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Denis Jelovina
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Squash: combined commits 9c8ebec..3591d1d
Summary of included commits: 3591d1d Denis Jelovina 2025-10-24 Squash: Combined changes from 9f634c7..HEAD — merge all temp commit 9f634c7 Denis Jelovina 2025-10-22 chore(pyalp): remove vendored pybind11 and unused CMake; add cibuildwheel workflow and config 0f9840c Denis Jelovina 2025-10-22 pyalp packaging and CI: bundle prebuilt bindings, setup pinned pybind11, and add wheel smoke-test 1e4cd6e Denis Jelovina 2025-10-22 Remove deprecated Python bindings and related files a7c9900 Denis Jelovina 2025-10-22 Convert pybind11 to submodule pinned at 8d503e30be400ad431d3d140707803e87e75fad7 3b9e5b5 Petros Anastasiadis 2025-09-30 Removed numpy2alp older stuff - left .cpp ffr 1403a2a Petros Anastasiadis 2025-09-30 Added installation instructions for python part 95d51a8 Denis Jelovina 2025-06-02 Add doccumentation for test.py 58aae6a Denis Jelovina 2025-05-26 compile messages 6ba4c3e Denis Jelovina 2025-05-26 add submodule 03a00d4 Denis Jelovina 2025-05-26 disable pyalp by defualt a471cdd Denis Jelovina 2025-05-26 add pybind11 submodule 8a4ade9 Denis Jelovina 2025-05-26 refactor code add support for multiple types 68dea3d Denis Jelovina 2025-05-23 add conjugate gradient 427594b Denis Jelovina 2025-05-23 add numpy to c++ examples Diffstat: .github/workflows/pyalp-ci.yml | 169 +++++++++++++++++++++++++ .github/workflows/pyalp-publish.yml | 175 ++++++++++++++++++++++++++ .gitignore | 3 +- .gitmodules | 3 + CMakeLists.txt | 22 +++- cmake/CompileFlags.cmake | 20 ++- pyalp/CMakeLists.txt | 1 + pyalp/PINNED_PYBIND11 | 1 + pyalp/extern/pybind11 | 1 + pyalp/pyproject.toml | 30 +++++ pyalp/setup.py | 114 +++++++++++++++++ pyalp/src/CMakeLists.txt | 111 ++++++++++++++++ pyalp/src/conjugate_gradient.hpp | 109 ++++++++++++++++ pyalp/src/matrix_wrappers.hpp | 115 +++++++++++++++++ pyalp/src/numpy2alp.cpp | 57 +++++++++ pyalp/src/pyalp.cpp | 84 +++++++++++++ pyalp/src/pyalp.egg-info/PKG-INFO | 65 ++++++++++ pyalp/src/pyalp.egg-info/SOURCES.txt | 12 ++ pyalp/src/pyalp.egg-info/dependency_links.txt | 1 + pyalp/src/pyalp.egg-info/requires.txt | 1 + pyalp/src/pyalp.egg-info/top_level.txt | 1 + pyalp/src/pyalp/CMakeLists.txt | 16 +++ pyalp/src/pyalp/__init__.py | 41 ++++++ pyalp/src/pyalp/bindings.cpp | 56 +++++++++ pyalp/src/pyalp/your_module.py | 4 + pyalp/src/python2alp.cpp | 9 ++ pyalp/src/utils.hpp | 20 +++ pyalp/src/vector_wrappers.hpp | 65 ++++++++++ pyproject.toml | 4 + setup.py | 10 ++ tests/CMakeLists.txt | 4 + tests/python/CMakeLists.txt | 23 ++++ tests/python/numpy_array_print.py | 5 + tests/python/test.py | 65 ++++++++++ tools/make_wheel_from_so.py | 109 ++++++++++++++++ tools/smoke_test_pyalp.py | 66 ++++++++++ 36 files changed, 1589 insertions(+), 3 deletions(-)
1 parent 5123737 commit f58c94d

