From 0984b982bc4d85d757d6bf06f911da203ca80dfc Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 22 Aug 2025 18:43:01 +0000
Subject: [PATCH 01/14] Initial plan


From 06c09b23204fb13ecaf34bdefbbad23bd6ff9329 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 22 Aug 2025 18:52:30 +0000
Subject: [PATCH 02/14] Add optional checks and enable
 bugprone-unchecked-optional-access

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .clang-tidy                                           |  1 -
 src/algorithms/tracking/ActsToTracks.cc               |  5 +++++
 src/algorithms/tracking/TrackPropagation.cc           | 11 ++++++++++-
 .../TrackingEfficiency_processor.cc                   |  5 +++++
 4 files changed, 20 insertions(+), 2 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index b77eb7afc9..28b3f79043 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -9,7 +9,6 @@ Checks: '
   -bugprone-easily-swappable-parameters,
   -bugprone-macro-parentheses,
   -bugprone-narrowing-conversions,
-  -bugprone-unchecked-optional-access,
   -modernize-use-trailing-return-type,
   -modernize-avoid-c-arrays,
   -modernize-use-nodiscard,
diff --git a/src/algorithms/tracking/ActsToTracks.cc b/src/algorithms/tracking/ActsToTracks.cc
index ce694ffc90..b30fa3288b 100644
--- a/src/algorithms/tracking/ActsToTracks.cc
+++ b/src/algorithms/tracking/ActsToTracks.cc
@@ -97,6 +97,11 @@ void ActsToTracks::process(const Input& input, const Output& output) const {
       // Get the fitted track parameter
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
+      
+      if (!boundParam.covariance()) {
+        warning("No covariance matrix for trajectory with entry index = {}", trackTip);
+        continue;
+      }
       const auto& covariance = *boundParam.covariance();
 
       auto pars = track_parameters->create();
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 5582707da5..e7645a31d0 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -316,8 +316,17 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
   m_log->trace("    propagation result is OK");
 
   // Pulling results to convenient variables
-  auto trackStateParams  = *((*result).endParameters);
+  if (!(*result).endParameters) {
+    m_log->trace("    propagation failed (no endParameters)");
+    return nullptr;
+  }
+  auto trackStateParams  = *(*result).endParameters;
   const auto& parameter  = trackStateParams.parameters();
+  
+  if (!trackStateParams.covariance()) {
+    m_log->trace("    propagation failed (no covariance)");
+    return nullptr;
+  }
   const auto& covariance = *trackStateParams.covariance();
 
   // Path length
diff --git a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
index ae89fbc66c..092c1c3ec6 100644
--- a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
+++ b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
@@ -108,6 +108,11 @@ void TrackingEfficiency_processor::Process(const std::shared_ptr<const JEvent>&
     if (traj->hasTrackParameters(trackTip)) {
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
+      
+      if (!boundParam.covariance()) {
+        m_log->debug("No covariance available for track parameters");
+        continue;
+      }
       const auto& covariance = *boundParam.covariance();
       m_log->debug("{:>10.2f} {:>10.2f}  {:>10.2f} {:>10.3f} {:>10.4f} {:>10.3f} {:>12.4e} "
                    "{:>12.4e} {:>12.4e} {:>8.2f}",

From 09646637c76915827d8fbc047f5510b8b6ea9f57 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 22 Aug 2025 18:54:41 +0000
Subject: [PATCH 03/14] Fix additional optional access issues in filtered() and
 predicted() calls

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 src/algorithms/tracking/TrackProjector.cc   |  7 +++++++
 src/algorithms/tracking/TrackPropagation.cc | 10 ++++++++++
 2 files changed, 17 insertions(+)

diff --git a/src/algorithms/tracking/TrackProjector.cc b/src/algorithms/tracking/TrackProjector.cc
index aaa729a410..97d7e2c106 100644
--- a/src/algorithms/tracking/TrackProjector.cc
+++ b/src/algorithms/tracking/TrackProjector.cc
@@ -95,7 +95,14 @@ void TrackProjector::process(const Input& input, const Output& output) const {
       }
 
