[med-svn] r4970 - in trunk/packages/mgltools/molkit/trunk/debian: . patches
Piotr Ożarowski
piotr at alioth.debian.org
Thu Jul 1 18:15:39 UTC 2010
Author: piotr
Date: 2010-07-01 18:15:24 +0000 (Thu, 01 Jul 2010)
New Revision: 4970
Added:
trunk/packages/mgltools/molkit/trunk/debian/patches/
trunk/packages/mgltools/molkit/trunk/debian/patches/fix_import_star.patch
trunk/packages/mgltools/molkit/trunk/debian/patches/fix_string_exceptions.patch
trunk/packages/mgltools/molkit/trunk/debian/patches/series
Modified:
trunk/packages/mgltools/molkit/trunk/debian/changelog
trunk/packages/mgltools/molkit/trunk/debian/control
trunk/packages/mgltools/molkit/trunk/debian/rules
Log:
* Non-maintainer upload.
* Build for all supported Python versions, add fix_import_star.patch
(closes: #586841)
* Add fix_string_exceptions.patch (closes: #585251)
* Architecture changed to all
Modified: trunk/packages/mgltools/molkit/trunk/debian/changelog
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/changelog 2010-07-01 18:12:02 UTC (rev 4969)
+++ trunk/packages/mgltools/molkit/trunk/debian/changelog 2010-07-01 18:15:24 UTC (rev 4970)
@@ -1,3 +1,13 @@
+mgltools-molkit (1.5.4.cvs.20090603-1.1) unstable; urgency=low
+
+ * Non-maintainer upload.
+ * Build for all supported Python versions, add fix_import_star.patch
+ (closes: #586841)
+ * Add fix_string_exceptions.patch (closes: #585251)
+ * Architecture changed to all
+
+ -- Piotr Ożarowski <piotr at debian.org> Wed, 30 Jun 2010 21:55:04 +0200
+
mgltools-molkit (1.5.4.cvs.20090603-1) unstable; urgency=low
* New upstream version.
Modified: trunk/packages/mgltools/molkit/trunk/debian/control
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/control 2010-07-01 18:12:02 UTC (rev 4969)
+++ trunk/packages/mgltools/molkit/trunk/debian/control 2010-07-01 18:15:24 UTC (rev 4970)
@@ -5,16 +5,16 @@
DM-Upload-Allowed: yes
XS-Autobuild: yes
Uploaders: Steffen Moeller <moeller at debian.org>, Sargis Dallakyan <sargis at scripps.edu>
-Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4), python2.5-dev, python-numpy
+Build-Depends: debhelper (>= 5.0.38), python-central (>= 0.5.6), cdbs (>= 0.4), python, python-numpy, quilt
Standards-Version: 3.8.1
-XS-Python-Version: 2.5
+XS-Python-Version: >= 2.5
Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mgltools/molkit/trunk/?rev=0&sc=0
Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mgltools/molkit/trunk/
Homepage: http://mgltools.scripps.edu/
Package: mgltools-molkit
XB-Python-Version: ${python:Versions}
-Architecture: any
+Architecture: all
Depends: ${shlibs:Depends}, ${misc:Depends}, ${python:Depends}, mgltools-pybabel, mgltools-dejavu, mgltools-bhtree, mgltools-sff, python-numpy
Recommends: mgltools-cmolkit
Suggests: pdb2pqr
Added: trunk/packages/mgltools/molkit/trunk/debian/patches/fix_import_star.patch
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/patches/fix_import_star.patch (rev 0)
+++ trunk/packages/mgltools/molkit/trunk/debian/patches/fix_import_star.patch 2010-07-01 18:15:24 UTC (rev 4970)
@@ -0,0 +1,18 @@
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
+@@ -384,11 +384,10 @@ class get_ligand_topology:
+ #
+ # Reformat the lists of lists of lists of ... that we get from the ring detection
+ #
+- from types import *
+- if type(item) is ListType:
++ if isinstance(item, (list, tuple)):
+ real_list=[]
+ for sub_item in item:
+- if not type(sub_item) is ListType:
++ if not isinstance(sub_item, (list, tuple)):
+ real_list.append(sub_item)
+ else:
+ self.get_items(sub_item)
Added: trunk/packages/mgltools/molkit/trunk/debian/patches/fix_string_exceptions.patch
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/patches/fix_string_exceptions.patch (rev 0)
+++ trunk/packages/mgltools/molkit/trunk/debian/patches/fix_string_exceptions.patch 2010-07-01 18:15:24 UTC (rev 4970)
@@ -0,0 +1,103 @@
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/NEWligand_topology.py
+@@ -405,7 +405,7 @@ class get_ligand_topology:
+ self.biglist.append(real_list)
+ return
+ else:
+- raise 'this should not happen'
++ raise Exception('this should not happen')
+
+ #
+ # -----
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/inputgen_pKa.py
+@@ -136,7 +136,9 @@ class inputGen:
+ #
+ # Not a known type
+ #
+- raise 'unknown type',type
++ # TODO: Exception() is used here instead of TypeError for backwards compatibility, fix it once sure that no TypeError is fine
++ #raise TypeError('unknown type',type)
++ raise Exception('unknown type',type)
+ return
+
+ def getText_sub(self):
+@@ -165,7 +167,7 @@ class inputGen:
+ text += " nlev 4\n"
+
+ else:
+- raise 'unknown method'
++ raise Exception('unknown method')
+ #
+ text += " mol 1\n"
+ text += " lpbe\n"
+@@ -214,7 +216,7 @@ class inputGen:
+ #
+ # Eh?
