Collection of fixes

.github/workflows/CI.yml

@@ -76,7 +76,7 @@ jobs:
           mkdir build && cd build
           cmake .. \
             -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-            -DPYTHON_EXECUTABLE=`which python3` \
+            -DPython3_EXECUTABLE=`which python3` \
             -DSERIALBOX_TESTING=ON \
             -DSERIALBOX_ENABLE_FORTRAN=${TEST_FORTRAN} \
             -DSERIALBOX_TESTING_FORTRAN=${TEST_FORTRAN} \

CMakeLists.txt

@@ -14,8 +14,8 @@
 set(CMAKE_INSTALL_PREFIX "${CMAKE_CURRENT_SOURCE_DIR}/install" CACHE PATH "CMake install prefix")
 
 cmake_policy(SET CMP0048 NEW)
-project(Serialbox LANGUAGES C CXX VERSION 2.6.1)
 cmake_minimum_required(VERSION 3.12.0)
+project(Serialbox LANGUAGES C CXX VERSION 2.6.1)
 
 set(CMAKE_CXX_EXTENSIONS OFF)
 set(CMAKE_C_EXTENSIONS OFF)
@@ -218,7 +218,7 @@ endif()
 
 #---------------------------------------- Python ---------------------------------------------------
 if(SERIALBOX_ENABLE_PYTHON)
-  find_package(PythonInterp 3.4)
+  find_package(Python3 COMPONENTS Interpreter)
 
   # Python tests are enabled by default if we can find "nose" and "numpy"
   set(ENABLE_PYTHON_TESTS OFF)

cmake/SerialboxTooling.cmake

@@ -89,12 +89,11 @@ function(serialbox_run_pp_ser)
 
   if(pp_ser_input)
     add_custom_command(OUTPUT ${pp_ser_output}
-                       COMMAND ${PYTHON_EXECUTABLE} ${SERIALBOX_PPSER} --verbose 
+                       COMMAND ${Python3_EXECUTABLE} ${SERIALBOX_PPSER} --verbose 
                                                                        --ignore-identical 
                                                                        --output-dir=${output_dir} 
                                                                        ${pp_ser_input}
                        DEPENDS ${pp_ser_input}
                        COMMENT "Preprocessing for serialization")
   endif()
 endfunction(serialbox_run_pp_ser)
-

cmake/modules/FindPythonModule.cmake

@@ -4,7 +4,7 @@
 #
 #   find_python_module(PyQt5 REQUIRED)
 #
-# The module makes use of the ${PYTHON_EXECUTABLE} which needs to be set before calling the 
+# The module makes use of the ${Python3_EXECUTABLE} which needs to be set before calling the 
 # find_python_module function.
 #
 # Variables defined by this cmake module:
@@ -25,7 +25,7 @@ function(find_python_module module)
     endif()
 
     # A module's location is usually a directory, but for binary modules it's a .so file.
-    execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c" 
+    execute_process(COMMAND "${Python3_EXECUTABLE}" "-c" 
       "import re, ${module}; print(re.compile('/__init__.py.*').sub('',${module}.__file__))"
       RESULT_VARIABLE _${module}_status 
       OUTPUT_VARIABLE _${module}_location
@@ -34,7 +34,7 @@ function(find_python_module module)
 
     # Set result
     if(NOT _${module}_status)
-      message(STATUS "Found Python module \"${module}\" for Python: ${PYTHON_EXECUTABLE}")
+      message(STATUS "Found Python module \"${module}\" for Python: ${Python3_EXECUTABLE}")
       set(PY_${module_upper}_PATH ${_${module}_location} 
           CACHE STRING "Location of Python module ${module}")
       set(PY_${module_upper}_FOUND TRUE
@@ -43,11 +43,10 @@ function(find_python_module module)
     else()
       set(PY_${module_upper}_FOUND FALSE)
         if(${module}_FIND_REQUIRED)
-          message(FATAL_ERROR "Could NOT find module ${module} for python ${PYTHON_EXECUTABLE}")
+          message(FATAL_ERROR "Could NOT find module ${module} for python ${Python3_EXECUTABLE}")
         else()
-          message(STATUS "Could NOT find \"${module}\" for python: ${PYTHON_EXECUTABLE}")
+          message(STATUS "Could NOT find \"${module}\" for python: ${Python3_EXECUTABLE}")
         endif()
     endif()
   endif(NOT PY_${module_upper}_FOUND)
 endfunction(find_python_module)
-

src/serialbox-python/setup.py

@@ -45,18 +45,17 @@ def build_extension(self, ext):
         # Can be set with Conda-Build, for example.
         cmake_generator = os.environ.get("CMAKE_GENERATOR", "")
 
