fix: update protobuf dependency to v5.29.5 (#111)

This PR upgrades the `protobuf` dependency and related dependencies
to a consistent version.

- update protobuf to v5.29.5
- downgrade protoc in devcontainer to v29.5
- update nipunn1313-mypy buf plugin to v3.6.0
- regenerate proto Python code with protobuf v5.29.5
- update uv.lock

fixes #110

Signed-off-by: Niels Pardon <par@zurich.ibm.com>

Author: nielspardon

.devcontainer/Dockerfile

@@ -5,9 +5,10 @@ SHELL ["/bin/bash", "-c"]
 RUN source "/home/vscode/.sdkman/bin/sdkman-init.sh" && sdk install java 25-graalce
 RUN mkdir -p ~/lib && cd ~/lib && curl -L -O http://www.antlr.org/download/antlr-4.13.2-complete.jar
 ENV ANTLR_JAR="~/lib/antlr-4.13.1-complete.jar"
-RUN cd ~ && curl -LO https://github.com/protocolbuffers/protobuf/releases/download/v30.2/protoc-30.2-linux-x86_64.zip && \
-    unzip protoc-30.2-linux-x86_64.zip -d ~/.local && \
-    rm protoc-30.2-linux-x86_64.zip
+# protoc 29.5 is the last version with protobuf python v5 which is compatible with protoletariat v3
+RUN cd ~ && curl -LO https://github.com/protocolbuffers/protobuf/releases/download/v29.5/protoc-29.5-linux-x86_64.zip && \
+    unzip protoc-29.5-linux-x86_64.zip -d ~/.local && \
+    rm protoc-29.5-linux-x86_64.zip
 RUN curl -sSL "https://github.com/bufbuild/buf/releases/download/v1.58.0/buf-$(uname -s)-$(uname -m)" -o ~/.local/bin/buf && chmod +x ~/.local/bin/buf
 RUN curl -LsSf https://astral.sh/uv/install.sh | sh
 USER root

buf.gen.yaml

@@ -2,5 +2,5 @@ version: v2
 plugins:
   - protoc_builtin: python
     out: src/substrait/gen
-  - remote: buf.build/community/nipunn1313-mypy:v3.5.0
+  - remote: buf.build/community/nipunn1313-mypy:v3.6.0
     out: src/substrait/gen

pyproject.toml

@@ -5,15 +5,15 @@ authors = [{name = "Substrait contributors", email = "substrait@googlegroups.com
 license = {text = "Apache-2.0"}
 readme = "README.md"
 requires-python = ">=3.9"
-dependencies = ["protobuf >= 3.20"]
+dependencies = ["protobuf >=3.19.1,<6"]
 dynamic = ["version"]
 
 [tool.setuptools_scm]
 write_to = "src/substrait/_version.py"
 
 [project.optional-dependencies]
 extensions = ["antlr4-python3-runtime", "pyyaml"]
-gen_proto = ["protobuf == 3.20.1", "protoletariat >= 2.0.0"]
+gen_proto = ["protobuf >=3.19.1,<6", "protoletariat >= 3.0.0"]
 sql = ["sqloxide", "deepdiff"]
 test = ["pytest >= 7.0.0", "antlr4-python3-runtime", "pyyaml", "sqloxide", "deepdiff", "duckdb<=1.2.2", "datafusion"]