-
Notifications
You must be signed in to change notification settings - Fork 34
Expand file tree
/
Copy path__init__.py
More file actions
135 lines (108 loc) · 3.72 KB
/
__init__.py
File metadata and controls
135 lines (108 loc) · 3.72 KB
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
#!/usr/bin/env python
##############################################################################
#
# (c) 2024-2026 The Trustees of Columbia University in the City of New York.
# All rights reserved.
#
# File coded by: Chris Farrow, Pavol Juhas, Simon Billinge, Billinge Group members.
#
# See GitHub contributions for a more detailed list of contributors.
# https://github.com/diffpy/diffpy.structure/graphs/contributors
#
# See LICENSE.rst for license information.
#
##############################################################################
"""Crystal structure container and parsers for structure formats.
Classes related to the structure of materials:
* Atom
* Lattice
* Structure
* PDFFitStructure
Other classes:
* SpaceGroup
* SymOp
* ExpandAsymmetricUnit
* GeneratorSite
* SymmetryConstraints
Exceptions:
* StructureFormatError
* LatticeError
* SymmetryError
"""
import os
import sys
import diffpy.structure as _structure
from diffpy.structure.atom import Atom
from diffpy.structure.lattice import Lattice
from diffpy.structure.parsers import get_parser
from diffpy.structure.pdffitstructure import PDFFitStructure
from diffpy.structure.structure import Structure
from diffpy.structure.structureerrors import LatticeError, StructureFormatError, SymmetryError
# package version
from diffpy.structure.version import __version__
from diffpy.utils._deprecator import build_deprecation_message, deprecated
# Deprecations -------------------------------------------------------
base = "diffpy.structure"
removal_version = "4.0.0"
loadStructure_deprecation_msg = build_deprecation_message(
base,
"loadStructure",
"load_structure",
removal_version,
)
# @deprecated
# custom deprecator for diffpy.Structure module
class DeprecatedStructureModule:
"""Proxy for backward compatibility of diffpy.Structure."""
def __getattr__(self, name):
import warnings
warnings.warn(
"Module 'diffpy.Structure' is deprecated and will be removed in version 4.0. "
"Use 'diffpy.structure' instead.",
DeprecationWarning,
stacklevel=2,
)
return getattr(_structure, name)
sys.modules["diffpy.Structure"] = DeprecatedStructureModule()
# top level routines
@deprecated(loadStructure_deprecation_msg)
def loadStructure(filename, fmt="auto", **kw):
"""This function has been deprecated and will be removed in version
4.0.0.
Please use diffpy.structure.load_structure instead.
"""
return load_structure(filename, fmt, **kw)
def load_structure(filename, fmt="auto", **kw):
"""Load new structure object from the specified file.
Parameters
----------
filename : str
Path to the file to be loaded.
fmt : str, Optional
Format of the structure file such as 'cif' or 'xyz'. Must be
one of the formats listed by the `parsers.inputFormats` function.
When 'auto', all supported formats are tried in a sequence.
kw : Optional
Extra keyword arguments that are passed to `parsers.getParser`
function. These configure the dedicated Parser object that
is used to read content in filename.
Returns
-------
stru : `Structure`, `PDFFitStructure`
The new Structure object loaded from the specified file.
Return a more specific PDFFitStructure type for 'pdffit'
and 'discus' formats.
"""
filename = os.fspath(filename)
p = get_parser(fmt, **kw)
rv = p.parse_file(filename)
return rv
# silence pyflakes checker
assert StructureFormatError and LatticeError and SymmetryError
assert Atom
assert Lattice
assert Structure
assert PDFFitStructure
# silence the pyflakes syntax checker
assert __version__ or True
# End of file