Fixes to the dirty/dirtyRecursive logic

Author: franzpoeschel

src/CustomHierarchy.cpp

@@ -634,7 +634,11 @@ void CustomHierarchy::flush_internal(
     {
         dataset.flush(name, flushParams, /* set_defaults = */ false);
     }
-    setDirty(false);
+    if (flushParams.flushLevel != FlushLevel::SkeletonOnly &&
+        flushParams.flushLevel != FlushLevel::CreateOrOpenFiles)
+    {
+        setDirty(false);
+    }
 }
 
 void CustomHierarchy::flush(

src/Iteration.cpp

@@ -360,12 +360,13 @@ void Iteration::flushIteration(internal::FlushParams const &flushParams)
         s.setParticlesPath(particlesPaths);
     }
 
-    if (access::write(IOHandler()->m_frontendAccess))
-    {
-        flushAttributes(flushParams);
-    }
-    if (flushParams.flushLevel != FlushLevel::SkeletonOnly)
+    if (flushParams.flushLevel != FlushLevel::SkeletonOnly &&
+        flushParams.flushLevel != FlushLevel::CreateOrOpenFiles)
     {
+        if (access::write(IOHandler()->m_frontendAccess))
+        {
+            flushAttributes(flushParams);
+        }
         setDirty(false);
         meshes.setDirty(false);
         particles.setDirty(false);

src/Series.cpp

@@ -1406,9 +1406,13 @@ void Series::flushFileBased(
     case Access::READ_WRITE:
     case Access::CREATE:
     case Access::APPEND: {
-        bool allDirty = dirty();
+        bool const allDirty = dirty();
         for (auto it = begin; it != end; ++it)
         {
+            /* reset the dirty bit for every iteration (i.e. file)
+             * otherwise only the first iteration will have updates attributes
+             */
+            setDirty(allDirty);
             // Phase 1
             switch (openIterationIfDirty(it->first, it->second))
             {
@@ -1459,12 +1463,7 @@ void Series::flushFileBased(
             {
                 IOHandler()->flush(flushParams);
             }
-            /* reset the dirty bit for every iteration (i.e. file)
-             * otherwise only the first iteration will have updates attributes
-             */
-            setDirty(allDirty);
         }
-        setDirty(false);
         break;
     }
     }

src/backend/Attributable.cpp

@@ -19,6 +19,7 @@
  * If not, see <http://www.gnu.org/licenses/>.
  */
 #include "openPMD/backend/Attributable.hpp"
+#include "openPMD/IO/AbstractIOHandler.hpp"
 #include "openPMD/Iteration.hpp"
 #include "openPMD/Series.hpp"
 #include "openPMD/auxiliary/DerefDynamicCast.hpp"
@@ -283,10 +284,10 @@ void Attributable::flushAttributes(internal::FlushParams const &flushParams)
         }
     }
     // Do this outside the if branch to also setDirty to dirtyRecursive
-    if (flushParams.flushLevel != FlushLevel::SkeletonOnly)
-    {
-        setDirty(false);
-    }
+    assert(
+        flushParams.flushLevel != FlushLevel::SkeletonOnly &&
+        flushParams.flushLevel != FlushLevel::CreateOrOpenFiles);
+    setDirty(false);
 }
 
 void Attributable::readAttributes(ReadMode mode)