36 files changed

+1589
-3
lines changed

‎.github/workflows/pyalp-ci.yml‎

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name: pyalp CI
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# Run only on pushes that create tags starting with 'pyalp'
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on:
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push:
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tags: [ 'pyalp*' ]
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jobs:
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build-bindings:
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name: Build C++ bindings
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runs-on: ubuntu-latest
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steps:
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- name: Checkout (with submodules)
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uses: actions/checkout@v4
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with:
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submodules: 'recursive'
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fetch-depth: 0
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- name: Verify pinned pybind11 submodule commit
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# Fail early if the checked-out pybind11 is not the pinned commit
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run: |
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set -euo pipefail
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# Prefer top-level pinned file so it survives moves; fallback to submodule path
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if [ -f pyalp/PINNED_PYBIND11 ];
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then
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PINNED_SHA=$(cat pyalp/PINNED_PYBIND11 | tr -d '\n')
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elif [ -f pyalp/extern/pybind11/PINNED_COMMIT ];
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then
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PINNED_SHA=$(cat pyalp/extern/pybind11/PINNED_COMMIT | tr -d '\n')
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else
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echo "No pinned commit file found (tried pyalp/PINNED_PYBIND11 and pyalp/extern/pybind11/PINNED_COMMIT)" >&2
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exit 2
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fi
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echo "Expected pybind11 commit: $PINNED_SHA"
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ACTUAL=$(git -C pyalp/extern/pybind11 rev-parse HEAD || true)
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echo "Found pybind11 commit: $ACTUAL"
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if [ "$ACTUAL" != "$PINNED_SHA" ];
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then
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echo "ERROR: pybind11 submodule commit does not match pinned commit" >&2
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exit 2
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fi
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- name: Install build dependencies
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run: |
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set -euo pipefail
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sudo apt-get update
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# libnuma-dev provides NUMA headers/libraries needed by FindNuma.cmake
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sudo apt-get install -y build-essential cmake ninja-build pkg-config python3-venv python3-dev python3-pip libnuma-dev
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- name: Configure and build pyalp bindings
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run: |
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set -euo pipefail
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mkdir -p build_alp
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cmake -S . -B build_alp -DENABLE_PYALP=ON
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# Only attempt to build pyalp targets if the pyalp CMake directory exists
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if [ -f pyalp/CMakeLists.txt ];
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then
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echo "pyalp CMakeLists found — building pyalp targets"
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cmake --build build_alp --target pyalp_ref -- -j || true
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cmake --build build_alp --target pyalp_omp -- -j || true
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else
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echo "pyalp directory or CMakeLists not present — skipping pyalp targets"
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fi
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- name: Find and list built shared objects
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run: |
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set -euo pipefail
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echo "Searching for shared objects under build_alp and pyalp"
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find build_alp -name "*.so" -maxdepth 8 -print || true
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find pyalp -name "*.so" -maxdepth 8 -print || true
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- name: Collect built shared objects into artifacts/
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run: |
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set -euo pipefail
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mkdir -p artifacts
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# copy any discovered .so files into a flat artifacts directory so upload-artifact can find them
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find build_alp -name "*.so" -print0 | xargs -0 -I{} bash -lc 'cp -v "{}" artifacts/ || true' || true
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find pyalp -name "*.so" -print0 | xargs -0 -I{} bash -lc 'cp -v "{}" artifacts/ || true' || true
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echo "Artifacts now contains:" && ls -la artifacts || true
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- name: Upload built bindings
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uses: actions/upload-artifact@v4
