ups, I forgot to update debian/rules, new patch attached -- Piotr Ożarowski Debian GNU/Linux Developer www.ozarowski.pl www.griffith.cc www.debian.org GPG Fingerprint: 1D2F A898 58DA AF62 1786 2DF7 AEF6 F1A2 A745 7645
diff -u mgltools-molkit-1.5.4.cvs.20090603/debian/control mgltools-molkit-1.5.4.cvs.20090603/debian/control --- mgltools-molkit-1.5.4.cvs.20090603/debian/control +++ mgltools-molkit-1.5.4.cvs.20090603/debian/control @@ -5,16 +5,16 @@ DM-Upload-Allowed: yes XS-Autobuild: yes Uploaders: Steffen Moeller <moel...@debian.org>, Sargis Dallakyan <sar...@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 diff -u mgltools-molkit-1.5.4.cvs.20090603/debian/rules mgltools-molkit-1.5.4.cvs.20090603/debian/rules --- mgltools-molkit-1.5.4.cvs.20090603/debian/rules +++ mgltools-molkit-1.5.4.cvs.20090603/debian/rules @@ -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 diff -u mgltools-molkit-1.5.4.cvs.20090603/debian/changelog mgltools-molkit-1.5.4.cvs.20090603/debian/changelog --- mgltools-molkit-1.5.4.cvs.20090603/debian/changelog +++ mgltools-molkit-1.5.4.cvs.20090603/debian/changelog @@ -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 <pi...@debian.org> Wed, 30 Jun 2010 21:55:04 +0200 + mgltools-molkit (1.5.4.cvs.20090603-1) unstable; urgency=low * New upstream version. only in patch2: unchanged: --- mgltools-molkit-1.5.4.cvs.20090603.orig/debian/patches/series +++ mgltools-molkit-1.5.4.cvs.20090603/debian/patches/series @@ -0,0 +1,2 @@ +fix_string_exceptions.patch +fix_import_star.patch only in patch2: unchanged: --- mgltools-molkit-1.5.4.cvs.20090603.orig/debian/patches/fix_string_exceptions.patch +++ mgltools-molkit-1.5.4.cvs.20090603/debian/patches/fix_string_exceptions.patch @@ -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 + + # only in patch2: unchanged: --- mgltools-molkit-1.5.4.cvs.20090603.orig/debian/patches/fix_import_star.patch +++ mgltools-molkit-1.5.4.cvs.20090603/debian/patches/fix_import_star.patch @@ -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)
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