2026
542e50a
raise PyRosettaIsNotInitializedError
klimaj Mar 25, 2026
6f98ca5
Disable verbose
klimaj Mar 25, 2026
ecf9fc0
Adding self.assertWarns(UserWarning) context manager test
klimaj Mar 25, 2026
a421b4d
Print if verbose
klimaj Mar 25, 2026
76a4d13
Update docstrings, logging and exception messages
klimaj Mar 25, 2026
0f25a71
Updating typing from distributed.client.Client to distributed.Client
klimaj Mar 25, 2026
964ad98
Update docstrings, logging and exception messages
klimaj Mar 25, 2026
3c10df1
git pull origin validate_tasks
klimaj Mar 25, 2026
b758765
Update warning and exception messages
klimaj Mar 25, 2026
6368c71
Update docstrings, warning and exception messages
klimaj Mar 25, 2026
d1626e3
Update docstrings, warning and exception messages
klimaj Mar 25, 2026
ad9725a
Update docstrings, warning and exception messages
klimaj Mar 26, 2026
149156f
Update import formatting
klimaj Mar 26, 2026
b49cc3c
Update docstrings and spacing
klimaj Mar 26, 2026
fc40891
Reformat imports
klimaj Mar 26, 2026
a0b9bb9
git pull origin main
klimaj Mar 30, 2026
ce0c4e6
Clarify skip_corrections keyword argument documentation of reproduce …
klimaj Mar 30, 2026
e42f24d
Clean up error message formatting; clarify produce docstring
klimaj Mar 30, 2026
afe3b52
Clean up nonce cache error messages
klimaj Mar 29, 2026
3dc6460
Clean up docstrings and error messages
klimaj Mar 30, 2026
164ee54
Fix spacing; format docstrings
klimaj Mar 30, 2026
e19037e
Fix newlines
klimaj Mar 30, 2026
25f90f7
Add docstrings
klimaj Mar 30, 2026
2dd1fe6
Fix spacing
klimaj Mar 30, 2026
fa4de97
Add pickle warnings to relevant docstrings
klimaj Mar 30, 2026
9d73ffb
Fix NoReturn typing
klimaj Mar 31, 2026
c50c596
Improve pickle warnings at main entrypoints
klimaj Mar 31, 2026
8878534
Import PackedPoseHasher to top-level
klimaj Mar 31, 2026
a21525b
Clarify ImportError message
klimaj Mar 31, 2026
bff0936
Fix import
klimaj Mar 31, 2026
b6132e0
Clean up
klimaj Mar 31, 2026
6eaf409
Type Security object
klimaj Mar 31, 2026
5944dc2
Remove duplicate globals
klimaj Mar 31, 2026
371f679
Clarify docstring
klimaj Mar 31, 2026
8e7b97f
Catch unsupported set type
klimaj Mar 31, 2026
00ec5f8
Catch unordered sets in _parse_protocols
klimaj Mar 31, 2026
31da6cb
Initial commit
klimaj Apr 1, 2026
c31e575
Improving type hints for user-facing API
klimaj Apr 1, 2026
36251bc
Fix imports
klimaj Apr 1, 2026
8a805f1
Add internal method type abstractions
klimaj Apr 1, 2026
7b589a3
Fix TypeVar assignments
klimaj Apr 1, 2026
a78f04b
Initial typing refactor
klimaj Apr 1, 2026
85b41f0
Update typing and docstrings
klimaj Apr 1, 2026
c87ea0d
Replace BaseException
klimaj Apr 1, 2026
c72ab47
Consolidate get_worker logic
klimaj Apr 1, 2026
68066e0
Merge branch 'main' of github.com:klimaj/rosetta into docstrings
klimaj Apr 3, 2026
e2ab1b8
Update type definitions
klimaj Apr 4, 2026
8ec63ec
Fix init_from_file_kwargs docstring section
klimaj Apr 4, 2026
803262d
Update attrs attributes for static type checking
klimaj Apr 4, 2026
db98164
Update attr syntax; use ExtraArgs class
klimaj Apr 4, 2026
cd498c5
Update version
klimaj Apr 4, 2026
51554ae
Clean up imports
klimaj Apr 4, 2026
5221d3d
Remove Generic types
klimaj Apr 4, 2026
33fc350
Consolidate generic callable type variables
klimaj Apr 5, 2026
3b21da5
Conditionally import AbstractSet and Deque
klimaj Apr 5, 2026
bd20f6b
Catch dict in reserve_scores; define PyRosettaProtocolType type variable
klimaj Apr 5, 2026
9f8d93a
Clean up imports
klimaj Apr 5, 2026
a88de88
Consolidate typing into type_defs.py
klimaj Apr 5, 2026
e2540f7
Add typing for Pose or PackedPose
klimaj Apr 5, 2026
5712c12
Fix typing
klimaj Apr 5, 2026
cc69ace
Clean up imports; add secure_read_pickle
klimaj Apr 5, 2026
6c6f1d2
Update typing
klimaj Apr 5, 2026
33742de
Parameterize typing
klimaj Apr 5, 2026
f8d8196
Update docstrings and typing
klimaj Apr 6, 2026
7f63657
Consolidate warning messages
klimaj Apr 6, 2026
9161c29
Fix docstring
klimaj Apr 6, 2026
b71f5e3
Fix docstring
klimaj Apr 6, 2026
1ae5414
Clean up imports and typing
klimaj Apr 7, 2026
fa50973
Update docstrings and an error message
klimaj Apr 7, 2026
9cdb577
Update distributed import
klimaj Apr 7, 2026
01163f9
Fix expected self.assertIn
klimaj Apr 7, 2026
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,15 @@
# (c) For more information, see http://www.rosettacommons.org. Questions about this can be
# (c) addressed to University of Washington CoMotion, email: license@uw.edu.


__author__ = "Jason C. Klima"

import warnings

from contextlib import suppress

from pyrosetta.distributed.cluster.core import PyRosettaCluster
from pyrosetta.distributed.cluster.toolkit import (
PackedPoseHasher,
Serialization,
export_init_file,
generate_dask_tls_security,
Expand All @@ -27,12 +28,13 @@
requires_packed_pose,
reserve_scores,
run,
secure_read_pickle,
update_scores,
)
from typing import List

from pyrosetta.distributed.cluster.type_defs import List

__all__: List[str] = [
"PackedPoseHasher",
"PyRosettaCluster",
"Serialization",
"export_init_file",
Expand All @@ -48,10 +50,10 @@
"requires_packed_pose",
"reserve_scores",
"run",
"secure_read_pickle",
"update_scores",
]
__version__: str = "4.1.0"

__version__: str = "5.0.0"

with warnings.catch_warnings() and suppress(NameError):
warnings.simplefilter("ignore", category=UserWarning)
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