Attachment 1648700 Details for Bug 1780849 – pymol-python3.patch

[patch] pymol-python3.patch

pymol-python3.patch (text/plain), 12.05 KB, created by Sergio Basto on 2019-12-31 01:30:47 UTC

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Creator: Sergio Basto

Created: 2019-12-31 01:30:47 UTC

Size: 12.05 KB

patch

obsolete

>diff -rup pymol-open-source-2.3.0.orig/test/headerTest.py pymol-open-source-2.3.0/test/headerTest.py
>--- pymol-open-source-2.3.0.orig/test/headerTest.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/headerTest.py	2019-12-31 00:58:56.747925023 +0000
>@@ -7,28 +7,28 @@ import os
> if len(sys.argv)>1:
> 	p = sys.argv[1:]
> else:
>-	print "Usage: pymol -cq ./headerTest.py -- MTZTestDirectory"
>+	print("Usage: pymol -cq ./headerTest.py -- MTZTestDirectory")
> 	sys.exit(1)
> 
> 
> for curPath in p:
>-	print "Processing MTZ files in path: '%s'" % curPath
>+	print("Processing MTZ files in path: '%s'" % curPath)
> 
> 	l = glob.glob(curPath + os.sep + "*.mtz")
> 
> 	d = {}
> 
> 	for mtzFile in l:
>-	    print "Processing %s." % mtzFile
>+	    print("Processing %s." % mtzFile)
> 	    d[mtzFile] = headering.MTZHeader(mtzFile)
> 
> 	for f in d:
>-	    print "Columns for file '%s':" % f
>+	    print("Columns for file '%s':" % f)
> 	    pprint.pprint(d[f].getColumns())
>-	    print ""
>+	    print("")
> 
> 	for f in d:
>-	    print "Columns of type W ofr file '%s':" % f
>+	    print("Columns of type W ofr file '%s':" % f)
> 	    pprint.pprint(d[f].getColumnsOfType("W"))
>-	    print ""
>+	    print("")
> 		
>diff -rup pymol-open-source-2.3.0.orig/test/inp/B01.py pymol-open-source-2.3.0/test/inp/B01.py
>--- pymol-open-source-2.3.0.orig/test/inp/B01.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/B01.py	2019-12-31 01:05:14.326755274 +0000
>@@ -50,7 +50,7 @@ def load():
>       try:
>          cmd.set("suspend_updates","1")  
>          cmd.delete('pdb')
>-         print file,last1,last2,c,"of",l
>+         print(file,last1,last2,c,"of",l)
>          last2 = last1
>          last1 = file
>          cmd.load(file,'pdb')
>diff -rup pymol-open-source-2.3.0.orig/test/inp/B02.py pymol-open-source-2.3.0/test/inp/B02.py
>--- pymol-open-source-2.3.0.orig/test/inp/B02.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/B02.py	2019-12-31 01:06:50.254201459 +0000
>@@ -26,7 +26,7 @@ def load():
> #        list.pop(0)
>     for file in list:
>         try:
>-            print file                     
>+            print(file)
>             cmd.delete('pdb')              
>             cmd.load(file,'pdb')           
>             cmd.orient('pdb')              
>diff -rup pymol-open-source-2.3.0.orig/test/inp/B04.py pymol-open-source-2.3.0/test/inp/B04.py
>--- pymol-open-source-2.3.0.orig/test/inp/B04.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/B04.py	2019-12-31 01:07:35.787938573 +0000
>@@ -42,15 +42,15 @@ def load():
>             l=f.readlines()
>             f.close()
>             if len(l):
>-               print
>+               print()
>                for a in l:
>-                  print a,
>+                  print(a,)
>                # save it so we have something to look at...
>                os.system("/bin/cp -f %s %s_s"%(cmp_file,cmp_file))