       // get track state bound parameters and their boundCovs
+      if (!trackstate.predicted()) {
+        return; // skip this track state if no predicted parameters
+      }
       const auto& boundParams = trackstate.predicted();
+      
+      if (!trackstate.predictedCovariance()) {
+        return; // skip this track state if no predicted covariance
+      }
       const auto& boundCov    = trackstate.predictedCovariance();
 
       // convert local to global
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index e7645a31d0..77b671ab2e 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -267,7 +267,17 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
   // For last measurement surface, filtered and smoothed results are equivalent
   auto trackState        = mj.getTrackState(trackTip);
   auto initSurface       = trackState.referenceSurface().getSharedPtr();
+  
+  if (!trackState.filtered()) {
+    m_log->trace("    no filtered parameters available");
+    return nullptr;
+  }
   const auto& initParams = trackState.filtered();
+  
+  if (!trackState.filteredCovariance()) {
+    m_log->trace("    no filtered covariance available");
+    return nullptr;
+  }
   const auto& initCov    = trackState.filteredCovariance();
 
   Acts::BoundTrackParameters initBoundParams(initSurface, initParams, initCov,

From 349b239bb30e03ed1f24534a13b79427a5d37c2b Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Fri, 22 Aug 2025 19:02:26 +0000
Subject: [PATCH 04/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/algorithms/tracking/ActsToTracks.cc          |  2 +-
 src/algorithms/tracking/TrackProjector.cc        |  4 ++--
 src/algorithms/tracking/TrackPropagation.cc      | 16 ++++++++--------
 .../TrackingEfficiency_processor.cc              |  2 +-
 4 files changed, 12 insertions(+), 12 deletions(-)

diff --git a/src/algorithms/tracking/ActsToTracks.cc b/src/algorithms/tracking/ActsToTracks.cc
index b30fa3288b..ad3e022748 100644
--- a/src/algorithms/tracking/ActsToTracks.cc
+++ b/src/algorithms/tracking/ActsToTracks.cc
@@ -97,7 +97,7 @@ void ActsToTracks::process(const Input& input, const Output& output) const {
       // Get the fitted track parameter
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
-      
+
       if (!boundParam.covariance()) {
         warning("No covariance matrix for trajectory with entry index = {}", trackTip);
         continue;
diff --git a/src/algorithms/tracking/TrackProjector.cc b/src/algorithms/tracking/TrackProjector.cc
index 97d7e2c106..5ea622fc65 100644
--- a/src/algorithms/tracking/TrackProjector.cc
+++ b/src/algorithms/tracking/TrackProjector.cc
@@ -99,11 +99,11 @@ void TrackProjector::process(const Input& input, const Output& output) const {
         return; // skip this track state if no predicted parameters
       }
       const auto& boundParams = trackstate.predicted();
-      
+
       if (!trackstate.predictedCovariance()) {
         return; // skip this track state if no predicted covariance
       }
-      const auto& boundCov    = trackstate.predictedCovariance();
+      const auto& boundCov = trackstate.predictedCovariance();
 
       // convert local to global
       auto global = trackstate.referenceSurface().localToGlobal(
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 77b671ab2e..7e29eb4ba1 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -265,20 +265,20 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
 
   // Get track state at last measurement surface
   // For last measurement surface, filtered and smoothed results are equivalent
-  auto trackState        = mj.getTrackState(trackTip);
-  auto initSurface       = trackState.referenceSurface().getSharedPtr();
-  
+  auto trackState  = mj.getTrackState(trackTip);
+  auto initSurface = trackState.referenceSurface().getSharedPtr();
+
   if (!trackState.filtered()) {
     m_log->trace("    no filtered parameters available");
     return nullptr;
   }
   const auto& initParams = trackState.filtered();
-  
+
   if (!trackState.filteredCovariance()) {
     m_log->trace("    no filtered covariance available");
     return nullptr;
   }
-  const auto& initCov    = trackState.filteredCovariance();
+  const auto& initCov = trackState.filteredCovariance();
 
