rpms/python-biopython/F-10 python-biopython-1.51-enable-flex.patch, NONE, 1.1 .cvsignore, 1.6, 1.7 python-biopython.spec, 1.11, 1.12 sources, 1.6, 1.7

[alexlan]

Author: alexlan

Update of /cvs/extras/rpms/python-biopython/F-10
In directory cvs1.fedora.phx.redhat.com:/tmp/cvs-serv19023

Modified Files:
	.cvsignore python-biopython.spec sources 
Added Files:
	python-biopython-1.51-enable-flex.patch 
Log Message:
* Tue Aug 18 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.51-1
- Update to upstream 1.51
- Drop mx {Build}Requires, no longer used upstream
- Remove Martel modules, no longer distributed upstream
- Add flex to BuildRequires, patch setup to build
  Bio.PDB.mmCIF.MMCIFlex as per upstream:
  http://bugzilla.open-bio.org/show_bug.cgi?id=2619


python-biopython-1.51-enable-flex.patch:
 setup.py |   12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

--- NEW FILE python-biopython-1.51-enable-flex.patch ---
--- setup.py.orig	2009-08-18 18:23:01.000000000 -0400
+++ setup.py	2009-08-18 18:23:22.000000000 -0400
@@ -304,12 +304,12 @@
               include_dirs=["Bio"]
               ),
 #Commented out due to the build dependency on flex, see Bug 2619
-#   Extension('Bio.PDB.mmCIF.MMCIFlex',
-#              ['Bio/PDB/mmCIF/lex.yy.c',
-#               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
-#              include_dirs=["Bio"],
-#              libraries=["fl"]
-#              ),
+   Extension('Bio.PDB.mmCIF.MMCIFlex',
+              ['Bio/PDB/mmCIF/lex.yy.c',
+               'Bio/PDB/mmCIF/MMCIFlexmodule.c'],
+              include_dirs=["Bio"],
+              libraries=["fl"]
+              ),
     Extension('Bio.Nexus.cnexus',
               ['Bio/Nexus/cnexus.c']
               ),


Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/python-biopython/F-10/.cvsignore,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -p -r1.6 -r1.7
--- .cvsignore	29 Sep 2008 08:07:25 -0000	1.6
+++ .cvsignore	18 Aug 2009 23:05:41 -0000	1.7
@@ -1 +1 @@
-biopython-1.48.tar.gz
+biopython-1.51.tar.gz


Index: python-biopython.spec
===================================================================
RCS file: /cvs/extras/rpms/python-biopython/F-10/python-biopython.spec,v
retrieving revision 1.11
retrieving revision 1.12
diff -u -p -r1.11 -r1.12
--- python-biopython.spec	29 Sep 2008 08:07:25 -0000	1.11
+++ python-biopython.spec	18 Aug 2009 23:05:41 -0000	1.12
@@ -2,25 +2,25 @@
 %{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
 
 Name:             python-biopython
-Version:          1.48
+Version:          1.51
 Release:          1%{?dist}
 Summary:          Python tools for computational molecular biology
 Source0:          http://biopython.org/DIST/biopython-%{version}.tar.gz
+Patch0:           python-biopython-1.51-enable-flex.patch
 License:          MIT
 Url:              http://www.biopython.org/
 Group:            Development/Libraries
 BuildRoot:        %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
 BuildRequires:    python-devel
+BuildRequires:    flex
 BuildRequires:    python-reportlab
-BuildRequires:    mx
-BuildRequires:    python-numeric
+BuildRequires:    numpy
 BuildRequires:    MySQL-python
-BuildRequires:    python-psycopg
+BuildRequires:    python-psycopg2
 Requires:         python-reportlab
-Requires:         mx
-Requires:         python-numeric
+Requires:         numpy
 Requires:         MySQL-python
-Requires:         python-psycopg
+Requires:         python-psycopg2
 Requires:         wise2
 
 %description
@@ -29,6 +29,8 @@ biology.
 
 %prep
 %setup -q -n biopython-%{version}
+# enable build of Bio.PDB.mmCIF.MMCIFlex (requires flex)
+%patch0 -p0
 
 # remove all execute bits from documentation and fix line endings
 find Scripts -type f -exec chmod -x {} 2>/dev/null ';'
@@ -40,17 +42,12 @@ find Bio -type f -exec chmod -x {} 2>/de
 # remove she-bang lines in .py files to keep rpmlint happy
 find Bio -type f -name "*.py" -exec sed -i '/^#![ ]*\/usr\/bin\/.*$/ d' {} 2>/dev/null ';'
 
-# answer interactive question "yes" to build Bio.KDTree
 %build
-env CFLAGS="$RPM_OPT_FLAGS" %{__python} setup.py build <<EOF
-y
-EOF
+env CFLAGS="$RPM_OPT_FLAGS" %{__python} setup.py build
 
 %install
 rm -rf $RPM_BUILD_ROOT
-%{__python} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython  <<EOF
-y
-EOF
+%{__python} setup.py install -O1 --skip-build --root=$RPM_BUILD_ROOT --install-data=%{_datadir}/python-biopython
 
 ## disable tests for the moment
 %check
@@ -68,12 +65,37 @@ rm -rf $RPM_BUILD_ROOT
 %endif
 %dir %{python_sitearch}/Bio
 %{python_sitearch}/Bio/*
-%dir %{python_sitearch}/Martel
-%{python_sitearch}/Martel/*
 %dir %{python_sitearch}/BioSQL
 %{python_sitearch}/BioSQL/*
 
 %changelog
+* Tue Aug 18 2009 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.51-1
+- Update to upstream 1.51
+- Drop mx {Build}Requires, no longer used upstream
+- Remove Martel modules, no longer distributed upstream
+- Add flex to BuildRequires, patch setup to build
+  Bio.PDB.mmCIF.MMCIFlex as per upstream:
+  http://bugzilla.open-bio.org/show_bug.cgi?id=2619
+
+* Sun Jul 26 2009 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.49-3
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_12_Mass_Rebuild
+
+* Thu Feb 26 2009 Fedora Release Engineering <rel-eng at lists.fedoraproject.org> - 1.49-2
+- Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
+
+* Mon Dec  1 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.49-1
+- Update to latest upstream (1.49) uses numpy and new API for psycopg2
+- [Build]Requires python-numeric -> numpy 
+- [Build]Requires python-psycopg -> python-psycopg2
+- Remove interactive question hack, no longer needed
+
+* Sun Nov 30 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.48-3
+- Temporarily disable python-psycopg dependency until it is rebuilt
+  for Python 2.6
+
+* Sat Nov 29 2008 Ignacio Vazquez-Abrams <ivazqueznet+rpm at gmail.com> - 1.48-2
+- Rebuild for Python 2.6
+
 * Mon Sep 29 2008 Alex Lancaster <alexlan[AT]fedoraproject org> - 1.48-1
 - Update to latest upstream (1.48)
 


Index: sources
===================================================================
RCS file: /cvs/extras/rpms/python-biopython/F-10/sources,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -p -r1.6 -r1.7
--- sources	29 Sep 2008 08:07:25 -0000	1.6
+++ sources	18 Aug 2009 23:05:42 -0000	1.7
@@ -1 +1 @@
-b049e3af8128bea68e4e86b55c6d0996  biopython-1.48.tar.gz
+e973cb96b44b47526d31b6a0039c686f  biopython-1.51.tar.gz