bgen-limix 4.2.1__tar.gz

bgen_limix-4.2.1/.clang-format

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bgen_limix-4.2.1/.github/workflows/ci.yml

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+name: CI
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+jobs:
+  test-c:
+    name: "C library (${{ matrix.os }}, ${{ matrix.build_type }})"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-15, windows-2025]
+        build_type: [Release, Debug]
+        include:
+          - os: ubuntu-24.04
+            sanitizers: ON
+          - os: macos-15
+            sanitizers: OFF
+          - os: windows-2025
+            sanitizers: OFF
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - uses: prefix-dev/setup-pixi@v0.9.6
+
+      - name: Configure CMake
+        run: >
+          pixi run cmake --preset pixi
+          -DCMAKE_BUILD_TYPE=${{ matrix.build_type }}
+          -DBGEN_BUILD_TESTS=ON
+          -DBGEN_BUILD_PYTHON=OFF
+          -DBGEN_ENABLE_SANITIZERS=${{ matrix.sanitizers }}
+
+      - name: Build
+        run: pixi run cmake --build build --config ${{ matrix.build_type }}
+
+      - name: Test (Linux / macOS)
+        if: runner.os != 'Windows'
+        run: pixi run ctest --test-dir build -C ${{ matrix.build_type }} --output-on-failure
+
+      - name: Test (Windows)
+        if: runner.os == 'Windows'
+        shell: pwsh
+        run: |
+          # pixi run resets PATH; prepend Library\bin for the conda DLLs
+          # (zlib-ng, zstd, libcurl …).  libstdc++ / libgcc are now statically
+          # linked via the MINGW target_link_options in CMakeLists.txt, so
+          # there is no MinGW DLL version conflict any more.
+          $pixi_bin = "${{ github.workspace }}\.pixi\envs\default\Library\bin"
+          $env:PATH = "$pixi_bin;C:\mingw64\bin;$env:PATH"
+          & "$pixi_bin\ctest.exe" --test-dir "${{ github.workspace }}\build" `
+            -C ${{ matrix.build_type }} --output-on-failure
+  test-python:
+    name: "Python (${{ matrix.os }})"
+    runs-on: ${{ matrix.os }}
+    strategy:
+      fail-fast: false
+      matrix:
+        os: [ubuntu-24.04, macos-14, windows-2022]
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          environments: test
+
+      - name: Build and test Python
+        run: pixi run -e test test-python
+
+  test-s3:
+    name: "S3 integration (MinIO)"
+    runs-on: ubuntu-24.04
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - uses: prefix-dev/setup-pixi@v0.9.6
+        with:
+          environments: test
+
+      - name: Start MinIO server
+        run: |
+          docker run -d --name minio-ci \
+            -p 19000:9000 \
+            -e MINIO_ROOT_USER=minio_access \
+            -e MINIO_ROOT_PASSWORD=minio_secret \
+            minio/minio server /data
+          # Wait for MinIO
+          for i in $(seq 1 30); do
+            curl -sf http://127.0.0.1:19000/minio/health/live && break
+            sleep 1
+          done
+
+      - name: Upload test data to MinIO
+        env:
+          AWS_ACCESS_KEY_ID: minio_access
+          AWS_SECRET_ACCESS_KEY: minio_secret
+          AWS_DEFAULT_REGION: us-east-1
+          AWS_ENDPOINT_URL: http://127.0.0.1:19000
+        run: |
+          pip install awscli --quiet
+          aws s3 mb s3://bgen-test --endpoint-url "$AWS_ENDPOINT_URL"
+          aws s3 cp test/data/example.14bits.bgen s3://bgen-test/example.14bits.bgen \
+            --endpoint-url "$AWS_ENDPOINT_URL"
+          # Public bucket for no-sign test
+          aws s3 mb s3://bgen-public --endpoint-url "$AWS_ENDPOINT_URL"
+          aws s3api put-bucket-policy --bucket bgen-public \
+            --policy '{"Version":"2012-10-17","Statement":[{"Effect":"Allow","Principal":"*","Action":"s3:GetObject","Resource":"arn:aws:s3:::bgen-public/*"}]}' \
+            --endpoint-url "$AWS_ENDPOINT_URL"
+          aws s3 cp test/data/example.14bits.bgen s3://bgen-public/example.14bits.bgen \
+            --endpoint-url "$AWS_ENDPOINT_URL"
+
+      - name: Configure & build (S3 enabled)
+        run: |
+          pixi run cmake --preset pixi \
+            -DCMAKE_BUILD_TYPE=Debug \
+            -DBGEN_BUILD_TESTS=ON \
+            -DBGEN_ENABLE_S3=ON
+          pixi run cmake --build build
+
+      - name: Run C S3 tests
+        env:
+          AWS_ACCESS_KEY_ID: minio_access
+          AWS_SECRET_ACCESS_KEY: minio_secret
+          AWS_DEFAULT_REGION: us-east-1
+          AWS_ENDPOINT_URL: http://127.0.0.1:19000
+          BGEN_TEST_S3_URI: s3://bgen-test/example.14bits.bgen
+          BGEN_TEST_S3_METAFILE: ${{ github.workspace }}/test/data/example.14bits.bgen.metafile
+        run: pixi run ./build/test/test_s3_open
+
+      - name: Run C S3 test (no-sign / public bucket)
+        env:
+          AWS_NO_SIGN_REQUEST: "1"
+          AWS_ENDPOINT_URL: http://127.0.0.1:19000
+          BGEN_TEST_S3_URI: s3://bgen-public/example.14bits.bgen
+          BGEN_TEST_S3_METAFILE: ${{ github.workspace }}/test/data/example.14bits.bgen.metafile
+        run: pixi run ./build/test/test_s3_open
+
+      - name: Install Python package with S3
+        run: |
+          pixi run -e test pip install --quiet "universal_pathlib>=0.2" "s3fs>=2024.1"
+          CMAKE_ARGS="-DBGEN_ENABLE_S3=ON" pixi run -e test pip install --no-build-isolation -e .
+
+      - name: Run Python S3/UPath tests
+        env:
+          BGEN_TEST_MINIO_ENDPOINT: http://127.0.0.1:19000
+          BGEN_TEST_MINIO_ACCESS: minio_access
+          BGEN_TEST_MINIO_SECRET: minio_secret
+          BGEN_TEST_S3_METAFILE: ${{ github.workspace }}/test/data/example.14bits.bgen.metafile
+        run: pixi run -e test pytest python/tests/test_s3_upath.py -v

