Fix CMake/GCC/clang warnings

CMakeLists.txt

@@ -27,7 +27,7 @@
 # License along with Mutation++.  If not, see
 # <http://www.gnu.org/licenses/>.
 #
-cmake_minimum_required(VERSION 3.5)
+cmake_minimum_required(VERSION 3.10...4.0)
 cmake_policy(SET CMP0048 NEW)
 set(CMAKE_CXX_STANDARD 14)
 
@@ -51,7 +51,6 @@ endif()
 #######################################################################
 
 if (SKBUILD)
-    add_subdirectory(thirdparty/pybind11)
     add_subdirectory(interface/python)
     set(CMAKE_POSITION_INDEPENDENT_CODE ON)
 endif()
@@ -217,7 +216,6 @@ option(ENABLE_COVERAGE "Generate coverage for codecov.io" OFF)
 list(APPEND LCOV_REMOVE_PATTERNS
     "'/usr/*'"
     "'*/tests/*'"
-    "'*/install/*'"
     "'*/examples/*'"
     "'*/thirdparty/*'"
 )

cmake/modules/ParseAndAddCatchTests.cmake

@@ -46,7 +46,7 @@
 #                                                                                                  #
 #==================================================================================================#
 
-cmake_minimum_required(VERSION 2.8.12)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 option(PARSE_CATCH_TESTS_VERBOSE "Print Catch to CTest parser debug messages" OFF)
 option(PARSE_CATCH_TESTS_NO_HIDDEN_TESTS "Exclude tests with [!hide], [.] or [.foo] tags" OFF)

examples/CMakeLists.txt

@@ -17,7 +17,7 @@
 # License along with Mutation++.  If not, see
 # <http://www.gnu.org/licenses/>.
 
-cmake_minimum_required(VERSION 2.8.2)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 # Append the PROJECT_BINARY_DIR to CMAKE_PREFIX_PATH in order to be able to 
 # find the configuration files at build time

examples/c++/CMakeLists.txt

@@ -18,7 +18,7 @@
 # License along with Mutation++.  If not, see
 # <http://www.gnu.org/licenses/>.
 
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 include(ListSubDirs)
 ListSubDirs(example_subdirs ${CMAKE_CURRENT_LIST_DIR})

examples/c++/CMakeLists.txt.shared

@@ -1,5 +1,5 @@
 cmake_policy(SET CMP0048 NEW)
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 get_filename_component(example_name ${CMAKE_CURRENT_SOURCE_DIR} NAME)
 

examples/c++/tutorial/CMakeLists.txt

@@ -1,5 +1,5 @@
 cmake_policy(SET CMP0048 NEW)
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 get_filename_component(example_name ${CMAKE_CURRENT_SOURCE_DIR} NAME)
 

examples/fortran/CMakeLists.txt.shared

@@ -1,5 +1,5 @@
 cmake_policy(SET CMP0048 NEW)
-cmake_minimum_required(VERSION 3.0)
+cmake_minimum_required(VERSION 3.10...4.0)
 
 get_filename_component(example_name ${CMAKE_CURRENT_SOURCE_DIR} NAME)
 

interface/fortran/CMakeLists.txt

@@ -19,7 +19,7 @@
 # <http://www.gnu.org/licenses/>.
 #
 
-cmake_minimum_required(VERSION 2.6)
+cmake_minimum_required(VERSION 3.10...4.0)
 cmake_policy(SET CMP0022 NEW)
 
 add_library(mutation++_fortran

interface/python/.gitignore

@@ -1,7 +1,7 @@
 ###Build###
 build/
 dist/
-mutationpp_python.egg-info/
+mutationpp.egg-info/
 *.so
 
 ###IDE###

interface/python/CMakeLists.txt

@@ -1,7 +1,21 @@
+if (CMAKE_VERSION VERSION_LESS 3.18)
+    set(PY_DEV_MODULE Development)
+else()
+    set(PY_DEV_MODULE Development.Module)
+endif()
+
+find_package(Python COMPONENTS Interpreter ${PY_DEV_MODULE} REQUIRED)
+
+execute_process(
+    COMMAND "${Python_EXECUTABLE}" -m pybind11 --cmakedir
+    OUTPUT_STRIP_TRAILING_WHITESPACE OUTPUT_VARIABLE pybind11_ROOT)
+
+find_package(pybind11 CONFIG REQUIRED)
+
 pybind11_add_module(_mutationpp
-        src/mutationpp_python.cpp
-        src/pyMixtureOptions.cpp
-        src/pyMixture.cpp
+    src/mutationpp_python.cpp
+    src/pyMixtureOptions.cpp
+    src/pyMixture.cpp
 )
 
 target_link_libraries(_mutationpp PRIVATE mutation++)

pyproject.toml

@@ -1,5 +1,5 @@
 [build-system]
-requires = ["setuptools", "wheel", "scikit-build", "cmake", "ninja"]
+requires = ["setuptools", "wheel", "pybind11", "scikit-build", "cmake", "ninja"]
 build-backend = "setuptools.build_meta"
 
 [tool.pytest.ini_options]

src/apps/bprime.cpp

@@ -59,7 +59,7 @@ using namespace Mutation::Utilities;
  * mole fractions at the wall versus temperature.
  */
 // Simply stores the command line options
-typedef struct {
+typedef struct Options {
     double T1;
     double T2;
     double dT;

src/apps/mppshock.cpp

@@ -38,7 +38,7 @@ class State
         m_P(p), m_V(u), m_T(T) {}
     State (const State&) = delete;
     State (State&&) = default;
-    State& operator=( const State &) = default;
+    State& operator=( const State &) = delete;
 
     double getP() const { return m_P; }
     double getV() const { return m_V; }

src/thermo/SpeciesNameFSM.cpp

@@ -55,7 +55,9 @@ bool SpeciesNameFSM::parse(const std::string& s)
     }
 
     // Run each character through the FSM
-    for_each(s.begin(), s.end(), std::bind1st(std::mem_fun(&SpeciesNameFSM::next), this));
+    using namespace std::placeholders;  // for _1,
+    for_each(s.begin(), s.end(),
+             std::bind(std::mem_fn(&SpeciesNameFSM::next), this, _1));
     next('\0');
 
     if (m_state == BadFormat) {

src/transport/CollisionIntegral.cpp

@@ -372,6 +372,7 @@ class FromAstColInt : public CollisionIntegral
         case Q22: return // A* Q11
             (m_ci1->compute(T)*m_ci2->compute(T));
         }
+        return 0; // LCOV_EXCL_LINE
     }
 
     /**
@@ -476,6 +477,7 @@ class FromBstColInt : public CollisionIntegral
         case Q13: return // (5*Q12 - B*Q11)/4
             (5.*m_ci3->compute(T)-m_ci1->compute(T)*m_ci2->compute(T))/4.;
         }
+        return 0; // LCOV_EXCL_LINE
     }
 
     /**
@@ -567,6 +569,7 @@ class FromCstColInt : public CollisionIntegral
         case Q12: return // C* Q11
             (m_ci1->compute(T)*m_ci2->compute(T));
         }
+        return 0; // LCOV_EXCL_LINE
     }
 
     /**