Author: bugman
Date: Tue Oct 16 22:25:24 2012
New Revision: 17874
URL: http://svn.gna.org/viewcvs/relax?rev=17874&view=rev
Log:
Merged revisions 17861-17866 via svnmerge from
svn+ssh://bugman@xxxxxxxxxxx/svn/relax/trunk
........
r17861 | bugman | 2012-10-16 14:55:24 +0200 (Tue, 16 Oct 2012) | 3 lines
The python print statements in the user manual are now function calls to be
Python 3 compatible.
........
r17862 | bugman | 2012-10-16 14:56:56 +0200 (Tue, 16 Oct 2012) | 3 lines
Another print statement to function Python 3 fix for the user manual.
........
r17863 | bugman | 2012-10-16 14:58:50 +0200 (Tue, 16 Oct 2012) | 6 lines
Python 3 fixes for the script for generating plots of magnetic field lines.
The command used was:
2to3 -w graphics/wizards/dipole_pair/VectorFieldPlot.py
........
r17864 | bugman | 2012-10-16 15:01:03 +0200 (Tue, 16 Oct 2012) | 3 lines
Python 3 fixes for non-used Python code - converted print statements to
function calls.
........
r17865 | bugman | 2012-10-16 15:02:16 +0200 (Tue, 16 Oct 2012) | 3 lines
Python 3 fixes for one of the test data scripts - print statement with
function call replacements.
........
r17866 | bugman | 2012-10-16 15:07:07 +0200 (Tue, 16 Oct 2012) | 3 lines
Removed a debugging printout.
........
Modified:
branches/frame_order_testing/ (props changed)
branches/frame_order_testing/docs/latex/intro.tex
branches/frame_order_testing/docs/latex/model-free.tex
branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
branches/frame_order_testing/extern/scientific_python/IO/PDB.py
branches/frame_order_testing/graphics/wizards/dipole_pair/VectorFieldPlot.py
branches/frame_order_testing/test_suite/shared_data/align_data/missing_data/generate_missing.py
branches/frame_order_testing/test_suite/system_tests/angles.py
Propchange: branches/frame_order_testing/
------------------------------------------------------------------------------
--- svnmerge-integrated (original)
+++ svnmerge-integrated Tue Oct 16 22:25:24 2012
@@ -1,1 +1,1 @@
-/trunk:1-17859
+/trunk:1-17859,17861-17866
Modified: branches/frame_order_testing/docs/latex/intro.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/intro.tex?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/intro.tex (original)
+++ branches/frame_order_testing/docs/latex/intro.tex Tue Oct 16 22:25:24 2012
@@ -155,12 +155,12 @@
This is the Python prompt which has been tailored specifically for relax.
You will hence have full access, if desired, to the power of the
Python\index{Python} programing language to manipulate your data. You can
for instance type
-\example{relax> print "Hello World"}
+\example{relax> print("Hello World")}
the result being
\begin{exampleenv}
-relax> print "Hello World" \\
+relax> print("Hello World") \\
Hello World \\
relax>
\end{exampleenv}
Modified: branches/frame_order_testing/docs/latex/model-free.tex
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/docs/latex/model-free.tex?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
--- branches/frame_order_testing/docs/latex/model-free.tex (original)
+++ branches/frame_order_testing/docs/latex/model-free.tex Tue Oct 16
22:25:24 2012
@@ -924,7 +924,7 @@
\\
\# Loop over the data pipe names. \\
for name in pipes: \\
-\hspace*{4ex} print ``$\backslash$n$\backslash$n\# '' + name + `` \#'' \\
+\hspace*{4ex} print(``$\backslash$n$\backslash$n\# '' + name + `` \#'') \\
\\
\hspace*{4ex} \# Create the data pipe. \\
