[SPARK-52844][PYTHON] Update protobuf Python package to 5.29.5

### What changes were proposed in this pull request?
Updating protobuf from 5.29.1 to 5.29.5

### Why are the changes needed?
- https://github.com/protocolbuffers/protobuf/releases/tag/v29.5
  - protocolbuffers/protobuf#20904
  - [Add recursion depth limits to pure python](protocolbuffers/protobuf@05ba1a8)
  - [Internal pure python fixes](protocolbuffers/protobuf@1ef3f01)

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

### How was this patch tested?
Passed all CI tests

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

Closes #51747 from eschcam/py-protobuf-update.

Authored-by: eschcam <cameron.scholes@est.tech>
Signed-off-by: Dongjoon Hyun <dongjoon@apache.org>

Author: eschcam

.github/workflows/build_and_test.yml

@@ -362,7 +362,7 @@ jobs:
     - name: Install Python packages (Python 3.11)
       if: (contains(matrix.modules, 'sql') && !contains(matrix.modules, 'sql-')) || contains(matrix.modules, 'connect') || contains(matrix.modules, 'yarn')
       run: |
-        python3.11 -m pip install 'numpy>=1.22' pyarrow pandas pyyaml 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 install 'numpy>=1.22' pyarrow pandas pyyaml scipy unittest-xml-reporting 'lxml==4.9.4' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5'
         python3.11 -m pip list
     # Run the tests.
     - name: Run tests
@@ -766,7 +766,7 @@ jobs:
         python-version: '3.11'
     - name: Install dependencies for Python CodeGen check
       run: |
-        python3.11 -m pip install 'black==23.12.1' 'protobuf==5.29.1' 'mypy==1.8.0' 'mypy-protobuf==3.3.0'
+        python3.11 -m pip install 'black==23.12.1' 'protobuf==5.29.5' '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_connect.yml

@@ -72,7 +72,7 @@ jobs:
           python packaging/client/setup.py sdist
           cd dist
           pip install pyspark*client-*.tar.gz
-          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' 'six==1.16.0' 'pandas==2.3.2' scipy 'plotly<6.0.0' 'mlflow>=2.8.1' coverage matplotlib openpyxl 'memory-profiler>=0.61.0' 'scikit-learn>=1.3.2' 'graphviz==0.20.3' 'torch<2.6.0' torchvision torcheval deepspeed unittest-xml-reporting
+          pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3' 'six==1.16.0' 'pandas==2.3.2' scipy 'plotly<6.0.0' 'mlflow>=2.8.1' coverage matplotlib openpyxl 'memory-profiler>=0.61.0' 'scikit-learn>=1.3.2' 'graphviz==0.20.3' 'torch<2.6.0' torchvision torcheval deepspeed unittest-xml-reporting
       - name: List Python packages
         run: python -m pip list
       - name: Run tests (local)

.github/workflows/build_python_connect35.yml

@@ -71,7 +71,7 @@ jobs:
           pip install 'numpy==1.25.1' 'pyarrow>=18.0.0' 'pandas<=2.0.3' scipy unittest-xml-reporting 'plotly<6.0.0' '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==5.29.1' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3'
+          pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5' '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

@@ -175,7 +175,7 @@ jobs:
       - name: Install Python packages (Python 3.11)
         if: contains(matrix.modules, 'resource-managers#yarn') || (contains(matrix.modules, 'sql#core')) || contains(matrix.modules, 'connect')
         run: |
-          python3.11 -m pip install 'numpy>=1.22' pyarrow pandas scipy unittest-xml-reporting 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1'
+          python3.11 -m pip install 'numpy>=1.22' pyarrow pandas scipy unittest-xml-reporting 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5'
           python3.11 -m pip list
       # Run the tests using script command.
       # BSD's script command doesn't support -c option, and the usage is different from Linux's one.