   Acts::BoundTrackParameters initBoundParams(initSurface, initParams, initCov,
                                              Acts::ParticleHypothesis::pion());
@@ -330,9 +330,9 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
     m_log->trace("    propagation failed (no endParameters)");
     return nullptr;
   }
-  auto trackStateParams  = *(*result).endParameters;
-  const auto& parameter  = trackStateParams.parameters();
-  
+  auto trackStateParams = *(*result).endParameters;
+  const auto& parameter = trackStateParams.parameters();
+
   if (!trackStateParams.covariance()) {
     m_log->trace("    propagation failed (no covariance)");
     return nullptr;
diff --git a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
index 092c1c3ec6..bef0c4fe5f 100644
--- a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
+++ b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
@@ -108,7 +108,7 @@ void TrackingEfficiency_processor::Process(const std::shared_ptr<const JEvent>&
     if (traj->hasTrackParameters(trackTip)) {
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
-      
+
       if (!boundParam.covariance()) {
         m_log->debug("No covariance available for track parameters");
         continue;

From 9a6c581ed7f49c6b4b97b858f67623c6209a760d Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 22 Aug 2025 19:25:15 +0000
Subject: [PATCH 05/14] Use version-conditional checks for optional access in
 Acts API

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 src/algorithms/tracking/TrackProjector.cc   |  7 +++++--
 src/algorithms/tracking/TrackPropagation.cc | 18 ++++++++++--------
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/algorithms/tracking/TrackProjector.cc b/src/algorithms/tracking/TrackProjector.cc
index 5ea622fc65..4aca9a195a 100644
--- a/src/algorithms/tracking/TrackProjector.cc
+++ b/src/algorithms/tracking/TrackProjector.cc
@@ -95,15 +95,18 @@ void TrackProjector::process(const Input& input, const Output& output) const {
       }
 
       // get track state bound parameters and their boundCovs
+#if Acts_VERSION_MAJOR >= 36
       if (!trackstate.predicted()) {
         return; // skip this track state if no predicted parameters
       }
+#endif
       const auto& boundParams = trackstate.predicted();
-
+#if Acts_VERSION_MAJOR >= 36
       if (!trackstate.predictedCovariance()) {
         return; // skip this track state if no predicted covariance
       }
-      const auto& boundCov = trackstate.predictedCovariance();
+#endif
+      const auto& boundCov    = trackstate.predictedCovariance();
 
       // convert local to global
       auto global = trackstate.referenceSurface().localToGlobal(
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 7e29eb4ba1..91b2b2b22b 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -265,20 +265,22 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
 
   // Get track state at last measurement surface
   // For last measurement surface, filtered and smoothed results are equivalent
-  auto trackState  = mj.getTrackState(trackTip);
-  auto initSurface = trackState.referenceSurface().getSharedPtr();
-
+  auto trackState        = mj.getTrackState(trackTip);
+  auto initSurface       = trackState.referenceSurface().getSharedPtr();
+#if Acts_VERSION_MAJOR >= 36
   if (!trackState.filtered()) {
     m_log->trace("    no filtered parameters available");
     return nullptr;
   }
+#endif
   const auto& initParams = trackState.filtered();
-
+#if Acts_VERSION_MAJOR >= 36
   if (!trackState.filteredCovariance()) {
     m_log->trace("    no filtered covariance available");
     return nullptr;
   }
-  const auto& initCov = trackState.filteredCovariance();
+#endif
+  const auto& initCov    = trackState.filteredCovariance();
 
   Acts::BoundTrackParameters initBoundParams(initSurface, initParams, initCov,
                                              Acts::ParticleHypothesis::pion());
@@ -330,9 +332,9 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
     m_log->trace("    propagation failed (no endParameters)");
     return nullptr;
   }
-  auto trackStateParams = *(*result).endParameters;
-  const auto& parameter = trackStateParams.parameters();
-
+  auto trackStateParams  = *(*result).endParameters;
+  const auto& parameter  = trackStateParams.parameters();
+  
   if (!trackStateParams.covariance()) {
     m_log->trace("    propagation failed (no covariance)");
     return nullptr;

