Manual changes to the codebase to prepare for formatting

1) Change OPENPMD_private macros so clang-format understands them

2) Put HDF5 lint back to the right place

3) Fix includes: sorting the includes via clang-format uncovered an include error.

Author: franzpoeschel

include/openPMD/IO/ADIOS/ADIOS1FilePosition.hpp

@@ -22,6 +22,7 @@
 
 #include "openPMD/IO/AbstractFilePosition.hpp"
 
+#include <string>
 
 namespace openPMD
 {

include/openPMD/RecordComponent.hpp

@@ -37,7 +37,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_protected
-#   define OPENPMD_protected protected
+#   define OPENPMD_protected protected:
 #endif
 
 
@@ -327,7 +327,10 @@ class RecordComponent : public BaseRecordComponent
 
     RecordComponent();
 
-OPENPMD_protected:
+// clang-format off
+OPENPMD_protected
+// clang-format on
+
     RecordComponent( std::shared_ptr< internal::RecordComponentData > );
 
     inline internal::RecordComponentData const & get() const

include/openPMD/Series.hpp

@@ -46,7 +46,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_private
-#   define OPENPMD_private private
+#   define OPENPMD_private private:
 #endif
 
 
@@ -421,7 +421,10 @@ class Series : public Attributable
      */
     WriteIterations writeIterations();
 
-OPENPMD_private:
+// clang-format off
+OPENPMD_private
+// clang-format on
+
     static constexpr char const * const BASEPATH = "/data/%T/";
 
     struct ParsedInput;

include/openPMD/backend/Attributable.hpp

@@ -35,7 +35,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_protected
-#   define OPENPMD_protected protected
+#   define OPENPMD_protected protected:
 #endif
 
 
@@ -259,7 +259,9 @@ class Attributable
      */
     MyPath myPath() const;
 
-OPENPMD_protected:
+// clang-format off
+OPENPMD_protected
+// clang-format on
 
     Series retrieveSeries() const;
 

include/openPMD/backend/BaseRecordComponent.hpp

@@ -26,7 +26,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_protected
-#   define OPENPMD_protected protected
+#   define OPENPMD_protected protected:
 #endif
 
 

include/openPMD/backend/Container.hpp

@@ -33,7 +33,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_protected
-#   define OPENPMD_protected protected
+#   define OPENPMD_protected protected:
 #endif
 
 
@@ -341,7 +341,10 @@ class Container : public Attributable
         return container().emplace(std::forward<Args>(args)...);
     }
 
-OPENPMD_protected:
+// clang-format off
+OPENPMD_protected
+// clang-format on
+
     Container( std::shared_ptr< ContainerData > containerData )
         : Attributable{ containerData }
         , m_containerData{ std::move( containerData ) }
@@ -368,7 +371,10 @@ class Container : public Attributable
         flushAttributes();
     }
 
-OPENPMD_private:
+// clang-format off
+OPENPMD_private
+// clang-format on
+
     Container() : Attributable{ nullptr }
     {
         Attributable::setData( m_containerData );

include/openPMD/backend/PatchRecordComponent.hpp

@@ -29,7 +29,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_private
-#   define OPENPMD_private private
+#   define OPENPMD_private private:
 #endif
 
 
@@ -88,7 +88,9 @@ class PatchRecordComponent : public BaseRecordComponent
     template< typename T >
     void store(uint64_t idx, T);
 
-OPENPMD_private:
+// clang-format off
+OPENPMD_private
+// clang-format on
 
     void flush(std::string const&);
     void read();
@@ -110,7 +112,10 @@ class PatchRecordComponent : public BaseRecordComponent
 
     PatchRecordComponent();
 
-OPENPMD_protected:
+// clang-format off
+OPENPMD_protected
+// clang-format on
+
     PatchRecordComponent(
         std::shared_ptr< internal::PatchRecordComponentData > );
 

include/openPMD/backend/Writable.hpp

@@ -28,7 +28,7 @@
 
 // expose private and protected members for invasive testing
 #ifndef OPENPMD_private
-#   define OPENPMD_private private
+#   define OPENPMD_private private:
 #endif
 
 
@@ -114,7 +114,10 @@ class Writable final
      */
     void seriesFlush();
 
-OPENPMD_private:
+// clang-format off
+OPENPMD_private
+// clang-format on
+
     void seriesFlush( FlushLevel );
     /*
      * These members need to be shared pointers since distinct instances of

src/IO/HDF5/HDF5IOHandler.cpp

@@ -1638,7 +1638,9 @@ HDF5IOHandlerImpl::readAttribute(Writable* writable,
                 char* m1 = H5Tget_member_name(attr_type, 1);
                 char* m2 = H5Tget_member_name(attr_type, 2);
                 if( m0 == nullptr || m1 == nullptr || m2 == nullptr )
+                    // clang-format off
                     isLegacyLibSplashAttr = false;  // NOLINT(bugprone-branch-clone)
+                // clang-format on
                 else if(strcmp("x", m0) != 0 || strcmp("y", m1) != 0 || strcmp("z", m2) != 0)
                     isLegacyLibSplashAttr = false;
                 H5free_memory(m2);

test/AuxiliaryTest.cpp

@@ -1,7 +1,7 @@
 // expose private and protected members for invasive testing
 #if openPMD_USE_INVASIVE_TESTS
-#   define OPENPMD_private public
-#   define OPENPMD_protected public
+#   define OPENPMD_private public:
+#   define OPENPMD_protected public:
 #endif
 #include "openPMD/config.hpp"
 #include "openPMD/backend/Writable.hpp"