Mercurial > repos > shellac > guppy_basecaller

annotate env/lib/python3.7/site-packages/humanfriendly/testing.py @ 0:26e78fe6e8c4 draft

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"planemo upload commit c699937486c35866861690329de38ec1a5d9f783"
author shellac
date Sat, 02 May 2020 07:14:21 -0400
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1 # Human friendly input/output in Python.
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2 #
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3 # Author: Peter Odding <peter@peterodding.com>
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4 # Last Change: March 6, 2020
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5 # URL: https://humanfriendly.readthedocs.io
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6
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7 """
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8 Utility classes and functions that make it easy to write :mod:`unittest` compatible test suites.
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9
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10 Over the years I've developed the habit of writing test suites for Python
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11 projects using the :mod:`unittest` module. During those years I've come to know
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12 :pypi:`pytest` and in fact I use :pypi:`pytest` to run my test suites (due to
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13 its much better error reporting) but I've yet to publish a test suite that
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14 *requires* :pypi:`pytest`. I have several reasons for doing so:
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15
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16 - It's nice to keep my test suites as simple and accessible as possible and
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17 not requiring a specific test runner is part of that attitude.
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18
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19 - Whereas :mod:`unittest` is quite explicit, :pypi:`pytest` contains a lot of
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20 magic, which kind of contradicts the Python mantra "explicit is better than
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21 implicit" (IMHO).
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22 """
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23
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24 # Standard library module
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25 import functools
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26 import logging
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27 import os
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28 import pipes
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29 import shutil
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30 import sys
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31 import tempfile
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32 import time
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33 import unittest
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34
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35 # Modules included in our package.
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36 from humanfriendly.compat import StringIO
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37 from humanfriendly.text import random_string
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38
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39 # Initialize a logger for this module.
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40 logger = logging.getLogger(__name__)
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41
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42 # A unique object reference used to detect missing attributes.
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43 NOTHING = object()
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44
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45 # Public identifiers that require documentation.
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46 __all__ = (
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47 'CallableTimedOut',
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48 'CaptureBuffer',
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49 'CaptureOutput',
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50 'ContextManager',
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51 'CustomSearchPath',
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52 'MockedProgram',
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53 'PatchedAttribute',
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54 'PatchedItem',
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55 'TemporaryDirectory',
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56 'TestCase',
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57 'configure_logging',
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58 'make_dirs',
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59 'retry',
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60 'run_cli',
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61 'skip_on_raise',
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62 'touch',
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63 )
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64
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65
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66 def configure_logging(log_level=logging.DEBUG):
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67 """configure_logging(log_level=logging.DEBUG)
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68 Automatically configure logging to the terminal.
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69
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70 :param log_level: The log verbosity (a number, defaults
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71 to :mod:`logging.DEBUG <logging>`).
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72
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73 When :mod:`coloredlogs` is installed :func:`coloredlogs.install()` will be
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74 used to configure logging to the terminal. When this fails with an
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75 :exc:`~exceptions.ImportError` then :func:`logging.basicConfig()` is used
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76 as a fall back.
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77 """
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78 try:
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79 import coloredlogs
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80 coloredlogs.install(level=log_level)
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81 except ImportError:
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82 logging.basicConfig(
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83 level=log_level,
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84 format='%(asctime)s %(name)s[%(process)d] %(levelname)s %(message)s',
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85 datefmt='%Y-%m-%d %H:%M:%S')
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86
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87
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88 def make_dirs(pathname):
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89 """
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90 Create missing directories.
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91
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92 :param pathname: The pathname of a directory (a string).
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93 """
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94 if not os.path.isdir(pathname):
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95 os.makedirs(pathname)
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96
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97
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98 def retry(func, timeout=60, exc_type=AssertionError):
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99 """retry(func, timeout=60, exc_type=AssertionError)
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100 Retry a function until assertions no longer fail.
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101
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102 :param func: A callable. When the callable returns
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103 :data:`False` it will also be retried.
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104 :param timeout: The number of seconds after which to abort (a number,
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105 defaults to 60).
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106 :param exc_type: The type of exceptions to retry (defaults
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107 to :exc:`~exceptions.AssertionError`).
