Author: semor
Date: Tue Jan 8 00:21:51 2008
New Revision: 4470
URL: http://svn.gna.org/viewcvs/relax?rev=4470&view=rev
Log:
Merged revisions 4440,4447,4449-4450,4452-4458,4461 via svnmerge from
svn+ssh://semor@xxxxxxxxxxx/svn/relax/1.3
........
r4440 | bugman | 2008-01-07 11:36:57 -0500 (Mon, 07 Jan 2008) | 3 lines
Created a directory for user scripts to be used as system/functional tests.
........
r4447 | bugman | 2008-01-07 11:59:23 -0500 (Mon, 07 Jan 2008) | 5 lines
Added the quit argument to the run() class method.
This is to allow the system/functional tests to run this method and to ask
relax not to quit.
........
r4449 | bugman | 2008-01-07 12:09:07 -0500 (Mon, 07 Jan 2008) | 5 lines
Created a script containing the commands used in the system test for
creating a model-free model.
The system test executes the script instead of running the commands itself.
........
r4450 | bugman | 2008-01-07 12:15:09 -0500 (Mon, 07 Jan 2008) | 5 lines
The script file is now passed into the interpreter run() method.
This change is like to break many things!!!
........
r4452 | bugman | 2008-01-07 12:19:07 -0500 (Mon, 07 Jan 2008) | 3 lines
Fixed the running of the script for the model-free m4 model creating system
test.
........
r4453 | bugman | 2008-01-07 12:28:57 -0500 (Mon, 07 Jan 2008) | 3 lines
Completely changed how the relax program introduction is handled.
........
r4454 | bugman | 2008-01-07 12:35:50 -0500 (Mon, 07 Jan 2008) | 3 lines
Added the ability to turn off the printing out of the script prior to its
execution.
........
r4455 | bugman | 2008-01-07 12:36:51 -0500 (Mon, 07 Jan 2008) | 3 lines
Turned off the printing of the script prior to its execution in the system
tests.
........
r4456 | bugman | 2008-01-07 12:42:18 -0500 (Mon, 07 Jan 2008) | 5 lines
Shifted the quit option from run() to __init__().
This will remove the need for all system tests using a script to ask the
interpreter to not exit.
........
r4457 | bugman | 2008-01-07 12:42:52 -0500 (Mon, 07 Jan 2008) | 3 lines
Made the 'intro_string', 'quit', and 'show_script' variables private.
........
r4458 | bugman | 2008-01-07 12:43:35 -0500 (Mon, 07 Jan 2008) | 3 lines
Passed the quit flag into the prompt mode of operation.
........
r4461 | semor | 2008-01-07 12:58:13 -0500 (Mon, 07 Jan 2008) | 3 lines
Fixed a typo in an import statement.
........
Added:
branches/consistency_tests_1.3/test_suite/system_tests/scripts/
- copied from r4461, 1.3/test_suite/system_tests/scripts/
Modified:
branches/consistency_tests_1.3/ (props changed)
branches/consistency_tests_1.3/prompt/interpreter.py
branches/consistency_tests_1.3/relax
branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
branches/consistency_tests_1.3/test_suite/system_tests/model_free.py
Propchange: branches/consistency_tests_1.3/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Jan 8 00:21:51 2008
@@ -1,1 +1,1 @@
-/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433
+/1.3:1-3320,3333-4175,4223,4241-4335,4338-4433,4440-4461
Modified: branches/consistency_tests_1.3/prompt/interpreter.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/prompt/interpreter.py?rev=4470&r1=4469&r2=4470&view=diff
==============================================================================
--- branches/consistency_tests_1.3/prompt/interpreter.py (original)
+++ branches/consistency_tests_1.3/prompt/interpreter.py Tue Jan 8 00:21:51
2008
@@ -78,12 +78,27 @@
class Interpreter:
- def __init__(self, relax):
- """The interpreter class."""
