Author: bugman
Date: Thu Jul 28 15:14:55 2011
New Revision: 13951
URL: http://svn.gna.org/viewcvs/relax?rev=13951&view=rev
Log:
Redesign of the main relax module.
The module has been renamed to 'relax.py', and the original file 'relax' is
now a very basic python
script which simply loads the module and runs the new start() function for
launching relax. The MS
Windows BAT file has also been updated to feed the module into python.
Added:
1.3/relax.py (contents, props changed)
- copied, changed from r13935, 1.3/relax
Modified:
1.3/relax
1.3/relax.bat
Modified: 1.3/relax
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax?rev=13951&r1=13950&r2=13951&view=diff
==============================================================================
--- 1.3/relax (original)
+++ 1.3/relax Thu Jul 28 15:14:55 2011
@@ -1,395 +1,7 @@
#! /usr/bin/env python
-###############################################################################
-#
#
-# relax
#
-#
#
-# Protein dynamics by NMR relaxation data analysis
#
-#
#
-# by Edward d'Auvergne
#
-#
#
-###############################################################################
-#
#
-# Licence
#
-#
#
-# relax, a program for relaxation data analysis.
#
-#
#
-# Copyright (C) 2001-2006 Edward d'Auvergne
#
-# Copyright (C) 2006-2011 the relax development team
#
-#
#
-# This program is free software; you can redistribute it and/or modify
#
-# it under the terms of the GNU General Public License as published by
#
-# the Free Software Foundation; either version 2 of the License, or
#
-# (at your option) any later version.
#
-#
#
-# This program is distributed in the hope that it will be useful,
#
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
#
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
#
-# GNU Library General Public License for more details.
#
-#
#
-# You should have received a copy of the GNU General Public License
#
-# along with this program; if not, write to the Free Software
#
-# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
#
-#
#
-###############################################################################
+# Import the relax module.
+import relax
-# First of all, store the relax installation path before the site-packages
mangle sys.path.
-from status import Status; status = Status()
-import sys
-status.install_path = sys.path[0]
-
-# Dependency checks.
-import dep_check
-
-# Python modules.
-from optparse import Option, OptionParser
-from os import F_OK, access, getpid, putenv
-if dep_check.profile_module:
- import profile
-import pstats
-from re import match
-from string import split, strip
-import sys
-
-# relax modules.
-from info import Info_box
-import generic_fns
-if dep_check.wx_module:
- import gui
-from prompt.gpl import gpl
-from prompt import interpreter
-import relax_errors
-from relax_io import io_streams_log, io_streams_tee
-import relax_warnings
-from test_suite.test_suite_runner import Test_suite_runner
-from version import version
-
-# Modify the environmental variables.
-putenv('PDBVIEWER', 'vmd')
-
-
-
-class Relax:
- """The main relax class.
-
- This contains information about the running state, for example the mode
of operation of relax,
- whether debugging is turned on, etc.
- """
-
- def __init__(self):
- """The top level class for initialising the program."""
-
- # Get and store the PID of this process.
- self.pid = getpid()
-
- # Setup the object containing the generic functions.
- self.generic = generic_fns
-
- # Process the command line arguments and determine the relax mode.
- mode, log_file, tee_file = self.arguments()
-
- # Set up the warning system.
- relax_warnings.setup(self.pedantic)
-
- # Show the version number and exit.
- if mode == 'version':
- print(('relax ' + version))
- sys.exit()
-
- # Show the relax info and exit.
- if mode == 'info':
- info = Info_box()
- print(info.sys_info())
- sys.exit()
-
- # Logging.
- if log_file:
- io_streams_log(log_file)
-
- # Tee.
- elif tee_file:
- io_streams_tee(tee_file)
-
- # Run the interpreter for the prompt or script modes.
- if mode == 'prompt' or mode == 'script':
- # Run the interpreter.