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108 :returns: The value returned by `func`.
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109 :raises: Once the timeout has expired :func:`retry()` will raise the
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110 previously retried assertion error. When `func` keeps returning
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111 :data:`False` until `timeout` expires :exc:`CallableTimedOut`
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112 will be raised.
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113
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114 This function sleeps between retries to avoid claiming CPU cycles we don't
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115 need. It starts by sleeping for 0.1 second but adjusts this to one second
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116 as the number of retries grows.
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117 """
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118 pause = 0.1
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119 timeout += time.time()
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120 while True:
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121 try:
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122 result = func()
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123 if result is not False:
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124 return result
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125 except exc_type:
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126 if time.time() > timeout:
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127 raise
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128 else:
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129 if time.time() > timeout:
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130 raise CallableTimedOut()
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131 time.sleep(pause)
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132 if pause < 1:
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133 pause *= 2
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134
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135
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136 def run_cli(entry_point, *arguments, **options):
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137 """
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138 Test a command line entry point.
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139
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140 :param entry_point: The function that implements the command line interface
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141 (a callable).
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142 :param arguments: Any positional arguments (strings) become the command
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143 line arguments (:data:`sys.argv` items 1-N).
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144 :param options: The following keyword arguments are supported:
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145
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146 **capture**
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147 Whether to use :class:`CaptureOutput`. Defaults
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148 to :data:`True` but can be disabled by passing
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149 :data:`False` instead.
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150 **input**
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151 Refer to :class:`CaptureOutput`.
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152 **merged**
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153 Refer to :class:`CaptureOutput`.
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154 **program_name**
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155 Used to set :data:`sys.argv` item 0.
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156 :returns: A tuple with two values:
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157
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158 1. The return code (an integer).
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159 2. The captured output (a string).
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160 """
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161 # Add the `program_name' option to the arguments.
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162 arguments = list(arguments)
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163 arguments.insert(0, options.pop('program_name', sys.executable))
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164 # Log the command line arguments (and the fact that we're about to call the
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165 # command line entry point function).
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166 logger.debug("Calling command line entry point with arguments: %s", arguments)
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167 # Prepare to capture the return code and output even if the command line
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168 # interface raises an exception (whether the exception type is SystemExit
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169 # or something else).
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170 returncode = 0
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171 stdout = None
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172 stderr = None
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173 try:
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174 # Temporarily override sys.argv.
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175 with PatchedAttribute(sys, 'argv', arguments):
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176 # Manipulate the standard input/output/error streams?
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177 options['enabled'] = options.pop('capture', True)
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178 with CaptureOutput(**options) as capturer:
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179 try:
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180 # Call the command line interface.
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181 entry_point()
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182 finally:
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183 # Get the output even if an exception is raised.
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184 stdout = capturer.stdout.getvalue()
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185 stderr = capturer.stderr.getvalue()
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186 # Reconfigure logging to the terminal because it is very
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187 # likely that the entry point function has changed the
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188 # configured log level.
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189 configure_logging()
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190 except BaseException as e:
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191 if isinstance(e, SystemExit):
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192 logger.debug("Intercepting return code %s from SystemExit exception.", e.code)
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193 returncode = e.code
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194 else:
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195 logger.warning("Defaulting return code to 1 due to raised exception.", exc_info=True)
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196 returncode = 1
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197 else:
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198 logger.debug("Command line entry point returned successfully!")
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199 # Always log the output captured on stdout/stderr, to make it easier to
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200 # diagnose test failures (but avoid duplicate logging when merged=True).
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201 is_merged = options.get('merged', False)
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202 merged_streams = [('merged streams', stdout)]
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203 separate_streams = [('stdout', stdout), ('stderr', stderr)]
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204 streams = merged_streams if is_merged else separate_streams
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205 for name, value in streams:
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206 if value:
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207 logger.debug("Output on %s:\n%s", name, value)
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208 else:
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209 logger.debug("No output on %s.", name)
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210 return returncode, stdout
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211
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212
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213 def skip_on_raise(*exc_types):
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214 """
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215 Decorate a test function to translation specific exception types to :exc:`unittest.SkipTest`.
