From 1305b2f09aaacea6e1364af18101bc246695ff81 Mon Sep 17 00:00:00 2001
From: alexlan <alexlan@fedoraproject.org>
Date: Apr 18 2007 06:38:32 +0000
Subject: Import FC-6 python-biopython.


---

diff --git a/.cvsignore b/.cvsignore
index e69de29..d73c5fe 100644
--- a/.cvsignore
+++ b/.cvsignore
@@ -0,0 +1 @@
+biopython-1.43.tar.gz
diff --git a/biopython-setup_test.patch b/biopython-setup_test.patch
new file mode 100644
index 0000000..04f0489
--- /dev/null
+++ b/biopython-setup_test.patch
@@ -0,0 +1,65 @@
+Index: setup.py
+===================================================================
+RCS file: /home/repository/biopython/biopython/setup.py,v
+retrieving revision 1.116
+diff -u -p -r1.116 setup.py
+--- setup.py	17 Mar 2007 19:21:04 -0000	1.116
++++ setup.py	11 Apr 2007 03:37:48 -0000
+@@ -238,11 +238,18 @@ class test_biopython(Command):
+     
+     """
+     description = "Automatically run the test suite for Biopython."
+-    user_options = []  # distutils complains if this is not here.
+-    def initialize_options(self):  # distutils wants this
+-        pass
+-    def finalize_options(self):    # this too
++
++    user_options = [
++        # provide the option to run tests in no-gui mode
++        ('no-gui', None, "Do not run in GUI mode")
++    ]
++
++    def initialize_options(self):
++        self.no_gui = None
++
++    def finalize_options(self):
+         pass
++
+     def run(self):
+         this_dir = os.getcwd()
+ 
+@@ -250,7 +257,10 @@ class test_biopython(Command):
+         os.chdir("Tests")
+         sys.path.insert(0, '')
+         import run_tests
+-        run_tests.main([])
++        if self.no_gui:
++            run_tests.main(['--no-gui'])
++        else:
++            run_tests.main([])
+ 
+         # change back to the current directory
+         os.chdir(this_dir)
+Index: Tests/run_tests.py
+===================================================================
+RCS file: /home/repository/biopython/biopython/Tests/run_tests.py,v
+retrieving revision 1.8
+diff -u -p -r1.8 run_tests.py
+--- Tests/run_tests.py	9 Mar 2007 23:36:43 -0000	1.8
++++ Tests/run_tests.py	11 Apr 2007 03:37:48 -0000
+@@ -56,7 +56,7 @@ def main(argv):
+ 
+     # get the command line options
+     try:
+-        opts, args = getopt.getopt(argv[1:], 'g',
++        opts, args = getopt.getopt(argv, 'g',
+ 				   ["generate", "no-gui", "help"])
+     except getopt.error, msg:
+         print msg
+@@ -316,5 +316,5 @@ def convert_string_newlines(line):
+     return line
+         
+ if __name__ == "__main__":
+-    sys.exit(main(sys.argv))
++    sys.exit(main(sys.argv[1:]))
+ 
diff --git a/python-biopython.spec b/python-biopython.spec
new file mode 100644
index 0000000..b27c30e
--- /dev/null
+++ b/python-biopython.spec
@@ -0,0 +1,84 @@
+%{!?python_sitelib: %define python_sitelib %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib()")}
+%{!?python_sitearch: %define python_sitearch %(%{__python} -c "from distutils.sysconfig import get_python_lib; print get_python_lib(1)")}
+
+Name:             python-biopython
+Version:          1.43
+Release:          3%{?dist}
+Summary:          Python tools for computational molecular biology
+Source0:          http://biopython.org/DIST/biopython-%{version}.tar.gz
+Patch0:           biopython-setup_test.patch
+License:          Biopython License Agreement
+Url:              http://www.biopython.org/
+Group:            Development/Libraries
+BuildRoot:        %{_tmppath}/%{name}-%{version}-%{release}-root-%(%{__id_u} -n)
+BuildRequires:    python-devel
+BuildRequires:    python-reportlab
+BuildRequires:    mx
+BuildRequires:    python-numeric
+BuildRequires:    MySQL-python
+BuildRequires:    python-psycopg
+Requires:         python-reportlab
+Requires:         mx
+Requires:         python-numeric
+Requires:         MySQL-python
+Requires:         python-psycopg
+
+%description
+A set of freely available Python tools for computational molecular
+biology.
+
+%prep
+%setup -q -n biopython-%{version}
+%patch0 -p0
+
+# remove all execute bits from documentation and fix line endings
+find Scripts -type f -exec chmod -x {} 2>/dev/null ';'
+find Doc -type f -exec chmod -x {} 2>/dev/null ';'
+find Doc -type f -exec sed -i 's/\r//' {} 2>/dev/null ';'
+
+# remove execute bits from Python modules
+find Bio -type f -exec chmod -x {} 2>/dev/null ';'
+# 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
+
+%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
+
+## disable tests for the moment
+%check
+%{?_with_check:%{__python} setup.py test --no-gui || :}
+
+%clean
+rm -rf $RPM_BUILD_ROOT
+
+%files
+%defattr(-,root,root,-)
+%doc Doc Scripts
+%doc CONTRIB DEPRECATED LICENSE NEWS README
+%dir %{python_sitearch}/Bio
+%{python_sitearch}/Bio/*
+%dir %{python_sitearch}/Martel
+%{python_sitearch}/Martel/*
+%dir %{python_sitearch}/BioSQL
+%{python_sitearch}/BioSQL/*
+
+%changelog
+* Mon Apr 17 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.43-3
+- Use python_sitearch macro to enable x86_64 builds work.
+
+* Mon Apr 16 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.43-2
+- Fix Source0 URL as per suggestion from Parag AN on #235989.
+
+* Mon Apr 02 2007 Alex Lancaster <alexl@users.sourceforge.net> 1.43-1
+- Initial Fedora package.
+
+
diff --git a/sources b/sources
index e69de29..d378292 100644
--- a/sources
+++ b/sources
@@ -0,0 +1 @@
+3c275b321bb1db7d8bda764913aaedcd  biopython-1.43.tar.gz