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1 ###############################################################################
2 # #
3 # relax #
4 # #
5 # Protein dynamics by NMR relaxation data analysis #
6 # #
7 # by Edward d'Auvergne #
8 # #
9 ###############################################################################
10 # #
11 # Licence #
12 # #
13 # relax, a program for relaxation data analysis. #
14 # #
15 # Copyright (C) 2001-2006 Edward d'Auvergne #
16 # Copyright (C) 2006-2016 the relax development team #
17 # #
18 # This program is free software; you can redistribute it and/or modify #
19 # it under the terms of the GNU General Public License as published by #
20 # the Free Software Foundation, either version 3 of the License, or #
21 # (at your option) any later version. #
22 # #
23 # This program is distributed in the hope that it will be useful, #
24 # but WITHOUT ANY WARRANTY; without even the implied warranty of #
25 # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the #
26 # GNU Library General Public License for more details. #
27 # #
28 # You should have received a copy of the GNU General Public License #
29 # along with this program; if not, write to the Free Software #
30 # #
31 ###############################################################################
32
33 # Module docstring.
34 """The main module for relax execution."""
35
36 # Dependency checks.
37 import dep_check
38
39 # Eliminate the ^[[?1034h escape code being produced on Linux systems by the import of the readline module.
40 import os
41 if 'TERM' in os.environ and os.environ['TERM'] == 'xterm':
42 os.environ['TERM'] = 'linux'
43
44 # Set up the Python 2 and 3 work-arounds.
45 import lib.compat
46
47 # Python modules.
48 import numpy
49 from optparse import Option, OptionGroup, OptionParser
50 from os import F_OK, access, getpid, putenv
51 if dep_check.cprofile_module:
52 import cProfile as profile
53 elif dep_check.profile_module:
54 import profile
55 import pstats
56 from pydoc import pager
57 import sys
58
59 # relax modules.
60 from info import Info_box
61 import lib.errors
62 from lib.io import io_streams_log, io_streams_tee
63 import lib.warnings
64 from multi import Application_callback, load_multiprocessor
65 from prompt import interpreter
66 from status import Status; status = Status()
67 import user_functions
68 import version
69
70
71 # Set up the user functions.
72 user_functions.initialise()
73
74 # Modify the environmental variables.
75 putenv('PDBVIEWER', 'vmd')
76
77
79 """Execute relax.
80
81 @keyword mode: Force a relax mode, overriding the command line.
82 @type mode: str
83 @keyword profile_flag: Change this flag to True for code profiling.
84 @type profile_flag: bool
85 """
86
87 # Normal relax operation.
88 relax = Relax()
89
90 # Override normal operation.
91 if mode:
92 # Override the mode.
93 relax.mode = mode
94
95 # Some defaults.
96 relax.script_file = None
97 relax.log_file = None
98 relax.tee_file = None
99 relax.multiprocessor_type = 'uni'
100 relax.n_processors = 1
101
102 # Process the command line arguments.
103 else:
104 relax.arguments()
105
106 # Store some start up info in the status object.
107 status.relax_mode = relax.mode
108
109 # Set up the multi-processor elements.
110 callbacks = Application_callback(master=relax)
111 verbosity = 0
112 if status.debug:
113 verbosity = 1
114 processor = load_multiprocessor(relax.multiprocessor_type, callbacks, processor_size=relax.n_processors, verbosity=verbosity)
115
116 # Place the processor fabric intro string into the info box.
117 info = Info_box()
118 info.multi_processor_string = processor.get_intro_string()
119
120 # Normal relax operation.
121 if not profile_flag:
122 # Execute relax in multi-processor mode (this includes the uni-processor for normal operation).
123 processor.run()
124
125 # relax in profiling mode.
126 else:
127 def print_stats(stats, status=0):
128 pstats.Stats(stats).sort_stats('time', 'name').print_stats()
129
130 # No profile module.
