Author: bugman
Date: Thu Sep 16 18:27:04 2010
New Revision: 11589
URL: http://svn.gna.org/viewcvs/relax?rev=11589&view=rev
Log:
Merged revisions 11587-11588 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r11587 | bugman | 2010-09-16 18:20:20 +0200 (Thu, 16 Sep 2010) | 3 lines
Renamed the results_folder arg to results_dir in the NOE auto-analysis, and
rearranged the args.
........
r11588 | bugman | 2010-09-16 18:22:30 +0200 (Thu, 16 Sep 2010) | 5 lines
Added a system test for the dauvergne_protocol auto-analysis code.
The test is not yet functional.
........
Added:
branches/bieri_gui/test_suite/shared_data/relaxation_data/13259_bug_reproducing_data/
- copied from r11588,
1.3/test_suite/shared_data/relaxation_data/13259_bug_reproducing_data/
branches/bieri_gui/test_suite/system_tests/scripts/model_free/full_analysis_trunc.py
- copied unchanged from r11588,
1.3/test_suite/system_tests/scripts/model_free/full_analysis_trunc.py
Modified:
branches/bieri_gui/ (props changed)
branches/bieri_gui/auto_analyses/noe.py
branches/bieri_gui/test_suite/system_tests/model_free.py
Propchange: branches/bieri_gui/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Thu Sep 16 18:27:04 2010
@@ -1,1 +1,1 @@
-/1.3:1-11575
+/1.3:1-11588
Modified: branches/bieri_gui/auto_analyses/noe.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/auto_analyses/noe.py?rev=11589&r1=11588&r2=11589&view=diff
==============================================================================
--- branches/bieri_gui/auto_analyses/noe.py (original)
+++ branches/bieri_gui/auto_analyses/noe.py Thu Sep 16 18:27:04 2010
@@ -35,11 +35,9 @@
class NOE_calc:
- def __init__(self, output_file='noe.out', seq_args=None,
pipe_name='noe', noe_ref=None, noe_ref_rmsd=None, noe_sat=None,
noe_sat_rmsd=None, unresolved=None, pdb_file=None, results_folder=None,
int_method='height', heteronuc='N', proton='H', heteronuc_pdb='N'):
+ def __init__(self, seq_args=None, pipe_name='noe', noe_ref=None,
noe_ref_rmsd=None, noe_sat=None, noe_sat_rmsd=None, unresolved=None,
pdb_file=None, output_file='noe.out', results_dir=None, int_method='height',
heteronuc='N', proton='H', heteronuc_pdb='N'):
"""Perform relaxation curve fitting.
- @keyword output_file: Name of the output file.
- @type output_file: str
@keyword seq_args: The sequence data (file name, dir,
mol_name_col, res_num_col, res_name_col, spin_num_col, spin_name_col, sep).
These are the arguments to the sequence.read() user function, for more
information please see the documentation for that function.
@type seq_args: list of lists of [str, None or str, None or
int, None or int, None or int, None or int, None or int, None or int, None or
int, None or str]
@keyword pipe_name: The name of the data pipe to create.
@@ -56,8 +54,10 @@
@type unresolved: str
@keyword pdb_file: Structure file in pdb format.
@type pdb_file: str
- @keyword results_folder:Folder where results files are placed in.
- @type results_folder: str
+ @keyword output_file: Name of the output file.
+ @type output_file: str
+ @keyword results_dir: Folder where results files are placed in.
+ @type results_dir: str
@keyword int_method: The integration method, one of 'height',
'point sum' or 'other'.
@type int_method: str
@keyword heteronuc: Name of heteronucleus of peak list.
@@ -70,16 +70,16 @@
# Store the args.
self.pipe_name = pipe_name
- self.output_file = output_file
self.noe_sat = noe_sat
self.noe_sat_rmsd = noe_sat_rmsd
self.noe_ref = noe_ref
self.noe_ref_rmsd =noe_ref_rmsd
self.unresolved = unresolved
self.pdb_file = pdb_file
- self.results_folder = results_folder
- if results_folder:
- self.grace_dir = results_folder+sep+'grace'
+ self.output_file = output_file
+ self.results_dir = results_dir
+ if results_dir:
+ self.grace_dir = results_dir+sep+'grace'
else:
self.grace_dir = None
self.int_method = int_method
@@ -135,7 +135,7 @@
self.interpreter.calc()
# Save the NOEs.
- self.interpreter.value.write(param='noe', file=self.output_file, dir
= self.results_folder, force=True)
+ self.interpreter.value.write(param='noe', file=self.output_file, dir
= self.results_dir, force=True)
# Create grace files.
self.interpreter.grace.write(y_data_type='ref', file='ref.agr',
dir=self.grace_dir, force=True)
@@ -143,10 +143,10 @@
self.interpreter.grace.write(y_data_type='noe', file='noe.agr',
dir=self.grace_dir, force=True)
# Write the results.
- self.interpreter.results.write(file='results',
dir=self.results_folder, force=True)
+ self.interpreter.results.write(file='results', dir=self.results_dir,
force=True)
# Save the program state.
- self.interpreter.state.save(state = 'save', dir=self.results_folder,
force=True)
+ self.interpreter.state.save(state = 'save', dir=self.results_dir,
force=True)
def check_vars(self):
Modified: branches/bieri_gui/test_suite/system_tests/model_free.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bieri_gui/test_suite/system_tests/model_free.py?rev=11589&r1=11588&r2=11589&view=diff
==============================================================================
--- branches/bieri_gui/test_suite/system_tests/model_free.py (original)
+++ branches/bieri_gui/test_suite/system_tests/model_free.py Thu Sep 16
18:27:04 2010
@@ -25,8 +25,10 @@
from math import pi
import platform
import numpy
+from os import sep
from re import search
-from os import sep
+from shutil import copytree, rmtree
+from tempfile import mkdtemp
# relax module imports.
from base_classes import SystemTestCase
@@ -69,6 +71,11 @@
def tearDown(self):
"""Reset the relax data storage object."""
+ # Remove temporary directories.
+ if hasattr(ds, 'tmpdir'):
+ rmtree(ds.tmpdir)
+
+ # Reset the relax data storage object.
ds.__reset__()
@@ -199,6 +206,21 @@
# Test the model.
self.assertEqual(cdp.mol[0].res[1].spin[0].model, 'm4')
self.assertEqual(cdp.mol[0].res[1].spin[0].params, ['S2', 'te',
'Rex'])
+
+
+ # FIXME!
+ def xxx_test_dauvergne_protocol(self):
+ """Check the execution of auto_analyses.dauvergne_protocol."""
+
+ # Create a temporary directory for dumping files.
+ ds.tmpdir = mkdtemp()
+
+ # Copy the files into the temporary directory.
+ path = __main__.install_path +
sep+'test_suite'+sep+'shared_data'+sep+'relaxation_data'+sep+'13259_bug_reproducing_data'
+ copytree(path, ds.tmpdir + sep + 'data')
+
+ # Execute the script.
+ self.interpreter.run(script_file=__main__.install_path +
sep+'test_suite'+sep+'system_tests'+sep+'scripts'+sep+'model_free'+sep+'full_analysis_trunc.py')
def test_generate_ri(self):
r11589 - in /branches/bieri_gui: ./ auto_analyses/ test_suite/shared_data/relaxation_data/13259_bug_reproducing_data/ test_s...