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216
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217 :param exc_types: One or more positional arguments give the exception
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218 types to be translated to :exc:`unittest.SkipTest`.
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219 :returns: A decorator function specialized to `exc_types`.
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220 """
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221 def decorator(function):
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222 @functools.wraps(function)
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223 def wrapper(*args, **kw):
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224 try:
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225 return function(*args, **kw)
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226 except exc_types as e:
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227 logger.debug("Translating exception to unittest.SkipTest ..", exc_info=True)
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228 raise unittest.SkipTest("skipping test because %s was raised" % type(e))
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229 return wrapper
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230 return decorator
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231
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232
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233 def touch(filename):
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234 """
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235 The equivalent of the UNIX :man:`touch` program in Python.
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236
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237 :param filename: The pathname of the file to touch (a string).
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238
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239 Note that missing directories are automatically created using
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240 :func:`make_dirs()`.
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241 """
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242 make_dirs(os.path.dirname(filename))
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243 with open(filename, 'a'):
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244 os.utime(filename, None)
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245
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246
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247 class CallableTimedOut(Exception):
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248
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249 """Raised by :func:`retry()` when the timeout expires."""
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250
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251
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252 class ContextManager(object):
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253
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254 """Base class to enable composition of context managers."""
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255
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256 def __enter__(self):
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257 """Enable use as context managers."""
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258 return self
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259
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260 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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261 """Enable use as context managers."""
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262
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263
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264 class PatchedAttribute(ContextManager):
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265
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266 """Context manager that temporary replaces an object attribute using :func:`setattr()`."""
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267
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268 def __init__(self, obj, name, value):
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269 """
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270 Initialize a :class:`PatchedAttribute` object.
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271
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272 :param obj: The object to patch.
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273 :param name: An attribute name.
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274 :param value: The value to set.
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275 """
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276 self.object_to_patch = obj
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277 self.attribute_to_patch = name
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278 self.patched_value = value
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279 self.original_value = NOTHING
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280
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281 def __enter__(self):
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282 """
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283 Replace (patch) the attribute.
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284
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285 :returns: The object whose attribute was patched.
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286 """
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287 # Enable composition of context managers.
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288 super(PatchedAttribute, self).__enter__()
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289 # Patch the object's attribute.
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290 self.original_value = getattr(self.object_to_patch, self.attribute_to_patch, NOTHING)
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291 setattr(self.object_to_patch, self.attribute_to_patch, self.patched_value)
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292 return self.object_to_patch
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293
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294 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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295 """Restore the attribute to its original value."""
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296 # Enable composition of context managers.
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297 super(PatchedAttribute, self).__exit__(exc_type, exc_value, traceback)
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298 # Restore the object's attribute.
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299 if self.original_value is NOTHING:
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300 delattr(self.object_to_patch, self.attribute_to_patch)
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301 else:
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302 setattr(self.object_to_patch, self.attribute_to_patch, self.original_value)
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303
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304
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305 class PatchedItem(ContextManager):
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306
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307 """Context manager that temporary replaces an object item using :meth:`~object.__setitem__()`."""
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308
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309 def __init__(self, obj, item, value):
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310 """
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311 Initialize a :class:`PatchedItem` object.
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312
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313 :param obj: The object to patch.
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314 :param item: The item to patch.
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315 :param value: The value to set.
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316 """
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317 self.object_to_patch = obj
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318 self.item_to_patch = item
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319 self.patched_value = value
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320 self.original_value = NOTHING
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321
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322 def __enter__(self):
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323 """
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324 Replace (patch) the item.
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325
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326 :returns: The object whose item was patched.
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327 """
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328 # Enable composition of context managers.
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329 super(PatchedItem, self).__enter__()
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330 # Patch the object's item.
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331 try:
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332 self.original_value = self.object_to_patch[self.item_to_patch]
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333 except KeyError:
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334 self.original_value = NOTHING
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335 self.object_to_patch[self.item_to_patch] = self.patched_value
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336 return self.object_to_patch
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337
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338 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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339 """Restore the item to its original value."""
