rpms/python-biopython/FC-6 biopython-setup_test.patch, NONE, 1.1 python-biopython.spec, NONE, 1.1 .cvsignore, 1.1, 1.2 sources, 1.1, 1.2

[Alex Lancaster (alexlan)]

Author: alexlan

Update of /cvs/extras/rpms/python-biopython/FC-6
In directory cvs-int.fedora.redhat.com:/tmp/cvs-serv15573/FC-6

Modified Files:
	.cvsignore sources 
Added Files:
	biopython-setup_test.patch python-biopython.spec 
Log Message:
Import FC-6 python-biopython.


biopython-setup_test.patch:

--- NEW FILE biopython-setup_test.patch ---
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:]))
 


--- NEW FILE python-biopython.spec ---
%{!?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 at users.sourceforge.net> 1.43-3
- Use python_sitearch macro to enable x86_64 builds work.

* Mon Apr 16 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.43-2
- Fix Source0 URL as per suggestion from Parag AN on #235989.

* Mon Apr 02 2007 Alex Lancaster <alexl at users.sourceforge.net> 1.43-1
- Initial Fedora package.




Index: .cvsignore
===================================================================
RCS file: /cvs/extras/rpms/python-biopython/FC-6/.cvsignore,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- .cvsignore	17 Apr 2007 16:59:59 -0000	1.1
+++ .cvsignore	18 Apr 2007 06:38:32 -0000	1.2
@@ -0,0 +1 @@
+biopython-1.43.tar.gz


Index: sources
===================================================================
RCS file: /cvs/extras/rpms/python-biopython/FC-6/sources,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- sources	17 Apr 2007 16:59:59 -0000	1.1
+++ sources	18 Apr 2007 06:38:32 -0000	1.2
@@ -0,0 +1 @@
+3c275b321bb1db7d8bda764913aaedcd  biopython-1.43.tar.gz