>                os.system("/bin/cp -f %s %s_s"%(ref_file,ref_file))               
>                os.system("/bin/cp -f %s %s_src"%(out_file,cmp_file))
>                os.system("/bin/cp -f %s %s_src"%(file,ref_file))
>-               print file
>+               print(file)
>             else:
>                sys.__stdout__.write(".")
>                sys.__stdout__.flush()
>diff -rup pymol-open-source-2.3.0.orig/test/inp/B06.py pymol-open-source-2.3.0/test/inp/B06.py
>--- pymol-open-source-2.3.0.orig/test/inp/B06.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/B06.py	2019-12-31 01:00:00.870564958 +0000
>@@ -26,7 +26,7 @@ def load():
> #   while list[0]!="pdb/f8/pdb1f8u":
> #      list.pop(0)
>    for file in list:
>-      print file
>+      print(file)
>       cmd.delete('pdb')
>       cmd.load(file,'pdb')
>       cmd.orient('pdb')
>diff -rup pymol-open-source-2.3.0.orig/test/inp/B07.py pymol-open-source-2.3.0/test/inp/B07.py
>--- pymol-open-source-2.3.0.orig/test/inp/B07.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/B07.py	2019-12-31 01:08:26.179647638 +0000
>@@ -33,10 +33,10 @@ def load():
>       idx = ch.insert_model(model)
> 
>       ch.pattern_orient_bonds(idx)
>-      print " %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)),
>+      print(" %5d"%cmd.count_atoms(),"%5d"%len(ch.pattern_get_string(idx)),)
>       ch.pattern_detect_chirality(idx)
>       pat = ch.pattern_get_string(idx)
>-      print "%5d"%len(pat),pat[0:22]+"..."+pat[-10:]
>+      print("%5d"%len(pat),pat[0:22]+"..."+pat[-10:])
> 
> cmd.feedback('disable','symmetry objectmolecule executive','everything')
> load()
>diff -rup pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py pymol-open-source-2.3.0/test/inp/C1050fitting.py
>--- pymol-open-source-2.3.0.orig/test/inp/C1050fitting.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/C1050fitting.py	2019-12-31 01:09:57.017123219 +0000
>@@ -5,11 +5,11 @@ from pymol import cmd
> 
> from random import random,seed
> 
>-print "BEGIN-LOG"
>+print("BEGIN-LOG")
> 
> seed(123)
> 
>-print "the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random()
>+print("the 1st random number should be %8.3f\notherwise the rest of the test is meaningless...\n"%pymol.random())
> 
> pymol.random = random
> 
>@@ -23,29 +23,29 @@ for a in xrange(1,11):
> 
> 
> cmd.frame(1)
>-print "%8.3f"%cmd.fit("ref","trg")
>+print("%8.3f"%cmd.fit("ref","trg"))
> 
> # asdf
> 
> 
> for a in xrange(1,14):
>-   print a,
>-   print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),
>-   print "%8.3f"%cmd.rms("ref","trg"),
>-   print "%8.3f"%cmd.rms_cur("ref","trg")
>+   print(a,)
>+   print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),)
>+   print("%8.3f"%cmd.rms("ref","trg"),)
>+   print("%8.3f"%cmd.rms_cur("ref","trg"))
> 
> cmd.frame(10)
> 
>-print "%8.3f"%cmd.fit("ref","trg")
>+print("%8.3f"%cmd.fit("ref","trg"))
> for a in xrange(1,14):
>-   print a,
>-   print "%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),
>-   print "%8.3f"%cmd.rms("ref","trg"),
>-   print "%8.3f"%cmd.rms_cur("ref","trg")
>+   print(a,)
>+   print("%8.3f"%cmd.fit("ref and resi %d"%a,"trg"),)
>+   print("%8.3f"%cmd.rms("ref","trg"),)
>+   print("%8.3f"%cmd.rms_cur("ref","trg"))