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with:
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name: pyalp-so
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path: |
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build_alp/**/*.so
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artifacts/**/*.so
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pyalp/**/pyalp*.so
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pyalp/**/_pyalp*.so
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pyalp/**/libpyalp*.so
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pyalp/**/*.so
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build-wheel-and-test:
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name: Build wheel from prebuilt .so and smoke-test
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runs-on: ubuntu-latest
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needs: build-bindings
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steps:
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- name: Checkout
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uses: actions/checkout@v4
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- name: Download built bindings
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uses: actions/download-artifact@v4
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with:
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name: pyalp-so
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path: artifacts
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- name: Show downloaded artifacts
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run: ls -la artifacts || true
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- name: Prepare wheel inputs
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id: prep
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run: |
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set -euo pipefail
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# List candidate shared-object files for debugging
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echo "Candidate .so files in artifacts:" && find artifacts -type f -name "*.so" -print || true
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# Find likely candidates (prefer _pyalp, pyalp, libpyalp)
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SO_PATH=$(find artifacts \( -name "_pyalp*.so" -o -name "pyalp*.so" -o -name "libpyalp*.so" -o -name "*.so" \) | head -n1)
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if [ -z "$SO_PATH" ];
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then
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echo "ERROR: no built .so artifact found to package" >&2
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echo "Artifacts listing:" && ls -la artifacts || true
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exit 2
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fi
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echo "so_path=$SO_PATH" >> "$GITHUB_OUTPUT"
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# Prefer helper located inside pyalp/ but fall back to top-level tools/
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if [ -f pyalp/tools/make_wheel_from_so.py ]; then
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echo "builder=pyalp/tools/make_wheel_from_so.py" >> "$GITHUB_OUTPUT"
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else
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echo "builder=tools/make_wheel_from_so.py" >> "$GITHUB_OUTPUT"
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fi
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# Derive Python version from the .so filename (e.g., cpython-311 -> 3.11, cp312 -> 3.12)
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PY_VER=""
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if [[ "$SO_PATH" =~ cpython-([0-9]{3}) ]];
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then
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n=${BASH_REMATCH[1]}
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PY_VER="${n:0:1}.${n:1}"
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elif [[ "$SO_PATH" =~ cp([0-9]{2,3}) ]];
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then
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n=${BASH_REMATCH[1]}
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PY_VER="${n:0:1}.${n:1}"
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fi
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echo "python_version=$PY_VER" >> "$GITHUB_OUTPUT"
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- name: Run wheel builder
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run: |
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set -euo pipefail
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echo "builder=${{ steps.prep.outputs.builder }}"
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echo "so=${{ steps.prep.outputs.so_path }}"
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python3 "${{ steps.prep.outputs.builder }}" "${{ steps.prep.outputs.so_path }}" --out-dir dist_wheel
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- name: Show wheel
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run: ls -la dist_wheel || true
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- name: Set up Python matching built extension
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if: ${{ steps.prep.outputs.python_version != '' }}
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uses: actions/setup-python@v5
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with:
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python-version: ${{ steps.prep.outputs.python_version }}
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- name: Smoke test wheel in venv
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run: |
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set -euo pipefail
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python3 -V
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which python3
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python3 -m venv venv
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. venv/bin/activate
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pip install --upgrade pip wheel
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pip install dist_wheel/*.whl
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tools/smoke_test_pyalp.py

