Let's try it another way

2026-06-04 13:44:21 +08:00 · 2026-01-31 14:22:09 +01:00
parent 2f997664c6
commit bdb9818a73
4 changed files with 220 additions and 28 deletions
--- a/.github/workflows/cmake-multi-platform.yml
+++ b/.github/workflows/cmake-multi-platform.yml
@@ -36,17 +36,10 @@ jobs:
      shell: bash
      run: echo "build-output-dir=${{ github.workspace }}/build" >> "$GITHUB_OUTPUT"

-    - name: Install boost
-      if: matrix.os == 'windows-latest'
-      uses: MarkusJx/install-boost@v2
-      id: install-boost
-      with:
-        boost_version: 1.88.0
-        
    - name: Install Catch2 Ubuntu
      if: matrix.os == 'ubuntu-latest'
      run: >
-        sudo apt-get update && sudo apt-get install catch2 libpython3-all-dev libboost1.88-all-dev
+        sudo apt-get update && sudo apt-get install catch2 libpython3-all-dev

    - name: setup python
      uses: actions/setup-python@v6
@@ -56,7 +49,7 @@ jobs:
    - name: Install Catch2 macOS
      if: matrix.os == 'macos-latest'
      run: >
-        brew install catch2 boost
+        brew install catch2

    - name: Install dependencies Window
      if: matrix.os == 'windows-latest'
@@ -67,7 +60,6 @@ jobs:
      run: >
        cmake -B ${{ steps.strings.outputs.build-output-dir }}
        -DCMAKE_CXX_COMPILER=${{ matrix.cpp_compiler }}
-        -DCMAKE_PREFIX_PATH=${{ steps.install-boost.outputs.BOOST_ROOT }} 
        -DCMAKE_BUILD_TYPE=Release
        -DBUILD_TESTING=ON
        -DBUILD_PYTHON_MODULE=ON
--- a/python-module/CMakeLists.txt
+++ b/python-module/CMakeLists.txt
@@ -35,7 +35,25 @@ if(NOT EXISTS ${Python_LIBRARIES})
 endif()

 # Boost 1.86 is required since it contains code required to use numpy 2.x
-find_package(Boost 1.86 REQUIRED COMPONENTS python)
+if(NOT WIN32)	# On Windows we need to build boost ourselves, to find the correct python lib
+	find_package(Boost 1.86 QUIET COMPONENTS python)
+endif()
+
+if(WIN32 OR NOT Boost_FOUND)
+	# boost is a huge project and directly downloading the 'alternate release'
+	# from github is much faster than recursively cloning the repo.
+	CPMAddPackage(
+		NAME Boost
+		VERSION 1.90.0
+		URL https://archives.boost.io/release/1.90.0/source/boost_1_90_0.tar.bz2
+		URL_HASH SHA256=49551aff3b22cbc5c5a9ed3dbc92f0e23ea50a0f7325b0d198b705e8ee3fc305
+		OPTIONS
+		"BOOST_ENABLE_CMAKE ON"
+		"BOOST_INCLUDE_LIBRARIES python"
+		"BOOST_ENABLE_PYTHON ON"
+		"CMAKE_POSITION_INDEPENDENT_CODE ON"
+	)
+endif()

 # ---------
 add_library(mkdssp_module SHARED dssp-python-plugin.cpp)
--- a/test/CMakeLists.txt
+++ b/test/CMakeLists.txt
@@ -1,33 +1,39 @@
 CPMFindPackage(
-	NAME Catch2 3
-	GIT_REPOSITORY https://github.com/catchorg/Catch2.git
-	GIT_TAG v3.4.0
-	EXCLUDE_FROM_ALL YES)
+    NAME Catch2 3
+    GIT_REPOSITORY https://github.com/catchorg/Catch2.git
+    GIT_TAG v3.4.0
+    EXCLUDE_FROM_ALL YES)

 add_executable(unit-test-dssp ${CMAKE_CURRENT_SOURCE_DIR}/unit-test-dssp.cpp ${PROJECT_SOURCE_DIR}/libdssp/src/dssp-io.cpp)

