Bug#586841: patch
tags 586841 + patch tags 585251 + patch thanks I will upload fixed package to DELAYED/7, please check attached debdiff and do maintainer upload if you think my changes are ok. I fixed all mgl* packages but some of them still have lintian errors, do not clean itself after the build (i.e. when built twice in a row, .diff.gz is different) or FTBFS in a non clean environment - I didn't fix those. Next patches will follow soon, if you don't want me to upload to DELAYED, ping me on IRC. -- 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 , Sargis Dallakyan -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/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 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/pdb2p
Bug#586841: patch
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 , Sargis Dallakyan -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 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 +=== +