- self.interpreter = interpreter.Interpreter()
- self.interpreter.run(self.script_file)
-
- # Execute the relax GUI.
- elif mode == 'gui':
- # Dependency check.
- if not dep_check.wx_module:
- sys.stderr.write("Please install the wx Python module to
access the relax GUI.\n\n")
- sys.exit()
-
- # Start the relax GUI wx application.
- app = gui.App(script=self.script_file)
- app.MainLoop()
-
- # Execute the relax test suite
- elif mode == 'test suite':
- # Load the interpreter and turn intros on.
- self.interpreter = interpreter.Interpreter(show_script=False,
quit=False, raise_relax_error=True)
- self.interpreter.on()
-
- # Run the tests.
- runner = Test_suite_runner(self.tests)
- runner.run_all_tests()
-
- # Execute the relax system tests.
- elif mode == 'system tests':
- # Load the interpreter and turn intros on.
- self.interpreter = interpreter.Interpreter(show_script=False,
quit=False, raise_relax_error=True)
- self.interpreter.on()
-
- # Run the tests.
- runner = Test_suite_runner(self.tests)
- runner.run_system_tests()
-
- # Execute the relax unit tests.
- elif mode == 'unit tests':
- # Run the tests.
- runner = Test_suite_runner(self.tests)
- runner.run_unit_tests()
-
- # Test mode.
- elif mode == 'test':
- self.test_mode()
-
- # Licence mode.
- elif mode == 'licence':
- self.licence()
-
- # Unknown mode.
- else:
- raise relax_errors.RelaxError("The '%s' mode is unknown." % mode)
-
-
- def arguments(self):
- """Function for processing the command line arguments."""
-
- # Parser object.
- parser = RelaxParser(self, usage="usage: %prog [options]
[script_file]")
-
- # Recognised command line options.
- parser.add_option('-d', '--debug', action='store_true',
dest='debug', default=0, help='enable debugging output')
- parser.add_option('-l', '--log', action='store', type='string',
dest='log', help='log relax output to the file LOG_FILE', metavar='LOG_FILE')
- parser.add_option('--licence', action='store_true', dest='licence',
default=0, help='display the licence')
- parser.add_option('-t', '--tee', action='store', type='string',
dest='tee', help='tee relax output to stdout and the file LOG_FILE',
metavar='LOG_FILE')
- parser.add_option('-g', '--gui', action='store_true', dest='gui',
default=0, help='launch the relax GUI')
- parser.add_option('-p', '--pedantic', action='store_true',
dest='pedantic', default=0, help='escalate all warnings to errors')
- parser.add_option('--test', action='store_true', dest='test',
default=0, help='run relax in test mode')
- parser.add_option('-x', '--test-suite', action='store_true',
dest='test_suite', default=0, help='execute the relax test suite')
- parser.add_option('-s', '--system-tests', action='store_true',
dest='system_tests', default=0, help='execute the relax system/functional
tests (part of the test suite)')
- parser.add_option('-u', '--unit-tests', action='store_true',
dest='unit_tests', default=0, help='execute the relax unit tests (part of the
test suite)')
- parser.add_option('-i', '--info', action='store_true', dest='info',
default=0, help='display information about this version of relax')
- parser.add_option('-v', '--version', action='store_true',
dest='version', default=0, help='show the version number and exit')
-
- # Parse the options.
- (options, args) = parser.parse_args()
-
- # Debugging flag.
- if options.debug:
- status.debug = True
-
- # Pedantic flag.
- self.pedantic = False
- if options.pedantic:
- self.pedantic = True
-
- # Logging.
- if options.log:
- # Exclusive modes.
- if options.tee:
- parser.error("the logging and tee options cannot be set
simultaneously")
-
- # The log file.
- log_file = options.log
-
- # Fail if the file already exists.
- if access(log_file, F_OK):
- parser.error("the log file " + repr(log_file) + " already
exists")
- else:
- log_file = None
-
- # Tee.