131 if not dep_check.profile_module:
132 sys.stderr.write("The profile module is not available, please install the Python development packages for profiling.\n\n")
133 sys.exit()
134
135 # Run relax in profiling mode.
136 profile.Profile.print_stats = print_stats
137 profile.runctx('processor.run()', globals(), locals())
138
139
140
142 """The main relax class.
143
144 This contains information about the running state, for example the mode of operation of relax,
145 whether debugging is turned on, etc.
146 """
147
149 """The top level class for initialising the program.
150
151 @keyword mode: Force a relax mode, overriding the command line.
152 @type mode: str
153 """
154
155 # Get and store the PID of this process.
156 self.pid = getpid()
157
158
160 """Execute relax.
161
162 This is the application callback method executed by the multi-processor framework.
163 """
164
165 # Set up the warning system.
166 lib.warnings.setup()
167
168 # Logging.
169 if self.log_file:
170 io_streams_log(self.log_file)
171
172 # Tee.
173 elif self.tee_file:
174 io_streams_tee(self.tee_file)
175
176 # Show the version number and exit.
177 if self.mode == 'version':
178 print('relax ' + version.version_full())
179 return
180
181 # Show the relax info and exit.
182 if self.mode == 'info':
183 # Initialise the information box.
184 info = Info_box()
185
186 # Print the program intro.
187 print(info.intro_text())
188
189 # Print the system info.
190 print(info.sys_info())
191
192 # Stop execution.
193 return
194
195 # Run the interpreter for the prompt or script modes.
196 if self.mode == 'prompt' or self.mode == 'script':
197 # Run the interpreter.
198 self.interpreter = interpreter.Interpreter()
199 self.interpreter.run(self.script_file)
200
201 # Execute the relax GUI.
202 elif self.mode == 'gui':
203 # Dependency check.
204 if not dep_check.wx_module:
205 sys.stderr.write("Please install the wx Python module to access the relax GUI.\n\n")
206 return
207
208 # Only import the module in this mode (to improve program start up speeds).
209 import gui
210
211 # Set the GUI flag in the status object.
212 status.show_gui = True
213
214 # Start the relax GUI wx application.
215 app = gui.App(script_file=self.script_file)
216 app.MainLoop()
217
218 # Execute the relax test suite
219 elif self.mode == 'test suite':
220 # Only import the module in the test modes (to improve program start up speeds).
221 from test_suite.test_suite_runner import Test_suite_runner
222
223 # Load the interpreter and turn intros on.
224 self.interpreter = interpreter.Interpreter(show_script=False, raise_relax_error=True)
225 self.interpreter.on()
226
227 # Run the tests.
228 runner = Test_suite_runner(self.tests, timing=self.test_timings)
229 runner.run_all_tests()
230
231 # Execute the relax system tests.
232 elif self.mode == 'system tests':
233 # Only import the module in the test modes (to improve program start up speeds).
234 from test_suite.test_suite_runner import Test_suite_runner
235
236 # Load the interpreter and turn intros on.
237 self.interpreter = interpreter.Interpreter(show_script=False, raise_relax_error=True)
238 self.interpreter.on()
239
240 # Run the tests.
241 runner = Test_suite_runner(self.tests, timing=self.test_timings)
242 runner.run_system_tests()
243
244 # Execute the relax unit tests.
245 elif self.mode == 'unit tests':
246 # Only import the module in the test modes (to improve program start up speeds).
247 from test_suite.test_suite_runner import Test_suite_runner
248
249 # Run the tests.
250 runner = Test_suite_runner(self.tests, timing=self.test_timings)
251 runner.run_unit_tests()
252
253 # Execute the relax GUI tests.
254 elif self.mode == 'GUI tests':
255 # Only import the module in the test modes (to improve program start up speeds).
256 from test_suite.test_suite_runner import Test_suite_runner
257
258 # Run the tests.