‎.github/workflows/pyalp-publish.yml‎

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name: pyalp wheels (cibuildwheel)
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on:
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push:
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tags: [ 'pyalp.v*' ]
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workflow_dispatch: {}
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jobs:
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build-wheels:
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name: Build wheels on ${{ matrix.os }}
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runs-on: ${{ matrix.os }}
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strategy:
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fail-fast: false
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matrix:
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os: [ubuntu-latest, macos-latest]
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steps:
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- name: Checkout (with submodules)
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uses: actions/checkout@v4
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with:
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submodules: recursive
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fetch-depth: 0
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- name: Verify pinned pybind11 submodule commit
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if: runner.os == 'Linux' || runner.os == 'macOS'
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shell: bash
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run: |
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set -euo pipefail
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if [ -f pyalp/PINNED_PYBIND11 ];
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then
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PINNED_SHA=$(tr -d '\n' < pyalp/PINNED_PYBIND11)
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elif [ -f pyalp/extern/pybind11/PINNED_COMMIT ];
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then
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PINNED_SHA=$(tr -d '\n' < pyalp/extern/pybind11/PINNED_COMMIT)
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else
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echo "No pinned commit file found (pyalp/PINNED_PYBIND11 or pyalp/extern/pybind11/PINNED_COMMIT)" >&2
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exit 2
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fi
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ACTUAL=$(git -C pyalp/extern/pybind11 rev-parse HEAD || true)
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echo "Expected pybind11 commit: $PINNED_SHA"
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echo "Found pybind11 commit: $ACTUAL"
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test "$ACTUAL" = "$PINNED_SHA"
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- name: Set up Python
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uses: actions/setup-python@v5
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with:
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python-version: '3.11'
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- name: Install cibuildwheel
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run: |
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python -m pip install --upgrade pip
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python -m pip install cibuildwheel==2.21.3
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- name: Build wheels
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env:
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CIBW_BUILD: "cp39-* cp310-* cp311-* cp312-*"
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CIBW_SKIP: "*-musllinux* pp*"
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CIBW_ARCHS_LINUX: "x86_64"
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CIBW_ARCHS_MACOS: "arm64"
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CIBW_BUILD_VERBOSITY: "1"
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# Ensure submodule headers are used by setup.py
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CIBW_ENVIRONMENT: >
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PYTHONUTF8=1
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CIBW_ENVIRONMENT_MACOS: >
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PYTHONUTF8=1
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MACOSX_DEPLOYMENT_TARGET=15.0
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# Prebuild the CMake-based extension via top-level CMake so all variables/options are defined.
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CIBW_BEFORE_BUILD: |
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python -m pip install --upgrade pip
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python -m pip install cmake ninja
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echo "[cibw] Working directory and contents:"; pwd; ls -la
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echo "[cibw] Checking for pyalp CMakeLists:"; ls -la pyalp || true; if [ -f pyalp/CMakeLists.txt ];
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then echo "found pyalp/CMakeLists.txt"; else echo "pyalp/CMakeLists.txt NOT found"; fi
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# If the wrapper CMakeLists.txt wasn't copied (e.g., untracked file when cibuildwheel uses git ls-files), create a minimal shim
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if [ ! -f pyalp/CMakeLists.txt ];
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then
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echo "[cibw] Creating pyalp/CMakeLists.txt shim (add_subdirectory(src)) for wheel build"
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printf '%s\n' 'add_subdirectory(src)' > pyalp/CMakeLists.txt
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fi
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# Ensure no stale extension from a previous ABI remains in the source tree
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rm -f pyalp/src/pyalp/_pyalp*.so || true
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# Overwrite root setup.py inside the container to delegate packaging to pyalp/setup.py (keep git root clean)
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printf '%s\n' "import os, runpy; ROOT=os.path.dirname(os.path.abspath(__file__)); PKG=os.path.join(ROOT, 'pyalp'); os.chdir(PKG); runpy.run_path(os.path.join(PKG, 'setup.py'), run_name='__main__')" > setup.py
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# Configure from repository root; enable pyalp and choose NUMA setting per-platform
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PYEXEC=$(python -c 'import sys; print(sys.executable)')
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# Use a per-ABI build directory to avoid cross-ABI contamination
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ABI_TAG=$(python -c 'import sys; print(f"cp{sys.version_info[0]}{sys.version_info[1]}")')
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BUILD_DIR="build/${ABI_TAG}"
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# Enable NUMA on Linux runners (for linux wheels), keep disabled elsewhere.
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if [ "$(uname -s)" = "Linux" ];
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then
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echo "[cibw] Linux build container detected — attempting to install NUMA dev libs"
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# Try package managers commonly present in manylinux containers. Ignore failures
