Author: bugman
Date: Wed Jan 21 20:15:35 2009
New Revision: 8564
URL: http://svn.gna.org/viewcvs/relax?rev=8564&view=rev
Log:
Merged revisions 8368-8563 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/1.3
........
r8436 | semor | 2009-01-13 20:23:13 +0100 (Tue, 13 Jan 2009) | 7 lines
Corrected a typo.
This was discussed in a thread starting at:
https://mail.gna.org/public/relax-devel/2009-01/msg00087.html
(Message-id: <496CD419.9020908@xxxxxxxxx>)
........
r8470 | bugman | 2009-01-15 13:52:12 +0100 (Thu, 15 Jan 2009) | 6 lines
Modified parse_token() to allow for '-' characters in molecule names
(derived from file names, etc.)
Instead of throwing a RelaxError if an invalid range is found, it is
assumed that the '-' character
does not signify a range and is treated as a string character which is part
of the token.
........
r8471 | bugman | 2009-01-15 14:01:40 +0100 (Thu, 15 Jan 2009) | 6 lines
Deletion of the test_parse_token_range_failx() unit test.
parse_token() no longer raises RelaxErrors with invalid range tokens (as
they are assumed to be
standard string characters instead).
........
r8492 | semor | 2009-01-15 20:10:18 +0100 (Thu, 15 Jan 2009) | 3 lines
Corrected mistakes in English.
........
r8501 | bugman | 2009-01-17 12:36:47 +0100 (Sat, 17 Jan 2009) | 3 lines
Updated the relax intro copyright notice for the relax development team to
2009!
........
Modified:
branches/bmrb/ (props changed)
branches/bmrb/docs/latex/fetch_docstrings.py
branches/bmrb/generic_fns/minimise.py
branches/bmrb/generic_fns/mol_res_spin.py
branches/bmrb/relax
branches/bmrb/specific_fns/model_free/mf_minimise.py
branches/bmrb/specific_fns/n_state_model.py
branches/bmrb/specific_fns/relax_fit.py
branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
Propchange: branches/bmrb/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Wed Jan 21 20:15:35 2009
@@ -1,1 +1,1 @@
-/1.3:1-8367
+/1.3:1-8563
Modified: branches/bmrb/docs/latex/fetch_docstrings.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/docs/latex/fetch_docstrings.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/docs/latex/fetch_docstrings.py (original)
+++ branches/bmrb/docs/latex/fetch_docstrings.py Wed Jan 21 20:15:35 2009
@@ -367,7 +367,7 @@
# R1 and R2.
string = self.safe_replacement(string, 'R1', 'R$_1$')
- string = self.safe_replacement(string, 'R2', 'R$_1$')
+ string = self.safe_replacement(string, 'R2', 'R$_2$')
# Model-free parameters.
Modified: branches/bmrb/generic_fns/minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/minimise.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/generic_fns/minimise.py (original)
+++ branches/bmrb/generic_fns/minimise.py Wed Jan 21 20:15:35 2009
@@ -192,10 +192,10 @@
@type min_algor: str
@param min_options: An array of options to be used by the
minimisation algorithm.
@type min_options: array of str
- @param func_tol: The function tolerence which, when reached,
terminates optimisation.
+ @param func_tol: The function tolerance which, when reached,
terminates optimisation.
Setting this to None turns of the check.
@type func_tol: None or float
- @param grad_tol: The gradient tolerence which, when reached,
terminates optimisation.
+ @param grad_tol: The gradient tolerance which, when reached,
terminates optimisation.
Setting this to None turns of the check.
@type grad_tol: None or float
@param max_iterations: The maximum number of iterations for the
algorithm.
Modified: branches/bmrb/generic_fns/mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/generic_fns/mol_res_spin.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/generic_fns/mol_res_spin.py (original)
+++ branches/bmrb/generic_fns/mol_res_spin.py Wed Jan 21 20:15:35 2009
@@ -1483,25 +1483,34 @@
indices.append(i)
# Range.
+ valid_range = True
if indices:
# Invalid range element, only one range char '-' and one
negative sign is allowed.
if len(indices) > 2:
- raise RelaxError, "The range element " + `element` + " is
invalid."
+ print "The range element " + `element` + " is invalid.
Assuming the '-' character does not specify a range."
+ valid_range = False
# Convert the two numbers to integers.
try:
start = int(element[:indices[0]])
end = int(element[indices[0]+1:])
except ValueError:
- raise RelaxError, "The range element " + `element` + " is
invalid as either the start or end of the range are not integers."
+ print "The range element " + `element` + " is invalid as
either the start or end of the range are not integers. Assuming the '-'
character does not specify a range."
+ valid_range = False
# Test that the starting number is less than the end.
- if start >= end:
- raise RelaxError, "The starting number of the range element
" + `element` + " needs to be less than the end number."
+ if valid_range and start >= end:
+ print "The starting number of the range element " +
`element` + " needs to be less than the end number. Assuming the '-'
character does not specify a range."
+ valid_range = False
# Create the range and append it to the list.
- for i in range(start, end+1):
- list.append(i)
+ if valid_range:
+ for i in range(start, end+1):
+ list.append(i)
+
+ # Just append the string (even though it might be junk).