259 runner = Test_suite_runner(self.tests, timing=self.test_timings)
260 runner.run_gui_tests()
261
262 # Execute the relax verification tests.
263 elif self.mode == 'verification tests':
264 # Only import the module in the test modes (to improve program start up speeds).
265 from test_suite.test_suite_runner import Test_suite_runner
266
267 # Run the tests.
268 runner = Test_suite_runner(self.tests, timing=self.test_timings)
269 runner.run_verification_tests()
270
271 # Test mode.
272 elif self.mode == 'test':
273 self.test_mode()
274
275 # Licence mode.
276 elif self.mode == 'licence':
277 self.licence()
278
279 # Unknown mode.
280 else:
281 raise lib.errors.RelaxError("The '%s' mode is unknown." % self.mode)
282
283
285 """Process the command line arguments."""
286
287 # Parser object.
288 parser = RelaxParser(self, usage="usage: %prog [options] [script_file]")
289
290 # Recognised command line options for the UI.
291 group = OptionGroup(parser, 'UI options')
292 group.add_option('-p', '--prompt', action='store_true', dest='prompt', default=0, help='launch relax in prompt mode after running any optionally supplied scripts')
293 group.add_option('-g', '--gui', action='store_true', dest='gui', default=0, help='launch the relax GUI')
294 group.add_option('-i', '--info', action='store_true', dest='info', default=0, help='display information about this version of relax')
295 group.add_option('-v', '--version', action='store_true', dest='version', default=0, help='show the version number and exit')
296 group.add_option('--licence', action='store_true', dest='licence', default=0, help='display the licence')
297 group.add_option('--test', action='store_true', dest='test', default=0, help='run relax in test mode')
298 parser.add_option_group(group)
299
300 # Recognised command line options for the multiprocessor.
301 group = OptionGroup(parser, 'Multi-processor options')
302 group.add_option('-m', '--multi', action='store', type='string', dest='multiprocessor', default='uni', help='set multi processor method')
303 group.add_option('-n', '--processors', action='store', type='int', dest='n_processors', default=-1, help='set number of processors (may be ignored)')
304 parser.add_option_group(group)
305
306 # Recognised command line options for IO redirection.
307 group = OptionGroup(parser, 'IO redirection options')
308 group.add_option('-l', '--log', action='store', type='string', dest='log', help='log relax output to the file LOG_FILE', metavar='LOG_FILE')
309 group.add_option('-t', '--tee', action='store', type='string', dest='tee', help='tee relax output to both stdout and the file LOG_FILE', metavar='LOG_FILE')
310 parser.add_option_group(group)
311
312 # Recognised command line options for the test suite.
313 group = OptionGroup(parser, 'Test suite options')
314 group.add_option('-x', '--test-suite', action='store_true', dest='test_suite', default=0, help='execute the full relax test suite')
315 group.add_option('-s', '--system-tests', action='store_true', dest='system_tests', default=0, help='execute the system/functional tests. Test names, revealed with the --time option, can be supplied to perform a subset of all tests.')
316 group.add_option('-u', '--unit-tests', action='store_true', dest='unit_tests', default=0, help='execute the unit tests. Module names, revealed with the --time option, can be supplied to perform a subset of all tests.')
317 group.add_option('--gui-tests', action='store_true', dest='gui_tests', default=0, help='execute the GUI tests. Test names, revealed with the --time option, can be supplied to perform a subset of all tests.')
318 group.add_option('--verification-tests', action='store_true', dest='verification_tests', default=0, help='execute the software verification tests. Test names, revealed with the --time option, can be supplied to perform a subset of all tests.')
319 group.add_option('--time', action='store_true', dest='tt', default=0, help='print out the timings of individual tests in the test suite')
320 group.add_option('--no-skip', action='store_true', dest='no_skip', default=0, help='a debugging option for relax developers to turn on all blacklisted tests, even those that will fail')
321 parser.add_option_group(group)
322
323 # Recognised command line options for debugging.
