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
|
#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Handling deprecation warnings and messages correctly.
"""
import os
import warnings
from dendropy.utility import metavar
DEPRECATION_WARNING_FILTER = None
_DEPRECATION_WARNINGS_CONFIGURED = False
class CriticalDeprecationWarning(UserWarning):
pass
def configure_deprecation_warning_behavior(warning_filter=None):
global DEPRECATION_WARNING_FILTER
global _DEPRECATION_WARNINGS_CONFIGURED
if warning_filter is None:
warning_filter = os.environ.get(metavar.DEPRECATION_WARNING_FILTER, "default")
DEPRECATION_WARNING_FILTER = warning_filter
warnings.simplefilter(DEPRECATION_WARNING_FILTER,
CriticalDeprecationWarning)
_DEPRECATION_WARNINGS_CONFIGURED = True
def _initialize_deprecation_warnings():
global _DEPRECATION_WARNINGS_CONFIGURED
if not _DEPRECATION_WARNINGS_CONFIGURED:
configure_deprecation_warning_behavior()
def dendropy_deprecation_warning(**kwargs):
_initialize_deprecation_warnings()
leader = " # "
stacklevel = kwargs.pop("stacklevel", 3)
if "message" in kwargs:
message = kwargs["message"]
elif "old_construct" in kwargs or "new_construct" in kwargs:
message = []
message.append("")
if "preamble" in kwargs:
message.append(leader + kwargs["preamble"])
message.append(leader + "Instead of:")
for construct in kwargs["old_construct"].split("\n"):
message.append(leader + " {}".format(construct))
message.append(leader + "Use:")
for construct in kwargs["new_construct"].split("\n"):
message.append(leader + " {}".format(construct))
if "epilog" in kwargs:
message.append(leader + kwargs["epilog"])
message = "\n".join(message)
_initialize_deprecation_warnings()
old_formatwarning = warnings.formatwarning
warnings.warn(
message=message,
category=CriticalDeprecationWarning,
stacklevel=stacklevel,
)
|
