haplokit 0.1.0__tar.gz

haplokit-0.1.0/.github/workflows/ci.yml

@@ -0,0 +1,69 @@
+name: ci
+
+on:
+  push:
+    branches: ["main"]
+  pull_request:
+
+jobs:
+  linux:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install system build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            cmake \
+            pkg-config \
+            libbz2-dev \
+            liblzma-dev \
+            libcurl4-openssl-dev \
+            zlib1g-dev
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[test]"
+          python -m pip install build
+
+      - name: Build vendored backend
+        run: |
+          cmake -S . -B build-wsl
+          cmake --build build-wsl --parallel
+
+      - name: Run Python tests
+        run: |
+          HAPLOKIT_CPP_BIN=$PWD/build-wsl/haplokit_cpp python -m pytest -q tests/python
+
+      - name: Run C++ tests
+        run: |
+          ctest --test-dir build-wsl --output-on-failure
+
+      - name: Build source distribution
+        run: |
+          python -m build --sdist
+
+      - name: Smoke test install from sdist
+        run: |
+          REPO_ROOT=$PWD
+          TMP_DIR=$(mktemp -d)
+          python -m venv "$TMP_DIR/.venv-sdist-smoke"
+          source "$TMP_DIR/.venv-sdist-smoke/bin/activate"
+          python -m pip install --upgrade pip
+          python -m pip install "$REPO_ROOT"/dist/*.tar.gz
+          cd "$TMP_DIR"
+          python -c "from pathlib import Path; import haplokit; assert (Path(haplokit.__file__).resolve().parent / '_bin' / 'haplokit_cpp').exists()"
+          haplokit view "$REPO_ROOT/data/var.sorted.vcf.gz" -r scaffold_1:4300-5000 --output-file smoke_out
+          python -c "from pathlib import Path; assert (Path('smoke_out') / 'hapresult.tsv').exists(); assert (Path('smoke_out') / 'hap_summary.tsv').exists()"

haplokit-0.1.0/.github/workflows/release.yml

@@ -0,0 +1,83 @@
+name: release
+
+on:
+  push:
+    tags:
+      - "v*"
+
+permissions:
+  contents: read
+  id-token: write
+
+jobs:
+  publish:
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+        with:
+          submodules: recursive
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.12"
+
+      - name: Install system build dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y \
+            build-essential \
+            cmake \
+            pkg-config \
+            libbz2-dev \
+            liblzma-dev \
+            libcurl4-openssl-dev \
+            zlib1g-dev
+
+      - name: Install Python dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install ".[test]"
+          python -m pip install build twine
+
+      - name: Build vendored backend
+        run: |
+          cmake -S . -B build-wsl
+          cmake --build build-wsl --parallel
+
+      - name: Run test suite
+        run: |
+          HAPLOKIT_CPP_BIN=$PWD/build-wsl/haplokit_cpp python -m pytest -q tests/python
+          ctest --test-dir build-wsl --output-on-failure
+
+      - name: Build source distribution
+        run: |
+          python -m build --sdist
+
+      - name: Smoke test install from sdist
+        run: |
+          REPO_ROOT=$PWD
+          TMP_DIR=$(mktemp -d)
+          python -m venv "$TMP_DIR/.venv-sdist-smoke"
+          source "$TMP_DIR/.venv-sdist-smoke/bin/activate"
+          python -m pip install --upgrade pip
+          python -m pip install "$REPO_ROOT"/dist/*.tar.gz
+          cd "$TMP_DIR"
+          python -c "from pathlib import Path; import haplokit; assert (Path(haplokit.__file__).resolve().parent / '_bin' / 'haplokit_cpp').exists()"
+          haplokit view "$REPO_ROOT/data/var.sorted.vcf.gz" -r scaffold_1:4300-5000 --output-file smoke_out
+          python -c "from pathlib import Path; assert (Path('smoke_out') / 'hapresult.tsv').exists(); assert (Path('smoke_out') / 'hap_summary.tsv').exists()"
+
+      - name: Check distribution metadata
+        run: |
+          twine check dist/*
+
+      - name: Upload distribution artifact
+        uses: actions/upload-artifact@v4
+        with:
+          name: pypi-dist
+          path: dist/*
+
+      - name: Publish to PyPI
+        uses: pypa/gh-action-pypi-publish@release/v1

haplokit-0.1.0/CMakeLists.txt

@@ -0,0 +1,70 @@
+cmake_minimum_required(VERSION 3.22)
+
+project(haplokit LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+include(CTest)
+enable_testing()
+
+include(cmake/htslib.cmake)
+haplokit_configure_htslib()
+
+add_library(haplokit_core
+    src/cpp/selector.cpp
+    src/cpp/vcf_reader.cpp
+    src/cpp/view_backend.cpp
+    src/cpp/gff_annotator.cpp
+    deps/gffsub/src/gff3_parser.cpp
+    deps/gffsub/src/gff3_filter.cpp
+    deps/gffsub/src/gff3_output.cpp
+)
+
+target_include_directories(haplokit_core
+    PUBLIC
+        ${CMAKE_CURRENT_SOURCE_DIR}/src/cpp
+        ${CMAKE_CURRENT_SOURCE_DIR}/deps/gffsub/src
+        ${CMAKE_CURRENT_SOURCE_DIR}/deps/nlohmann
+        ${HAPLOKIT_HTSLIB_INCLUDE_DIRS}
+)
+
+target_link_libraries(haplokit_core PUBLIC ${HAPLOKIT_HTSLIB_TARGET} ${HAPLOKIT_HTSLIB_EXTRA_LIBS})
+add_dependencies(haplokit_core haplokit_htslib_build)
+
+add_executable(haplokit_cpp
+    src/cpp/main.cpp
+)
+
+target_link_libraries(haplokit_cpp PRIVATE haplokit_core)
+
+if(BUILD_TESTING)
+    add_executable(vcf_reader_test
+        tests/cpp/vcf_reader_test.cpp
+    )
+
+    target_link_libraries(vcf_reader_test PRIVATE haplokit_core)
+
+    add_executable(view_backend_test
+        tests/cpp/view_backend_test.cpp
+    )
+
+    target_link_libraries(view_backend_test PRIVATE haplokit_core)
+
+    add_test(
+        NAME vcf_reader_test
+        COMMAND vcf_reader_test
+    )
+
+    add_test(
+        NAME view_backend_test
+        COMMAND view_backend_test
+    )
+
+    set_tests_properties(
+        vcf_reader_test view_backend_test
+        PROPERTIES
+            WORKING_DIRECTORY ${CMAKE_SOURCE_DIR}
+    )
+endif()