-        # Set Python_EXECUTABLE instead if you use PYBIND11_FINDPYTHON
+        # Set Python3_EXECUTABLE instead if you use PYBIND11_FINDPYTHON
         # EXAMPLE_VERSION_INFO shows you how to pass a value into the C++ code
         # from Python.
         cmake_args = [
             "-DCMAKE_LIBRARY_OUTPUT_DIRECTORY={}".format(extdir),
-            "-DPYTHON_EXECUTABLE={}".format(sys.executable),
+            "-DPython3_EXECUTABLE={}".format(sys.executable),
             "-DCMAKE_BUILD_TYPE={}".format(cfg),  # not used on MSVC, but no harm
             "-DSERIALBOX_ENABLE_FORTRAN=false",
             "-DCMAKE_BUILD_RPATH={}".format(origin),
             "-DSERIALBOX_ENABLE_SDB=false",
             "-DSERIALBOX_ASYNC_API=false",
-
         ]
         build_args = []
         # Adding CMake arguments set as environment variable
@@ -70,6 +69,7 @@ def build_extension(self, ext):
         ]
         if sys.platform == "darwin":
             from distutils import sysconfig
+
             vars = sysconfig.get_config_vars()
             vars["SO"] = ".dylib"
             vars["EXT_SUFFIX"] = ".dylib"
@@ -89,7 +89,6 @@ def build_extension(self, ext):
                     pass
 
         else:
-
             # Single config generators are handled "normally"
             single_config = any(x in cmake_generator for x in {"NMake", "Ninja"})
 
@@ -151,7 +150,9 @@ def _get_origin(self):
     author="Serialbox Developers",
     packages=find_packages(),
     install_requires=["numpy"],
-    ext_modules=[CMakeExtension("libSerialboxC", sourcedir=os.path.join(DIR, "../../"))],
+    ext_modules=[
+        CMakeExtension("libSerialboxC", sourcedir=os.path.join(DIR, "../../"))
+    ],
     cmdclass={"build_ext": CMakeBuild},
     zip_safe=False,
 )

src/serialbox/core/hash/Hash.h

@@ -36,6 +36,7 @@ class Hash {
   ///
   /// \return Hex representation as string of the computed hash
   virtual std::string hash(const void* data, int length) = 0;
+  virtual ~Hash() = default;
 };
 
 } // namespace serialbox

src/serialbox/core/hash/SHA256.cpp

@@ -19,6 +19,7 @@
 //===------------------------------------------------------------------------------------------===//
 
 #include "serialbox/core/hash/SHA256.h"
+#include <cstdint>
 #include <cstdlib>
 #include <cstring>
 #include <sstream>

test/serialbox-python/run_python_tests.sh.cmake

@@ -23,7 +23,7 @@ export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:${PROJECT_BINARY_DIR}/src/serialbox-c"
 #
 # Check if nose exists
 #
-"${PYTHON_EXECUTABLE}" -c "import nose"
+"${Python3_EXECUTABLE}" -c "import nose"
 if [ "$?" == "1" ]; then
   echo ">> Python tests require module 'nose'"
   exit 1
@@ -33,10 +33,10 @@ fi
 # Run serialbox python tests with nose
 #
 cd "${PYTHON_TEST_DIR}/serialbox"
-"${PYTHON_EXECUTABLE}" -m "nose"
+"${Python3_EXECUTABLE}" -m "nose"
 
 #
 # Run the sdb tests with nose
 #
 cd "${PYTHON_TEST_DIR}/sdb/sdbcore"
-"${PYTHON_EXECUTABLE}" -m "nose"
+"${Python3_EXECUTABLE}" -m "nose"