[PWGJE] Fix wrong headers. Remove unused files. Fix includes.

PWGJE/Core/JetTaggingUtilities.h

@@ -163,7 +163,7 @@
 
     int motherStatusCode = std::abs(mother.getGenStatusCode());
 
     if (motherStatusCode == 23 || motherStatusCode == 33 || motherStatusCode == 43 || motherStatusCode == 63) {
       return mother.globalIndex();
     }
   }
@@ -191,7 +191,7 @@
 
     int motherStatusCode = std::abs(mother.getGenStatusCode());
 
     if (motherStatusCode == 23 || motherStatusCode == 33 || motherStatusCode == 43 || motherStatusCode == 63 || (motherStatusCode == 51 && mother.template mothers_first_as<T>().pdgCode() == 21)) {
       return mother.globalIndex();
     }
   }
@@ -394,13 +394,13 @@
   bool charmQuark = false;
   for (auto const& mcpart : mcparticles) {
     int pdgcode = mcpart.pdgCode();
     if (std::abs(pdgcode) == 21 || (std::abs(pdgcode) >= 1 && std::abs(pdgcode) <= 5)) {
       double dR = jetutilities::deltaR(jet, mcpart);
 
       if (dR < jet.r() / 100.f) {
         if (std::abs(pdgcode) == 5) {
           return JetTaggingSpecies::beauty; // Beauty jet
         } else if (std::abs(pdgcode) == 4) {
           charmQuark = true;
         }
       }
@@ -429,15 +429,15 @@
 
   for (auto const& mcpart : mcparticles) {
     int pdgcode = mcpart.pdgCode();
     if (std::abs(pdgcode) == 21 || (std::abs(pdgcode) >= 1 && std::abs(pdgcode) <= 5)) {
       double dR = jetutilities::deltaR(jet, mcpart);
 
       if (dR < jet.r() / 100.f) {
         if (std::abs(pdgcode) == 5) {
           return JetTaggingSpecies::beauty; // Beauty jet
         } else if (std::abs(pdgcode) == 4) {
           charmQuark = true;
         } else if (std::abs(pdgcode) == 3) {
           strangeQuark = true;
         }
       }
@@ -541,7 +541,7 @@
  * positive value is expected from secondary vertex
  *
  * @param jet
- * @param track which is needed aod::JTrackExtras
+ * @param track which is needed o2::aod::JTrackExtras
  */
 template <typename T, typename U>
 int getGeoSign(T const& jet, U const& track)
@@ -962,7 +962,7 @@
 
   trkLabels["trkVtxIndex"] = std::vector<int>(nTrks, -1);
   if (count.size() != 0) {                        // If there is any SV cluster not only PV cluster
     for (auto& [idx, avgDistance] : avgDistances) // o2-linter: disable=const-ref-in-for-loop
       avgDistance /= count[idx];
 
     nVertices += avgDistances.size();

PWGJE/Core/MlResponseHfTagging.h

@@ -18,11 +18,10 @@
 
 #include "Tools/ML/MlResponse.h"
 
-#include <onnxruntime_cxx_api.h>
-
 #include <Framework/Logger.h>
 
 #include <onnxruntime_c_api.h>
+#include <onnxruntime_cxx_api.h>
 
 #include <cstddef>
 #include <cstdint>
@@ -330,6 +329,7 @@ class TensorAllocator
 {
  protected:
   Ort::MemoryInfo memInfo;
+
  public:
   TensorAllocator()
     : memInfo(Ort::MemoryInfo::CreateCpu(OrtAllocatorType::OrtArenaAllocator, OrtMemType::OrtMemTypeDefault))
@@ -426,7 +426,7 @@ class GNNBjetAllocator : public TensorAllocator
   }
   ~GNNBjetAllocator() = default;
 