 target_include_directories(unit-test-dssp PRIVATE
-	${CMAKE_CURRENT_SOURCE_DIR}/src
-	${CMAKE_CURRENT_SOURCE_DIR}/include
+    ${CMAKE_CURRENT_SOURCE_DIR}/src
+    ${CMAKE_CURRENT_SOURCE_DIR}/include
 )

 target_link_libraries(unit-test-dssp PRIVATE dssp cifpp::cifpp Catch2::Catch2)

 if(MSVC)
-	# Specify unwind semantics so that MSVC knowns how to handle exceptions
-	target_compile_options(unit-test-dssp PRIVATE /EHsc)
+    # Specify unwind semantics so that MSVC knowns how to handle exceptions
+    target_compile_options(unit-test-dssp PRIVATE /EHsc)
 endif()

 add_test(NAME unit-test-dssp COMMAND $<TARGET_FILE:unit-test-dssp>
-	--data-dir ${CMAKE_CURRENT_SOURCE_DIR}
-	--rsrc-dir ${CIFPP_DATA_DIR})
+    --data-dir ${CMAKE_CURRENT_SOURCE_DIR}
+    --rsrc-dir ${CIFPP_DATA_DIR})

 if(BUILD_PYTHON_MODULE)
-	find_package(Python REQUIRED Interpreter)
+    find_package(Python REQUIRED Interpreter)

