Author: bugman
Date: Wed Oct 17 13:29:50 2012
New Revision: 17893
URL: http://svn.gna.org/viewcvs/relax?rev=17893&view=rev
Log:
Merged revisions 17878-17892 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17878 | bugman | 2012-10-16 23:15:21 +0200 (Tue, 16 Oct 2012) | 3 lines
Fix for the API documentation for the rename of the 'scripts' to
'devel_scripts' directory at r17708.
........
r17879 | bugman | 2012-10-16 23:30:35 +0200 (Tue, 16 Oct 2012) | 6 lines
API documentation fix - a circular import has been broken.
This was only a circular import when the gui package is imported from an
external program like
Epydoc.
........
r17880 | bugman | 2012-10-16 23:37:14 +0200 (Tue, 16 Oct 2012) | 6 lines
Improvements to the API documentation compilation.
The excluded files and directories, as well as hidden ones, are no longer
included in the list of
files/directories to add to the documentation.
........
r17881 | bugman | 2012-10-17 09:32:20 +0200 (Wed, 17 Oct 2012) | 3 lines
Updated the relax prompt mode figure in the intro chapter of the user
manual to the more modern prompt.
........
r17882 | bugman | 2012-10-17 10:40:58 +0200 (Wed, 17 Oct 2012) | 5 lines
Fix for the relax user manual compilation.
The full path for an icon in the graphics directory was being used.
........
r17883 | bugman | 2012-10-17 10:53:40 +0200 (Wed, 17 Oct 2012) | 3 lines
Import fix for the relax GUI tests for a problem only recently introduced.
........
r17884 | bugman | 2012-10-17 11:01:23 +0200 (Wed, 17 Oct 2012) | 3 lines
The setup.py application building script now complains if the Python
setuptools are not installed.
........
r17885 | bugman | 2012-10-17 11:25:53 +0200 (Wed, 17 Oct 2012) | 6 lines
Added some bug catching code for the observer objects.
In some rare cases a registered method's key was set to None. This is now
caught and a RelaxError
thrown to prevent later indecipherable errors.
........
r17886 | bugman | 2012-10-17 11:30:59 +0200 (Wed, 17 Oct 2012) | 3 lines
Added some special RelaxErrors for data pipe bundles.
........
r17887 | bugman | 2012-10-17 11:31:44 +0200 (Wed, 17 Oct 2012) | 3 lines
Missing import of the sys module.
........
r17888 | bugman | 2012-10-17 11:33:35 +0200 (Wed, 17 Oct 2012) | 3 lines
Added some error checking for the data pipe bundle in the auto model-free
analysis GUI code.
........
r17889 | bugman | 2012-10-17 11:37:13 +0200 (Wed, 17 Oct 2012) | 3 lines
Added data pipe bundle error checking for the GUI pipe editor window
associate_auto() method.
........
r17890 | bugman | 2012-10-17 11:45:31 +0200 (Wed, 17 Oct 2012) | 3 lines
Another attempt at fixing a nasty circular import in the relax GUI.
........
r17891 | bugman | 2012-10-17 11:59:14 +0200 (Wed, 17 Oct 2012) | 3 lines
Fix for the State.test_load_state_no_gui() GUI test - the data pipe bundle
is now given.
........
r17892 | bugman | 2012-10-17 11:59:46 +0200 (Wed, 17 Oct 2012) | 3 lines
More error checking for the associate_auto() method of the data pipe editor
window.
........