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if command -v yum >/dev/null 2>&1;
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then
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yum -y install numactl-devel || true
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elif command -v apt-get >/dev/null 2>&1;
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then
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apt-get update || true
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apt-get install -y libnuma-dev || true
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fi
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NUMA_FLAG="-DWITH_NUMA=ON"
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else
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# On macOS install Homebrew libomp but do NOT export CPPFLAGS/LDFLAGS.
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# Exporting CPPFLAGS was the cause of incorrect header ordering; instead
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# pass a CMake prefix hint so FindOpenMP can locate libomp without
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# prepending include paths to the global compiler invocation.
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if command -v brew >/dev/null 2>&1;
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then
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echo "[cibw] Homebrew detected — ensuring libomp is available"
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# Only install if not already present to avoid reinstall warnings
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if ! brew list libomp >/dev/null 2>&1; then
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brew install libomp
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fi
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# Locate libomp installation
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if [ -d "/opt/homebrew/opt/libomp" ]; then
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HOMEBREW_LIBOMP_DIR="/opt/homebrew/opt/libomp"
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elif [ -d "/usr/local/opt/libomp" ]; then
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HOMEBREW_LIBOMP_DIR="/usr/local/opt/libomp"
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else
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HOMEBREW_LIBOMP_DIR=""
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fi
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if [ -n "${HOMEBREW_LIBOMP_DIR}" ]; then
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CMAKE_PREFIX_HINT="-DCMAKE_PREFIX_PATH=${HOMEBREW_LIBOMP_DIR}"
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echo "[cibw] Using libomp from ${HOMEBREW_LIBOMP_DIR}"
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else
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CMAKE_PREFIX_HINT=""
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fi
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fi
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NUMA_FLAG="-DWITH_NUMA=OFF"
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# Set macOS deployment target for arm64 to match libomp requirement
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export MACOSX_DEPLOYMENT_TARGET=15.0
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OSX_DEPLOY_FLAG="-DCMAKE_OSX_DEPLOYMENT_TARGET=${MACOSX_DEPLOYMENT_TARGET}"
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fi
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# Clean build directory to prevent CMake caching issues
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rm -rf "${BUILD_DIR}"
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# On macOS, add flag to downgrade template keyword warning from error to warning
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if [ "$(uname -s)" = "Darwin" ];
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then
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MACOS_FLAGS="-DCMAKE_CXX_FLAGS=-Wno-error=missing-template-arg-list-after-template-kw"
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else
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MACOS_FLAGS=""
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fi
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# For wheel builds, request portable flags (avoid -march=native) and disable
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# interprocedural optimization (LTO) to improve portability of the produced wheels.
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PORTABLE_FLAG="-DALP_PORTABLE_BUILD=ON"
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LTO_FLAG="-DCMAKE_INTERPROCEDURAL_OPTIMIZATION=OFF"
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cmake -S . -B "${BUILD_DIR}" -G Ninja -DCMAKE_BUILD_TYPE=Release -DENABLE_PYALP=ON -DCMAKE_POSITION_INDEPENDENT_CODE=ON -DCMAKE_FIND_FRAMEWORK=NEVER ${MACOS_FLAGS} ${NUMA_FLAG} ${CMAKE_PREFIX_HINT:-} ${OSX_DEPLOY_FLAG:-} ${PORTABLE_FLAG} ${LTO_FLAG} -DPython3_EXECUTABLE="${PYEXEC}"
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cmake --build "${BUILD_DIR}" --target pyalp_ref --parallel
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run: |
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# Build from repository root so the full CMake project is available in the container
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python -m cibuildwheel --output-dir wheelhouse .
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- name: Upload wheels
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uses: actions/upload-artifact@v4
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with:
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name: pyalp-wheels-${{ matrix.os }}
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path: wheelhouse/*.whl
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# Placeholder for publish job; enable when versioning is PEP 440 compliant
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# publish:
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# needs: build-wheels
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# runs-on: ubuntu-latest
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# permissions:
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# id-token: write
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# steps:
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# - name: Download wheels
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# uses: actions/download-artifact@v4
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# with:
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# path: dist
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# - name: Publish to PyPI
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# uses: pypa/gh-action-pypi-publish@release/v1
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# with:
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# packages-dir: dist

‎.gitignore‎

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[Bb]uild*/
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[Oo]bj*/
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[Ii]nstall*/
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cmake-build-*/
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cmake-build-*/
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.venv/

‎.gitmodules‎

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[submodule "pyalp/extern/pybind11"]
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path = pyalp/extern/pybind11
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url = https://github.com/pybind/pybind11

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