\hspace*{4ex} pipe.create(name, `mf') \\
Modified:
branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
--- branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
(original)
+++ branches/frame_order_testing/extern/scientific_python/IO/FortranFormat.py
Tue Oct 16 22:25:24 2012
@@ -33,8 +33,8 @@
>>>s = ' 59999'
>>>format = FortranFormat('2I4')
>>>line = FortranLine(s, format)
- >>>print line[0]
- >>>print line[1]
+ >>>print(line[0])
+ >>>print(line[1])
prints::
@@ -46,7 +46,7 @@
>>>format = FortranFormat('2D15.5')
>>>line = FortranLine([3.1415926, 2.71828], format)
- >>>print str(line)
+ >>>print(str(line))
prints::
Modified: branches/frame_order_testing/extern/scientific_python/IO/PDB.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/extern/scientific_python/IO/PDB.py?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
--- branches/frame_order_testing/extern/scientific_python/IO/PDB.py (original)
+++ branches/frame_order_testing/extern/scientific_python/IO/PDB.py Tue Oct
16 22:25:24 2012
@@ -45,10 +45,10 @@
Example::
>>>conf = Structure('example.pdb')
- >>>print conf
+ >>>print(conf)
>>>for residue in conf.residues:
>>> for atom in residue:
- >>> print atom
+ >>> print(atom)
@undocumented: atom_format
@undocumented: anisou_format
Modified:
branches/frame_order_testing/graphics/wizards/dipole_pair/VectorFieldPlot.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/graphics/wizards/dipole_pair/VectorFieldPlot.py?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
---
branches/frame_order_testing/graphics/wizards/dipole_pair/VectorFieldPlot.py
(original)
+++
branches/frame_order_testing/graphics/wizards/dipole_pair/VectorFieldPlot.py
Tue Oct 16 22:25:24 2012
@@ -205,7 +205,7 @@
def __get_arrowname(self, fillcolor='#000000'):
if 'arrows' not in dir(self):
self.arrows = {}
- if fillcolor not in self.arrows.iterkeys():
+ if fillcolor not in iter(self.arrows.keys()):
arrow = etree.SubElement(self.__get_defs(), 'path')
self.arrows[fillcolor] = arrow
arrow.set('id', 'arrow' + str(len(self.arrows)))
@@ -544,7 +544,7 @@
obj = etree.SubElement(self.symbols, name)
else:
obj = etree.SubElement(group, name)
- for i, j in params.iteritems():
+ for i, j in params.items():
obj.set(str(i), str(j))
return obj
@@ -561,7 +561,7 @@
outfile.write(etree.tostring(self.svg, xml_declaration=True,
pretty_print=True, encoding='utf-8'))
outfile.close()
- print 'image written to', filename + '.svg'
+ print('image written to', filename + '.svg')
@@ -606,7 +606,7 @@
if v != None: d_near *= 1.3 - cosv(v, self.first_point - p)
type_near = 'start'
mon = []
- for ptype, poles in self.field.elements.iteritems():
+ for ptype, poles in self.field.elements.items():
if ptype not in ['monopoles', 'dipoles'] or len(poles) == 0:
continue
for pole in poles:
@@ -679,7 +679,7 @@
(dpole * abs(cv) < xtol) and (l > 1e-3)):
# path is closed
nodes[-1]['v_out'] = None
- print 'closed at', pretty_vec(p)
+ print('closed at', pretty_vec(p))
break
elif (h > 0.99 * dpole and (cv > 0.9 or
(cv > 0. and dpole * abs(sv) < ytol))):
@@ -755,7 +755,7 @@
# create a corner
# use second-order formulas instead of runge-kutta
p += hc * v2
- print 'corner at', pretty_vec(p)
+ print('corner at', pretty_vec(p))
v = vnorm(2. * v2 - v)
nodes.append({'p':p.copy(),'v_in':v*hc,'corner':True})
l += h
@@ -779,7 +779,7 @@
adif = angle_dif(a1, a0)
if (abs(adif) / (.8*hh)**2 > corner_limit or
abs(a0) + abs(a1) >= pi / 2.):