-
- # Place the program class structure under self.relax
+ def __init__(self, relax, intro_string=None, show_script=True,
quit=True):
+ """The interpreter class.
+
+ @param relax: The relax instance.
+ @type relax: instance
+ @param intro_string: The string to print at the start of
execution.
+ @type intro_string: str
+ @param show_script: If true, the relax will print the script
contents prior to executing
+ the script.
+ @type show_script: bool
+ @param quit: If true, the default, then relax will exit
after running the run()
+ method.
+ @type quit: bool
+ """
+
+ # Place the arguments in the class namespace.
self.relax = relax
-
+ self.__intro_string = intro_string
+ self.__show_script = show_script
+ self.__quit_flag = quit
+
# The prompts.
sys.ps1 = 'relax> '
sys.ps2 = 'relax| '
@@ -137,11 +152,16 @@
self._Vmd = Vmd(relax)
- def run(self):
+ def run(self, script_file=None):
"""Run the python interpreter.
The namespace of this function is the namespace seen inside the
interpreter. All user
accessible functions, classes, etc, should be placed in this
namespace.
+
+
+ @param script_file: The script file to be executed. For the
interpreter mode, this
+ should be left as None.
+ @type script_file: None or str
"""
# Python modules.
@@ -216,12 +236,12 @@
readline.parse_and_bind("tab: complete")
# Execute the script file if given.
- if self.relax.script_file:
+ if script_file:
# Turn on the function intro flag.
self.intro = 1
# Run the script.
- run_script(intro=self.relax.intro_string, local=self.local,
script_file=self.relax.script_file, quit=1)
+ run_script(intro=self.__intro_string, local=self.local,
script_file=script_file, quit=self.__quit_flag,
show_script=self.__show_script)
# Test for the dummy mode for generating documentation (then exit).
elif hasattr(self.relax, 'dummy_mode'):
@@ -231,7 +251,7 @@
# Go to the prompt.
else:
- prompt(intro=self.relax.intro_string, local=self.local)
+ prompt(intro=self.__intro_string, local=self.local,
quit=self.__quit_flag)
def _off(self):
@@ -317,7 +337,7 @@
more = 0
-def interact_script(self, intro, local, script_file, quit):
+def interact_script(self, intro, local, script_file, quit, show_script=True):
"""Replacement function for 'code.InteractiveConsole.interact'.
This will execute the script file.
@@ -331,20 +351,21 @@
local['self'].intro = 1
# Print the script.
- try:
- file = open(script_file, 'r')
- except IOError, warning:
+ if show_script:
try:
- raise RelaxError, "The script file '" + script_file + "' does
not exist."
- except AllRelaxErrors, instance:
- sys.stdout.write(instance.__str__())
- sys.stdout.write("\n")
- return
- sys.stdout.write("script = " + `script_file` + "\n")
-
sys.stdout.write("----------------------------------------------------------------------------------------------------\n")
- sys.stdout.write(file.read())
-
sys.stdout.write("----------------------------------------------------------------------------------------------------\n")
- file.close()
+ file = open(script_file, 'r')
+ except IOError, warning:
+ try:
+ raise RelaxError, "The script file '" + script_file + "'
does not exist."
+ except AllRelaxErrors, instance:
+ sys.stdout.write(instance.__str__())
+ sys.stdout.write("\n")
+ return
+ sys.stdout.write("script = " + `script_file` + "\n")
+
sys.stdout.write("----------------------------------------------------------------------------------------------------\n")
+ sys.stdout.write(file.read())
+
sys.stdout.write("----------------------------------------------------------------------------------------------------\n")
+ file.close()
# Execute the script.
try:
@@ -384,7 +405,7 @@
console.interact(intro, local)
-def run_script(intro=None, local=None, script_file=None, quit=1):
+def run_script(intro=None, local=None, script_file=None, quit=1,
show_script=True):
"""Python interpreter emulation.
This function replaces 'code.interact'.