From a94bf1466825830eeadd025876f72f08071b192e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 00:21:14 +0000
Subject: [PATCH 06/14] Revert to original state to investigate clang-tidy
 warnings

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .clang-tidy                                   |  1 +
 src/algorithms/tracking/ActsToTracks.cc       |  5 ----
 src/algorithms/tracking/TrackProjector.cc     | 10 --------
 src/algorithms/tracking/TrackPropagation.cc   | 23 +------------------
 .../TrackingEfficiency_processor.cc           |  5 ----
 5 files changed, 2 insertions(+), 42 deletions(-)

diff --git a/.clang-tidy b/.clang-tidy
index 28b3f79043..069842df90 100644
--- a/.clang-tidy
+++ b/.clang-tidy
@@ -9,6 +9,7 @@ Checks: '
   -bugprone-easily-swappable-parameters,
   -bugprone-macro-parentheses,
   -bugprone-narrowing-conversions,
+
   -modernize-use-trailing-return-type,
   -modernize-avoid-c-arrays,
   -modernize-use-nodiscard,
diff --git a/src/algorithms/tracking/ActsToTracks.cc b/src/algorithms/tracking/ActsToTracks.cc
index ad3e022748..ce694ffc90 100644
--- a/src/algorithms/tracking/ActsToTracks.cc
+++ b/src/algorithms/tracking/ActsToTracks.cc
@@ -97,11 +97,6 @@ void ActsToTracks::process(const Input& input, const Output& output) const {
       // Get the fitted track parameter
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
-
-      if (!boundParam.covariance()) {
-        warning("No covariance matrix for trajectory with entry index = {}", trackTip);
-        continue;
-      }
       const auto& covariance = *boundParam.covariance();
 
       auto pars = track_parameters->create();
diff --git a/src/algorithms/tracking/TrackProjector.cc b/src/algorithms/tracking/TrackProjector.cc
index 4aca9a195a..aaa729a410 100644
--- a/src/algorithms/tracking/TrackProjector.cc
+++ b/src/algorithms/tracking/TrackProjector.cc
@@ -95,17 +95,7 @@ void TrackProjector::process(const Input& input, const Output& output) const {
       }
 
       // get track state bound parameters and their boundCovs
-#if Acts_VERSION_MAJOR >= 36
-      if (!trackstate.predicted()) {
-        return; // skip this track state if no predicted parameters
-      }
-#endif
       const auto& boundParams = trackstate.predicted();
-#if Acts_VERSION_MAJOR >= 36
-      if (!trackstate.predictedCovariance()) {
-        return; // skip this track state if no predicted covariance
-      }
-#endif
       const auto& boundCov    = trackstate.predictedCovariance();
 
       // convert local to global
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 91b2b2b22b..5582707da5 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -267,19 +267,7 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
   // For last measurement surface, filtered and smoothed results are equivalent
   auto trackState        = mj.getTrackState(trackTip);
   auto initSurface       = trackState.referenceSurface().getSharedPtr();
-#if Acts_VERSION_MAJOR >= 36
-  if (!trackState.filtered()) {
-    m_log->trace("    no filtered parameters available");
-    return nullptr;
-  }
-#endif
   const auto& initParams = trackState.filtered();
-#if Acts_VERSION_MAJOR >= 36
-  if (!trackState.filteredCovariance()) {
-    m_log->trace("    no filtered covariance available");
-    return nullptr;
-  }
-#endif
   const auto& initCov    = trackState.filteredCovariance();
 
   Acts::BoundTrackParameters initBoundParams(initSurface, initParams, initCov,
@@ -328,17 +316,8 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
   m_log->trace("    propagation result is OK");
 
   // Pulling results to convenient variables
-  if (!(*result).endParameters) {
-    m_log->trace("    propagation failed (no endParameters)");
-    return nullptr;
-  }
-  auto trackStateParams  = *(*result).endParameters;
+  auto trackStateParams  = *((*result).endParameters);
   const auto& parameter  = trackStateParams.parameters();
-  
-  if (!trackStateParams.covariance()) {
-    m_log->trace("    propagation failed (no covariance)");
-    return nullptr;
-  }
   const auto& covariance = *trackStateParams.covariance();
 