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340 # Enable composition of context managers.
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341 super(PatchedItem, self).__exit__(exc_type, exc_value, traceback)
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342 # Restore the object's item.
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343 if self.original_value is NOTHING:
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344 del self.object_to_patch[self.item_to_patch]
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345 else:
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346 self.object_to_patch[self.item_to_patch] = self.original_value
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347
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348
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349 class TemporaryDirectory(ContextManager):
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350
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351 """
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352 Easy temporary directory creation & cleanup using the :keyword:`with` statement.
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353
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354 Here's an example of how to use this:
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355
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356 .. code-block:: python
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357
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358 with TemporaryDirectory() as directory:
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359 # Do something useful here.
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360 assert os.path.isdir(directory)
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361 """
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362
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363 def __init__(self, **options):
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364 """
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365 Initialize a :class:`TemporaryDirectory` object.
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366
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367 :param options: Any keyword arguments are passed on to
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368 :func:`tempfile.mkdtemp()`.
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369 """
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370 self.mkdtemp_options = options
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371 self.temporary_directory = None
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372
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373 def __enter__(self):
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374 """
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375 Create the temporary directory using :func:`tempfile.mkdtemp()`.
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376
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377 :returns: The pathname of the directory (a string).
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378 """
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379 # Enable composition of context managers.
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380 super(TemporaryDirectory, self).__enter__()
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381 # Create the temporary directory.
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382 self.temporary_directory = tempfile.mkdtemp(**self.mkdtemp_options)
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383 return self.temporary_directory
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384
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385 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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386 """Cleanup the temporary directory using :func:`shutil.rmtree()`."""
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387 # Enable composition of context managers.
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388 super(TemporaryDirectory, self).__exit__(exc_type, exc_value, traceback)
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389 # Cleanup the temporary directory.
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390 if self.temporary_directory is not None:
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391 shutil.rmtree(self.temporary_directory)
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392 self.temporary_directory = None
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393
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394
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395 class MockedHomeDirectory(PatchedItem, TemporaryDirectory):
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396
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397 """
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398 Context manager to temporarily change ``$HOME`` (the current user's profile directory).
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399
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400 This class is a composition of the :class:`PatchedItem` and
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401 :class:`TemporaryDirectory` context managers.
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402 """
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403
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404 def __init__(self):
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405 """Initialize a :class:`MockedHomeDirectory` object."""
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406 PatchedItem.__init__(self, os.environ, 'HOME', os.environ.get('HOME'))
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407 TemporaryDirectory.__init__(self)
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408
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409 def __enter__(self):
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410 """
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411 Activate the custom ``$PATH``.
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412
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413 :returns: The pathname of the directory that has
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414 been added to ``$PATH`` (a string).
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415 """
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416 # Get the temporary directory.
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417 directory = TemporaryDirectory.__enter__(self)
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418 # Override the value to patch now that we have
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419 # the pathname of the temporary directory.
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420 self.patched_value = directory
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421 # Temporary patch $HOME.
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422 PatchedItem.__enter__(self)
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423 # Pass the pathname of the temporary directory to the caller.
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424 return directory
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425
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426 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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427 """Deactivate the custom ``$HOME``."""
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428 super(MockedHomeDirectory, self).__exit__(exc_type, exc_value, traceback)
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429
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430
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431 class CustomSearchPath(PatchedItem, TemporaryDirectory):
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432
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433 """
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434 Context manager to temporarily customize ``$PATH`` (the executable search path).
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435
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436 This class is a composition of the :class:`PatchedItem` and
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437 :class:`TemporaryDirectory` context managers.
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438 """
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439
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440 def __init__(self, isolated=False):
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441 """
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442 Initialize a :class:`CustomSearchPath` object.
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443
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444 :param isolated: :data:`True` to clear the original search path,
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445 :data:`False` to add the temporary directory to the
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446 start of the search path.
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447 """
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448 # Initialize our own instance variables.
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449 self.isolated_search_path = isolated
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450 # Selectively initialize our superclasses.
