add option h5fortran_IGNORE_CONDA_LIBRARIES

add option h5fortran_python for testing

fixes #48

Author: scivision

.github/workflows/ci.yml

@@ -4,7 +4,6 @@ env:
   HOMEBREW_NO_INSTALL_CLEANUP: 1
   CTEST_NO_TESTS_ACTION: error
   CTEST_PARALLEL_LEVEL: 0
-  CMAKE_BUILD_PARALLEL_LEVEL: 4
   CMAKE_INSTALL_PREFIX: ~/libs
   CMAKE_PREFIX_PATH: ~/libs
 

.github/workflows/composite-pkg/action.yml

@@ -8,7 +8,7 @@ runs:
 
   - uses: actions/setup-python@v5
     with:
-      python-version: '3.12'
+      python-version: '3.13'
 
   - name: Python pkgs
     shell: bash

CMakeLists.txt

@@ -25,7 +25,7 @@ endif()
 # --- avoid Anaconda libraries
 find_package(Python COMPONENTS Interpreter)
 
-if(DEFINED ENV{CONDA_PREFIX})
+if(DEFINED ENV{CONDA_PREFIX} AND h5fortran_IGNORE_CONDA_LIBRARIES)
   list(APPEND CMAKE_IGNORE_PREFIX_PATH $ENV{CONDA_PREFIX})
   list(APPEND CMAKE_IGNORE_PATH $ENV{CONDA_PREFIX}/bin)
   # need CMAKE_IGNORE_PATH for CMake < 3.23

CMakePresets.json

@@ -6,7 +6,10 @@
   "name": "default",
   "binaryDir": "${sourceDir}/build",
   "cacheVariables": {
-    "CMAKE_COMPILE_WARNING_AS_ERROR": true
+    "CMAKE_COMPILE_WARNING_AS_ERROR": true,
+    "h5fortran_BUILD_TESTING": true,
+    "h5fortran_find": true,
+    "h5fortran_python": true
   }
 },
 {
@@ -29,7 +32,7 @@
   "description": "Build with code coverage enabled.",
   "cacheVariables": {
     "CMAKE_BUILD_TYPE": "Debug",
-    "h5fortran_COVERAGE": true
+    "h5fortran_coverage": true
   }
 }
 ],

cmake/CheckHDF5.cmake

@@ -19,7 +19,7 @@ endmacro()
 
 function(hdf5_run_err_diag stderr)
 
-if(DEFINED ENV{CONDA_PREFIX})
+if(DEFINED ENV{CONDA_PREFIX} AND h5fortran_IGNORE_CONDA_LIBRARIES)
   message(WARNING "suggest running 'conda deactivate' and re-running cmake as Conda may be interfering with HDF5 library.")
 elseif(WIN32 AND stderr MATCHES "0xc0000135")
   message(STATUS "test run error may be due to missing HDF5 DLLs in PATH

cmake/compilers.cmake

@@ -55,14 +55,14 @@ add_compile_options(
 endif()
 
 # --- code coverage
-if(h5fortran_COVERAGE)
+if(h5fortran_coverage)
   include(${CMAKE_CURRENT_LIST_DIR}/Modules/CodeCoverage.cmake)
   append_coverage_compiler_flags()
   set(COVERAGE_EXCLUDES ${PROJECT_SOURCE_DIR}/test)
 endif()
 
 # --- clang-tidy
-if(tidy AND h5fortran_IS_TOP_LEVEL)
+if(h5fortran_tidy AND h5fortran_IS_TOP_LEVEL)
   find_program(CLANG_TIDY_EXE NAMES "clang-tidy" REQUIRED)
   set(CMAKE_C_CLANG_TIDY ${CLANG_TIDY_EXE})
   set(CMAKE_CXX_CLANG_TIDY ${CLANG_TIDY_EXE})

options.cmake

@@ -2,13 +2,16 @@ message(STATUS "${PROJECT_NAME} ${PROJECT_VERSION} CMake ${CMAKE_VERSION} Toolch
 
 include(GNUInstallDirs)
 
-option(h5fortran_find "try to find libraries" on)
+option(h5fortran_find "try to find HDF5 library" ON)
 
-option(h5fortran_COVERAGE "Code coverage tests")
-option(tidy "Run clang-tidy on the code")
+option(h5fortran_coverage "Code coverage tests")
+option(h5fortran_tidy "Run clang-tidy on the code")
 
-option(matlab "check HDF5 file writes with Matlab")
-option(concepts "conceptual testing, for devs only" off)
+option(h5fortran_matlab "check HDF5 file writes with Matlab")
+option(h5fortran_python "check HDF5 file writes with Python")
+
+option(h5fortran_IGNORE_CONDA_LIBRARIES "If ON, CMake will not search for the
+hdf5 libraries in a Conda environment." ON)
 
 option(h5fortran_BUILD_TESTING "build tests" ${h5fortran_IS_TOP_LEVEL})
 

test/CMakeLists.txt

@@ -15,6 +15,20 @@ set(attr_file ${CMAKE_CURRENT_BINARY_DIR}/test_attr_py.h5)
 set(shape_file ${CMAKE_CURRENT_BINARY_DIR}/test_shape.h5)
 set(string_file ${CMAKE_CURRENT_BINARY_DIR}/test_string_py.h5)
 