+ #
+- raise 'type not set'
++ raise Exception('type not set')
+
+ #
+ # ------
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligand_topology.py
+@@ -399,7 +399,7 @@ class get_ligand_topology:
+ self.biglist.append(real_list)
+ return
+ else:
+- raise 'this should not happen'
++ raise Exception('this should not happen')
+
+ #
+ # -----
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/ligandclean/ligff.py
+@@ -354,7 +354,7 @@ class ligand_charge_handler(MOL2MOLECULE
+ if BondiiRadiiDict.has_key(ele):
+ radius = BondiiRadiiDict[ele]
+ else:
+- raise 'radius not known for',ele
++ raise Exception('radius not known for',ele)
+ #
+ # Store the radii and charges
+ #
+Index: mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/pka.py
+===================================================================
+--- mgltools-molkit-1.5.4.cvs.20090603.orig/MolKit/pdb2pqr/pdb2pka/pka.py
++++ mgltools-molkit-1.5.4.cvs.20090603/MolKit/pdb2pqr/pdb2pka/pka.py
+@@ -867,7 +867,7 @@ class pKaRoutines:
+ if abs(totphi)<0.01 or abs(totcrg)<0.01:
+ print 'total abs phi',totphi
+ print 'total abs crg',totcrg
+- raise 'Something is rotten'
++ raise Exception('Something is rotten')
+ print
+ print
+ return energy
+@@ -1071,7 +1071,7 @@ class pKaRoutines:
+ #
+ if get_neutral_state:
+ if not neutral_state:
+- raise "no neutral state for",residue.resSeq
++ raise Exception("no neutral state for",residue.resSeq)
+ return neutral_state
+ #
+ # Make sure that the charges add up to integers by adding extra atoms
+@@ -1129,7 +1129,7 @@ class pKaRoutines:
+ if added is None and sum>0.001:
+ print sum
+ print atomnames
+- raise 'Could not find integer charge state'
++ raise Exception('Could not find integer charge state')
+ return atomnames
+
+ #
Added: trunk/packages/mgltools/molkit/trunk/debian/patches/series
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/patches/series (rev 0)
+++ trunk/packages/mgltools/molkit/trunk/debian/patches/series 2010-07-01 18:15:24 UTC (rev 4970)
@@ -0,0 +1,2 @@
+fix_string_exceptions.patch
+fix_import_star.patch
Modified: trunk/packages/mgltools/molkit/trunk/debian/rules
===================================================================
--- trunk/packages/mgltools/molkit/trunk/debian/rules 2010-07-01 18:12:02 UTC (rev 4969)
+++ trunk/packages/mgltools/molkit/trunk/debian/rules 2010-07-01 18:15:24 UTC (rev 4970)
@@ -13,7 +13,7 @@
include /usr/share/cdbs/1/rules/debhelper.mk
include /usr/share/cdbs/1/class/python-distutils.mk
-#include /usr/share/cdbs/1/rules/simple-patchsys.mk
+include /usr/share/cdbs/1/rules/patchsys-quilt.mk
clean::
find . -name CVS -a -type d| xargs -r rm -r
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