> 
> 
> a = 1
>-print "%8.3f"%cmd.fit("ref","trg")
>+print("%8.3f"%cmd.fit("ref","trg"))
> for b in xrange(1,11):
>    cmd._dump_floats(cmd.intra_fit("trg and resi %d"%a,b))
>    cmd._dump_floats(cmd.intra_rms("trg",b))
>@@ -56,7 +56,7 @@ cmd.do("intra_fit (trg and resi 1),10")
> cmd.do("intra_rms (trg),10")
> cmd.do("intra_rms_cur (trg),10")
> 
>-print "END-LOG"
>+print("END-LOG")
> 
> 
> 
>diff -rup pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py pymol-open-source-2.3.0/test/inp/C1060controlling.py
>--- pymol-open-source-2.3.0.orig/test/inp/C1060controlling.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/C1060controlling.py	2019-12-31 01:12:25.376266687 +0000
>@@ -2,30 +2,30 @@
> 
> from pymol import cmd
> 
>-print "BEGIN-LOG"
>+print("BEGIN-LOG")
> 
>-print cmd.set_key('F1',lambda :cmd.turn('x',10))
>-print cmd.set_key('F12',lambda :cmd.turn('x',10))
>+print(cmd.set_key('F1',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('F12',lambda :cmd.turn('x',10)))
> 
>-print cmd.set_key('left',lambda :cmd.turn('x',10))
>-print cmd.set_key('right',lambda :cmd.turn('x',10))
>-print cmd.set_key('pgup',lambda :cmd.turn('x',10))
>-print cmd.set_key('pgdn',lambda :cmd.turn('x',10))
>-print cmd.set_key('home',lambda :cmd.turn('x',10))
>-print cmd.set_key('insert',lambda :cmd.turn('x',10))
>+print(cmd.set_key('left',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('right',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('pgup',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('pgdn',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('home',lambda :cmd.turn('x',10)))
>+print(cmd.set_key('insert',lambda :cmd.turn('x',10)))
> 
>-print cmd.set_key('ALT-A',lambda :cmd.turn('y',10))
>+print(cmd.set_key('ALT-A',lambda :cmd.turn('y',10)))
> 
>-print cmd.set_key('CTRL-C',lambda :cmd.turn('z',10))
>+print(cmd.set_key('CTRL-C',lambda :cmd.turn('z',10)))
> 
>-print cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10))
>+print(cmd.set_key('SHFT-F1', lambda :cmd.turn('z',10)))
> 
>-print cmd.set_key('ALT-F1', lambda :cmd.turn('y',10))
>+print(cmd.set_key('ALT-F1', lambda :cmd.turn('y',10)))
> 
>-print cmd.set_key('CTRL-F8', lambda :cmd.move('x',1))
>+print(cmd.set_key('CTRL-F8', lambda :cmd.move('x',1)))
> 
> 
>-print "END-LOG"
>+print("END-LOG")
> 
> 
> 
>diff -rup pymol-open-source-2.3.0.orig/test/inp/C1100do.py pymol-open-source-2.3.0/test/inp/C1100do.py
>--- pymol-open-source-2.3.0.orig/test/inp/C1100do.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/C1100do.py	2019-12-31 01:12:44.051158878 +0000
>@@ -2,7 +2,7 @@
> 
> from pymol import cmd
> 
>-print "BEGIN-LOG"
>+print("BEGIN-LOG")
> 
> cmd.do("""
> load dat/pept.pdb
>@@ -27,16 +27,16 @@ cmd.do('ray')
> 
> # see if when can embed Python blocks inside of PyMOL inside of Python
> 
>-cmd.do('for a in range(1,10):\\\n   print a\\\n   print a+10')
>+cmd.do('for a in range(1,10):\\\n   print (a)\\\n   print (a+10)')
> 
> cmd.do(r"""
> for a in range(11,21):\
>-  print a\
>-  print a+10
>+  print (a)\
>+  print (a+10)
>   """)
> 
> 
>-print "END-LOG"
>+print("END-LOG")
> 
> 
> 
>diff -rup pymol-open-source-2.3.0.orig/test/inp/C2000returns.py pymol-open-source-2.3.0/test/inp/C2000returns.py