324 group = OptionGroup(parser, 'Debugging options')
325 group.add_option('-d', '--debug', action='store_true', dest='debug', default=0, help='enable debugging output')
326 group.add_option('--error-state', action='store_true', dest='error_state', default=0, help='save a pickled state file when a RelaxError occurs')
327 group.add_option('--traceback', action='store_true', dest='traceback', default=0, help='show stack tracebacks on all RelaxErrors and RelaxWarnings')
328 group.add_option('-e', '--escalate', action='store_true', dest='escalate', default=0, help='escalate all warnings to errors')
329 group.add_option('--numpy-raise', action='store_true', dest='numpy_raise', default=0, help='convert numpy warnings to errors')
330 parser.add_option_group(group)
331
332 # Parse the options.
333 (options, args) = parser.parse_args()
334
335 # Debugging options: Debugging flag, escalate flag, traceback flag, and numpy warning to error conversion.
336 if options.debug:
337 status.debug = True
338 if options.escalate:
339 lib.warnings.ESCALATE = True
340 if options.traceback:
341 status.traceback = True
342 lib.warnings.TRACEBACK = True
343 if options.numpy_raise:
344 numpy.seterr(all='raise')
345 if options.error_state:
346 lib.errors.SAVE_ERROR_STATE = True
347
348 # Script prompt interactive inspection flag.
349 if options.prompt:
350 status.prompt = True
351
352 # Logging.
353 if options.log:
354 # Exclusive modes.
355 if options.tee:
356 parser.error("the logging and tee options cannot be set simultaneously")
357
358 # The log file.
359 self.log_file = options.log
360
361 # Fail if the file already exists.
362 if access(self.log_file, F_OK):
363 parser.error("the log file " + repr(self.log_file) + " already exists")
364 else:
365 self.log_file = None
366
367 # Tee.
368 if options.tee:
369 # Exclusive modes.
370 if options.log:
371 parser.error("the tee and logging options cannot be set simultaneously")
372
373 # The tee file.
374 self.tee_file = options.tee
375
376 # Fail if the file already exists.
377 if access(self.tee_file, F_OK):
378 parser.error("the tee file " + repr(self.tee_file) + " already exists")
379 else:
380 self.tee_file = None
381
382 # Test suite mode, therefore the args are the tests to run and not a script file.
383 if options.test_suite or options.system_tests or options.unit_tests or options.gui_tests or options.verification_tests:
384 # Store the arguments.
385 self.tests = args
386
387 # Test timings.
388 self.test_timings = False
389 if options.tt:
390 self.test_timings = True
391
392 # Run blacklisted tests.
393 status.skip_blacklisted_tests = True
394 if options.no_skip:
395 status.skip_blacklisted_tests = False
396
397 # The argument is a script.
398 else:
399 # Number of positional arguments should only be 0 or 1. 1 should be the script file.
400 if len(args) > 1:
401 parser.error("incorrect number of arguments")
402
403 # Script file.
404 self.script_file = None
405 if len(args) == 1:
406 self.script_file = args[0]
407
408 # Test if the script file exists.
409 if not access(self.script_file, F_OK):
410 parser.error("the script file " + repr(self.script_file) + " does not exist")
411
412 # Set the multi-processor type and number.
413 self.multiprocessor_type = options.multiprocessor
414 self.n_processors = options.n_processors
415
416 # Checks for the multiprocessor mode.
417 if self.multiprocessor_type == 'mpi4py' and not dep_check.mpi4py_module:
418 parser.error(dep_check.mpi4py_message)
419
420
421 # Determine the relax mode and test for mutually exclusive modes.
422 #################################################################
423
424 # Show the version number.
425 if options.version:
426 self.mode = 'version'
427
428 # Show the info about this relax version.
429 elif options.info:
430 self.mode = 'info'
431
432 # Run the relax tests.
