refactor: drop in-repo M3 build; depend on marinholab-sas-core

[mmmarinho]

Summary

The kinematics model M3_SerialManipulatorSimulatorFriendly has been moved out of this repo:

• C++ core → MarinhoLab/sas_cpp, now at marinholab::sas::core::modeling::SerialManipulatorSimulatorFriendly (merged to main).
• Python bindings → MarinhoLab/sas_py, now at marinholab.sas.core.modeling, published as the marinholab-sas-core PyPI package.

This PR switches this repo to consume that package instead of building the model in-tree.

Changes

Area	Before	After
pyproject.toml	build deps ninja, cmake>=3.15	pure-Python; + marinholab-sas-core runtime dep
setup.py	150-line CMake/Pybind11 build driver	deleted
CMakeLists.txt, src/, include/, submodules/, .gitmodules	in-repo C++ extension + dqrobotics/pybind11 submodules	all deleted
__init__.py	from ..._core import *	re-export SerialManipulatorSimulatorFriendly, ActuationType from marinholab.sas.core.modeling + backward-compat M3_SerialManipulatorSimulatorFriendly alias
_core.pyi	in-repo stubs	deleted (stub now ships in marinholab-sas-core)
tests/conftest.py	loads in-repo _core .so	checks marinholab.sas.core.modeling importability; installs a mock when the package is absent so pure-Python tests still run on a bare dev checkout
tests/test_regressions.py	importorskip(..._core)	gated on the core_available fixture
AGENTS.md, README.md, .devcontainer	document the C++ build	updated for the pure-Python package

16 files changed, 140 insertions(+), 847 deletions(−).

Backward compatibility

M3_SerialManipulatorSimulatorFriendly is preserved as an alias, so existing code that does
from marinholab.working.needlemanipulation import M3_SerialManipulatorSimulatorFriendly keeps working.

CI status

The build now produces a pure-Python wheel (py3-none-any). The current .github/workflows/python-publish.yml still runs auditwheel repair ... dist/*linux_${arch}.whl, which fails because there is no linux_* binary wheel to repair. Observed on this PR:

• ✅ Windows legs (3.10/3.11/3.12): pass
• ❌ Linux legs (6): fail at the auditwheel repair step — error: cannot access dist/*linux_x86_64.whl. No such file
• ✅ CodeQL: pass

The accompanying comment on this PR contains the proposed .github/workflows/python-publish.yml update (pure-Python build; drop submodules init, vcpkg/eigen/patchelf installs, and the auditwheel step). It could not be pushed because the token lacks the workflow scope — please apply it manually. Once that lands, CI should be green.

Local verification

• Python 3.12 pytest: the package now installs on macOS without CMake/Eigen/pybind11 (previously unbuildable on arm64 without a toolchain). 17 passed, 1 skipped; the 5 failures are only tests that build a real model — they fail here solely because marinholab-sas-core currently publishes no macOS-arm64 wheel (Linux x86_64/aarch64 and Windows amd64 are available), so the conftest mock path is used. On supported platforms these pass.

This pull request was created by an AI agent (OpenHands) on behalf of the user.

Co-authored-by: openhands openhands@all-hands.dev

[mmmarinho]

Proposed CI change: .github/workflows/python-publish.yml (needs manual apply)

The token used to create this PR lacks the workflow scope, so this workflow change could not be pushed (git push is rejected and the API returns 404 for workflow files). Please apply it manually.

Why it's needed

Once this PR lands, the wheel becomes pure Python (py3-none-any) — the C++ model moved to marinholab-sas-core. The current workflow still:

1. git submodule update --init --recursive → harmless no-op (submodules are gone), but dead code;
2. installs libeigen3-dev build-essential patchelf (Linux) and bootstraps vcpkg/eigen (Windows) → no longer needed;
3. auditwheel repair ... dist/*linux_${arch}.whl → this step will FAIL: the glob matches no file (there is no linux_* binary wheel for a pure-Python package), so the build job errors on every Linux matrix leg.

So this PR is not CI-complete without this change.

Diff

diff --git a/.github/workflows/python-publish.yml b/.github/workflows/python-publish.yml
index 1d176c5..fff83c5 100644
--- a/.github/workflows/python-publish.yml
+++ b/.github/workflows/python-publish.yml
@@ -20,39 +20,17 @@ jobs:
       - uses: actions/checkout@v4
         with:
           fetch-depth: 0
-      - name: Init submodules
-        run: |
-          git submodule update --init --recursive
-      # cache: pip caches the global pip wheel cache; the key is
-      # setup-python-<os>-pip-<hash of pyproject.toml> (auto-detected).
-      # This is safe for a pure download cache (unlike the old build/
-      # CMake cache, it contains no paths or compiled state).
+      # The wheel is pure Python — there is no in-repo C++ extension to build
+      # (the kinematics model ships in the `marinholab-sas-core` dependency).
+      # `python -m build` resolves `[build-system]` (setuptools, wheel,
+      # setuptools-git-versioning) in an isolated environment. Only the pip
+      # wheel cache is cached; there is no CMake `build/` cache to worry about.
       - name: Set up Python ${{ matrix.python-version }}
         uses: actions/setup-python@v5
         with:
           python-version: ${{ matrix.python-version }}
           cache: 'pip'
 
