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
+===
+
