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New Data Structures for HOOMD objects #776

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3a1f3ed
Add __len__ and __getitem__ to TypeConverterSequence
b-butler Sep 4, 2020
98ae61d
Add initial data structures
b-butler Sep 4, 2020
9f995f1
Make ParameterDict inherit from MutableMapping
b-butler Sep 4, 2020
4bdf676
Move TypeParameterDict and ParameterDict to their own files
b-butler Sep 4, 2020
f931f23
Update ParameterDict to use _HOOMDDataStructures
b-butler Sep 4, 2020
4459f18
Fix Fourier params definition
b-butler Sep 4, 2020
26f378a
Change TypeParameterDict.to_dict -> to_base
b-butler Sep 4, 2020
4753574
Change _HOOMDDataStructures._handle_update method
b-butler Sep 4, 2020
6914870
Update TypeParameterDict classes to use _HOOMDDataStructures
b-butler Sep 4, 2020
8079a5c
Add __{get,set}attr__ methods for _HOOMDDict
b-butler Sep 4, 2020
ba434d3
Add __str__ and __repr__ methods to data structure classes
b-butler Sep 4, 2020
714d8a7
Require _HOOMDDataStructures to have parent's
b-butler Sep 4, 2020
c965622
Fix bug in finding correct validation for data structure classes
b-butler Sep 4, 2020
af2db9e
Fix bug in _HOOMDDict.__getattr__
b-butler Sep 5, 2020
a8e5275
Update Data structures to handle becoming obsolete
b-butler Sep 5, 2020
0aaefc2
Update hpmc tests with new data structures
b-butler Sep 5, 2020
54c64b9
Merge branch 'master' into refactor/data-structures
b-butler Nov 17, 2020
408ac0a
Add documentation of data types.
b-butler Nov 17, 2020
712f332
Document HOOMD data structure types
b-butler Nov 17, 2020
41187e8
Remove old _param_dict file
b-butler Nov 17, 2020
eb06546
Add documentation for data structures
b-butler Dec 4, 2020
7f162d5
Apply suggestions from code review
b-butler Dec 7, 2020
b99cf0a
Remove docstrings on data structures.
b-butler Dec 7, 2020
366c3db
Add documentation for hoomd.data.data_structures._get_inner_typeconve…
b-butler Dec 7, 2020
5408df9
General data structure refactoring
b-butler Dec 7, 2020
3ee64bc
Fix bugs in synced data structures
b-butler Dec 8, 2020
adf845f
Apply suggestions from code review
b-butler Dec 8, 2020
431e449
Refactor ``_SyncedDataStructure.to_base`` methods
b-butler Dec 8, 2020
591d1b9
Update error messages and Warnings in hoomd.data.data_structures
b-butler Dec 8, 2020
b27dce3
Fix __setattr__ for ``HOOMDDict``
b-butler Dec 8, 2020
68457f1
Remove conditional from HOOMDSet.add
b-butler Dec 8, 2020
f5070ee
Rename ``hoomd.data.param_dict`` to ``parameter_dict``
b-butler Dec 8, 2020
8f2aac7
Remove hoomd.data.typeparam.TypeParameter.__deepcopy__
b-butler Dec 8, 2020
4da5cbe
Update documentation in ``hoomd.data.type_param``
b-butler Dec 8, 2020
0b20724
Fix method typo and simplify ``to_base`` for ``TypeParameterDict``
b-butler Dec 8, 2020
ac8c31e
Use ``_data`` in ``ParameterDict`` and simply ``to_base``
b-butler Dec 8, 2020
82262c1
Fix copying ``TypeParameter``.
b-butler Dec 8, 2020
f5fd4db
Remove non-complient `__deepcopy__` for ParameterDict
b-butler Dec 8, 2020
97702a4
Merge branch 'master' into refactor/data-structures
b-butler Dec 8, 2020
f634596
yapf formatting for new files
b-butler Dec 8, 2020
3b4f41b
Use """ for docstrings
b-butler Dec 8, 2020
77b57b0
Improve documentation for _get_inner_typeconverter
b-butler Dec 8, 2020
6e0d0e8
Remove :members: and from TypeParameter and add docstring
b-butler Dec 8, 2020
b9166c4
Use f-strings in more places
b-butler Dec 8, 2020
c3a6966
Fix ``to_base`` method of HOOMD data structures
b-butler Dec 8, 2020
68dbfc1
check_dict in ``hpmc.pytest.test_shape`` doesn't capture all Attribut…
b-butler Dec 8, 2020
ec38de6
Fix sphinx builds for data structures
b-butler Dec 16, 2020
44fd51f
Merge branch 'master' into refactor/data-structures
b-butler Dec 16, 2020
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2 changes: 1 addition & 1 deletion hoomd/custom/custom_operation.py
Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
from abc import abstractmethod

from hoomd.operation import _TriggeredOperation
from hoomd.data.parameterdicts import ParameterDict
from hoomd.data.param_dict import ParameterDict
from hoomd.custom.custom_action import Action, _AbstractLoggable
from hoomd.trigger import Trigger
from hoomd import _hoomd
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4 changes: 3 additions & 1 deletion hoomd/data/CMakeLists.txt
Original file line number Diff line number Diff line change
@@ -1,13 +1,15 @@
set(files __init__.py
array.py
data_structures.py
local_access.py
local_access_cpu.py
local_access_gpu.py
parameterdicts.py
param_dict.py
smart_default.py
syncedlist.py
typeconverter.py
typeparam.py
type_param_dict.py
)

install(FILES ${files}
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