@@ -396,7 +417,7 @@
# The console.
console = InteractiveConsole(local)
- console.interact(intro, local, script_file, quit)
+ console.interact(intro, local, script_file, quit,
show_script=show_script)
def runcode(self, code):
Modified: branches/consistency_tests_1.3/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/relax?rev=4470&r1=4469&r2=4470&view=diff
==============================================================================
--- branches/consistency_tests_1.3/relax (original)
+++ branches/consistency_tests_1.3/relax Tue Jan 8 00:21:51 2008
@@ -139,14 +139,14 @@
elif tee_file and mode != 'thread':
tee(tee_file)
+ # Create a string to pass to the interpreter to print.
+ intro_string = self.get_intro_string()
+
# Run the interpreter for the prompt or script modes.
if mode == 'prompt' or mode == 'script':
- # Create a string to pass to the interpreter to print.
- self.set_intro_string()
-
# Run the interpreter.
- self.interpreter = interpreter.Interpreter(self)
- self.interpreter.run()
+ self.interpreter = interpreter.Interpreter(self, intro_string)
+ self.interpreter.run(self.script_file)
# Threading mode.
elif mode == 'thread':
@@ -167,11 +167,8 @@
# Execute the relax test suite
elif mode == 'test suite':
- # Create a string to pass to the interpreter to print.
- self.set_intro_string()
-
# Load the interpreter and turn intros on.
- self.interpreter = interpreter.Interpreter(self)
+ self.interpreter = interpreter.Interpreter(self,
show_script=False, quit=False)
self.interpreter._on()
# Run the tests.
@@ -180,11 +177,8 @@
# Execute the relax system tests.
elif mode == 'system tests':
- # Create a string to pass to the interpreter to print.
- self.set_intro_string()
-
# Load the interpreter and turn intros on.
- self.interpreter = interpreter.Interpreter(self)
+ self.interpreter = interpreter.Interpreter(self,
show_script=False, quit=False)
self.interpreter._on()
# Run the tests.
@@ -193,9 +187,6 @@
# Execute the relax unit tests.
elif mode == 'unit tests':
- # Create a string to pass to the interpreter to print.
- self.set_intro_string()
-
# Run the tests.
runner = Test_suite_runner(self)
runner.run_unit_tests()
@@ -366,14 +357,12 @@
return mode, log_file, tee_file
- def licence(self):
- """Function for displaying the licence."""
-
- help(gpl)
-
-
- def set_intro_string(self):
- """Create the program introduction."""
+ def get_intro_string(self):
+ """Create the program introduction.
+
+ @return: The program introduction string.
+ @type return: str
+ """
# The width of the printout.
if self.platform == 'Windows' or self.platform == 'Microsoft':
@@ -382,36 +371,45 @@
width = 100
# Some new lines.
- self.intro_string = '\n\n\n'
+ intro_string = '\n\n\n'
# Program name and version.
string = "relax " + self.version
- self.intro_string = self.intro_string + self.spacing(string, width)
+ '\n\n'
+ intro_string = intro_string + self.spacing(string, width) + '\n\n'
# Program description.
string = "Protein dynamics by NMR relaxation data analysis"
- self.intro_string = self.intro_string + self.spacing(string, width)
+ '\n\n'
+ intro_string = intro_string + self.spacing(string, width) + '\n\n'
# Copyright printout.
string = "Copyright (C) 2001-2006 Edward d'Auvergne"
- self.intro_string = self.intro_string + self.spacing(string, width)
+ '\n'
+ intro_string = intro_string + self.spacing(string, width) + '\n'
string = "Copyright (C) 2006-2008 the relax development team"
- self.intro_string = self.intro_string + self.spacing(string, width)
+ '\n\n'
+ intro_string = intro_string + self.spacing(string, width) + '\n\n'