-	add_test(NAME python_module COMMAND ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/test-python.py")
-	set_tests_properties(python_module PROPERTIES
-		ENVIRONMENT
-			"PYTHONPATH=$<TARGET_FILE_DIR:mkdssp_module>;LIBCIFPP_DATA_DIR=${CIFPP_DATA_DIR}"
-		WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
-endif()
+    add_test(NAME python_module COMMAND ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/test-python.py")
+    set_tests_properties(python_module PROPERTIES
+        ENVIRONMENT
+        "PYTHONPATH=$<TARGET_FILE_DIR:mkdssp_module>;LIBCIFPP_DATA_DIR=${CIFPP_DATA_DIR}"
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+
+    add_test(NAME python_module_numpy COMMAND ${Python_EXECUTABLE} "${CMAKE_CURRENT_SOURCE_DIR}/test_numpy2_compat.py")
+    set_tests_properties(python_module_numpy PROPERTIES
+        ENVIRONMENT
+        "PYTHONPATH=$<TARGET_FILE_DIR:mkdssp_module>;LIBCIFPP_DATA_DIR=${CIFPP_DATA_DIR}"
+        WORKING_DIRECTORY "${CMAKE_CURRENT_SOURCE_DIR}")
+endif()
--- a/test/test_numpy2_compat.py
+++ b/test/test_numpy2_compat.py
@@ -0,0 +1,176 @@
+"""
+DSSP numpy 2.x compatibility test script
+This script tests whether the DSSP module works correctly with numpy 2.x
+"""
+
+import sys
+import os
+import gzip
+import traceback
+
+def find_test_file():
+    """Find the test CIF file in the repository"""
+    # Possible paths relative to script location
+    possible_paths = [
+        "test/1cbs.cif.gz",  # From repository root
+        "../test/1cbs.cif.gz",  # From python-module directory
+        "1cbs.cif.gz",  # From test directory
+    ]
+    
+    for path in possible_paths:
+        if os.path.exists(path):
+            return path
+    
+    return None
+
+def test_numpy_version():
+    """Check numpy version"""
+    try:
+        import numpy as np
+        print(f"✓ numpy version: {np.__version__}")
+        major_version = int(np.__version__.split('.')[0])
+        if major_version >= 2:
+            print("✓ numpy 2.x detected")
+        else:
+            print(f"⚠ numpy {np.__version__} detected (not 2.x)")
+        return True
+    except ImportError as e:
+        print(f"✗ Failed to import numpy: {e}")
+        return False
+
+def test_mkdssp_import():
+    """Test mkdssp module import"""
+    try:
+        import mkdssp
+        print("✓ Successfully imported mkdssp module")
+        return True
+    except ImportError as e:
+        print(f"✗ Failed to import mkdssp: {e}")
+        traceback.print_exc()
+        return False
+
+def test_basic_functionality():
+    """Test basic functionality"""
+    try:
+        from mkdssp import dssp, TestBond, helix_type, chain_break_type, helix_position_type, structure_type
+        print("✓ Successfully imported all mkdssp classes/functions")
+        
+        # Find test file
+        test_file = find_test_file()
+        if test_file is None:
+            print("✗ Could not find test file (1cbs.cif.gz)")
+            print("  Please run this script from the repository root or test directory")
+            return False
+        
+        print(f"✓ Found test file: {test_file}")
+        
+        # Read test file
+        try:
+            with gzip.open(test_file, "rt") as f:
+                file_content = f.read()
+            print("✓ Successfully read test file")
+        except Exception as e:
+            print(f"✗ Failed to read test file: {e}")
+            return False
+        
+        # Test DSSP object creation
+        try:
+            dssp_obj = dssp(file_content)
+            print("✓ Successfully created DSSP object")
+        except Exception as e:
+            print(f"✗ Failed to create DSSP object: {e}")
+            traceback.print_exc()
+            return False
+        
+        # Test statistics
+        try:
+            stats = dssp_obj.statistics
+            print(f"✓ Successfully retrieved statistics")
+            print(f"  - Residues: {stats.residues}")
+            print(f"  - Chains: {stats.chains}")
+            print(f"  - H-bonds: {stats.H_bonds}")
+        except Exception as e:
+            print(f"✗ Failed to retrieve statistics: {e}")
+            traceback.print_exc()
+            return False
+        
+        # Test iteration
+        try:
+            count = 0
+            for res in dssp_obj:
+                count += 1
+                if count == 1:
+                    # Check first residue
+                    print(f"  - First residue: {res.asym_id} {res.seq_id} {res.compound_id}")
+            print(f"✓ Successfully iterated through {count} residues")
+        except Exception as e:
+            print(f"✗ Failed to iterate through residues: {e}")
+            traceback.print_exc()
+            return False
+        
+        # Test TestBond function
+        try:
+            a = dssp_obj.get('A', 137)
+            b = dssp_obj.get('A', 6)
+            result = TestBond(a, b)
+            print(f"✓ Successfully tested TestBond function: {result}")
+        except Exception as e:
+            print(f"✗ Failed to test TestBond function: {e}")
+            traceback.print_exc()
+            return False
+        
+        return True
+        
+    except Exception as e:
+        print(f"✗ Basic functionality test failed: {e}")
+        traceback.print_exc()
+        return False
+
+def main():
+    """Main test function"""
+    print("=" * 60)
+    print("DSSP numpy 2.x Compatibility Test")
+    print("=" * 60)
+    print()
+    
+    all_passed = True
+    
+    # Test 1: Check numpy version
+    print("Test 1: Check numpy version")
+    if not test_numpy_version():
+        all_passed = False
+    print()
+    
+    # Test 2: Import mkdssp
+    print("Test 2: Import mkdssp module")
+    if not test_mkdssp_import():
+        all_passed = False
+        print("\n⚠ Cannot import mkdssp, skipping remaining tests")
+        print_summary(False)
+        return 1
+    print()
+    
+    # Test 3: Basic functionality
+    print("Test 3: Test basic functionality")
+    if not test_basic_functionality():
+        all_passed = False
+    print()
+    
+    # Summary
+    print_summary(all_passed)
+    
+    return 0 if all_passed else 1
+
+def print_summary(all_passed):
+    """Print test summary"""
+    print("=" * 60)
+    if all_passed:
+        print("✓ All tests passed!")
+        print("✓ DSSP appears to be compatible with numpy 2.x")
+    else:
+        print("✗ Some tests failed")
+        print("✗ There may be compatibility issues with numpy 2.x")
+    print("=" * 60)
+
+if __name__ == "__main__":
+    sys.exit(main())