[med-svn] r19159 - trunk/packages/python-biopython/trunk/debian/patches
Andreas Tille
tille at moszumanska.debian.org
Sat May 9 05:47:13 UTC 2015
Author: tille
Date: 2015-05-09 05:47:12 +0000 (Sat, 09 May 2015)
New Revision: 19159
Removed:
trunk/packages/python-biopython/trunk/debian/patches/fix_test_problem_on_powerpc.patch
Modified:
trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch
trunk/packages/python-biopython/trunk/debian/patches/series
Log:
Refreshed patches
Deleted: trunk/packages/python-biopython/trunk/debian/patches/fix_test_problem_on_powerpc.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/fix_test_problem_on_powerpc.patch 2015-05-09 05:41:29 UTC (rev 19158)
+++ trunk/packages/python-biopython/trunk/debian/patches/fix_test_problem_on_powerpc.patch 2015-05-09 05:47:12 UTC (rev 19159)
@@ -1,207 +0,0 @@
-Author: Michiel de Hoon <mjldehoon at yahoo.com>
-Last-Update: Fri, 29 Aug 2014 20:37:24 -0700
-Bug-Debian: http://bugs.debian.org/751277
-Forwarded-Upstream: yes
-Description: Fix issue in test suite on PowerPC (and hopefully mips, s390x)
-
---- a/Bio/Cluster/clustermodule.c
-+++ b/Bio/Cluster/clustermodule.c
-@@ -27,31 +27,79 @@
- /* -- Helper routines ------------------------------------------------------- */
- /* ========================================================================== */
-
-+#if PY_MAJOR_VERSION < 3
-+static char
-+extract_single_character(PyObject* object, const char variable[],
-+ const char allowed[])
-+{ char c = '\0';
-+ const char* data;
-+ Py_ssize_t n;
-+ if (PyString_Check(object))
-+ { n = PyString_GET_SIZE(object);
-+ if (n==1) {
-+ data = PyString_AS_STRING(object);
-+ c = data[0];
-+ }
-+ }
-+ else if (PyUnicode_Check(object))
-+ { n = PyUnicode_GET_SIZE(object);
-+ if (n==1) {
-+ Py_UNICODE* u = PyUnicode_AS_UNICODE(object);
-+ Py_UNICODE ch = u[0];
-+ if (ch < 128) c = ch;
-+ }
-+ }
-+ else
-+ { PyErr_Format(PyExc_ValueError, "%s should be a string", variable);
-+ return 0;
-+ }
-+ if (!c)
-+ { PyErr_Format(PyExc_ValueError,
-+ "%s should be a single character", variable);
-+ return 0;
-+ }
-+ else if (!strchr(allowed, c))
-+ { PyErr_Format(PyExc_ValueError,
-+ "unknown %s function specified (should be one of '%s')",
-+ variable, allowed);
-+ return 0;
-+ }
-+ return c;
-+}
-+#else
-+static char
-+extract_single_character(PyObject* object, const char variable[],
-+ const char allowed[])
-+{ Py_UCS4 ch;
-+ Py_ssize_t n;
-+ if (!PyUnicode_Check(object))
-+ { PyErr_Format(PyExc_ValueError, "%s should be a string", variable);
-+ return 0;
-+ }
-+ if (PyUnicode_READY(object)==-1) return 0;
-+ n = PyUnicode_GET_LENGTH(object);
-+ if (n!=1)
-+ { PyErr_Format(PyExc_ValueError,
-+ "%s should be a single character", variable);
-+ return 0;
-+ }
-+ ch = PyUnicode_READ_CHAR(object, 0);
-+ if (ch < 128)
-+ { const char c = ch;
-+ if (strchr(allowed, c)) return c;
-+ }
-+ PyErr_Format(PyExc_ValueError,
-+ "unknown %s function specified (should be one of '%s')",
-+ variable, allowed);
-+ return 0;
-+}
-+#endif
-+
- static int
- distance_converter(PyObject* object, void* pointer)
- { char c;
-- const char* data;
-- const char known_distances[] = "ebcauxsk";
--#if PY_MAJOR_VERSION < 3
-- if (PyString_Check(object))
-- data = PyString_AsString(object);
-- else
--#endif
-- if (PyUnicode_Check(object))
-- data = PyUnicode_AS_DATA(object);
-- else
-- { PyErr_SetString(PyExc_ValueError, "distance should be a string");
-- return 0;
-- }
-- if (strlen(data)!=1)
-- { PyErr_SetString(PyExc_ValueError, "distance should be a single character");
-- return 0;
-- }
-- c = data[0];
-- if (!strchr(known_distances, c))
-- { PyErr_Format(PyExc_ValueError, "unknown distance function specified (should be one of '%s')", known_distances);
-- return 0;
-- }
-+ c = extract_single_character(object, "dist", "ebcauxsk");
-+ if (c==0) return 0;
- *((char*)pointer) = c;
- return 1;