Added:
branches/cst/graphics/screenshots/relax_prompt_mode.eps.gz
- copied unchanged from r17892,
trunk/graphics/screenshots/relax_prompt_mode.eps.gz
branches/cst/graphics/screenshots/relax_prompt_mode.png
- copied unchanged from r17892,
trunk/graphics/screenshots/relax_prompt_mode.png
Modified:
branches/cst/ (props changed)
branches/cst/docs/latex/curvefit.tex
branches/cst/docs/latex/intro.tex
branches/cst/gui/__init__.py
branches/cst/gui/analyses/auto_model_free.py
branches/cst/gui/misc.py
branches/cst/gui/pipe_editor.py
branches/cst/gui/relax_gui.py
branches/cst/relax_errors.py
branches/cst/scons/manuals.py
branches/cst/setup.py
branches/cst/status.py
branches/cst/test_suite/gui_tests/state.py
branches/cst/test_suite/test_suite_runner.py
Propchange: branches/cst/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Oct 17 13:29:50 2012
@@ -1,1 +1,1 @@
-/trunk:1-17871
+/trunk:1-17892
Modified: branches/cst/docs/latex/curvefit.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/latex/curvefit.tex?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/docs/latex/curvefit.tex (original)
+++ branches/cst/docs/latex/curvefit.tex Wed Oct 17 13:29:50 2012
@@ -32,7 +32,7 @@
\subsection{Temperature control and calibration} \label{sect: temperature
control and calibration}
-\includegraphics[bb=0 0 18
18]{/data/relax/relax-trunk/graphics/oxygen_icons/128x128/status/weather-clear}
+\includegraphics[bb=0 0 18
18]{graphics/oxygen_icons/128x128/status/weather-clear}
Before starting with the spectral processing, it should be noted that proper
temperature control and calibration are essential for relaxation data. Small
temperature changes can have an effect on the viscosity and hence global
tumbling of the molecule being studied and, as the molecular diffusion tensor
is the major contributor to relaxation, any non-consistent data will likely
lead to artificial motions appearing in subsequent model-free analyses.
Modified: branches/cst/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/docs/latex/intro.tex?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/docs/latex/intro.tex (original)
+++ branches/cst/docs/latex/intro.tex Wed Oct 17 13:29:50 2012
@@ -175,7 +175,7 @@
% Prompt screenshot
\begin{figure}
-\centerline{\includegraphics[width=0.9\textwidth, bb=14 14 861
561]{graphics/screenshots/relax_prompt_1_3_8}}
+\centerline{\includegraphics[width=0.9\textwidth, bb=14 14 1088
821]{graphics/screenshots/relax_prompt_mode}}
\caption[Prompt screenshot]{A screenshot of relax being run in the primary
prompt mode.}\label{fig: relax prompt}
\end{figure}
Modified: branches/cst/gui/__init__.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/gui/__init__.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/gui/__init__.py (original)
+++ branches/cst/gui/__init__.py Wed Oct 17 13:29:50 2012
@@ -38,10 +38,10 @@
import generic_fns
from graphics import IMAGE_PATH
from relax_errors import RelaxError
-from relax_gui import Main
from status import Status; status = Status()
# relax GUI module imports.
+from gui import relax_gui
from gui.uf_objects import Uf_storage; uf_store = Uf_storage()
@@ -100,7 +100,7 @@
self.show_splash()
# Build the GUI.
- self.gui = Main(parent=None, id=-1, title="")
+ self.gui = relax_gui.Main(parent=None, id=-1, title="")
# Make it the main application component.
self.SetTopWindow(self.gui)
Modified: branches/cst/gui/analyses/auto_model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/gui/analyses/auto_model_free.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/gui/analyses/auto_model_free.py (original)
+++ branches/cst/gui/analyses/auto_model_free.py Wed Oct 17 13:29:50 2012
@@ -39,6 +39,7 @@
from generic_fns.pipes import has_bundle, has_pipe
from graphics import fetch_icon
from physical_constants import NH_BOND_LENGTH
+from relax_errors import RelaxError
from relax_string import LIST, PARAGRAPH, SECTION, SUBSECTION, TITLE
from specific_fns.setup import get_specific_fn
from status import Status; status = Status()
@@ -209,6 +210,10 @@
ds.relax_gui.analyses[data_index].local_tm_models = ['tm0',
'tm1', 'tm2', 'tm3', 'tm4', 'tm5', 'tm6', 'tm7', 'tm8', 'tm9']
ds.relax_gui.analyses[data_index].mf_models = ['m0', 'm1', 'm2',
'm3', 'm4', 'm5', 'm6', 'm7', 'm8', 'm9']
ds.relax_gui.analyses[data_index].max_iter = 30
+
+ # Error checking.