bgen_limix-4.2.1/.github/workflows/wheels.yml

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+name: Build wheels
+
+on:
+  push:
+    branches: [main]
+    tags: ["v*"]
+  pull_request:
+    branches: [main]
+  workflow_dispatch:
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  # Only cancel-in-progress if it's NOT a tag push (so automated/manual release pushes don't get canceled by subsequent commits)
+  cancel-in-progress: ${{ github.ref_type != 'tag' }}
+
+jobs:
+  build_sdist:
+    name: Build sdist
+    runs-on: ubuntu-24.04
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Build sdist
+        run: pipx run build --sdist
+
+      - uses: actions/upload-artifact@v7.0.1
+        with:
+          name: cibw-sdist
+          path: dist/*.tar.gz
+
+
+  build_wheels:
+    name: Wheels on ${{ matrix.label }}
+    runs-on: ${{ matrix.os }}
+    permissions:
+      contents: read
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+          - os: ubuntu-24.04
+            label: ubuntu-24.04-x86_64
+          - os: ubuntu-24.04-arm
+            label: ubuntu-24.04-aarch64
+          - os: macos-15
+            label: macos-15
+          - os: windows-2025
+            label: windows-2025
+
+    steps:
+      - uses: actions/checkout@v6.0.2
+
+      - name: Build wheels
+        uses: pypa/cibuildwheel@v3.4.1
+        env:
+          # Build for CPython 3.11 only — stable ABI (abi3) wheel works for all 3.11+
+          CIBW_BUILD: "cp311-*"
+          # nanobind-backend (split mode) ships no musllinux wheels, so those builds can't install it
+          CIBW_SKIP: "*-musllinux*"
+          # Test the built wheels
+          CIBW_TEST_REQUIRES: pytest
+          CIBW_TEST_COMMAND: pytest {project}/python/tests -v
+          # macOS: build universal2 wheels on the ARM runner
+          CIBW_ARCHS_MACOS: "native"
+          # Windows: build AMD64 only
+          CIBW_ARCHS_WINDOWS: "AMD64"
+          # Install OpenSSL headers needed by fetched curl on Linux
+          CIBW_BEFORE_BUILD_LINUX: >
+            (command -v yum && yum install -y openssl-devel) ||
+            (command -v apk && apk add openssl-dev) || true
+
+      - uses: actions/upload-artifact@v7.0.1
+        with:
+          name: cibw-wheels-${{ matrix.label }}
+          path: ./wheelhouse/*.whl
+
+  publish:
+    name: Publish to PyPI
+    needs: [build_sdist, build_wheels]
+    runs-on: ubuntu-24.04
+    if: github.event_name == 'push' && startsWith(github.ref, 'refs/tags/v')
+    permissions:
+      id-token: write
+
+    steps:
+      - uses: actions/download-artifact@v8.0.1
+        with:
+          pattern: cibw-*
+          path: dist
+          merge-multiple: true
+
+      - uses: pypa/gh-action-pypi-publish@v1.14.0

