From 461161cf9dff9d29e143f7ec601f91d19dea1638 Mon Sep 17 00:00:00 2001
From: alexlan <alexlan@fedoraproject.org>
Date: Aug 18 2009 22:45:19 +0000
Subject: - 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

---

diff --git a/.cvsignore b/.cvsignore
index 674539c..ce7aaed 100644
--- a/.cvsignore
+++ b/.cvsignore
@@ -1 +1 @@
-biopython-1.49.tar.gz
+biopython-1.51.tar.gz
diff --git a/python-biopython-1.51-enable-flex.patch b/python-biopython-1.51-enable-flex.patch
new file mode 100644
index 0000000..0fca77b
--- /dev/null
+++ b/python-biopython-1.51-enable-flex.patch
@@ -0,0 +1,21 @@
+--- 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']
+               ),
diff --git a/python-biopython.spec b/python-biopython.spec
index d5c5998..1307231 100644
--- a/python-biopython.spec
+++ b/python-biopython.spec
@@ -2,22 +2,22 @@
 %{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
 
 Name:             python-biopython
-Version:          1.49
-Release:          2%{?dist}
+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:    numpy
 BuildRequires:    MySQL-python
 BuildRequires:    python-psycopg2
 Requires:         python-reportlab
-Requires:         mx
 Requires:         numpy
 Requires:         MySQL-python
 Requires:         python-psycopg2
@@ -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 ';'
@@ -63,12 +65,21 @@ 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@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@lists.fedoraproject.org> - 1.49-2
 - Rebuilt for https://fedoraproject.org/wiki/Fedora_11_Mass_Rebuild
 
diff --git a/sources b/sources
index 360a1d7..49be4d6 100644
--- a/sources
+++ b/sources
@@ -1 +1 @@
-d233d4944f0c17d5927ca32c5a30d5b3  biopython-1.49.tar.gz
+e973cb96b44b47526d31b6a0039c686f  biopython-1.51.tar.gz