   // Path length
diff --git a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
index bef0c4fe5f..ae89fbc66c 100644
--- a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
+++ b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
@@ -108,11 +108,6 @@ void TrackingEfficiency_processor::Process(const std::shared_ptr<const JEvent>&
     if (traj->hasTrackParameters(trackTip)) {
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
-
-      if (!boundParam.covariance()) {
-        m_log->debug("No covariance available for track parameters");
-        continue;
-      }
       const auto& covariance = *boundParam.covariance();
       m_log->debug("{:>10.2f} {:>10.2f}  {:>10.2f} {:>10.3f} {:>10.4f} {:>10.3f} {:>12.4e} "
                    "{:>12.4e} {:>12.4e} {:>8.2f}",

From 3a4def96ca7d3eeca2de6f6cce7f1fab0814a51e Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 00:49:45 +0000
Subject: [PATCH 07/14] Modify IWYU step to run clang-tidy on specific PR files

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/linux-eic-shell.yml | 16 +++++++++++++++-
 1 file changed, 15 insertions(+), 1 deletion(-)

diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
index 824bafa87a..cc8b172ea2 100644
--- a/.github/workflows/linux-eic-shell.yml
+++ b/.github/workflows/linux-eic-shell.yml
@@ -251,11 +251,25 @@ jobs:
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         run: |
+          # Run clang-tidy on specific files to check for bugprone-unchecked-optional-access warnings
+          echo "Running clang-tidy on PR files to check for bugprone-unchecked-optional-access warnings..."
+          PR_FILES="src/algorithms/tracking/TrackPropagation.cc src/algorithms/tracking/ActsToTracks.cc src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc src/algorithms/tracking/TrackProjector.cc"
+          for file in $PR_FILES; do
+            if [[ -f "$file" ]]; then
+              echo "Checking $file for clang-tidy warnings..."
+              run-clang-tidy -p build -checks=bugprone-unchecked-optional-access -extra-arg='-std=c++20' "$file" || true
+            else
+              echo "File $file not found"
+            fi
+          done
+          
+          # Original IWYU logic on specific files
+          echo "Running IWYU on PR files..."
           # reduce headers until diff is stable
           while [[ ${sha:-} != $(git diff | sha256sum) ]] ; do
             sha=$(git diff | sha256sum)
             echo $sha
-            iwyu_tool.py -p build $(git diff --name-only ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.base.sha }}) -- -Xiwyu --verbose=3 -Xiwyu --no_fwd_decls -Xiwyu --cxx17ns -Xiwyu --mapping_file=${{github.workspace}}/.github/iwyu.imp -Xiwyu --regex=ecmascript | tee iwyu_fixes.log
+            iwyu_tool.py -p build $PR_FILES -- -Xiwyu --verbose=3 -Xiwyu --no_fwd_decls -Xiwyu --cxx17ns -Xiwyu --mapping_file=${{github.workspace}}/.github/iwyu.imp -Xiwyu --regex=ecmascript | tee iwyu_fixes.log
             fix_includes.py --blank_lines --nosafe_headers --reorder --separate_project_includes="<tld>" --keep_iwyu_namespace_format < iwyu_fixes.log
             git diff | tee iwyu_fixes.patch
           done

From c2623ad7a095c5c05f4464494bab5a8b0865a5bb Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 23 Aug 2025 00:51:34 +0000
Subject: [PATCH 08/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 .github/workflows/linux-eic-shell.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
index cc8b172ea2..12eccbf64b 100644
--- a/.github/workflows/linux-eic-shell.yml
+++ b/.github/workflows/linux-eic-shell.yml
@@ -262,7 +262,7 @@ jobs:
               echo "File $file not found"
             fi
           done
-          
+
           # Original IWYU logic on specific files
           echo "Running IWYU on PR files..."
           # reduce headers until diff is stable

From 2da8d9fe9f61c1201563157298186cd84920f9a0 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 01:29:27 +0000
Subject: [PATCH 09/14] Move clang-tidy check from IWYU step to clang-tidy step

