refactor: compile-time BLAS ILP64/LP64 selection and external pointer mode

.github/workflows/CI_PublishTestPyPI.yml

@@ -46,16 +46,13 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux_2_28"
           CIBW_BUILD: "${{ matrix.py_tag }}-*"
-          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.deployment_target || '11.0' }} SPARSEIR_USE_BLAS=1"
+          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.deployment_target || '11.0' }}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
           CIBW_SKIP: "*-manylinux_i686 *-musllinux_i686"
           # Install OpenBLAS using micromamba (conda-forge) - separate for manylinux and musllinux
           CIBW_BEFORE_ALL_MANYLINUX: "curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && ./bin/micromamba create -y -p /opt/openblas && ./bin/micromamba install -y -c conda-forge openblas -p /opt/openblas --no-deps"
           CIBW_BEFORE_ALL_MUSLLINUX: "apk add --no-cache bzip2 && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && ./bin/micromamba create -y -p /opt/openblas && ./bin/micromamba install -y -c conda-forge openblas -p /opt/openblas --no-deps"
           CIBW_BEFORE_ALL_MACOS: "brew install openblas"
-          # Set environment variables to help CMake find OpenBLAS
-          CIBW_ENVIRONMENT_MANYLINUX: "SPARSEIR_USE_BLAS=1"
-          CIBW_ENVIRONMENT_MUSLLINUX: "SPARSEIR_USE_BLAS=1"
         with:
           package-dir: ./python
           output-dir: dist

.github/workflows/PublishPyPI.yml

@@ -91,16 +91,13 @@ jobs:
           CIBW_BUILD_VERBOSITY: 1
           CIBW_MANYLINUX_X86_64_IMAGE: "manylinux_2_28"
           CIBW_BUILD: "${{ matrix.py_tag }}-*"
-          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.deployment_target || '11.0' }} SPARSEIR_USE_BLAS=1"
+          CIBW_ENVIRONMENT_MACOS: "MACOSX_DEPLOYMENT_TARGET=${{ matrix.deployment_target || '11.0' }}"
           CIBW_ARCHS: ${{ matrix.cibw_archs }}
           CIBW_SKIP: "*-manylinux_i686 *-musllinux_i686"
           # Install OpenBLAS using micromamba (conda-forge) - separate for manylinux and musllinux
           CIBW_BEFORE_ALL_MANYLINUX: "curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && ./bin/micromamba create -y -p /opt/openblas && ./bin/micromamba install -y -c conda-forge openblas -p /opt/openblas --no-deps"
           CIBW_BEFORE_ALL_MUSLLINUX: "apk add --no-cache bzip2 && curl -Ls https://micro.mamba.pm/api/micromamba/linux-64/latest | tar -xvj bin/micromamba && ./bin/micromamba create -y -p /opt/openblas && ./bin/micromamba install -y -c conda-forge openblas -p /opt/openblas --no-deps"
           CIBW_BEFORE_ALL_MACOS: "brew install openblas"
-          # Set environment variables to help CMake find OpenBLAS
-          CIBW_ENVIRONMENT_MANYLINUX: "SPARSEIR_USE_BLAS=1"
-          CIBW_ENVIRONMENT_MUSLLINUX: "SPARSEIR_USE_BLAS=1"
         with:
           package-dir: ./python
           output-dir: dist

.github/workflows/test_cxx_backend.yml

@@ -2,7 +2,7 @@ name: Test C++ Backend
 
 on:
   push:
-    branches: [ "main", "459-restructure-directories" ]
+    branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
   workflow_dispatch:
@@ -40,9 +40,44 @@ jobs:
         working-directory: capi_sample
         run: ./run_sample.sh
 