-  // Copy operator for initializing GNNBjetAllocator using Configurable values
+  // Copy operator for initializing GNNBjetAllocator using o2::framework::Configurable values
   GNNBjetAllocator& operator=(const GNNBjetAllocator& other)
   {
     nJetFeat = other.nJetFeat;

PWGJE/DataModel/JetTagging.h

@@ -18,11 +18,11 @@
 #ifndef PWGJE_DATAMODEL_JETTAGGING_H_
 #define PWGJE_DATAMODEL_JETTAGGING_H_
 
-#include "RecoDecay.h"
-
 #include "PWGJE/Core/JetTaggingUtilities.h"
 #include "PWGJE/DataModel/Jet.h" // IWYU pragma: keep
 
+#include "Common/Core/RecoDecay.h"
+
 #include <Framework/ASoA.h>
 
 #include <Rtypes.h>

PWGJE/JetFinders/Duplicates/jetFinderDataCharged1.cxx

@@ -13,9 +13,8 @@
 //
 /// \author Nima Zardoshti <nima.zardoshti@cern.ch>
 
-#include "PWGJE/JetFinders/jetFinder.cxx"
-
 #include "PWGJE/DataModel/Jet.h"
+#include "PWGJE/JetFinders/jetFinder.h"
 
 #include <Framework/AnalysisTask.h>
 #include <Framework/ConfigContext.h>
@@ -24,6 +23,10 @@
 
 #include <vector>
 
+using namespace o2;
+using namespace o2::framework;
+using namespace o2::framework::expressions;
+
 using JetFinderDataCharged1 = JetFinderTask<aod::Charged1Jets, aod::Charged1JetConstituents, aod::Charged1EventWiseSubtractedJets, aod::Charged1EventWiseSubtractedJetConstituents>;
 
 WorkflowSpec defineDataProcessing(ConfigContext const& cfgc)

PWGJE/JetFinders/Duplicates/jetFinderMCDCharged1.cxx

@@ -13,9 +13,8 @@
 //
 /// \author Nima Zardoshti <nima.zardoshti@cern.ch>
 
-#include "PWGJE/JetFinders/jetFinder.cxx"
-
 #include "PWGJE/DataModel/Jet.h"
+#include "PWGJE/JetFinders/jetFinder.h"
 
 #include <Framework/AnalysisTask.h>
 #include <Framework/ConfigContext.h>
@@ -24,6 +23,10 @@
 
 #include <vector>
 
+using namespace o2;
+using namespace o2::framework;
+using namespace o2::framework::expressions;
+
 using JetFinderMCDetectorLevelCharged1 = JetFinderTask<aod::Charged1MCDetectorLevelJets, aod::Charged1MCDetectorLevelJetConstituents, aod::Charged1MCDetectorLevelEventWiseSubtractedJets, aod::Charged1MCDetectorLevelEventWiseSubtractedJetConstituents>;
 
 WorkflowSpec defineDataProcessing(ConfigContext const& cfgc)

PWGJE/JetFinders/Duplicates/jetFinderMCPCharged1.cxx

@@ -13,9 +13,8 @@
 //
 /// \author Nima Zardoshti <nima.zardoshti@cern.ch>
 
-#include "PWGJE/JetFinders/jetFinder.cxx"
-
 #include "PWGJE/DataModel/Jet.h"
+#include "PWGJE/JetFinders/jetFinder.h"
 
 #include <Framework/AnalysisTask.h>
 #include <Framework/ConfigContext.h>
@@ -24,6 +23,10 @@
 
 #include <vector>
 
+using namespace o2;
+using namespace o2::framework;
+using namespace o2::framework::expressions;
+
 using JetFinderMCParticleLevelCharged1 = JetFinderTask<aod::Charged1MCParticleLevelJets, aod::Charged1MCParticleLevelJetConstituents, aod::Charged1MCParticleLevelEventWiseSubtractedJets, aod::Charged1MCParticleLevelEventWiseSubtractedJetConstituents>;
 
 WorkflowSpec defineDataProcessing(ConfigContext const& cfgc)