bgen_limix-4.2.1/.gitignore

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+.cache/
+.ccls-cache/
+
+compile_commands.json
+
+.tags*
+
+build*/
+
+# pixi
+.pixi/
+pixi.lock
+
+# Python
+__pycache__/
+*.py[cod]
+*.egg-info/
+dist/
+*.so
+*.pyd
+.pytest_cache/
+
+# Object files
+*.o
+*.ko
+*.obj
+*.elf
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Libraries
+*.lib
+*.a
+*.la
+*.lo
+
+# Shared objects (inc. Windows DLLs)
+*.dll
+*.so
+*.so.*
+*.dylib
+
+# Executables
+*.exe
+*.out
+*.app
+*.i*86
+*.x86_64
+*.hex
+
+# Debug files
+*.dSYM/
+*.su

bgen_limix-4.2.1/.pre-commit-config.yaml

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+---
+repos:
+  - repo: https://github.com/pre-commit/pre-commit-hooks
+    rev: v6.0.0
+    hooks:
+      - id: trailing-whitespace
+      - id: end-of-file-fixer
+      - id: check-yaml
+      - id: check-toml
+      - id: check-merge-conflict
+  - repo: https://github.com/astral-sh/ruff-pre-commit
+    rev: v0.15.15
+    hooks:
+      - id: ruff
+        args: [--fix]
+      - id: ruff-format
+  - repo: https://github.com/pre-commit/mirrors-clang-format
+    rev: v22.1.5
+    hooks:
+      - id: clang-format
+        types_or: [c, c++]
+  - repo: https://github.com/cheshirekow/cmake-format-precommit
+    rev: v0.6.13
+    hooks:
+      - id: cmake-format
+  - repo: https://github.com/rbubley/mirrors-prettier
+    rev: v3.8.3
+    hooks:
+      - id: prettier
+        types_or: [yaml, markdown]

bgen_limix-4.2.1/.vscode/launch.json

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+{
+    "configurations": [
+        {
+            "type": "cmake",
+            "request": "launch",
+            "name": "Debug portfile(s)",
+            "cmakeDebugType": "external",
+            "pipeName": "/tmp/vcpkg_ext_portfile_dbg",
+            "preLaunchTask": "Debug vcpkg commands"
+        }
+    ]
+}

bgen_limix-4.2.1/.vscode/settings.json

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+{
+    "workbench.colorCustomizations": {}
+}

bgen_limix-4.2.1/AGENTS.md

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+C library + Python bindings for BGEN format (specs 1.2 & 1.3). C11/C++17, CMake + Ninja, pixi for env management.
+
+Build & test: `pixi run test` (runs both C and Python test suites).
+C only: `cmake --preset pixi -DCMAKE_BUILD_TYPE=Release && cmake --build build && ctest --test-dir build`.
+Python: `pixi run build-python && pixi run test-python`. The Python build (`python/CMakeLists.txt`, driven by scikit-build via `cmake.source-dir = "python"`) reuses a pre-installed bgen via `find_package(bgen)` when available. The bgen C library is built as a pixi package (`[package]` in `pixi.toml`) using `pixi-build-cmake`, which selects the correct platform toolchain (MSVC on Windows, clang on macOS, gcc on Linux). Running `pixi install` (done automatically by `pixi run`) builds and installs bgen into the environment before the Python build step. If no pre-built bgen is found (e.g. cibuildwheel / PyPI sdist), the Python build falls back to building the C library from source.
+
+Key CMake options: `BGEN_ENABLE_S3` (needs libcurl + OpenSSL), `BGEN_BUILD_TESTS`.
+System deps resolved via conda-forge (pixi): zlib-ng, zstd, almosthere, nanobind.
+Pre-built build dirs: `build` (pixi preset), `build-s3` (S3 enabled), `build-no-s3`.