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451 PatchedItem.__init__(self, os.environ, 'PATH', self.current_search_path)
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452 TemporaryDirectory.__init__(self)
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453
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454 def __enter__(self):
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455 """
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456 Activate the custom ``$PATH``.
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457
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458 :returns: The pathname of the directory that has
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459 been added to ``$PATH`` (a string).
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460 """
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461 # Get the temporary directory.
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462 directory = TemporaryDirectory.__enter__(self)
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463 # Override the value to patch now that we have
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464 # the pathname of the temporary directory.
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465 self.patched_value = (
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466 directory if self.isolated_search_path
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467 else os.pathsep.join([directory] + self.current_search_path.split(os.pathsep))
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468 )
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469 # Temporary patch the $PATH.
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470 PatchedItem.__enter__(self)
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471 # Pass the pathname of the temporary directory to the caller
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472 # because they may want to `install' custom executables.
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473 return directory
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474
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475 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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476 """Deactivate the custom ``$PATH``."""
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477 super(CustomSearchPath, self).__exit__(exc_type, exc_value, traceback)
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478
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479 @property
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480 def current_search_path(self):
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481 """The value of ``$PATH`` or :data:`os.defpath` (a string)."""
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482 return os.environ.get('PATH', os.defpath)
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483
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484
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485 class MockedProgram(CustomSearchPath):
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486
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487 """
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488 Context manager to mock the existence of a program (executable).
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489
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490 This class extends the functionality of :class:`CustomSearchPath`.
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491 """
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492
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493 def __init__(self, name, returncode=0, script=None):
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494 """
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495 Initialize a :class:`MockedProgram` object.
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496
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497 :param name: The name of the program (a string).
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498 :param returncode: The return code that the program should emit (a
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499 number, defaults to zero).
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500 :param script: Shell script code to include in the mocked program (a
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501 string or :data:`None`). This can be used to mock a
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502 program that is expected to generate specific output.
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503 """
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504 # Initialize our own instance variables.
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505 self.program_name = name
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506 self.program_returncode = returncode
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507 self.program_script = script
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508 self.program_signal_file = None
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509 # Initialize our superclasses.
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510 super(MockedProgram, self).__init__()
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511
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512 def __enter__(self):
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513 """
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514 Create the mock program.
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515
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516 :returns: The pathname of the directory that has
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517 been added to ``$PATH`` (a string).
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518 """
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519 directory = super(MockedProgram, self).__enter__()
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520 self.program_signal_file = os.path.join(directory, 'program-was-run-%s' % random_string(10))
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521 pathname = os.path.join(directory, self.program_name)
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522 with open(pathname, 'w') as handle:
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523 handle.write('#!/bin/sh\n')
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524 handle.write('echo > %s\n' % pipes.quote(self.program_signal_file))
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525 if self.program_script:
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526 handle.write('%s\n' % self.program_script.strip())
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527 handle.write('exit %i\n' % self.program_returncode)
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528 os.chmod(pathname, 0o755)
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529 return directory
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530
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531 def __exit__(self, *args, **kw):
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532 """
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533 Ensure that the mock program was run.
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534
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535 :raises: :exc:`~exceptions.AssertionError` when
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536 the mock program hasn't been run.
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537 """
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538 try:
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539 assert self.program_signal_file and os.path.isfile(self.program_signal_file), \
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540 ("It looks like %r was never run!" % self.program_name)
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541 finally:
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542 return super(MockedProgram, self).__exit__(*args, **kw)
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543
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544
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545 class CaptureOutput(ContextManager):
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546
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547 """
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548 Context manager that captures what's written to :data:`sys.stdout` and :data:`sys.stderr`.
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549
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550 .. attribute:: stdin
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551
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552 The :class:`~humanfriendly.compat.StringIO` object used to feed the standard input stream.
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553
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554 .. attribute:: stdout
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555
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556 The :class:`CaptureBuffer` object used to capture the standard output stream.
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557
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558 .. attribute:: stderr
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559
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560 The :class:`CaptureBuffer` object used to capture the standard error stream.
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561 """
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562
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563 def __init__(self, merged=False, input='', enabled=True):
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564 """
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565 Initialize a :class:`CaptureOutput` object.
