[SPARK-50564][PYTHON] Upgrade protobuf Python package to 5.29.1

### What changes were proposed in this pull request?
This PR aims to upgrade protobuf Python package from 5.28.3 to 5.29.1.

### Why are the changes needed?
To bring the latest bug fixes, such as
- Fix a python bug when assign an empty Struct at creation. (protocolbuffers/protobuf#18977) (protocolbuffers/protobuf@bb0d575), this one only introduced since 5.28.x
- Fix cord handling in DynamicMessage and oneofs. (protocolbuffers/protobuf@9e8b30c)
- Fix packed reflection handling bug in edition 2023. (protocolbuffers/protobuf@4c92328)
- Fix ContainerBase::DeepCopy to not modify the source object. (protocolbuffers/protobuf@9fa1f4f)

Full release notes as follows:
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.0-rc1
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.0-rc2
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.0-rc3
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.0
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.1
- https://pypi.org/project/protobuf/5.29.1/

### Does this PR introduce _any_ user-facing change?
No

### How was this patch tested?
Pass Github Actions

### Was this patch authored or co-authored using generative AI tooling?
No

Closes #49170 from LuciferYang/protobuf-python-5.29.1.

Lead-authored-by: yangjie01 <yangjie01@baidu.com>
Co-authored-by: YangJie <yangjie01@baidu.com>
Signed-off-by: Dongjoon Hyun <dongjoon@apache.org>

.github/workflows/build_and_test.yml

@@ -340,7 +340,7 @@ jobs:
     - name: Install Python packages (Python 3.11)
       if: (contains(matrix.modules, 'sql') && !contains(matrix.modules, 'sql-')) || contains(matrix.modules, 'connect')
       run: |
-        python3.11 -m pip install 'numpy>=1.20.0' pyarrow pandas scipy unittest-xml-reporting 'lxml==4.9.4' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.28.3'
+        python3.11 -m pip install 'numpy>=1.20.0' pyarrow pandas scipy unittest-xml-reporting 'lxml==4.9.4' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1'
         python3.11 -m pip list
     # Run the tests.
     - name: Run tests
@@ -726,7 +726,7 @@ jobs:
         python-version: '3.11'
     - name: Install dependencies for Python CodeGen check
       run: |
-        python3.11 -m pip install 'black==23.9.1' 'protobuf==5.28.3' 'mypy==1.8.0' 'mypy-protobuf==3.3.0'
+        python3.11 -m pip install 'black==23.9.1' 'protobuf==5.29.1' 'mypy==1.8.0' 'mypy-protobuf==3.3.0'
         python3.11 -m pip list
     - name: Python CodeGen check for branch-3.5
       if: inputs.branch == 'branch-3.5'

.github/workflows/build_python_connect35.yml

@@ -70,7 +70,7 @@ jobs:
           pip install 'numpy==1.25.1' 'pyarrow==12.0.1' 'pandas<=2.0.3' scipy unittest-xml-reporting plotly>=4.8 'mlflow>=2.3.1' coverage 'matplotlib==3.7.2' openpyxl 'memory-profiler==0.60.0' 'scikit-learn==1.1.*'
 
           # Add Python deps for Spark Connect.
-          pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.28.3' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3'
+          pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3'
 
           # Add torch as a testing dependency for TorchDistributor
           pip install 'torch==2.0.1' 'torchvision==0.15.2' torcheval

.github/workflows/maven_test.yml

@@ -178,7 +178,7 @@ jobs:
       - name: Install Python packages (Python 3.11)
         if: (contains(matrix.modules, 'sql#core')) || contains(matrix.modules, 'connect')
         run: |
-          python3.11 -m pip install 'numpy>=1.20.0' pyarrow pandas scipy unittest-xml-reporting 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.28.3'
+          python3.11 -m pip install 'numpy>=1.20.0' pyarrow pandas scipy unittest-xml-reporting 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1'
           python3.11 -m pip list
       # Run the tests.
       - name: Run tests

.github/workflows/python_macos_test.yml

@@ -134,7 +134,7 @@ jobs:
           python${{matrix.python}} -m pip install --ignore-installed 'blinker>=1.6.2'
           python${{matrix.python}} -m pip install --ignore-installed 'six==1.16.0'
           python${{matrix.python}} -m pip install numpy 'pyarrow>=15.0.0' 'six==1.16.0' 'pandas==2.2.3' scipy 'plotly>=4.8' 'mlflow>=2.8.1' coverage matplotlib openpyxl 'memory-profiler>=0.61.0' 'scikit-learn>=1.3.2' unittest-xml-reporting && \
-          python${{matrix.python}} -m pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.28.3' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3' && \
+          python${{matrix.python}} -m pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3' && \
           python${{matrix.python}} -m pip cache purge && \
           python${{matrix.python}} -m pip list
       # Run the tests.

dev/create-release/spark-rm/Dockerfile

@@ -102,7 +102,7 @@ RUN pypy3 -m pip install numpy 'six==1.16.0' 'pandas==2.2.3' scipy coverage matp
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=15.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2 twine==3.4.1"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0"
 
 # Install Python 3.10 packages
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10

dev/infra/Dockerfile

@@ -96,7 +96,7 @@ RUN pypy3 -m pip install numpy 'six==1.16.0' 'pandas==2.2.3' scipy coverage matp
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 # Install Python 3.10 packages
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10

dev/requirements.txt

@@ -61,7 +61,7 @@ py
 grpcio>=1.67.0
 grpcio-status>=1.67.0
 googleapis-common-protos>=1.65.0
-protobuf==5.28.3
+protobuf==5.29.1
 
 # Spark Connect python proto generation plugin (optional)
 mypy-protobuf==3.3.0

dev/spark-test-image/python-309/Dockerfile

@@ -69,7 +69,7 @@ RUN apt-get update && apt-get install -y \
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 # Install Python 3.9 packages
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.9

dev/spark-test-image/python-310/Dockerfile

@@ -65,7 +65,7 @@ RUN apt-get update && apt-get install -y \
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 # Install Python 3.10 packages
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.10

dev/spark-test-image/python-311/Dockerfile

@@ -69,7 +69,7 @@ RUN apt-get update && apt-get install -y \
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 # Install Python 3.11 packages
 RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.11

dev/spark-test-image/python-312/Dockerfile

@@ -69,7 +69,7 @@ RUN apt-get update && apt-get install -y \
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
 # Python deps for Spark Connect
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 # Install Python 3.12 at the last stage to avoid breaking the existing Python installations
 RUN apt-get update && apt-get install -y \

dev/spark-test-image/python-313/Dockerfile

@@ -68,7 +68,7 @@ RUN apt-get update && apt-get install -y \
 
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.2.3 scipy plotly>=4.8 mlflow>=2.8.1 coverage matplotlib openpyxl memory-profiler>=0.61.0 scikit-learn>=1.3.2"
-ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.28.3 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
 
 
 # Install Python 3.13 packages