- if options.tee:
- # Exclusive modes.
- if options.log:
- parser.error("the tee and logging options cannot be set
simultaneously")
-
- # The tee file.
- tee_file = options.tee
-
- # Fail if the file already exists.
- if access(tee_file, F_OK):
- parser.error("the tee file " + repr(tee_file) + " already
exists")
- else:
- tee_file = None
-
- # Test suite mode, therefore the args are the tests to run and not a
script file.
- if options.test_suite or options.system_tests or options.unit_tests:
- self.tests = args
-
- # The argument is a script.
- else:
- # Number of positional arguments should only be 0 or 1. 1
should be the script file.
- if len(args) > 1:
- parser.error("incorrect number of arguments")
-
- # Script file.
- self.script_file = None
- if len(args) == 1:
- self.script_file = args[0]
-
- # Test if the script file exists.
- if not access(self.script_file, F_OK):
- parser.error("the script file " + repr(self.script_file)
+ " does not exist")
-
-
- # Determine the relax mode and test for mutually exclusive modes.
- #################################################################
-
- # Show the version number.
- if options.version:
- mode = 'version'
-
- # Show the info about this relax version.
- elif options.info:
- mode = 'info'
-
- # Run the relax tests.
- elif options.test_suite or options.system_tests or
options.unit_tests:
- # Exclusive modes.
- if options.test:
- parser.error("executing the relax test suite and running
relax in test mode are mutually exclusive")
- elif options.licence:
- parser.error("executing the relax test suite and running
relax in licence mode are mutually exclusive")
-
- # Set the mode.
- if options.test_suite:
- mode = 'test suite'
- elif options.system_tests:
- mode = 'system tests'
- elif options.unit_tests:
- mode = 'unit tests'
-
- # Test mode.
- elif options.test:
- # Make sure no script is supplied.
- if self.script_file:
- parser.error("a script should not be supplied in test mode")
-
- # Exclusive modes.
- if options.test_suite or options.system_tests or
options.unit_tests:
- parser.error("the relax test mode and executing the test
suite are mutually exclusive")
- elif options.licence:
- parser.error("the relax modes test and licence are mutually
exclusive")
-
- # Set the mode.
- mode = 'test'
-
- # Licence mode.
- elif options.licence:
- # Make sure no script is supplied.
- if self.script_file:
- parser.error("a script should not be supplied in test mode")
-
- # Exclusive modes.
- if options.test_suite or options.system_tests or
options.unit_tests:
- parser.error("the relax licence mode and executing the test
suite are mutually exclusive")
- elif options.test:
- parser.error("the relax modes licence and test are mutually
exclusive")
-
- # Set the mode.
- mode = 'licence'
-
- # GUI.
- elif options.gui:
- # Exclusive models.
- if options.test_suite or options.system_tests or
options.unit_tests:
- parser.error("the relax GUI mode and testing modes are
mutually exclusive")
- elif options.licence:
- parser.error("the relax GUI mode and licence mode are
mutually exclusive")
-
- # Missing wx module.
- if not dep_check.wx_module:
- parser.error("To use the GUI, the wx python module must be
installed.")
-
- # Set the mode.
- mode = 'gui'
-
- # Script mode.
- elif self.script_file:
- mode = 'script'
-
- # Prompt mode (default).
- else:
- mode = 'prompt'
-
- # Return.
- return mode, log_file, tee_file
-
-
- def licence(self):
- """Function for displaying the licence."""
-
- help(gpl)
-
-
- def test_mode(self):
- """Relax test mode code."""
-
- # Don't actually do anything.
- return
-
-
-class RelaxParser(OptionParser):
- 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):
- """Subclassed OptionParser class with a replacement error
function."""
-
- # Relax base class.
- self.relax = relax
-
- # Run the __init__ method of the OptionParser class.
- OptionParser.__init__(self, usage, option_list, option_class,
version, conflict_handler, description, formatter, add_help_option, prog)
-
-
- def error(self, message):
- """Replacement error function."""