>--- pymol-open-source-2.3.0.orig/test/inp/C2000returns.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/C2000returns.py	2019-12-31 01:14:11.048656595 +0000
>@@ -1,6 +1,6 @@
> # -c
> 
>-print "BEGIN-LOG"
>+print("BEGIN-LOG")
> 
> import pymol
> from pymol import cmd
>@@ -8,18 +8,18 @@ from pymol import cmd
> # need to do this for all supported file types because the load routines diverge...
> 
> def x(st):
>-   print st
>+   print(st)
>    cmd.set("raise_exceptions",0)
>    valu = eval(st)
>-   print valu
>+   print(valu)
>    if cmd.is_error(valu):
>       cmd.set("raise_exceptions",1)
>       try:
>-         print eval(st)
>+         print(eval(st))
>       except pymol.CmdException:
>-         print "CmdException raised."
>+         print("CmdException raised.")
>       except cmd.QuietException:
>-         print "QuietException raised."
>+         print("QuietException raised.")
> 
> map(x,[
> 'cmd.load("dat/pept.pdb")' ,
>@@ -55,12 +55,12 @@ map(x,[
> cmd.delete("all")
> cmd.load("dat/pept.pdb")
> mdl = cmd.get_model("pept")
>-print mdl.__class__
>-print len(mdl.atom)
>+print(mdl.__class__)
>+print(len(mdl.atom))
> 
> mdl = cmd.get_model("none")
>-print mdl.__class__
>-print len(mdl.atom)
>+print(mdl.__class__)
>+print(len(mdl.atom))
> 
> map( x, [
> 'cmd.get_model("nonexistent")',
>@@ -119,7 +119,7 @@ map( x, [
> 
> 
> 
>-print "END-LOG"
>+print("END-LOG")
> 
> TODO="""
> 
>diff -rup pymol-open-source-2.3.0.orig/test/inp/T04.py pymol-open-source-2.3.0/test/inp/T04.py
>--- pymol-open-source-2.3.0.orig/test/inp/T04.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/inp/T04.py	2019-12-31 01:00:30.116396114 +0000
>@@ -34,7 +34,7 @@ def centers():
>          cmd.center("(resi %d)"%resi)
>          time.sleep(random.random()*0.30)
>       except: 
>-         print "exception"
>+         print("exception")
> 
> t = threading.Thread(target=centers)
> t.setDaemon(1)
>@@ -146,7 +146,7 @@ def carts():
>          time.sleep(random.random()*0.03)
> 
>       except:
>-         print "exception"
>+         print("exception")
> 
> t = threading.Thread(target=carts)
> t.setDaemon(1)
>diff -rup pymol-open-source-2.3.0.orig/test/win.py pymol-open-source-2.3.0/test/win.py
>--- pymol-open-source-2.3.0.orig/test/win.py	2019-02-11 14:08:10.000000000 +0000
>+++ pymol-open-source-2.3.0/test/win.py	2019-12-31 01:15:21.879273187 +0000
>@@ -58,10 +58,10 @@ for test in tests:
>       tst = re.sub(r".*/|.*\\","",ifil) # get exact test name without suffix
>       tst = re.sub(r"\..*","",tst)
>       
>-      print " run_tests: "+tst+"..."
>+      print(" run_tests: "+tst+"...")
>       
>       syscmd = cmmd+" -x -d pwd "+opt+" "+ifil+" > tmp.txt 2>&1"
>-      print syscmd
>+      print(syscmd)
>       #os.system("c:\\pymolws\\pymol.exe")
>       os.system(syscmd)
>       # generate log file
>@@ -94,10 +94,10 @@ for test in tests:
>          if (not lf) and not (lg):
>             break
>          if string.strip(lf)!=string.strip(lg):
>-            print "<",lf
>-            print ">",lg
>+            print("<",lf)
>+            print(">",lg)
> 
>-print "done"
>+print("done")
> time.sleep(360)
> 
> #

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Attachments on bug 1780849: 1648700