# Program licence and help (80 characters wide).
if width == 80:
- self.intro_string = self.intro_string + "This is free software
which you are welcome to modify and redistribute under\n"
- self.intro_string = self.intro_string + "the conditions of the
GNU General Public License (GPL). This program,\n"
- self.intro_string = self.intro_string + "including all modules,
is licensed under the GPL and comes with absolutely no\n"
- self.intro_string = self.intro_string + "warranty. For details
type 'GPL'. Assistance in using this program can be\n"
- self.intro_string = self.intro_string + "accessed by typing
'help'.\n"
+ intro_string = intro_string + "This is free software which you
are welcome to modify and redistribute under\n"
+ intro_string = intro_string + "the conditions of the GNU General
Public License (GPL). This program,\n"
+ intro_string = intro_string + "including all modules, is
licensed under the GPL and comes with absolutely no\n"
+ intro_string = intro_string + "warranty. For details type
'GPL'. Assistance in using this program can be\n"
+ intro_string = intro_string + "accessed by typing 'help'.\n"
# Program licence and help (100 characters wide).
else:
- self.intro_string = self.intro_string + "This is free software
which you are welcome to modify and redistribute under the conditions of
the\n"
- self.intro_string = self.intro_string + "GNU General Public
License (GPL). This program, including all modules, is licensed under the
GPL\n"
- self.intro_string = self.intro_string + "and comes with
absolutely no warranty. For details type 'GPL'. Assistance in using this
program\n"
- self.intro_string = self.intro_string + "can be accessed by
typing 'help'.\n"
+ intro_string = intro_string + "This is free software which you
are welcome to modify and redistribute under the conditions of the\n"
+ intro_string = intro_string + "GNU General Public License (GPL).
This program, including all modules, is licensed under the GPL\n"
+ intro_string = intro_string + "and comes with absolutely no
warranty. For details type 'GPL'. Assistance in using this program\n"
+ intro_string = intro_string + "can be accessed by typing
'help'.\n"
+
+ # Return the string.
+ return intro_string
+
+
+ def licence(self):
+ """Function for displaying the licence."""
+
+ help(gpl)
def spacing(self, string, width=100):
Modified: branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/system_tests/__init__.py?rev=4470&r1=4469&r2=4470&view=diff
==============================================================================
--- branches/consistency_tests_1.3/test_suite/system_tests/__init__.py
(original)
+++ branches/consistency_tests_1.3/test_suite/system_tests/__init__.py Tue
Jan 8 00:21:51 2008
@@ -42,7 +42,7 @@
__all__ = ['angles',
'consistency_tests',
'diffusion_tensor',
- 'generic.py',
+ 'generic',
'jw_mapping',
'main',
'model_free',
Modified: branches/consistency_tests_1.3/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/consistency_tests_1.3/test_suite/system_tests/model_free.py?rev=4470&r1=4469&r2=4470&view=diff
==============================================================================
--- branches/consistency_tests_1.3/test_suite/system_tests/model_free.py
(original)
+++ branches/consistency_tests_1.3/test_suite/system_tests/model_free.py Tue
Jan 8 00:21:51 2008
@@ -82,14 +82,8 @@
def test_create_m4(self):
"""Creating model m4 with parameters {S2, te, Rex} using
model_free.create_model()."""
- # Path of the files.
- path = sys.path[-1] +
'/test_suite/system_tests/data/model_free/S2_0.970_te_2048_Rex_0.149'
-
- # Read the sequence.
- self.relax.interpreter._Sequence.read(file='noe.500.out', dir=path)
-
- # Select the model.
- self.relax.interpreter._Model_free.create_model(model='m4',
equation='mf_orig', params=['S2', 'te', 'Rex'], spin_id=None)
+ # Execute the script.
+
self.relax.interpreter.run(script_file='test_suite/system_tests/scripts/create_m4.py')
# Alias the current data pipe.
cdp = relax_data_store[relax_data_store.current_pipe]
r4470 - in /branches/consistency_tests_1.3: ./ prompt/ test_suite/system_tests/ test_suite/system_tests/scripts/