Modernize Dockerfile to build against current Python and GraphBLAS

The Dockerfile had bit-rotted: the python:3.10-slim-buster base image
no longer builds (Debian buster apt repos are gone), and the most recent
commit simultaneously dropped Python <=3.10 support in pyproject.toml
while leaving the Dockerfile pinned to Python 3.10. Several install
paths and cmake flags were also out of date for SuiteSparse:GraphBLAS
10.x.

Changes:

- Bump base image from python:3.10-slim-buster (EOL) to
  python:3.12-slim-bookworm. Update hardcoded python3.10 site-packages
  paths to python3.12 in three places.

- Update GraphBLAS header copy: 10.x installs the header at
  /usr/include/suitesparse/GraphBLAS.h, not /usr/include/GraphBLAS.h,
  and create_headers.py looks for it at
  ${sys.prefix}/include/suitesparse/GraphBLAS.h.

- Replace deprecated `python3 setup.py install` with
  `pip install --no-build-isolation --no-deps .`. The pip-driven path
  is required by modern setuptools, and pip is added to the build-time
  install list along with pycparser/setuptools/wheel/setuptools-git-versioning
  which the build now needs explicitly.

- Add cmake flags matching CI in suitesparse.sh:
  -DCMAKE_BUILD_TYPE=Release, -DJITINIT=2, -DGRAPHBLAS_USE_JIT=OFF.
  The JIT flags avoid segfaults in tests; without them GraphBLAS may
  attempt JIT compilation at runtime.

- Replace stale -DGBCOMPACT cmake flag with the current name -DCOMPACT,
  and give ARG COMPACT a default of 0 so the substitution is non-empty
  when the build-arg is omitted.

- Make `git tag ${VERSION}` idempotent: wrap with `(... || true)` so
  the build does not fail when ${VERSION} matches an existing tag in
  the source tree (which is now the case for the current 10.3.1.0
  release tag).

- Fix Docker COPY collapsing the libgraphblas symlink chain
  (libgraphblas.so -> .so.10 -> .so.10.3.1) into three identical 67MB
  regular files. Copy only the real versioned library
  (libgraphblas.so.*.*.*) and recreate symlinks via `ln -sf` in a RUN
  step. Apply the same fix to libgomp in the final stage. This removes
  the `ldconfig: ... is not a symbolic link` warnings and saves ~130MB.

- Cleanup: remove unused `ARG SUITESPARSE` redeclaration in the psg
  stage, fix the lowercase `as` -> `AS` for FromAsCasing warnings,
  and switch `ENV PYTHONUNBUFFERED 1` to the modern `ENV key=value`
  form.

- Drop the bizarre `WORKDIR /build/GraphBLAS/build` that was set
  *before* the GraphBLAS git clone, producing the path
  /build/GraphBLAS/build/GraphBLAS/build. The clone now happens
  directly under /build.

Built and verified by running the doctests inside the produced image:

  $ docker build --build-arg SUITESPARSE=v10.3.1 \\
                 --build-arg VERSION=10.3.1.0 \\
                 -t psg-test:latest .
  $ docker run --rm psg-test:latest python3 -c "
      import suitesparse_graphblas; suitesparse_graphblas.initialize()
      from suitesparse_graphblas.tests.test_doctest import test_run_doctests
      test_run_doctests()"

  -> 268 doctests pass, supports_complex=True

Author: michelp

Dockerfile

@@ -1,47 +1,71 @@
-ARG BASE_CONTAINER=python:3.10-slim-buster
-FROM ${BASE_CONTAINER} as suitesparse
+ARG BASE_CONTAINER=python:3.12-slim-bookworm
+FROM ${BASE_CONTAINER} AS suitesparse
 ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update && apt-get install -yq build-essential cmake git
 
 ARG SUITESPARSE
-ARG COMPACT
+ARG COMPACT=0
 
 WORKDIR /build
 RUN git clone https://github.com/eliben/pycparser.git --depth 1
 
-WORKDIR /build/GraphBLAS/build
+# Use `-DJITINIT=2` so that the JIT functionality is available, but disabled by default.
+# Level 2, "run", means that pre-JIT kernels may be used, which does not require a compiler at runtime.
+# Disable JIT entirely to avoid segfaulting in tests (matches CI in suitesparse.sh).
 RUN git clone https://github.com/DrTimothyAldenDavis/GraphBLAS.git --depth 1 --branch ${SUITESPARSE} \
     && cd GraphBLAS/build \
-    && cmake .. -DCMAKE_INSTALL_PREFIX=/usr -DGBCOMPACT=${COMPACT} \
+    && cmake .. \
+        -DCMAKE_BUILD_TYPE=Release \
+        -DCMAKE_INSTALL_PREFIX=/usr \
+        -DCOMPACT=${COMPACT} \
+        -DJITINIT=2 \
+        -DGRAPHBLAS_USE_JIT=OFF \
     && make -j$(nproc) \
     && make install
 