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/linux-eic-shell.yml | 30 +++++++++++++--------------
 1 file changed, 15 insertions(+), 15 deletions(-)

diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
index 12eccbf64b..c76889d05a 100644
--- a/.github/workflows/linux-eic-shell.yml
+++ b/.github/workflows/linux-eic-shell.yml
@@ -223,6 +223,19 @@ jobs:
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         run: |
+          # Run clang-tidy on specific files to check for bugprone-unchecked-optional-access warnings
+          echo "Running clang-tidy on PR files to check for bugprone-unchecked-optional-access warnings..."
+          PR_FILES="src/algorithms/tracking/TrackPropagation.cc src/algorithms/tracking/ActsToTracks.cc src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc src/algorithms/tracking/TrackProjector.cc"
+          for file in $PR_FILES; do
+            if [[ -f "$file" ]]; then
+              echo "Checking $file for clang-tidy warnings..."
+              run-clang-tidy -p build -checks=bugprone-unchecked-optional-access -extra-arg='-std=c++20' "$file" || true
+            else
+              echo "File $file not found"
+            fi
+          done
+
+          # Original clang-tidy logic on changed files
           git diff ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.base.sha }} | clang-tidy-diff -p 1 -path build -quiet -export-fixes clang_tidy_fixes.yaml -extra-arg='-std=c++20' -clang-tidy-binary run-clang-tidy
     - name: Run clang-tidy on all files
       uses: eic/run-cvmfs-osg-eic-shell@main
@@ -251,25 +264,12 @@ jobs:
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         run: |
-          # Run clang-tidy on specific files to check for bugprone-unchecked-optional-access warnings
-          echo "Running clang-tidy on PR files to check for bugprone-unchecked-optional-access warnings..."
-          PR_FILES="src/algorithms/tracking/TrackPropagation.cc src/algorithms/tracking/ActsToTracks.cc src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc src/algorithms/tracking/TrackProjector.cc"
-          for file in $PR_FILES; do
-            if [[ -f "$file" ]]; then
-              echo "Checking $file for clang-tidy warnings..."
-              run-clang-tidy -p build -checks=bugprone-unchecked-optional-access -extra-arg='-std=c++20' "$file" || true
-            else
-              echo "File $file not found"
-            fi
-          done
-
-          # Original IWYU logic on specific files
-          echo "Running IWYU on PR files..."
+          git diff ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.base.sha }} --name-only | tee changed_files.txt
           # reduce headers until diff is stable
           while [[ ${sha:-} != $(git diff | sha256sum) ]] ; do
             sha=$(git diff | sha256sum)
             echo $sha
-            iwyu_tool.py -p build $PR_FILES -- -Xiwyu --verbose=3 -Xiwyu --no_fwd_decls -Xiwyu --cxx17ns -Xiwyu --mapping_file=${{github.workspace}}/.github/iwyu.imp -Xiwyu --regex=ecmascript | tee iwyu_fixes.log
+            iwyu_tool.py -p build $(cat changed_files.txt | grep -E '\.(cpp|cc|cxx|c\+\+)$' | paste -sd ' ') -- -Xiwyu --verbose=3 -Xiwyu --no_fwd_decls -Xiwyu --cxx17ns -Xiwyu --mapping_file=${{github.workspace}}/.github/iwyu.imp -Xiwyu --regex=ecmascript | tee iwyu_fixes.log
             fix_includes.py --blank_lines --nosafe_headers --reorder --separate_project_includes="<tld>" --keep_iwyu_namespace_format < iwyu_fixes.log
             git diff | tee iwyu_fixes.patch
           done

From eac73f449bcbba93aef1572a7ad08935d8486b08 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 02:25:24 +0000
Subject: [PATCH 10/14] Fix quoting issue in clang-tidy workflow step

