[nanvix] E: Bake ninja and Cython into toolchain image

[esaurez]

[nanvix] E: Bake ninja and Cython into toolchain image

Adds ninja-build, python3-pip, and Cython<3 to the toolchain-python docker image so that meson- and Cython-based Python extension cross-builds (numpy, scipy, ...) work out-of-the-box, without an apt/pip preamble on every docker run invocation.

What changed in .nanvix/docker/Dockerfile:

• Added python3-pip and ninja-build to the apt install list.
• Added pip3 install --break-system-packages 'Cython<3' (pinned for numpy 1.26.x compatibility; lift the pin when bumping numpy).
• Added rm -rf /usr/include/python3.12 after the install. The python3-pip / ninja-build apt packages transitively pull in libpython3.12-dev, whose headers under /usr/include/python3.12 would otherwise be picked up by meson's regen step ahead of the Nanvix cross sysroot headers and silently corrupt the cross-build.
• Comment block explaining the rationale for each addition and the /usr/include/python3.12 purge.

Why this matters:

The numpy .so cross-build (validated end-to-end on 2026-05-27 with the STB_WEAK loader fix landed) requires two tools that were not present in the image as shipped:

• ninja — meson's default backend; missing it makes every meson-based Python extension build fail immediately.
• Cython — used by numpy/_build_utils/tempita.py to template .pyx.in files; without it the numpy.random codegen step fails.

Before this change, the workaround was to inject:

apt-get update -qq
apt-get install -qq -y --no-install-recommends ninja-build python3-pip
pip3 install --quiet --break-system-packages 'Cython<3'
rm -rf /usr/include/python3.12

into every numpy build invocation, which (a) was fragile, (b) required the docker container to have outbound network access on every build (non-hermetic), and (c) re-paid the apt install cost in CI every run.

Validated locally:

• docker build -f .nanvix/docker/Dockerfile -t toolchain-python:pr13 .nanvix/docker/ succeeds.
• docker run --rm <image> bash -c 'ninja --version' → 1.11.1.
• docker run --rm <image> bash -c 'python3 -c "import Cython; print(Cython.__version__)"' → 0.29.37.
• docker run --rm <image> bash -c 'ls /usr/include/python3.12' → exits non-zero / "No such file or directory".

Co-authored-by: Copilot 223556219+Copilot@users.noreply.github.com

[Copilot]

Pull request overview

Updates the Nanvix toolchain-python Docker image to include additional build-time dependencies needed for cross-compiling third-party Python extension modules (notably meson/ninja and Cython-based projects like numpy/scipy), aiming to remove per-build apt/pip bootstrapping.

Changes:

• Install python3-pip and ninja-build in the toolchain image.
• Install Cython<3 via pip for numpy 1.26.x compatibility.
• Purge host Python headers under /usr/include/python3.12 to avoid meson accidentally consuming host headers instead of the Nanvix sysroot.

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