.github/workflows/pages.yml

@@ -63,7 +63,7 @@ jobs:
          pip install 'sphinx==4.5.0' mkdocs 'pydata_sphinx_theme>=0.13' sphinx-copybutton nbsphinx numpydoc jinja2 markupsafe 'pyzmq<24.0.0' \
             ipython ipython_genutils sphinx_plotly_directive 'numpy>=1.22' pyarrow 'pandas==2.3.2' 'plotly>=4.8' 'docutils<0.18.0' \
             'flake8==3.9.0' 'mypy==1.8.0' 'pytest==7.1.3' 'pytest-mypy-plugins==1.9.3' 'black==23.12.1' \
-            'pandas-stubs==1.2.0.53' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1' 'grpc-stubs==1.24.11' 'googleapis-common-protos-stubs==2.2.0' \
+            'pandas-stubs==1.2.0.53' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5' 'grpc-stubs==1.24.11' 'googleapis-common-protos-stubs==2.2.0' \
             'sphinxcontrib-applehelp==1.0.4' 'sphinxcontrib-devhelp==1.0.2' 'sphinxcontrib-htmlhelp==2.0.1' 'sphinxcontrib-qthelp==1.0.3' 'sphinxcontrib-serializinghtml==1.1.5'
       - name: Install Ruby for documentation generation
         uses: ruby/setup-ruby@v1

.github/workflows/python_hosted_runner_test.yml

@@ -151,7 +151,7 @@ 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${{matrix.python}} -m pip install numpy 'pyarrow>=21.0.0' 'six==1.16.0' 'pandas==2.3.2' scipy 'plotly<6.0.0' 'mlflow>=2.8.1' coverage matplotlib openpyxl 'memory-profiler>=0.61.0' 'scikit-learn>=1.3.2' unittest-xml-reporting && \
-          python${{matrix.python}} -m pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3' && \
+          python${{matrix.python}} -m pip install 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5' 'googleapis-common-protos==1.65.0' 'graphviz==0.20.3' && \
           python${{matrix.python}} -m pip cache purge
       - name: List Python packages
         run: python${{matrix.python}} -m pip list

dev/create-release/spark-rm/Dockerfile

@@ -94,7 +94,7 @@ ENV R_LIBS_SITE="/usr/local/lib/R/site-library:${R_LIBS_SITE}:/usr/lib/R/library
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.3.2 scipy plotly<6.0.0 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==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.5 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/infra/Dockerfile

@@ -96,7 +96,7 @@ RUN pypy3 -m pip install numpy 'six==1.16.0' 'pandas==2.3.0' scipy coverage matp
 
 ARG BASIC_PIP_PKGS="numpy pyarrow>=18.0.0 six==1.16.0 pandas==2.3.0 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==5.29.1 googleapis-common-protos==1.65.0 graphviz==0.20.3"
+ARG CONNECT_PIP_PKGS="grpcio==1.67.0 grpcio-status==1.67.0 protobuf==5.29.5 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

@@ -64,7 +64,7 @@ py
 grpcio>=1.67.0
 grpcio-status>=1.67.0
 googleapis-common-protos>=1.65.0
-protobuf==5.29.1
+protobuf==5.29.5
 
 # Spark Connect python proto generation plugin (optional)
 mypy-protobuf==3.3.0

dev/spark-test-image/docs/Dockerfile

@@ -90,6 +90,6 @@ RUN curl -sS https://bootstrap.pypa.io/get-pip.py | python3.11
 RUN python3.11 -m pip install 'sphinx==4.5.0' mkdocs 'pydata_sphinx_theme>=0.13' sphinx-copybutton nbsphinx numpydoc jinja2 markupsafe 'pyzmq<24.0.0' \
   ipython ipython_genutils sphinx_plotly_directive 'numpy>=1.22' pyarrow 'pandas==2.3.2' 'plotly>=4.8' 'docutils<0.18.0' \
   'flake8==3.9.0' 'mypy==1.8.0' 'pytest==7.1.3' 'pytest-mypy-plugins==1.9.3' 'black==23.12.1' \
-  'pandas-stubs==1.2.0.53' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.1' 'grpc-stubs==1.24.11' 'googleapis-common-protos-stubs==2.2.0' \
+  'pandas-stubs==1.2.0.53' 'grpcio==1.67.0' 'grpcio-status==1.67.0' 'protobuf==5.29.5' 'grpc-stubs==1.24.11' 'googleapis-common-protos-stubs==2.2.0' \
   'sphinxcontrib-applehelp==1.0.4' 'sphinxcontrib-devhelp==1.0.2' 'sphinxcontrib-htmlhelp==2.0.1' 'sphinxcontrib-qthelp==1.0.3' 'sphinxcontrib-serializinghtml==1.1.5' \
   && python3.11 -m pip cache purge