+  test-cxx-backend-ilp64:
+    runs-on: ubuntu-latest
+    name: C++ backend with ILP64 BLAS
+    timeout-minutes: 60  # Allow up to 60 minutes for ILP64 tests
+
+    steps:
+      - uses: actions/checkout@v5
+
+      - name: Install dependencies with ILP64 BLAS
+        run: |
+          sudo apt update && sudo apt install -y libeigen3-dev libopenblas64-0 libopenblas64-dev
+
+      - name: Build and test C++ backend with ILP64
+        working-directory: backend/cxx
+        run: |
+          rm -rf build
+          mkdir -p build && cd build
+          cmake .. -DSPARSEIR_BUILD_TESTING=ON -DSPARSEIR_USE_BLAS_ILP64=ON
+          cmake --build . -j$(nproc)
+          ctest --output-on-failure --verbose -j$(nproc)
+
+      - name: Build and test capi_test against ILP64 backend
+        working-directory: capi_test
+        env:
+          SPARSEIR_USE_BLAS_ILP64: 1
+        run: ./test_with_cxx_backend.sh
+
+      - name: Build and run capi_sample with ILP64
+        working-directory: capi_sample
+        env:
+          SPARSEIR_USE_BLAS_ILP64: 1
+        run: ./run_sample.sh
+
   test-cxx-backend-rollup:
     runs-on: ubuntu-latest
-    needs: test-cxx-backend
+    needs: 
+      - test-cxx-backend
+      - test-cxx-backend-ilp64
     if: always()
     steps:
       - name: All tests passed

.github/workflows/test_fortran.yml

@@ -2,7 +2,7 @@ name: Test Fortran Bindings
 
 on:
   push:
-    branches: [ "main", "459-restructure-directories" ]
+    branches: [ "main" ]
   pull_request:
     branches: [ "main" ]
   workflow_dispatch:

.github/workflows/test_python.yml

@@ -4,7 +4,6 @@ on:
   push:
     branches:
       - main
-      - 459-restructure-directories
   pull_request:
     branches:
       - main
@@ -50,21 +49,11 @@ jobs:
         with:
           enable-cache: true
 
-      - name: Setup build environment
+      - name: Setup and run tests
         working-directory: python
-        run: python3 setup_build.py
-
-      - name: Run uv sync
-        working-directory: python
-        run: uv sync
-        env:
-          SPARSEIR_USE_BLAS: 1
-
-      - name: Run tests
-        working-directory: python
-        run: uv run pytest tests/ -v
-        env:
-          SPARSEIR_USE_BLAS: 1
+        run: |
+          chmod +x run_tests.sh
+          ./run_tests.sh
 
   test-python-rollup:
     runs-on: ubuntu-latest

CMakeLists.txt

@@ -49,65 +49,32 @@ endif()
 
 # Eigen3
 # BLAS/LAPACK options
-option(SPARSEIR_USE_BLAS "Enable BLAS support" OFF)
-option(SPARSEIR_USE_ILP64 "Enable ILP64 BLAS interface (requires SPARSEIR_USE_BLAS=ON)" OFF)
-
-# BLAS/LAPACK search and configuration
-if(SPARSEIR_USE_BLAS)
-    add_compile_definitions(SPARSEIR_USE_BLAS)
-    message(STATUS "BLAS support enabled")
-
-    # ILP64 support
-    if(SPARSEIR_USE_ILP64)
-        add_compile_definitions(SPARSEIR_USE_ILP64)
-        message(STATUS "ILP64 BLAS interface enabled")
-    else()
-        message(STATUS "LP64 BLAS interface enabled (default)")
-    endif()
+option(SPARSEIR_USE_BLAS_ILP64 "Enable ILP64 BLAS interface (64-bit integers)" OFF)
+
+# BLAS search and configuration (always enabled)
+message(STATUS "BLAS support enabled")
+
+# Set BLAS integer size based on SPARSEIR_USE_BLAS_ILP64
+if(SPARSEIR_USE_BLAS_ILP64)
+    set(BLA_SIZEOF_INTEGER 8)
+    message(STATUS "Searching for ILP64 BLAS interface (64-bit integers)")
+else()
+    set(BLA_SIZEOF_INTEGER 4)
+    message(STATUS "Searching for LP64 BLAS interface (32-bit integers, default)")
+endif()
+
+# Find BLAS package using standard CMake FindBLAS
+find_package(BLAS REQUIRED)
 