-
- # Usage message.
- self.print_usage(sys.stderr)
-
- # Raise a clean error.
- try:
- raise relax_errors.RelaxError(message)
- except relax_errors.AllRelaxErrors, instance:
- sys.stderr.write(instance.__str__())
-
- # Exit.
- sys.exit()
-
-
-if __name__ == "__main__":
- # Change this flag to True for code profiling.
- profile_flag = False
-
- # Normal relax operation.
- if not profile_flag:
- Relax()
-
- # relax in profiling mode.
- else:
- def print_stats(stats, status=0):
- pstats.Stats(stats).sort_stats('cumulative',
'name').print_stats()
-
- # No profile module.
- if not dep_check.profile_module:
- sys.stderr.write("The profile module is not available, please
install the Python development packages for profiling.\n\n")
- sys.exit()
-
- # Run relax in profiling mode.
- profile.Profile.print_stats = print_stats
- profile.run('Relax()')
+# Start relax.
+relax.start()
Modified: 1.3/relax.bat
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax.bat?rev=13951&r1=13950&r2=13951&view=diff
==============================================================================
--- 1.3/relax.bat (original)
+++ 1.3/relax.bat Thu Jul 28 15:14:55 2011
@@ -18,4 +18,4 @@
rem Run relax using python. %~dp0 will expand to the path where relax is
found
rem and %0 is simply 'relax'. %* will send all the remaining arguments to
rem relax.
-python "%~dp0%0" %*
+python "%~dp0%0.py" %*
Copied: 1.3/relax.py (from r13935, 1.3/relax)
URL:
http://svn.gna.org/viewcvs/relax/1.3/relax.py?p2=1.3/relax.py&p1=1.3/relax&r1=13935&r2=13951&rev=13951&view=diff
==============================================================================
--- 1.3/relax (original)
+++ 1.3/relax.py Thu Jul 28 15:14:55 2011
@@ -1,5 +1,3 @@
-#! /usr/bin/env python
-
###############################################################################
#
#
# relax
#
@@ -66,6 +64,32 @@
# Modify the environmental variables.
putenv('PDBVIEWER', 'vmd')
+
+
+def start(profile_flag=False):
+ """Execute relax.
+
+ @keyword profile_flag: Change this flag to True for code profiling.
+ @type profile_flag: bool
+ """
+
+ # Normal relax operation.
+ if not profile_flag:
+ Relax()
+
+ # relax in profiling mode.
+ else:
+ def print_stats(stats, status=0):
+ pstats.Stats(stats).sort_stats('cumulative',
'name').print_stats()
+
+ # No profile module.
+ if not dep_check.profile_module:
+ sys.stderr.write("The profile module is not available, please
install the Python development packages for profiling.\n\n")
+ sys.exit()
+
+ # Run relax in profiling mode.
+ profile.Profile.print_stats = print_stats
+ profile.run('Relax()')
@@ -345,6 +369,7 @@
return
+
class RelaxParser(OptionParser):
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):
"""Subclassed OptionParser class with a replacement error
function."""
@@ -372,24 +397,6 @@
sys.exit()
+# Start relax if this file is passed to Python.
if __name__ == "__main__":
- # Change this flag to True for code profiling.
- profile_flag = False
-
- # Normal relax operation.
- if not profile_flag:
- Relax()
-
- # relax in profiling mode.
- else:
- def print_stats(stats, status=0):
- pstats.Stats(stats).sort_stats('cumulative',
'name').print_stats()
-
- # No profile module.
- if not dep_check.profile_module:
- sys.stderr.write("The profile module is not available, please
install the Python development packages for profiling.\n\n")
- sys.exit()
-
- # Run relax in profiling mode.
- profile.Profile.print_stats = print_stats
- profile.run('Relax()')
+ start()
r13951 - in /1.3: relax relax.bat relax.py