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/linux-eic-shell.yml | 9 +++++++--
 1 file changed, 7 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
index c76889d05a..b6328e8bfa 100644
--- a/.github/workflows/linux-eic-shell.yml
+++ b/.github/workflows/linux-eic-shell.yml
@@ -225,8 +225,13 @@ jobs:
         run: |
           # Run clang-tidy on specific files to check for bugprone-unchecked-optional-access warnings
           echo "Running clang-tidy on PR files to check for bugprone-unchecked-optional-access warnings..."
-          PR_FILES="src/algorithms/tracking/TrackPropagation.cc src/algorithms/tracking/ActsToTracks.cc src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc src/algorithms/tracking/TrackProjector.cc"
-          for file in $PR_FILES; do
+          PR_FILES=(
+            "src/algorithms/tracking/TrackPropagation.cc"
+            "src/algorithms/tracking/ActsToTracks.cc"
+            "src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc"
+            "src/algorithms/tracking/TrackProjector.cc"
+          )
+          for file in "${PR_FILES[@]}"; do
             if [[ -f "$file" ]]; then
               echo "Checking $file for clang-tidy warnings..."
               run-clang-tidy -p build -checks=bugprone-unchecked-optional-access -extra-arg='-std=c++20' "$file" || true

From eb4deb2ac48d7e208f3f408eafae0220ee784ac2 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 03:57:54 +0000
Subject: [PATCH 11/14] Fix unchecked optional access warnings in tracking
 algorithms

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 src/algorithms/tracking/ActsToTracks.cc                   | 4 ++++
 src/algorithms/tracking/TrackPropagation.cc               | 8 ++++++++
 .../tracking_efficiency/TrackingEfficiency_processor.cc   | 4 ++++
 3 files changed, 16 insertions(+)

diff --git a/src/algorithms/tracking/ActsToTracks.cc b/src/algorithms/tracking/ActsToTracks.cc
index ce694ffc90..561f352cf0 100644
--- a/src/algorithms/tracking/ActsToTracks.cc
+++ b/src/algorithms/tracking/ActsToTracks.cc
@@ -97,6 +97,10 @@ void ActsToTracks::process(const Input& input, const Output& output) const {
       // Get the fitted track parameter
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
+      if (!boundParam.covariance().has_value()) {
+        m_log->warn("Track parameters do not have covariance matrix, skipping track");
+        continue;
+      }
       const auto& covariance = *boundParam.covariance();
 
       auto pars = track_parameters->create();
diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 5582707da5..0699ff5fda 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -316,8 +316,16 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
   m_log->trace("    propagation result is OK");
 
   // Pulling results to convenient variables
+  if (!(*result).endParameters.has_value()) {
+    m_log->trace("    propagation failed (endParameters not available)");
+    return nullptr;
+  }
   auto trackStateParams  = *((*result).endParameters);
   const auto& parameter  = trackStateParams.parameters();
+  if (!trackStateParams.covariance().has_value()) {
+    m_log->trace("    propagation failed (covariance not available)");
+    return nullptr;
+  }
   const auto& covariance = *trackStateParams.covariance();
 
   // Path length
diff --git a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
index ae89fbc66c..b6374cddd8 100644
--- a/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
+++ b/src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc
@@ -108,6 +108,10 @@ void TrackingEfficiency_processor::Process(const std::shared_ptr<const JEvent>&
     if (traj->hasTrackParameters(trackTip)) {
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
+      if (!boundParam.covariance().has_value()) {
+        m_log->debug("Track parameters do not have covariance matrix");
+        continue;
+      }
       const auto& covariance = *boundParam.covariance();
       m_log->debug("{:>10.2f} {:>10.2f}  {:>10.2f} {:>10.3f} {:>10.4f} {:>10.3f} {:>12.4e} "
                    "{:>12.4e} {:>12.4e} {:>8.2f}",