-    # Find BLAS package
-    if(SPARSEIR_USE_ILP64)
-        # For ILP64, check if BLAS_LIBRARIES is already set by user
-        if(BLAS_LIBRARIES)
-            message(STATUS "ILP64 BLAS library specified: ${BLAS_LIBRARIES}")
-            # Verify the library exists
-            if(NOT EXISTS "${BLAS_LIBRARIES}")
-                message(FATAL_ERROR "Specified ILP64 BLAS library not found: ${BLAS_LIBRARIES}")
-            endif()
-            set(BLAS_FOUND TRUE)
-        else()
-            # Try to find ILP64 BLAS automatically
-            find_library(BLAS_LIBRARIES
-                NAMES openblas64
-                PATHS /usr/lib/x86_64-linux-gnu /usr/lib /usr/local/lib
-                NO_DEFAULT_PATH
-            )
-            if(BLAS_LIBRARIES)
-                message(STATUS "ILP64 BLAS found automatically: ${BLAS_LIBRARIES}")
-                set(BLAS_FOUND TRUE)
-            else()
-                message(FATAL_ERROR "ILP64 BLAS (libopenblas64) not found. You can specify it with -DBLAS_LIBRARIES=/path/to/libopenblas64.so")
-            endif()
-        endif()
+if(BLAS_FOUND)
+    message(STATUS "BLAS found: ${BLAS_LIBRARIES}")
+    if(SPARSEIR_USE_BLAS_ILP64)
+        message(STATUS "BLAS with ILP64 interface (BLA_SIZEOF_INTEGER=8)")
     else()
-        # For LP64, use standard CMake BLAS finder
-        find_package(BLAS REQUIRED)
-        if(BLAS_FOUND)
-            message(STATUS "BLAS found: ${BLAS_LIBRARIES}")
-        else()
-            message(FATAL_ERROR "BLAS not found")
-        endif()
+        message(STATUS "BLAS with LP64 interface (BLA_SIZEOF_INTEGER=4)")
     endif()
-
-    # CMake's find_package(BLAS) should provide include directories
-    #if(BLAS_INCLUDE_DIRS)
-        #include_directories(${BLAS_INCLUDE_DIRS})
-        #message(STATUS "BLAS include directories: ${BLAS_INCLUDE_DIRS}")
-    #else()
-        #message(FATAL_ERROR "BLAS include directories not found")
-    #endif()
-elseif(SPARSEIR_USE_ILP64)
-    message(FATAL_ERROR "SPARSEIR_USE_ILP64 requires SPARSEIR_USE_BLAS=ON")
+else()
+    message(FATAL_ERROR "BLAS not found")
 endif()
 
 
@@ -187,23 +154,22 @@ set_target_properties(sparseir PROPERTIES
 
 target_link_libraries(sparseir PRIVATE Eigen3::Eigen Threads::Threads)
 
-# Add BLAS/LAPACK linking
-if(SPARSEIR_USE_BLAS)
-    if(SPARSEIR_USE_ILP64 OR BLAS_FOUND)
-        target_link_libraries(sparseir PRIVATE ${BLAS_LIBRARIES})
-        message(STATUS "Linked BLAS libraries: ${BLAS_LIBRARIES}")
-    else()
-        message(FATAL_ERROR "BLAS libraries not found")
+# Add BLAS linking (always enabled)
+# Link BLAS privately, but ensure it's not dropped by linker
+# This allows dlopen/dlsym to find BLAS symbols at runtime
+if(SPARSEIR_USE_BLAS_ILP64 OR BLAS_FOUND)
+    target_link_libraries(sparseir PRIVATE ${BLAS_LIBRARIES})
+    message(STATUS "Linked BLAS libraries: ${BLAS_LIBRARIES}")
+
+    # Ensure BLAS dependency is retained even if symbols are not directly used
+    # This is necessary for dynamic symbol resolution at runtime
+    if(NOT APPLE)
+        target_link_options(sparseir PRIVATE "LINKER:--no-as-needed")
     endif()
 else()
-    message(STATUS "BLAS linking disabled")
+    message(FATAL_ERROR "BLAS libraries not found - BLAS is required")
 endif()
 
-if(SPARSEIR_USE_LAPACKE AND LAPACK_FOUND)
-    target_link_libraries(sparseir PRIVATE ${LAPACK_LIBRARIES})
-endif()
-
-
 # macOS-specific configuration
 if(APPLE AND ACCELERATE_FRAMEWORK)
     target_link_libraries(sparseir PRIVATE ${ACCELERATE_FRAMEWORK})