Update checkout github action version

Also fixes clang-formatting

Author: anthoak13

.github/workflows/CI-tests.yml

@@ -18,7 +18,7 @@ jobs:
     runs-on: ubuntu-latest
     container: anthoak13/attpcroot-deps
     steps:
-    - uses: actions/checkout@v4
+    - uses: actions/checkout@v6
 
     - name: Configure CMake
       # Configure CMake in a 'build' subdirectory. `CMAKE_BUILD_TYPE` is only required if you are using a single-configuration generator such as make.

.github/workflows/main.yml

@@ -8,7 +8,7 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v2
+    - uses: actions/checkout@v6
     - name: Run clang-format
       uses: DoozyX/clang-format-lint-action@v0.17
       # These are optional (defaults displayed)

AtTools/AtELossBetheBlochTest.cxx

@@ -1,4 +1,5 @@
 #include "AtELossBetheBloch.h"
+
 #include "AtELossCATIMA.h"
 
 #include <catima/catima.h>
@@ -286,17 +287,16 @@ TEST_F(AtELossBetheBlochVsCATIMAFixture, CATIMAComparison_EnergyStraggling)
       double eIni, eFin;
    };
    const Case cases[] = {
-      {1.0, 0.75 * mass},     // narrow: ~25% energy loss
-      {5.0, 3.58164 * mass},  // narrow: ~28% energy loss
-      {5.0, 1.0},             // wide: 80% energy loss
-      {10.0, 1.0},            // wide: 90% energy loss, exercises Bragg-peak region
+      {1.0, 0.75 * mass},    // narrow: ~25% energy loss
+      {5.0, 3.58164 * mass}, // narrow: ~28% energy loss
+      {5.0, 1.0},            // wide: 80% energy loss
+      {10.0, 1.0},           // wide: 90% energy loss, exercises Bragg-peak region
    };
    for (auto &c : cases) {
       double bbSigma = bb.GetElossStraggling(c.eIni, c.eFin);
       double catimaSigma = catima.GetElossStraggling(c.eIni, c.eFin);
       ASSERT_GT(bbSigma, 0.0) << "BB straggling zero for E0=" << c.eIni;
       ASSERT_GT(catimaSigma, 0.0) << "CATIMA straggling zero for E0=" << c.eIni;
-      EXPECT_NEAR(bbSigma, catimaSigma, 0.10 * catimaSigma)
-         << "Energy straggling mismatch for E0=" << c.eIni << " MeV";
+      EXPECT_NEAR(bbSigma, catimaSigma, 0.10 * catimaSigma) << "Energy straggling mismatch for E0=" << c.eIni << " MeV";
    }
 }

AtTools/AtELossCATIMA.cxx

@@ -44,7 +44,8 @@ double AtELossCATIMA::GetRange(double energyIni, double energyFin) const
    double remainingEnergy{energyIni};
    double range{0};
    while (remainingEnergy > energyFin) {
-      catima::Result result = catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
+      catima::Result result =
+         catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
       double dEdx = result.dEdxi * fDensity;
       double DE = dEdx * fRangeStepSize / 10.;
 
@@ -65,7 +66,8 @@ double AtELossCATIMA::GetEnergy(double energyIni, double distance) const
    double remainingEnergy{energyIni};
    double range{0};
    while (range < distance) {
-      catima::Result result = catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
+      catima::Result result =
+         catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
       double dEdx = result.dEdxi * fDensity;
       double DE{};
 
@@ -142,8 +144,9 @@ AtELossCATIMA::GetBraggCurve(double energy, double rangeStepSize, double totalFr
    double range{};
    while (remainingEnergy / energy > totalFractionELoss) {
 
-      catima::Result result = catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
-      double dEdx = result.dEdxi * fDensity; // MeV/cm
+      catima::Result result =
+         catima::calculate(*fProjectile, *fMaterial, remainingEnergy / fProjectileMassAmu, fConfig);
+      double dEdx = result.dEdxi * fDensity;                    // MeV/cm
       braggCurve.push_back(std::make_pair(dEdx / 10.0, range)); // store in MeV/mm
 
       double DE = dEdx * rangeStepSize / 10.;

scripts/formatAll.sh

@@ -2,16 +2,25 @@
 
 #Break if something errors
 set -e
-echo "Indenting all source (.cxx) and header files (.h)"
+echo "Indenting all source (.cxx, .C) and header files (.h)"
 
-#Make sure $VMCWORKDIR is set. 
+#Make sure $VMCWORKDIR is set.
 if [ -z "$VMCWORKDIR" ]
 then
     echo "VMCWORKDIR is unset. Please run config.sh on build directory first. Aborting..."
     return
 fi
 
-find -L $VMCWORKDIR -type f | grep -w h$ | xargs -I fname clang-format -i --verbose fname
-find -L $VMCWORKDIR -type f | grep -w cxx$ | xargs -I fname clang-format -i --verbose fname
+# Directories excluded from formatting (matches .github/workflows/main.yml)
+EXCLUDE_DIRS="macro scripts compiled resources include geometry build .venv lib bin"
+
+# Build a prune expression for find
+PRUNE_EXPR=""
+for dir in $EXCLUDE_DIRS; do
+    PRUNE_EXPR="$PRUNE_EXPR -path $VMCWORKDIR/$dir -prune -o"
+done
+
+find -L $VMCWORKDIR $PRUNE_EXPR -type f \( -name "*.h" -o -name "*.cxx" -o -name "*.C" \) -print \
+    | xargs -I fname clang-format-17 -i --verbose fname
 
 echo "Success! Indented all source and header files"