+# --- Python h5py
+if(NOT DEFINED h5py_ok AND Python_EXECUTABLE)
+  execute_process(COMMAND ${Python_EXECUTABLE} -c "import h5py"
+  RESULT_VARIABLE ret
+  ERROR_VARIABLE err
+  )
+  message(VERBOSE "${ret} ${err}")
+  if(ret EQUAL 0)
+    set(h5py_ok true CACHE BOOL "h5py OK")
+  else()
+    set(h5py_ok false CACHE BOOL "h5py not OK")
+  endif()
+endif()
+
 # --- fundamental HDF5 library check
 
 add_executable(test_minimal test_minimal.f90)
@@ -57,13 +71,16 @@ endfunction(setup_test)
 
 # --- setup unit tests
 
-set(test_names array attributes attributes_read
+set(test_names array attributes
 cast deflate_write deflate_read deflate_props destructor exist
-groups layout lt scalar shape string string_read version write
+groups layout lt scalar shape string version write
 fail_read_size_mismatch fail_read_rank_mismatch fail_nonexist_variable)
 if(HAVE_IEEE_ARITH)
   list(APPEND test_names fill)
 endif()
+if(h5py_ok)
+  list(APPEND test_names attributes_read string_read)
+endif()
 
 setup_test("${test_names}")
 
@@ -85,7 +102,7 @@ REQUIRED_FILES ${CMAKE_CURRENT_BINARY_DIR}/deflate1.h5
 LABELS deflate
 )
 
-if(h5fortran_COVERAGE)
+if(h5fortran_coverage)
 setup_target_for_coverage_gcovr_html(
 NAME coverage
 EXECUTABLE ${CMAKE_CTEST_COMMAND}
@@ -99,27 +116,15 @@ if(WIN32 AND CMAKE_VERSION VERSION_GREATER_EQUAL 3.22)
   )
 endif()
 
-# --- Python h5py
-if(NOT DEFINED h5py_ok)
-  execute_process(COMMAND ${Python_EXECUTABLE} -c "import h5py"
-  RESULT_VARIABLE ret
-  ERROR_VARIABLE err
-  )
-  message(VERBOSE "${ret} ${err}")
-  if(ret EQUAL 0)
-    set(h5py_ok true CACHE BOOL "h5py OK")
-  else()
-    set(h5py_ok false CACHE BOOL "h5py not OK")
-  endif()
-endif()
+# --- attributes
+
+if(h5py_ok)
 
 set_property(TEST string_read PROPERTY FIXTURES_REQUIRED h5str)
 set_property(TEST string_read PROPERTY REQUIRED_FILES ${string_file})
 
-# --- attributes
-
 add_test(NAME PythonAttributes
-COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/generate_attributes.py ${attr_file}
+COMMAND Python::Interpreter ${CMAKE_CURRENT_SOURCE_DIR}/generate_attributes.py ${attr_file}
 )
 
 set_property(TEST PythonAttributes PROPERTY FIXTURES_SETUP h5attr)
@@ -130,26 +135,26 @@ set_property(TEST attributes_read PROPERTY REQUIRED_FILES ${attr_file})
 # --- shape
 
 add_test(NAME PythonShape
-COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/check_shape.py ${shape_file}
+COMMAND Python::Interpreter ${CMAKE_CURRENT_SOURCE_DIR}/check_shape.py ${shape_file}
 )
 
 set_property(TEST PythonShape PROPERTY REQUIRED_FILES ${shape_file})
 set_property(TEST PythonShape PROPERTY FIXTURES_REQUIRED h5shape)
 
 # --- String
 add_test(NAME PythonString
-COMMAND ${Python_EXECUTABLE} ${CMAKE_CURRENT_SOURCE_DIR}/generate_string_data.py ${string_file}
+COMMAND Python::Interpreter ${CMAKE_CURRENT_SOURCE_DIR}/generate_string_data.py ${string_file}
 )
 
 set_property(TEST PythonString PROPERTY FIXTURES_SETUP h5str)
 
-set_property(TEST string_read PythonAttributes PythonShape PythonString attributes_read PROPERTY DISABLED $<NOT:$<BOOL:${h5py_ok}>>)
-
 set_property(TEST PythonAttributes PythonShape PythonString PROPERTY LABELS python)
 
+endif()
+
 # --- Matlab HDF5
 
-if(matlab)
+if(h5fortran_matlab)
 find_package(Matlab COMPONENTS MAIN_PROGRAM REQUIRED)
 
 set(matlab_cmd "i=h5info('${shape_file}', '/d7').Dataspace.Size; assert(all(i == [2, 1, 3, 4, 7, 6, 5]))")
@@ -163,7 +168,7 @@ REQUIRED_FILES ${shape_file}
 FIXTURES_REQUIRED h5shape
 )
 
-endif(matlab)
+endif()
 
 # --- h5ls