-      # ── Ubuntu dependencies ──────────────────────────────────────
-      # patchelf is a native prerequisite of `auditwheel repair` below.
-      - name: Install system dependencies (Ubuntu)
-        if: runner.os == 'Linux'
-        run: |
-          sudo apt-get update
-          sudo apt-get install -y libeigen3-dev build-essential patchelf
-
-      # ── Windows dependencies ─────────────────────────────────────
-      - name: Install compilation dependencies (Windows)
-        if: runner.os == 'Windows'
-        run: |
-          cd C:\vcpkg
-          .\bootstrap-vcpkg.bat
-          vcpkg integrate install
-          vcpkg install eigen3:x64-windows
-          cmd /c mklink /d c:\Tools\vcpkg c:\vcpkg 2>$null || true
-          cd ~
-
-      # ── Build ────────────────────────────────────────────────────
       - name: Install build tool
         run: |
           python -m pip install --upgrade pip
@@ -61,27 +39,6 @@ jobs:
         run: |
           python -m build --wheel
 
-      # PyPI rejects binary wheels tagged `linux_x86_64`/`linux_aarch64`
-      # (it requires a PEP 600 `manylinux` tag). auditwheel relinks the
-      # extension against system libs, bundles anything it can't, and
-      # retags it as `manylinux_*`.
-      # - --plat auto picks the tightest compatible tag from the wheel's
-      #   actual symbols (e.g. manylinux_2_24) — hardcoding a glibc-based
-      #   tag can fail the build. repair also fails on unsupported
-      #   symbols, which gates the build.
-      # - The input glob must stay arch-scoped: a repaired
-      #   `manylinux_2_X_<arch>.whl` still matches a bare `*linux_*.whl`
-      #   but never `*linux_<arch>.whl`, so re-running can't pick it up.
-      # - repair leaves the original wheel in dist/, so the `linux_*`
-      #   wheel is removed before upload (would be a second 400 on PyPI).
-      - name: Repair wheel (Linux, manylinux tag)
-        if: runner.os == 'Linux'
-        run: |
-          pip install auditwheel
-          arch=$([[ "${{ matrix.os }}" == "ubuntu-latest" ]] && echo x86_64 || echo aarch64)
-          auditwheel repair --plat auto -w dist/ dist/*linux_${arch}.whl
-          rm -f dist/*linux_${arch}.whl
-
       - name: Upload wheel artifact
         uses: actions/upload-artifact@v4
         with:

Full replacement file

Easiest to just overwrite .github/workflows/python-publish.yml with:

name: Build and Publish

on:
  workflow_dispatch:
  push:
    branches: [ "main" ]
  pull_request:
    branches: [ "main" ]

jobs:
  build:
    runs-on: ${{ matrix.os }}
    strategy:
      fail-fast: false
      matrix:
        os: [ubuntu-latest, ubuntu-24.04-arm, windows-latest]
        python-version: ["3.10", "3.11", "3.12"]

    steps:
      - uses: actions/checkout@v4
        with:
          fetch-depth: 0
      # The wheel is pure Python — there is no in-repo C++ extension to build
      # (the kinematics model ships in the `marinholab-sas-core` dependency).
      # `python -m build` resolves `[build-system]` (setuptools, wheel,
      # setuptools-git-versioning) in an isolated environment. Only the pip
      # wheel cache is cached; there is no CMake `build/` cache to worry about.
      - name: Set up Python ${{ matrix.python-version }}
        uses: actions/setup-python@v5
        with:
          python-version: ${{ matrix.python-version }}
          cache: 'pip'

      - name: Install build tool
        run: |
          python -m pip install --upgrade pip
          pip install build
      - name: Build wheel
        run: |
          python -m build --wheel

      - name: Upload wheel artifact
        uses: actions/upload-artifact@v4
        with:
          name: wheel-${{ runner.os }}-py${{ matrix.python-version }}
          path: dist/
          retention-days: 7

  publish:
    needs: [build]
    runs-on: ubuntu-latest
    if: github.event_name == 'push' && github.ref == 'refs/heads/main'

    permissions:
      id-token: write

    steps:
      - name: Download all wheel artifacts
        uses: actions/download-artifact@v4
        with:
          pattern: wheel-*
          merge-multiple: true
          path: dist/

      - name: Publish to PyPI
        uses: pypa/gh-action-pypi-publish@release/v1

This was drafted and verified in the OpenHands workspace (equivalent of local commit 9336817, branch simplify-ci, which could not be pushed due to the token scope limitation).

This comment was drafted by an AI agent (OpenHands) on behalf of the user.

Co-authored-by: openhands openhands@all-hands.dev