+ if ds.relax_gui.analyses[data_index].pipe_bundle == None:
+ raise RelaxError("The pipe bundle must be supplied.")
# Alias the data.
self.data = ds.relax_gui.analyses[data_index]
Modified: branches/cst/gui/misc.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/gui/misc.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/gui/misc.py (original)
+++ branches/cst/gui/misc.py Wed Oct 17 13:29:50 2012
@@ -27,6 +27,7 @@
from copy import deepcopy
import os
import platform
+import sys
from textwrap import wrap
import wx
Modified: branches/cst/gui/pipe_editor.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/gui/pipe_editor.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/gui/pipe_editor.py (original)
+++ branches/cst/gui/pipe_editor.py Wed Oct 17 13:29:50 2012
@@ -30,6 +30,7 @@
from data import Relax_data_store; ds = Relax_data_store()
from generic_fns.pipes import cdp_name, delete, get_bundle, get_type,
pipe_names, switch
from graphics import fetch_icon
+from relax_errors import RelaxError
from status import Status; status = Status()
# relax GUI module imports.
@@ -323,9 +324,15 @@
if not hasattr(ds, 'relax_gui'):
self.gui.init_data()
- # The type.
+ # The type and data pipe bundle.
type = get_type(self.selected_pipe)
bundle = get_bundle(self.selected_pipe)
+
+ # Error checking.
+ if self.selected_pipe == None:
+ raise RelaxError("No data pipe has been selected - this is not
possible.")
+ if bundle == None:
+ raise RelaxError("The selected data pipe is not associated with
a data pipe bundle.")
# The name.
names = {
Modified: branches/cst/gui/relax_gui.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/gui/relax_gui.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/gui/relax_gui.py (original)
+++ branches/cst/gui/relax_gui.py Wed Oct 17 13:29:50 2012
@@ -44,7 +44,6 @@
from relax_errors import RelaxNoPipeError
from relax_io import io_streams_restore
from status import Status; status = Status()
-import test_suite.test_suite_runner
from version import version
# relax GUI module imports.
@@ -587,7 +586,8 @@
# Prevent all new GUI elements from being shown.
status.show_gui = False
- # Run the tests.
+ # Run the tests (with the import here to break a nasty circular
import).
+ import test_suite.test_suite_runner
runner = test_suite.test_suite_runner.Test_suite_runner([],
from_gui=True, categories=categories)
runner.run_all_tests()
Modified: branches/cst/relax_errors.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/relax_errors.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/relax_errors.py (original)
+++ branches/cst/relax_errors.py Wed Oct 17 13:29:50 2012
@@ -830,6 +830,19 @@
# Data pipe errors.
###################
+# The data pipe bundle already exists.
+class RelaxBundleError(BaseError):
+ def __init__(self, bundle):
+ self.text = "The data pipe bundle '%s' already exists." % bundle
+
+# No data pipe bundles exist.
+class RelaxNoBundleError(BaseError):
+ def __init__(self, bundle=None):
+ if bundle != None:
+ self.text = "The data pipe bundle '%s' has not been created
yet." % bundle
+ else:
+ self.text = "No data pipe bundles currently exist. Please use
the pipe.bundle user function first."
+
# The data pipe already exists.
class RelaxPipeError(BaseError):
def __init__(self, pipe):
Modified: branches/cst/scons/manuals.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/scons/manuals.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/scons/manuals.py (original)
+++ branches/cst/scons/manuals.py Wed Oct 17 13:29:50 2012
@@ -100,13 +100,13 @@
# exclude
# The list of objects to exclude.
exclude = [
+ 'devel_scripts',
'extern',
'graphics',
'minfx.scipy_subset',
'multi.test_implementation',
'multi.test_implementation2',
- 'sample_scripts',
- 'scripts'
+ 'sample_scripts'
]
# output
@@ -268,6 +268,14 @@
if file in blacklist:
continue
+ # The excluded ones.