433 elif options.test_suite or options.system_tests or options.unit_tests or options.gui_tests or options.verification_tests:
434 # Exclusive modes.
435 if options.test:
436 parser.error("executing the relax test suite and running relax in test mode are mutually exclusive")
437 elif options.licence:
438 parser.error("executing the relax test suite and running relax in licence mode are mutually exclusive")
439
440 # Set the mode.
441 if options.test_suite:
442 self.mode = 'test suite'
443 elif options.system_tests:
444 self.mode = 'system tests'
445 elif options.unit_tests:
446 self.mode = 'unit tests'
447 elif options.gui_tests:
448 self.mode = 'GUI tests'
449 elif options.verification_tests:
450 self.mode = 'verification tests'
451
452 # Set the status flag.
453 status.test_mode = True
454
455 # Test mode.
456 elif options.test:
457 # Make sure no script is supplied.
458 if self.script_file:
459 parser.error("a script should not be supplied in test mode")
460
461 # Exclusive modes.
462 if options.test_suite or options.system_tests or options.unit_tests or options.gui_tests or options.verification_tests:
463 parser.error("the relax test mode and executing the test suite are mutually exclusive")
464 elif options.licence:
465 parser.error("the relax modes test and licence are mutually exclusive")
466
467 # Set the mode.
468 self.mode = 'test'
469
470 # Licence mode.
471 elif options.licence:
472 # Make sure no script is supplied.
473 if self.script_file:
474 parser.error("a script should not be supplied in test mode")
475
476 # Exclusive modes.
477 if options.test_suite or options.system_tests or options.unit_tests or options.gui_tests or options.verification_tests:
478 parser.error("the relax licence mode and executing the test suite are mutually exclusive")
479 elif options.test:
480 parser.error("the relax modes licence and test are mutually exclusive")
481
482 # Set the mode.
483 self.mode = 'licence'
484
485 # GUI.
486 elif options.gui:
487 # Exclusive models.
488 if options.test_suite or options.system_tests or options.unit_tests or options.gui_tests or options.verification_tests:
489 parser.error("the relax GUI mode and testing modes are mutually exclusive")
490 elif options.licence:
491 parser.error("the relax GUI mode and licence mode are mutually exclusive")
492
493 # Missing wx module.
494 if not dep_check.wx_module:
495 # Not installed.
496 if dep_check.wx_module_message == "No module named 'wx'":
497 parser.error("To use the GUI, the wxPython module must be installed.")
498
499 # Broken.
500 else:
501 parser.error("The wxPython installation is broken:\n%s." % dep_check.wx_module_message)
502
503 # Set the mode.
504 self.mode = 'gui'
505
506 # Script mode.
507 elif self.script_file:
508 self.mode = 'script'
509
510 # Prompt mode (default).
511 else:
512 self.mode = 'prompt'
513
514
516 """Function for displaying the licence."""
517
518 # Present the GPL using paging.
519 file = open('docs/COPYING')
520 pager(file.read())
521
522
528
529
530
532 - def __init__(self, relax, usage=None, option_list=None, option_class=Option, version=None, conflict_handler="error", description=None, formatter=None, add_help_option=1, prog=None):
533 """Subclassed OptionParser class with a replacement error function."""
534
535 # Relax base class.
536 self.relax = relax
537
538 # Run the __init__ method of the OptionParser class.
539 OptionParser.__init__(self, usage, option_list, option_class, version, conflict_handler, description, formatter, add_help_option, prog)
540
541
543 """Replacement error function."""
544
545 # Usage message.
546 self.print_usage(sys.stderr)
547
548 # Raise a clean error.
549 try:
550 raise lib.errors.RelaxError(message)
551 except lib.errors.AllRelaxErrors:
552 instance = sys.exc_info()[1]
553 sys.stderr.write(instance.__str__())
554
555 # Exit.
556 sys.exit()
557
558
559 # Start relax if this file is passed to Python.
560 if __name__ == "__main__":
561 start()
562
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