-FROM ${BASE_CONTAINER} as psg
-ARG SUITESPARSE
+FROM ${BASE_CONTAINER} AS psg
 ARG VERSION
-ENV PYTHONUNBUFFERED 1
+ENV PYTHONUNBUFFERED=1
 
-COPY --from=suitesparse  /usr/include/GraphBLAS.h /usr/local/include/
-COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgraphblas* /usr/lib/x86_64-linux-gnu/
-COPY --from=suitesparse /build/pycparser/utils/fake_libc_include/* /usr/local/lib/python3.10/site-packages/pycparser/utils/fake_libc_include/
+COPY --from=suitesparse /usr/include/suitesparse/GraphBLAS.h /usr/local/include/suitesparse/GraphBLAS.h
+# Copy only the real versioned library; recreate symlinks (Docker COPY collapses cross-stage symlinks).
+COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgraphblas.so.*.*.* /usr/lib/x86_64-linux-gnu/
+RUN cd /usr/lib/x86_64-linux-gnu \
+    && REAL=$(ls libgraphblas.so.*.*.*) \
+    && SOMAJOR=libgraphblas.so.$(echo "$REAL" | sed -E 's/libgraphblas\.so\.([0-9]+).*/\1/') \
+    && ln -sf "$REAL" "$SOMAJOR" \
+    && ln -sf "$SOMAJOR" libgraphblas.so \
+    && ldconfig
 
 RUN apt-get update && apt-get install -yq build-essential git
-RUN pip3 install numpy cffi pytest cython
+RUN pip3 install --break-system-packages numpy cffi pytest cython pycparser setuptools wheel setuptools-git-versioning
+
+COPY --from=suitesparse /build/pycparser/utils/fake_libc_include/* /usr/local/lib/python3.12/site-packages/pycparser/utils/fake_libc_include/
 
 RUN mkdir -p /psg
 ADD . /psg
 
 WORKDIR /psg
-RUN git tag ${VERSION} && \
+# `git tag || true` so the build is idempotent when ${VERSION} already matches an existing tag in the source tree.
+RUN (git tag ${VERSION} || true) && \
     python3 suitesparse_graphblas/create_headers.py && \
-    python3 setup.py install && \
+    pip3 install --break-system-packages --no-build-isolation --no-deps . && \
     ldconfig
 
 #RUN pytest --pyargs suitesparse_graphblas.tests
 RUN apt-get -y --purge remove git python3-pip && apt-get clean
 
 FROM ${BASE_CONTAINER}
-COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgraphblas* /usr/lib/x86_64-linux-gnu/
-COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgomp* /usr/lib/x86_64-linux-gnu/
-COPY --from=psg /usr/local/lib/python3.10/site-packages /usr/local/lib/python3.10/site-packages
+COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgraphblas.so.*.*.* /usr/lib/x86_64-linux-gnu/
+COPY --from=suitesparse /usr/lib/x86_64-linux-gnu/libgomp.so.*.*.* /usr/lib/x86_64-linux-gnu/
+COPY --from=psg /usr/local/lib/python3.12/site-packages /usr/local/lib/python3.12/site-packages
+RUN cd /usr/lib/x86_64-linux-gnu \
+    && GBREAL=$(ls libgraphblas.so.*.*.*) \
+    && GBSOMAJOR=libgraphblas.so.$(echo "$GBREAL" | sed -E 's/libgraphblas\.so\.([0-9]+).*/\1/') \
+    && ln -sf "$GBREAL" "$GBSOMAJOR" \
+    && ln -sf "$GBSOMAJOR" libgraphblas.so \
+    && GMREAL=$(ls libgomp.so.*.*.*) \
+    && GMSOMAJOR=libgomp.so.$(echo "$GMREAL" | sed -E 's/libgomp\.so\.([0-9]+).*/\1/') \
+    && ln -sf "$GMREAL" "$GMSOMAJOR" \
+    && ldconfig