+ else:
+ list.append(element)
# Number or name.
else:
Modified: branches/bmrb/relax
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/relax?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/relax (original)
+++ branches/bmrb/relax Wed Jan 21 20:15:35 2009
@@ -15,7 +15,7 @@
# relax, a program for relaxation data analysis.
#
#
#
# Copyright (C) 2001-2006 Edward d'Auvergne
#
-# Copyright (C) 2006-2008 the relax development team
#
+# Copyright (C) 2006-2009 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
#
@@ -335,7 +335,7 @@
# Copyright printout.
string = "Copyright (C) 2001-2006 Edward d'Auvergne"
intro_string = intro_string + self.spacing(string, width) + '\n'
- string = "Copyright (C) 2006-2008 the relax development team"
+ string = "Copyright (C) 2006-2009 the relax development team"
intro_string = intro_string + self.spacing(string, width) + '\n\n'
# Program licence and help (80 characters wide).
Modified: branches/bmrb/specific_fns/model_free/mf_minimise.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/model_free/mf_minimise.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/specific_fns/model_free/mf_minimise.py (original)
+++ branches/bmrb/specific_fns/model_free/mf_minimise.py Wed Jan 21 20:15:35
2009
@@ -722,10 +722,10 @@
@type min_algor: str
@keyword min_options: An array of options to be used by the
minimisation algorithm.
@type min_options: array of str
- @keyword func_tol: The function tolerence which, when
reached, terminates optimisation.
+ @keyword func_tol: The function tolerance which, when
reached, terminates optimisation.
Setting this to None turns of the check.
@type func_tol: None or float
- @keyword grad_tol: The gradient tolerence which, when
reached, terminates optimisation.
+ @keyword grad_tol: The gradient tolerance which, when
reached, terminates optimisation.
Setting this to None turns of the check.
@type grad_tol: None or float
@keyword max_iterations: The maximum number of iterations for the
algorithm.
Modified: branches/bmrb/specific_fns/n_state_model.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/n_state_model.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/specific_fns/n_state_model.py (original)
+++ branches/bmrb/specific_fns/n_state_model.py Wed Jan 21 20:15:35 2009
@@ -1187,10 +1187,10 @@
@type min_algor: str
@param min_options: An array of options to be used by the
minimisation algorithm.
@type min_options: array of str
- @param func_tol: The function tolerence which, when reached,
terminates optimisation.
+ @param func_tol: The function tolerance which, when reached,
terminates optimisation.
Setting this to None turns of the check.
@type func_tol: None or float
- @param grad_tol: The gradient tolerence which, when reached,
terminates optimisation.
+ @param grad_tol: The gradient tolerance which, when reached,
terminates optimisation.
Setting this to None turns of the check.
@type grad_tol: None or float
@param max_iterations: The maximum number of iterations for the
algorithm.
Modified: branches/bmrb/specific_fns/relax_fit.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/specific_fns/relax_fit.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/specific_fns/relax_fit.py (original)
+++ branches/bmrb/specific_fns/relax_fit.py Wed Jan 21 20:15:35 2009
@@ -591,10 +591,10 @@
@type min_algor: str
@keyword min_options: An array of options to be used by the
minimisation algorithm.
@type min_options: array of str
- @keyword func_tol: The function tolerence which, when
reached, terminates optimisation.
+ @keyword func_tol: The function tolerance which, when
reached, terminates optimisation.
Setting this to None turns of the check.
@type func_tol: None or float
- @keyword grad_tol: The gradient tolerence which, when
reached, terminates optimisation.
+ @keyword grad_tol: The gradient tolerance which, when
reached, terminates optimisation.
Setting this to None turns of the check.
@type grad_tol: None or float
@keyword max_iterations: The maximum number of iterations for the
algorithm.
Modified:
branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
URL:
http://svn.gna.org/viewcvs/relax/branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py?rev=8564&r1=8563&r2=8564&view=diff
==============================================================================
--- branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py
(original)
+++ branches/bmrb/test_suite/unit_tests/_generic_fns/test_mol_res_spin.py Wed
Jan 21 20:15:35 2009
@@ -985,20 +985,6 @@
self.assertEqual(list[5], 'Gly')
- def test_parse_token_range_fail1(self):
- """Failure of the generic_fns.mol_res_spin.parse_token() function on
the string '1-5-7'."""
-
- # Parse the invalid token.
- self.assertRaises(RelaxError, mol_res_spin.parse_token, '1-5-7')
-
-
- def test_parse_token_range_fail2(self):
- """Failure of the generic_fns.mol_res_spin.parse_token() function on
the string '1--3'."""
-
- # Parse the invalid token.
- self.assertRaises(RelaxError, mol_res_spin.parse_token, '1--3')
-
-
def test_residue_loop(self):
"""Test the proper operation of the residue loop with residue
selection.
r8564 - in /branches/bmrb: ./ docs/latex/ generic_fns/ specific_fns/ specific_fns/model_free/ test_suite/unit_tests/_generic...