Merge branch 'master' of http://github.com/sphenix-collaboration/coresoftware

Author: Michael Peters

.github/workflows/fix-eof-newline-coderabbit-docstrings.yml

@@ -0,0 +1,106 @@
+name: Fix missing final newline (CodeRabbit docstring PRs)
+
+on:
+  pull_request_target:
+    types: [opened, synchronize, reopened]
+
+permissions:
+  contents: write
+  pull-requests: read
+
+jobs:
+  fix_eof_newline:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Guard - only CodeRabbit docstring PRs from same repo
+        id: guard
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          AUTHOR='${{ github.event.pull_request.user.login }}'
+          BASE_REPO='${{ github.event.pull_request.base.repo.full_name }}'
+          HEAD_REPO='${{ github.event.pull_request.head.repo.full_name }}'
+          TITLE='${{ github.event.pull_request.title }}'
+
+          if [[ "$AUTHOR" != "coderabbitai[bot]" ]]; then
+            echo "run=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # Safety: only push to branches within the same repo
+          if [[ "$BASE_REPO" != "$HEAD_REPO" ]]; then
+            echo "run=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          # only run for docstring PRs
+          if ! echo "$TITLE" | grep -qi "docstring"; then
+            echo "run=false" >> "$GITHUB_OUTPUT"
+            exit 0
+          fi
+
+          echo "run=true" >> "$GITHUB_OUTPUT"
+
+      - name: Checkout PR head
+        if: steps.guard.outputs.run == 'true'
+        uses: actions/checkout@v4
+        with:
+          ref: ${{ github.event.pull_request.head.ref }}
+          repository: ${{ github.event.pull_request.head.repo.full_name }}
+          fetch-depth: 0
+
+      - name: Append final newline when missing (changed files only)
+        if: steps.guard.outputs.run == 'true'
+        shell: bash
+        run: |
+          set -euo pipefail
+
+          BASE_SHA="${{ github.event.pull_request.base.sha }}"
+          HEAD_SHA="${{ github.event.pull_request.head.sha }}"
+
+          files=$(git diff --name-only "$BASE_SHA" "$HEAD_SHA" -- \
+            '*.C' '*.c' '*.cc' '*.cpp' '*.cxx' '*.h' '*.hh' '*.hpp' '*.hxx' || true)
+
+          if [[ -z "${files}" ]]; then
+            echo "No relevant files changed."
+            exit 0
+          fi
+
+          changed=0
+          for f in $files; do
+            [[ -f "$f" ]] || continue
+
+            # For non-empty files: ensure last byte is '\n'
+            if [[ -s "$f" ]]; then
+              last_byte="$(tail -c 1 "$f" || true)"
+              if [[ "$last_byte" != $'\n' ]]; then
+                printf '\n' >> "$f"
+                echo "Fixed EOF newline: $f"
+                changed=1
+              fi
+            fi
+          done
+
+          if [[ "$changed" -eq 0 ]]; then
+            echo "All files already end with a newline."
+            exit 0
+          fi
+
+          git status --porcelain
+          git add -A
+
+          git config user.name "github-actions[bot]"
+          git config user.email "github-actions[bot]@users.noreply.github.com"
+
+          git commit -m "Fix missing final newline in docstring PR"
+
+      - name: Push fix commit back to PR branch
+        if: steps.guard.outputs.run == 'true'
+        shell: bash
+        run: |
+          set -euo pipefail
+          # If no commit was created, pushing will fail; so only push if HEAD is ahead.
+          if git rev-parse HEAD~1 >/dev/null 2>&1; then
+            git push origin "HEAD:${{ github.event.pull_request.head.ref }}"
+          fi

calibrations/tpc/dEdx/Makefile.am

@@ -2,7 +2,7 @@ AUTOMAKE_OPTIONS = foreign
 
 AM_CPPFLAGS = \
   -I$(includedir) \
-  -I$(OFFLINE_MAIN)/include \
+  -isystem$(OFFLINE_MAIN)/include \
   -isystem$(ROOTSYS)/include
 
 AM_LDFLAGS = \
@@ -14,7 +14,7 @@ pkginclude_HEADERS = \
   dEdxFitter.h \
   GlobaldEdxFitter.h \
   bethe_bloch.h
- 
+
 lib_LTLIBRARIES = \
   libdedxfitter.la
 
@@ -26,8 +26,8 @@ libdedxfitter_la_LIBADD = \
   -lphool \
   -ltrack_io \
   -lg4detectors \
+  -ltrackbase_historic \
   -ltrackbase_historic_io \
-  -ltrack_reco \
   -lglobalvertex \
   -lSubsysReco
 

calibrations/tpc/dEdx/configure.ac

@@ -6,10 +6,10 @@ AC_PROG_CXX(CC g++)
 
 LT_INIT([disable-static])
 
-dnl   no point in suppressing warnings people should 
-dnl   at least see them, so here we go for g++: -Wall
+dnl   enable more warnings and make them fatal
+dnl this package needs openmp which requires -fopenmp for clang
 if test $ac_cv_prog_gxx = yes; then
-   CXXFLAGS="$CXXFLAGS -Wall -Werror"
+   CXXFLAGS="$CXXFLAGS -Wall -Wshadow -Wextra -Werror"
 fi
 
