allpy: bc1a7595d9d1 allpy/util.py

allpy

view allpy/util.py @ 1107:bc1a7595d9d1

Clean rewrite or markup_to_file.py util; --markup is now optional and allows specifying multiple markups as a comma-separated list

author	Daniil Alexeyevsky <dendik@kodomo.fbb.msu.ru>
date	Thu, 14 Jun 2012 19:05:28 +0400
parents	c1091715f8a3
children	0736e1bbd186

line source

1 """Miscellanous utilities.

2 """

3 import sys

4 import warnings

5 import os

6 import inspect

7 import functools

8 from tempfile import mkstemp

9 from StringIO import StringIO

11 def unzip(seq):

12 """The oppozite of zip() builtin."""

13 a, b = [], []

14 for x, y in seq:

15 a.append(x)

16 b.append(y)

17 return a, b

19 def open(filename, mode='r'):

20 """Open file. Return stdin/stdout for filename '-'."""

21 if filename == '-':

22 if 'w' in mode or 'a' in mode or '+' in mode:

23 return sys.stdout

24 if 'r' in mode:

25 return sys.stdin

26 raise AssertionError("Unknown file mode: %s" % mode)

27 else:

28 return file(filename, mode)

30 def remove_each(string, substrings):

31 """Remove each of substrings from string."""

32 for sub in substrings:

33 string = string.replace(sub, "")

34 return string

36 class UserDict(dict):

37 """Clone of dict that user may add attributes to."""

38 pass

40 class UserList(list):

41 """Clone of list that user may add attributes to."""

42 pass

44 class UserString(str):

45 """Clone of str that user may add attributes to."""

46 pass

48 def deprecated(message=None, what=None, in_favor=None, removed_in=None):

49 """Warn about function being deprecated."""

50 if not message:

51 if what is None:

52 frame = inspect.currentframe().f_back

53 caller = []

54 if inspect.getmodule(frame):

55 caller.append(inspect.getmodule(frame).__name__)

56 if 'self' in frame.f_locals:

57 caller.append(frame.f_locals['self'].__class__.__name__)

58 elif 'cls' in frame.f_locals:

59 caller.append(frame.f_locals['cls'].__name__)

60 caller.append(frame.f_code.co_name)

61 what = ".".join(caller) + "(...)"

62 message = "{0} is deprecated".format(what)

63 if in_favor:

64 message = "{0} in favor of {1}".format(message, in_favor)

65 if removed_in:

66 message = "{0}; will be removed in allpy version {1}".format(message, removed_in)

67 warnings.warn(message, DeprecationWarning, stacklevel=2)

69 def Deprecated(message=None, in_favor=None, removed_in=None):

70 def decorator(function):

71 @functools.wraps(function)

72 def decorated(*args, **kws):

73 text = "{0} is deprecated".format(function)

74 if in_favor:

75 text = "{0} in favor of {1}".format(text, in_favor)

76 if removed_in:

77 text = "{0}\n\nWill be removed in allpy version {1}.".format(text, removed_in)

78 if message:

79 text = "{0}\n\n{1}".format(text, message)

80 warnings.warn(text, DeprecationWarning, stacklevel=2)

81 return function(*args, **kws)

82 return decorated

83 return decorator

85 class Silence(object):

86 """Context manager for use with `with`.

88 Run code in context without any message to the screen, but show all output

89 that was there if an error occured. E.g.::

91 with Silence():

92 structure = PDBParser().get_structure(name, file)

94 There are two mutually exclusive ways of silencing:

96 1. By replacing OS'es stdout/stderr with tempfile (called `dup`)

97 2. By replacing python's sys.stdout/sys.stderr with StringIO (`hide`)

99 For each of ways you may specify values: 'stdout', 'stderr' or 'both'.

100 E.g::

101

102 with Silence(dup="both"):

103 check_call(["mucle", alignment])

104

105 `Silence()` is equivalent to `Silence(hide='stderr')`

106 """

107

108 def __init__(self, hide=None, dup=None):

109 if dup is None and hide is None:

110 hide = "stderr"

111 assert not (dup is not None and hide is not None)

112 self.stderr = self.stdout = self.dup_stderr = self.dup_stdout = False

113 if dup == "stdout" or dup == "both":

114 self.dup_stdout = True

115 if dup == "stderr" or dup == "both":

116 self.dup_stderr = True

117 if hide == "stdout" or hide == "both":

118 self.stdout = True

119 if hide == "stderr" or hide == "both":

120 self.stderr = True

121

122 def __enter__(self):

123 assert not (self.stderr and self.dup_stderr)

124 assert not (self.stdout and self.dup_stdout)

125 if self.dup_stdout or self.dup_stderr:

126 fd, name = mkstemp(prefix="allpy-silent-")

127 self.captured_dup = os.fdopen(fd)

128 self.captured_dup_name = name

129 if self.dup_stdout:

130 self.dup_stdout = os.dup(sys.stdout.fileno())

131 os.dup2(self.captured_dup.fileno(), sys.stdout.fileno())

132 if self.dup_stderr:

133 self.dup_stderr = os.dup(sys.stderr.fileno())

134 os.dup2(self.captured_dup.fileno(), sys.stderr.fileno())

135 if self.stdout or self.stderr:

136 self.captured_output = StringIO()

137 if self.stdout:

138 self.stdout, sys.stdout = sys.stdout, self.captured_output

139 if self.stderr:

140 self.stderr, sys.stderr = sys.stderr, self.captured_output

141

142 def __exit__(self, exc_type, exc_value, traceback):

143 if self.stdout or self.stderr:

144 if self.stdout:

145 sys.stdout = self.stdout

146 if self.stderr:

147 sys.stderr = self.stderr

148 if exc_type is not None:

149 sys.stderr.write(self.captured_output.getvalue())

150 if self.dup_stdout or self.dup_stderr:

151 if self.dup_stdout:

152 os.dup2(self.dup_stdout, sys.stdout.fileno())

153 os.close(self.dup_stdout)

154 if self.dup_stderr:

155 os.dup2(self.dup_stderr, sys.stderr.fileno())

156 os.close(self.dup_stderr)

157 if exc_type is not None:

158 self.captured_dup.seek(0)

159 sys.stderr.write(self.captured_dup.read())

160 os.unlink(self.captured_dup_name)

161

162 # vim: set et ts=4 sts=4 sw=4: