patch upb CopyFrom error in protobuf-python 4.24.0

easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0-GCCcore-12.3.0.eb

@@ -10,7 +10,12 @@ toolchain = {'name': 'GCCcore', 'version': '12.3.0'}
 
 source_urls = ['https://pypi.python.org/packages/source/p/protobuf']
 sources = ['protobuf-%(version)s.tar.gz']
-checksums = ['5d0ceb9de6e08311832169e601d1fc71bd8e8c779f3ee38a97a78554945ecb85']
+patches = ['%(name)s-%(version)s_fix-upb-copyfrom.patch']
+checksums = [
+    {'protobuf-4.24.0.tar.gz': '5d0ceb9de6e08311832169e601d1fc71bd8e8c779f3ee38a97a78554945ecb85'},
+    {'protobuf-python-4.24.0_fix-upb-copyfrom.patch':
+     '9afea4c68ee54d7278ec61a7e7d91c0aad2e7b0d63ba22f2200d0df2fac34de7'},
+]
 
 builddependencies = [('binutils', '2.40')]
 

easybuild/easyconfigs/p/protobuf-python/protobuf-python-4.24.0_fix-upb-copyfrom.patch

@@ -0,0 +1,39 @@
+From 57636ce03ac1e2aab3a362a61a6664981e21cda5 Mon Sep 17 00:00:00 2001
+From: Jie Luo <[email protected]>
+Date: Thu, 24 Aug 2023 14:27:41 -0700
+Subject: [PATCH] upb CopyFrom the default empty message should just clear
+ instead of deep copy from memory
+
+fix https://github.com/protocolbuffers/protobuf/issues/13485
+
+PiperOrigin-RevId: 559870202
+---
+ python/message.c | 15 +++++++++------
+ 1 file changed, 9 insertions(+), 6 deletions(-)
+
+diff --git a/python/message.c b/python/message.c
+index afdd4311a..e61eebb23 100644
+--- a/python/message.c
++++ b/python/message.c
+@@ -1237,12 +1237,15 @@ static PyObject* PyUpb_Message_CopyFrom(PyObject* _self, PyObject* arg) {
+   PyUpb_Message* other = (void*)arg;
+   PyUpb_Message_EnsureReified(self);
+
+-  PyObject* tmp = PyUpb_Message_Clear(self);
+-  Py_DECREF(tmp);
+-
+-  upb_Message_DeepCopy(self->ptr.msg, other->ptr.msg,
+-                       upb_MessageDef_MiniTable(other->def),
+-                       PyUpb_Arena_Get(self->arena));
++  const upb_Message* other_msg = PyUpb_Message_GetIfReified((PyObject*)other);
++  if (other_msg) {
++    upb_Message_DeepCopy(self->ptr.msg, other_msg,
++                         upb_MessageDef_MiniTable(other->def),
++                         PyUpb_Arena_Get(self->arena));
++  } else {
++    PyObject* tmp = PyUpb_Message_Clear(self);
++    Py_DECREF(tmp);
++  }
+   PyUpb_Message_SyncSubobjs(self);
+
+   Py_RETURN_NONE;