- }
-@@ -59,28 +107,8 @@ distance_converter(PyObject* object, voi
- static int
- method_treecluster_converter(PyObject* object, void* pointer)
- { char c;
-- const char* data;
-- const char known_methods[] = "csma";
--#if PY_MAJOR_VERSION < 3
-- if (PyString_Check(object))
-- data = PyString_AsString(object);
-- else
--#endif
-- if (PyUnicode_Check(object))
-- data = PyUnicode_AS_DATA(object);
-- else
-- { PyErr_SetString(PyExc_ValueError, "method should be a string");
-- return 0;
-- }
-- if (strlen(data)!=1)
-- { PyErr_SetString(PyExc_ValueError, "method should be a single character");
-- return 0;
-- }
-- c = data[0];
-- if (!strchr(known_methods, c))
-- { PyErr_Format(PyExc_ValueError, "unknown method function specified (should be one of '%s')", known_methods);
-- return 0;
-- }
-+ c = extract_single_character(object, "method", "csma");
-+ if (c==0) return 0;
- *((char*)pointer) = c;
- return 1;
- }
-@@ -88,28 +116,8 @@ method_treecluster_converter(PyObject* o
- static int
- method_kcluster_converter(PyObject* object, void* pointer)
- { char c;
-- const char* data;
-- const char known_methods[] = "am";
--#if PY_MAJOR_VERSION < 3
-- if (PyString_Check(object))
-- data = PyString_AsString(object);
-- else
--#endif
-- if (PyUnicode_Check(object))
-- data = PyUnicode_AS_DATA(object);
-- else
-- { PyErr_SetString(PyExc_ValueError, "method should be a string");
-- return 0;
-- }
-- if (strlen(data)!=1)
-- { PyErr_SetString(PyExc_ValueError, "method should be a single character");
-- return 0;
-- }
-- c = data[0];
-- if (!strchr(known_methods, c))
-- { PyErr_Format(PyExc_ValueError, "unknown method function specified (should be one of '%s')", known_methods);
-- return 0;
-- }
-+ c = extract_single_character(object, "method", "am");
-+ if (c==0) return 0;
- *((char*)pointer) = c;
- return 1;
- }
-@@ -117,31 +125,12 @@ method_kcluster_converter(PyObject* obje
- static int
- method_clusterdistance_converter(PyObject* object, void* pointer)
- { char c;
-- const char* data;
-- const char known_methods[] = "amsxv";
--#if PY_MAJOR_VERSION < 3
-- if (PyString_Check(object))
-- data = PyString_AsString(object);
-- else
--#endif
-- if (PyUnicode_Check(object))
-- data = PyUnicode_AS_DATA(object);
-- else
-- { PyErr_SetString(PyExc_ValueError, "method should be a string");
-- return 0;
-- }
-- if (strlen(data)!=1)
-- { PyErr_SetString(PyExc_ValueError, "method should be a single character");
-- return 0;
-- }
-- c = data[0];
-- if (!strchr(known_methods, c))
-- { PyErr_Format(PyExc_ValueError, "unknown method function specified (should be one of '%s')", known_methods);
-- return 0;
-- }
-+ c = extract_single_character(object, "method", "amsxv");
-+ if (c==0) return 0;
- *((char*)pointer) = c;
- return 1;
- }
-+
- /* -- data ------------------------------------------------------------------ */
-
- static double**
Modified: trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch 2015-05-09 05:41:29 UTC (rev 19158)
+++ trunk/packages/python-biopython/trunk/debian/patches/remove_mathml-qname.patch 2015-05-09 05:47:12 UTC (rev 19159)
@@ -4,9 +4,9 @@
Forwarded-Upstream: yes
Description: Remove non DFSG free DTD
---- biopython-1.64.orig/Bio/Entrez/DTDs/modules.ent
-+++ biopython-1.64/Bio/Entrez/DTDs/modules.ent
-@@ -350,13 +350,6 @@
+--- a/Bio/Entrez/DTDs/modules.ent
++++ b/Bio/Entrez/DTDs/modules.ent
+@@ -350,13 +350,6 @@ Version Reason/Occasion
"mathmlsetup.ent" >
Modified: trunk/packages/python-biopython/trunk/debian/patches/series
===================================================================
--- trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-09 05:41:29 UTC (rev 19158)
+++ trunk/packages/python-biopython/trunk/debian/patches/series 2015-05-09 05:47:12 UTC (rev 19159)
@@ -1,2 +1 @@
remove_mathml-qname.patch
-fix_test_problem_on_powerpc.patch
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