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ARG-RHE code release (#51)
- This PR contains the functions used in ARG-RHE experiments. It also contains the genotype mapping, linear association testing and ARG matrix multiplication routines. - Adds CRoaring via FetchContent. - Update to latest macos build agents as in ASMC. - Also adds ASMC py-vers-full/py-vers-pr change in build-wheels.yml to reduce CI load. - Upgrade GitHub actions. - Python code moved into src/arg-needle-lib as recommented in cibuildwheel to avoid copying any source artifacts into wheel. - Some tests marked as conditional on OS due to differences in msprime simulation.
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‎.github/workflows/build-wheels.yml‎

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include:
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- os: ubuntu-24.04
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arch: x86_64
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py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
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py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
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py-vers-pr: cp311-*
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before-all: |
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dnf -y install boost-devel eigen3-devel wget
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dnf -y install epel-release
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mdt: ""
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- os: ubuntu-24.04-arm
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arch: aarch64
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py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
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py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
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py-vers-pr: cp312-*
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before-all: |
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dnf -y install boost-devel eigen3-devel wget
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dnf -y install epel-release
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dnf -y install hdf5-devel
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extra-env: ""
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mdt: ""
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- os: macos-13
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- os: macos-15-intel
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arch: x86_64
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py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
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py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
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py-vers-pr: cp313-*
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before-all: brew install boost eigen hdf5
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extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
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mdt: 13
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extra-env: CC=clang CXX=clang++
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mdt: 15.0
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- os: macos-14
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arch: arm64
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py-vers: cp39-* cp310-* cp311-* cp312-* cp313-*
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py-vers-full: cp39-* cp310-* cp311-* cp312-* cp313-* cp314-*
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py-vers-pr: cp314-*
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before-all: brew install boost eigen hdf5
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extra-env: CC="$(brew --prefix llvm@15)/bin/clang" CXX="$(brew --prefix llvm@15)/bin/clang++" HOMEBREW_NO_INSTALLED_DEPENDENTS_CHECK=1
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mdt: 14
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extra-env: CC=clang CXX=clang++
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mdt: 14.0
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env:
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CIBW_BUILD: ${{ matrix.py-vers }}
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CIBW_BUILD: ${{ github.event_name != 'pull_request' && matrix.py-vers-full || matrix.py-vers-pr }}
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CIBW_SKIP: cp3*-musllinux_*
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CIBW_ARCHS: ${{ matrix.arch }}
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CIBW_MANYLINUX_X86_64_IMAGE: manylinux_2_28
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steps:
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- name: checkout repo & submodules
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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with:
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fetch-depth: 0
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- name: Build wheels
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uses: pypa/cibuildwheel@v2.22.0
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uses: pypa/cibuildwheel@v3.2.0
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- uses: actions/upload-artifact@v4
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with:
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steps:
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- name: Download wheels from cloud runners
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uses: actions/download-artifact@v4
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uses: actions/download-artifact@v5
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with:
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pattern: wheels-cloud-*
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merge-multiple: true
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path: wheels
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- uses: pypa/gh-action-pypi-publish@v1.12.4
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- uses: pypa/gh-action-pypi-publish@v1.13.0
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with:
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user: __token__
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password: ${{ secrets.PYPI_TOKEN }}

‎.github/workflows/sync.yml‎

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runs-on: ubuntu-latest
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steps:
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- name: Checkout private repo
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uses: actions/checkout@v3
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uses: actions/checkout@v5
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with:
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fetch-depth: 0
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persist-credentials: false
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runs-on: ubuntu-latest
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steps:
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- name: Checkout public repo
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uses: actions/checkout@v3
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uses: actions/checkout@v5
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with:
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fetch-depth: 0
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persist-credentials: false

‎.github/workflows/tests-examples-macos.yml‎

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steps:
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- name: checkout repo & submodules
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: install system packages
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run: |
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- name: run example visit
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run: ./example/example_visit
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working-directory: build_dir
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- name: run example sumstats
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run: ./example/example_sumstats
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working-directory: build_dir

‎.github/workflows/tests-examples-ubuntu.yml‎

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steps:
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- name: checkout repo & submodules
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: install system packages
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run: |
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- name: run example visit
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run: ./example/example_visit
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working-directory: build_dir
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- name: run example sumstats
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run: ./example/example_sumstats
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working-directory: build_dir

‎.github/workflows/tests-python.yml‎

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- name: checkout repo
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uses: actions/checkout@v4
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uses: actions/checkout@v5
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- name: set up Python
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uses: actions/setup-python@v5
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uses: actions/setup-python@v6
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with:
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python-version: ${{ matrix.python-version }}
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‎.gitignore‎

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.idea/
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cmake-build*/
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# VSCode
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.vscode/

‎CMakeLists.txt‎

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pybind11
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GIT_REPOSITORY https://github.com/pybind/pybind11
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GIT_TAG 7c33cdc2d39c7b99a122579f53bc94c8eb3332ff # Version 2.13.5
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)
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FetchContent_GetProperties(pybind11)
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if (NOT pybind11_POPULATED)
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endif ()
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endif ()
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include(FetchContent)
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FetchContent_Declare(
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roaring
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GIT_REPOSITORY https://github.com/RoaringBitmap/CRoaring.git
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GIT_TAG v4.4.2
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GIT_SHALLOW TRUE
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)
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set(ENABLE_ROARING_TESTS OFF CACHE INTERNAL "")
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set(ROARING_BUILD_STATIC ON CACHE INTERNAL "")
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set(ROARING_BUILD_LTO OFF CACHE INTERNAL "")
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FetchContent_GetProperties(roaring)
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# Use FetchContent_Populate and add_subdirectory instead of FetchContent_MakeAvailable
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# to avoid copying roaring include headers and other install files into built wheel.
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FetchContent_Populate(roaring)
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add_subdirectory(${roaring_SOURCE_DIR} ${roaring_BINARY_DIR} EXCLUDE_FROM_ALL)
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target_compile_options(roaring PRIVATE -Wno-deprecated-declarations)
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set_target_properties(roaring PROPERTIES POSITION_INDEPENDENT_CODE TRUE)
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add_subdirectory(src)
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add_subdirectory(example)
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‎PyPI_README.md‎

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This repository contains arg-needle-lib, which implements an ARG data structure and ARG-based analyses such as genealogy-wide association.
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Prebuilt CPython wheels are available for Linux (compatible with glibc ≥ 2.28) and macOS (built on macOS 15 for x86_64 and macOS 14 for arm64).
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| Platform \ CPython | ≤3.8 | 3.9 | 3.10 | 3.11 | 3.12 | 3.13 | 3.14 |
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|-----------------------------| ---- | --- | ---- | ---- | ---- | ---- | ---- |
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| Linux x86_64 | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
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| Linux aarch64 | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
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| macOS Intel (x86_64) | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
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| macOS Apple Silicon (arm64) | ❌ | ✅ | ✅ | ✅ | ✅ | ✅ | ✅ |
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## Quickstart
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### Install the Python module from PyPI

‎arg_needle_lib‎

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‎example/CMakeLists.txt‎

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add_executable(example_visit example_visit.cpp)
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target_link_libraries(example_visit PRIVATE arg_needle_lib)
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add_executable(example_sumstats example_sumstats.cpp)
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target_link_libraries(example_sumstats PRIVATE arg_needle_lib)

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