- print 'end edge at', pretty_vec(p)
+ print('end edge at', pretty_vec(p))
# direction after corner changes again -> end
line
nodes[-1]['v_out'] = None
break
@@ -829,7 +829,7 @@
h = vabs(nodes[-1]['p'] - p)
nodes[-2]['v_out'] = f(nodes[-2]['p']) * h
nodes[-1]['v_in'] = f(nodes[-1]['p']) * h
- print 'stopped at', pretty_vec(nodes[-1]['p'])
+ print('stopped at', pretty_vec(nodes[-1]['p']))
break
# adapt step carefully
@@ -846,9 +846,9 @@
nodes[-1]['v_out'] = None
if i == maxn:
- print maxn, 'integration steps exceeded at', pretty_vec(p)
+ print(maxn, 'integration steps exceeded at', pretty_vec(p))
if l >= maxr:
- print 'integration boundary', str(maxr), 'exceeded at',
pretty_vec(p)
+ print('integration boundary', str(maxr), 'exceeded at',
pretty_vec(p))
return nodes
def __is_loop(self, nodes, path_close_tol):
@@ -995,7 +995,7 @@
if num_success > 2 and N < N_old: num_success = 2
if num_success >= 3: break
if num >= 25:
- print 'polyline creation did not converge after', num,
'tries!'
+ print('polyline creation did not converge after', num,
'tries!')
break
ratios = [ratio * N / n for ratio in ratios]
@@ -1114,7 +1114,7 @@
'''
def __init__ (self, elements={}):
self.elements = {}
- for name, params in elements.iteritems():
+ for name, params in elements.items():
self.add_element(name, params)
'''
@@ -1259,4 +1259,4 @@
### append your specific field creation here ###
# see http://commons.wikimedia.org/wiki/File:VFPt_charges_plus_minus.svg for
an example
-#print "individual image description code must be inserted at the end of
this program's source code!"
+#print("individual image description code must be inserted at the end of
this program's source code!")
Modified:
branches/frame_order_testing/test_suite/shared_data/align_data/missing_data/generate_missing.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/shared_data/align_data/missing_data/generate_missing.py?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
---
branches/frame_order_testing/test_suite/shared_data/align_data/missing_data/generate_missing.py
(original)
+++
branches/frame_order_testing/test_suite/shared_data/align_data/missing_data/generate_missing.py
Tue Oct 16 22:25:24 2012
@@ -144,7 +144,7 @@
# Loop over the interatomic data.
for interatom in interatomic_loop():
- print interatom.spin_id1, interatom.spin_id2
+ print(interatom.spin_id1, interatom.spin_id2)
# Deselected containers.
if not interatom.select:
continue
@@ -161,7 +161,7 @@
elif spin1._res_num == missing[i][j][0] and spin1.name ==
missing[i][j][1]:
skip = True
if skip:
- print "\tskip"
+ print("\tskip")
continue
# No vector.
Modified: branches/frame_order_testing/test_suite/system_tests/angles.py
URL:
http://svn.gna.org/viewcvs/relax/branches/frame_order_testing/test_suite/system_tests/angles.py?rev=17874&r1=17873&r2=17874&view=diff
==============================================================================
--- branches/frame_order_testing/test_suite/system_tests/angles.py (original)
+++ branches/frame_order_testing/test_suite/system_tests/angles.py Tue Oct 16
22:25:24 2012
@@ -66,7 +66,6 @@
# Checks for the first 12 residues.
for i in range(12):
- print((cdp.mol[0].res[i].spin[0]))
# Check the residue and spin info.
self.assertEqual(cdp.mol[0].res[i].num, i+1)
self.assertEqual(cdp.mol[0].res[i].name, res_name[i])
r17874 - in /branches/frame_order_testing: ./ docs/latex/ extern/scientific_python/IO/ graphics/wizards/dipole_pair/ test_su...