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566
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567 :param merged: :data:`True` to merge the streams,
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568 :data:`False` to capture them separately.
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569 :param input: The data that reads from :data:`sys.stdin`
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570 should return (a string).
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571 :param enabled: :data:`True` to enable capturing (the default),
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572 :data:`False` otherwise. This makes it easy to
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573 unconditionally use :class:`CaptureOutput` in
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574 a :keyword:`with` block while preserving the
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575 choice to opt out of capturing output.
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576 """
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577 self.stdin = StringIO(input)
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578 self.stdout = CaptureBuffer()
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579 self.stderr = self.stdout if merged else CaptureBuffer()
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580 self.patched_attributes = []
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581 if enabled:
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582 self.patched_attributes.extend(
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583 PatchedAttribute(sys, name, getattr(self, name))
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584 for name in ('stdin', 'stdout', 'stderr')
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585 )
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586
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587 def __enter__(self):
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588 """Start capturing what's written to :data:`sys.stdout` and :data:`sys.stderr`."""
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589 super(CaptureOutput, self).__enter__()
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590 for context in self.patched_attributes:
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591 context.__enter__()
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592 return self
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593
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594 def __exit__(self, exc_type=None, exc_value=None, traceback=None):
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595 """Stop capturing what's written to :data:`sys.stdout` and :data:`sys.stderr`."""
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596 super(CaptureOutput, self).__exit__(exc_type, exc_value, traceback)
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597 for context in self.patched_attributes:
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598 context.__exit__(exc_type, exc_value, traceback)
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599
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600 def get_lines(self):
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601 """Get the contents of :attr:`stdout` split into separate lines."""
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602 return self.get_text().splitlines()
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603
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604 def get_text(self):
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605 """Get the contents of :attr:`stdout` as a Unicode string."""
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606 return self.stdout.get_text()
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607
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608 def getvalue(self):
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609 """Get the text written to :data:`sys.stdout`."""
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610 return self.stdout.getvalue()
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611
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612
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613 class CaptureBuffer(StringIO):
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614
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615 """
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616 Helper for :class:`CaptureOutput` to provide an easy to use API.
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617
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618 The two methods defined by this subclass were specifically chosen to match
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619 the names of the methods provided by my :pypi:`capturer` package which
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620 serves a similar role as :class:`CaptureOutput` but knows how to simulate
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621 an interactive terminal (tty).
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622 """
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623
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624 def get_lines(self):
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625 """Get the contents of the buffer split into separate lines."""
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626 return self.get_text().splitlines()
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627
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628 def get_text(self):
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629 """Get the contents of the buffer as a Unicode string."""
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630 return self.getvalue()
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631
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632
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633 class TestCase(unittest.TestCase):
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634
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635 """Subclass of :class:`unittest.TestCase` with automatic logging and other miscellaneous features."""
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636
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637 def __init__(self, *args, **kw):
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638 """
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639 Initialize a :class:`TestCase` object.
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640
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641 Any positional and/or keyword arguments are passed on to the
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642 initializer of the superclass.
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643 """
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644 super(TestCase, self).__init__(*args, **kw)
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645
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646 def setUp(self, log_level=logging.DEBUG):
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647 """setUp(log_level=logging.DEBUG)
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648 Automatically configure logging to the terminal.
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649
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650 :param log_level: Refer to :func:`configure_logging()`.
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651
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652 The :func:`setUp()` method is automatically called by
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653 :class:`unittest.TestCase` before each test method starts.
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654 It does two things:
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655
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656 - Logging to the terminal is configured using
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657 :func:`configure_logging()`.
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658
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659 - Before the test method starts a newline is emitted, to separate the
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660 name of the test method (which will be printed to the terminal by
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661 :mod:`unittest` or :pypi:`pytest`) from the first line of logging
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662 output that the test method is likely going to generate.
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663 """
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664 # Configure logging to the terminal.
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665 configure_logging(log_level)
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666 # Separate the name of the test method (printed by the superclass
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667 # and/or py.test without a newline at the end) from the first line of
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668 # logging output that the test method is likely going to generate.
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669 sys.stderr.write("\n")