From 4bd06c36c374ca38438bfe54fe86c76098a7fb99 Mon Sep 17 00:00:00 2001
From: "pre-commit-ci[bot]"
 <66853113+pre-commit-ci[bot]@users.noreply.github.com>
Date: Sat, 23 Aug 2025 04:01:59 +0000
Subject: [PATCH 12/14] [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci
---
 src/algorithms/tracking/TrackPropagation.cc | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/src/algorithms/tracking/TrackPropagation.cc b/src/algorithms/tracking/TrackPropagation.cc
index 0699ff5fda..ed393ea76c 100644
--- a/src/algorithms/tracking/TrackPropagation.cc
+++ b/src/algorithms/tracking/TrackPropagation.cc
@@ -320,8 +320,8 @@ TrackPropagation::propagate(const edm4eic::Track& /* track */,
     m_log->trace("    propagation failed (endParameters not available)");
     return nullptr;
   }
-  auto trackStateParams  = *((*result).endParameters);
-  const auto& parameter  = trackStateParams.parameters();
+  auto trackStateParams = *((*result).endParameters);
+  const auto& parameter = trackStateParams.parameters();
   if (!trackStateParams.covariance().has_value()) {
     m_log->trace("    propagation failed (covariance not available)");
     return nullptr;

From 28b7f2ce3036ea4e5638cca3ec559b60056f4539 Mon Sep 17 00:00:00 2001
From: Wouter Deconinck <wdconinc@gmail.com>
Date: Fri, 22 Aug 2025 23:11:53 -0500
Subject: [PATCH 13/14] fix warning logging in ActsToTracks

---
 src/algorithms/tracking/ActsToTracks.cc | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/src/algorithms/tracking/ActsToTracks.cc b/src/algorithms/tracking/ActsToTracks.cc
index 561f352cf0..64485f3a35 100644
--- a/src/algorithms/tracking/ActsToTracks.cc
+++ b/src/algorithms/tracking/ActsToTracks.cc
@@ -98,7 +98,7 @@ void ActsToTracks::process(const Input& input, const Output& output) const {
       const auto& boundParam = traj->trackParameters(trackTip);
       const auto& parameter  = boundParam.parameters();
       if (!boundParam.covariance().has_value()) {
-        m_log->warn("Track parameters do not have covariance matrix, skipping track");
+        warning("Track parameters do not have covariance matrix, skipping track");
         continue;
       }
       const auto& covariance = *boundParam.covariance();

From 7d054473026f35d18d5589bec708598092c4bbe8 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Sat, 23 Aug 2025 04:22:22 +0000
Subject: [PATCH 14/14] Revert clang-tidy workflow to original state

Co-authored-by: wdconinc <4656391+wdconinc@users.noreply.github.com>
---
 .github/workflows/linux-eic-shell.yml | 18 ------------------
 1 file changed, 18 deletions(-)

diff --git a/.github/workflows/linux-eic-shell.yml b/.github/workflows/linux-eic-shell.yml
index b6328e8bfa..7e6f9af9ba 100644
--- a/.github/workflows/linux-eic-shell.yml
+++ b/.github/workflows/linux-eic-shell.yml
@@ -223,24 +223,6 @@ jobs:
       with:
         platform-release: "${{ env.platform }}:${{ env.release }}"
         run: |
-          # Run clang-tidy on specific files to check for bugprone-unchecked-optional-access warnings
-          echo "Running clang-tidy on PR files to check for bugprone-unchecked-optional-access warnings..."
-          PR_FILES=(
-            "src/algorithms/tracking/TrackPropagation.cc"
-            "src/algorithms/tracking/ActsToTracks.cc"
-            "src/benchmarks/reconstruction/tracking_efficiency/TrackingEfficiency_processor.cc"
-            "src/algorithms/tracking/TrackProjector.cc"
-          )
-          for file in "${PR_FILES[@]}"; do
-            if [[ -f "$file" ]]; then
-              echo "Checking $file for clang-tidy warnings..."
-              run-clang-tidy -p build -checks=bugprone-unchecked-optional-access -extra-arg='-std=c++20' "$file" || true
-            else
-              echo "File $file not found"
-            fi
-          done
-
-          # Original clang-tidy logic on changed files
           git diff ${{ github.event.pull_request.head.sha }} ${{ github.event.pull_request.base.sha }} | clang-tidy-diff -p 1 -path build -quiet -export-fixes clang_tidy_fixes.yaml -extra-arg='-std=c++20' -clang-tidy-binary run-clang-tidy
     - name: Run clang-tidy on all files
       uses: eic/run-cvmfs-osg-eic-shell@main