 AC_CONFIG_FILES([Makefile])

generators/Herwig/HepMCTrigger/HepMCJetTrigger.cc

@@ -31,14 +31,14 @@ HepMCJetTrigger::HepMCJetTrigger(float trigger_thresh, int n_incom, bool up_lim,
 int HepMCJetTrigger::process_event(PHCompositeNode* topNode)
 {
   // std::cout << "HepMCJetTrigger::process_event(PHCompositeNode *topNode) Processing Event" << std::endl;
-  n_evts++;
   if (this->set_event_limit == true)
   {  // needed to keep all HepMC output at the same number of events
     if (n_good >= this->goal_event_number)
     {
       return Fun4AllReturnCodes::ABORTEVENT;
     }
   }
+  n_evts++;
   PHHepMCGenEventMap* phg = findNode::getClass<PHHepMCGenEventMap>(topNode, "PHHepMCGenEventMap");
   if (!phg)
   {

generators/Herwig/HepMCTrigger/HepMCJetTrigger.h

@@ -47,16 +47,18 @@ class HepMCJetTrigger : public SubsysReco
   /// Called at the end of all processing.
 
   /// Reset
+  int getNevts(){return this->n_evts;}
+  int getNgood(){return this->n_good;}
 
  private:
   bool isGoodEvent(HepMC::GenEvent* e1);
   std::vector<fastjet::PseudoJet> findAllJets(HepMC::GenEvent* e1);
   int jetsAboveThreshold(const std::vector<fastjet::PseudoJet>& jets) const;
   float threshold{0.};
   int goal_event_number{1000};
+  bool set_event_limit{false};
   int n_evts{0};
   int n_good{0};
-  bool set_event_limit{false};
 };
 
 #endif  // HEPMCJETTRIGGER_H

generators/Herwig/HepMCTrigger/HepMCParticleTrigger.cc

@@ -68,14 +68,14 @@ HepMCParticleTrigger::HepMCParticleTrigger(float trigger_thresh, int n_incom, bo
 int HepMCParticleTrigger::process_event(PHCompositeNode* topNode)
 {
   // std::cout << "HepMCParticleTrigger::process_event(PHCompositeNode *topNode) Processing Event" << std::endl;
-  n_evts++;
   if (this->set_event_limit == true)
   {  // needed to keep all HepMC output at the same number of events
     if (n_good >= this->goal_event_number)
     {
       return Fun4AllReturnCodes::ABORTEVENT;
     }
   }
+  n_evts++;
   bool good_event{false};
   PHHepMCGenEventMap* phg = findNode::getClass<PHHepMCGenEventMap>(topNode, "PHHepMCGenEventMap");
   if (!phg)

generators/Herwig/HepMCTrigger/HepMCParticleTrigger.h

@@ -66,6 +66,8 @@ class HepMCParticleTrigger : public SubsysReco
   void SetPzHighLow(double, double);
 
   void SetStableParticleOnly(bool b) { m_doStableParticleOnly = b; }
+  int getNevts(){return this->n_evts;}
+  int getNgood(){return this->n_good;}
 
  private:
   bool isGoodEvent(HepMC::GenEvent* e1);
@@ -76,9 +78,9 @@ class HepMCParticleTrigger : public SubsysReco
   bool m_doStableParticleOnly{true};
   float threshold{0.};
   int goal_event_number{1000};
+  bool set_event_limit{false};
   int n_evts{0};
   int n_good{0};
-  bool set_event_limit{false};
 
   float _theEtaHigh{1.1};
   float _theEtaLow{-1.1};

generators/PHPythia8/PHPythia8.cc

@@ -123,17 +123,13 @@ int PHPythia8::Init(PHCompositeNode *topNode)
   std::cout << "PHPythia8 random seed: " << seed << std::endl;
 
 
-  // this is empirical - something in the pythia8::init() method interferes
-  // with our macros (it sets the tpc drift verlocity back to 0)
-  // not the feintest idea right now what this could be
-  // but saving the old cout state and restoring it aftwerwards
-  // gets our tpc drift velocity back
+// pythia again messes with the cout formatting
   std::ios old_state(nullptr);
-  old_state.copyfmt(std::cout);
+  old_state.copyfmt(std::cout); // save current state
 
   m_Pythia8->init();
 
-  std::cout.copyfmt(old_state);
+  std::cout.copyfmt(old_state); // restore state to saved state
 
   return Fun4AllReturnCodes::EVENT_OK;
 }
@@ -211,6 +207,9 @@ int PHPythia8::process_event(PHCompositeNode * /*topNode*/)
   bool passedGen = false;
   bool passedTrigger = false;
   //  int genCounter = 0;
+// pythia again messes with the cout formatting in its event loop
+  std::ios old_state(nullptr);
+  old_state.copyfmt(std::cout); // save current state
 
   while (!passedTrigger)
   {
@@ -286,6 +285,7 @@ int PHPythia8::process_event(PHCompositeNode * /*topNode*/)
   if (!success)
   {
     std::cout << "PHPythia8::process_event - Failed to add event to HepMC record!" << std::endl;
+    std::cout.copyfmt(old_state); // restore state to saved state
     return Fun4AllReturnCodes::ABORTRUN;
   }
 
@@ -306,6 +306,8 @@ int PHPythia8::process_event(PHCompositeNode * /*topNode*/)
 
   ++m_EventCount;
 
+  std::cout.copyfmt(old_state); // restore state to saved state
+
   // save statistics
   if (m_IntegralNode)
   {