+ if file in exclude:
+ continue
+
+ # Hidden files and directories.
+ if search('^\.', file):
+ continue
+
# Otherwise add it.
epydoc_cmd = "%s %s" % (epydoc_cmd, file)
@@ -310,7 +318,7 @@
head_lines = []
# The Google analytics JS.
- file = open(status.install_path + sep + 'scripts' + sep +
'google_analytics.js')
+ file = open(status.install_path + sep + 'devel_scripts' + sep +
'google_analytics.js')
for line in file.readlines():
head_lines.append(line)
file.close()
Modified: branches/cst/setup.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/setup.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/setup.py (original)
+++ branches/cst/setup.py Wed Oct 17 13:29:50 2012
@@ -38,7 +38,11 @@
from os import getcwd, listdir, sep, walk
from os.path import relpath, sep
from re import search
-from setuptools import setup
+try:
+ from setuptools import setup
+except ImportError:
+ print("ImportError: To run setup.py, please installed the Python
setuptools (see http://pypi.python.org/pypi/setuptools)")
+ setup = None
import sys
# relax module imports.
Modified: branches/cst/status.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/status.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/status.py (original)
+++ branches/cst/status.py Wed Oct 17 13:29:50 2012
@@ -452,6 +452,10 @@
if key in self._keys:
raise RelaxError("The observer '%s' already exists." % key)
+ # Blank key.
+ if key == None:
+ raise RelaxError("The observer key must be supplied.")
+
# Debugging.
if self._status.debug:
if method_name:
Modified: branches/cst/test_suite/gui_tests/state.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/gui_tests/state.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/test_suite/gui_tests/state.py (original)
+++ branches/cst/test_suite/gui_tests/state.py Wed Oct 17 13:29:50 2012
@@ -93,7 +93,7 @@
self.app.gui.state_load(file_name=file)
# Create a data pipe bundle.
- self._execute_uf(uf_name='pipe.bundle', pipe='a')
+ self._execute_uf(uf_name='pipe.bundle', pipe='a', bundle='test
bundle')
# Show the pipe editor.
self.app.gui.show_pipe_editor(None)
Modified: branches/cst/test_suite/test_suite_runner.py
URL:
http://svn.gna.org/viewcvs/relax/branches/cst/test_suite/test_suite_runner.py?rev=17893&r1=17892&r2=17893&view=diff
==============================================================================
--- branches/cst/test_suite/test_suite_runner.py (original)
+++ branches/cst/test_suite/test_suite_runner.py Wed Oct 17 13:29:50 2012
@@ -39,8 +39,8 @@
# relax module imports.
if dep_check.wx_module:
- from gui.interpreter import Interpreter
- from gui.relax_gui import Main
+ from gui import relax_gui
+ from gui import interpreter
from test_suite.relax_test_runner import GuiTestRunner, RelaxTestRunner
from status import Status; status = Status()
@@ -121,7 +121,7 @@
app = wx.App(redirect=False)
# Build the GUI.
- app.gui = Main(parent=None, id=-1, title="")
+ app.gui = relax_gui.Main(parent=None, id=-1, title="")
# Execute the GUI tests.
gui_runner = GUI_test_runner()
@@ -130,8 +130,8 @@
# Clean up for the GUI, if not in GUI mode.
if status.test_mode:
# Terminate the interpreter thread to allow the tests to
cleanly exit.
- interpreter = Interpreter()
- interpreter.exit()
+ interpreter_thread = interpreter.Interpreter()
+ interpreter_thread.exit()
# Stop the GUI main loop.
app.ExitMainLoop()
r17893 - in /branches/cst: ./ docs/latex/ graphics/screenshots/ gui/ gui/analyses/ scons/ test_suite/ test_suite/gui_tests/