Clang compliance

.github/workflows/build.yml

@@ -34,8 +34,7 @@ jobs:
         if: runner.os == 'Linux'
         run: |
           sudo apt-get update
-          sudo apt-get install -y build-essential libeigen3-dev libfftw3-dev libhdf5-dev libopenmpi-dev libomp-dev
-          sudo pip install numpy
+          sudo apt-get install -y build-essential libeigen3-dev libfftw3-dev libhdf5-dev libopenmpi-dev libomp-dev python3-numpy
 
 
       - name: Setup submodule and build

CMakeLists.txt

@@ -62,7 +62,7 @@ set(CMAKE_FIND_PACKAGE_SORT_DIRECTION DEC)
 
 find_package(MPI REQUIRED COMPONENTS C CXX)
 find_package(OpenMP)
-find_package(FFTW)
+find_package(FFTW REQUIRED)
 find_package(HDF5 COMPONENTS C CXX HL REQUIRED)
 find_package(TIRPC)	       # Check for alternative Sun rpc support
 find_package(Eigen3 REQUIRED)

expui/BiorthBasis.cc

@@ -368,7 +368,7 @@ namespace BasisClasses
   {
     // Sanity check on derived class type
     //
-    if (typeid(*coef) != typeid(CoefClasses::SphStruct))
+    if (typeid(coef.get()) != typeid(CoefClasses::SphStruct*))
       throw std::runtime_error("Spherical::set_coefs: you must pass a CoefClasses::SphStruct");
 
     // Sanity check on dimensionality
@@ -1431,7 +1431,7 @@ namespace BasisClasses
 
   void Cylindrical::set_coefs(CoefClasses::CoefStrPtr coef)
   {
-    if (typeid(*coef) != typeid(CoefClasses::CylStruct))
+    if (typeid(coef.get()) != typeid(CoefClasses::CylStruct*))
       throw std::runtime_error("Cylindrical::set_coefs: you must pass a CoefClasses::CylStruct");
 
     CoefClasses::CylStruct* cf = dynamic_cast<CoefClasses::CylStruct*>(coef.get());
@@ -1708,7 +1708,7 @@ namespace BasisClasses
   {
     // Sanity check on derived class type
     //
-    if (typeid(*coef) != typeid(CoefClasses::CylStruct))
+    if (typeid(coef.get()) != typeid(CoefClasses::CylStruct*))
       throw std::runtime_error("FlatDisk::set_coefs: you must pass a CoefClasses::CylStruct");
 
     // Sanity check on dimensionality
@@ -2140,7 +2140,7 @@ namespace BasisClasses
   {
     // Sanity check on derived class type
     //
-    if (typeid(*coef) != typeid(CoefClasses::SlabStruct))
+    if (typeid(coef) != typeid(CoefClasses::SlabStruct*))
       throw std::runtime_error("Slab::set_coefs: you must pass a CoefClasses::SlabStruct");
 
     // Sanity check on dimensionality
@@ -2572,7 +2572,7 @@ namespace BasisClasses
   {
     // Sanity check on derived class type
     //
-    if (typeid(*coef) != typeid(CoefClasses::CubeStruct))
+    if (typeid(coef.get()) != typeid(CoefClasses::CubeStruct*))
       throw std::runtime_error("Cube::set_coefs: you must pass a CoefClasses::CubeStruct");
 
     // Sanity check on dimensionality

expui/CoefContainer.cc

@@ -72,7 +72,7 @@ namespace MSSA
       unpack_cylfld();
     }
     else {
-      throw std::runtime_error(std::string("CoefDB::unpack_channels(): can not reflect coefficient type=") + typeid(*coefs.get()).name());
+      throw std::runtime_error(std::string("CoefDB::unpack_channels(): can not reflect coefficient type=") + typeid(coefs.get()).name());
     }
 
     return coefs;
@@ -91,7 +91,7 @@ namespace MSSA
     else if (dynamic_cast<CoefClasses::CylFldCoefs*>(coefs.get()))
       { } // Do nothing
     else {
-      throw std::runtime_error(std::string("CoefDB::background(): can not reflect coefficient type=") + typeid(*coefs.get()).name());
+      throw std::runtime_error(std::string("CoefDB::background(): can not reflect coefficient type=") + typeid(coefs.get()).name());
     }
   }
 
@@ -112,7 +112,7 @@ namespace MSSA
     else if (dynamic_cast<CoefClasses::CylFldCoefs*>(coefs.get()))
       pack_cylfld();
     else {
-      throw std::runtime_error(std::string("CoefDB::pack_channels(): can not reflect coefficient type=") + typeid(*coefs.get()).name());
+      throw std::runtime_error(std::string("CoefDB::pack_channels(): can not reflect coefficient type=") + typeid(coefs.get()).name());
     }
   }
 

exputil/BarrierWrapper.cc

@@ -101,12 +101,13 @@ void BarrierWrapper::light_operator(const string& label,
 
 				// Compare adjacent strings in the list
     if (localid==0) {
-      char tmp[cbufsz];		// Working buffer
+				// Working buffer
+      auto tmp = std::make_unique<char[]>(cbufsz);
       bool firstime   = true;
-      string one, two = strncpy(tmp, &bufferT[0], cbufsz);
+      string one, two = strncpy(tmp.get(), &bufferT[0], cbufsz);
       for (int n=1; n<commsize; n++) {
 	one = two;
-	two = strncpy(tmp, &bufferT[cbufsz*n], cbufsz);
+	two = strncpy(tmp.get(), &bufferT[cbufsz*n], cbufsz);
 	if (one.compare(two) != 0) {
 	  if (firstime) {
 	    cout << std::string(60,'-') << std::endl << left

exputil/EmpCylSL.cc

@@ -5875,7 +5875,7 @@ void EmpCylSL::dump_images(const string& OUTFILE,
   //============
   // Open files
   //============
-  std::ofstream out[Number];
+  auto out = std::make_unique<std::ofstream[]>(Number);
   for (int j=0; j<Number; j++) {
     Name = OUTFILE + Types[j] + ".eof_recon";
     out[j].open(Name.c_str());

exputil/GaussCore.c

@@ -26,19 +26,18 @@
 /*
    Forward declaration for function QQp:
 */
-static int QQp();
+static int QQp(double, double*, double*);
 
 /*
    Function to test a real value for exceeding -1,
    and quit on an error if condition not met.
 */
-void GaussCheck(value)
-double value;
+void GaussCheck(double value)
 {
-    if (value <= (-1.0)) {
-	fprintf(stderr, "Gauss package: parameter out of range: %g\n", value);
-	exit(1);
-    }
+  if (value <= (-1.0)) {
+    fprintf(stderr, "Gauss package: parameter out of range: %g\n", value);
+    exit(1);
+  }
 }
 
 
@@ -54,11 +53,8 @@ static int n1;
 /*
    The workhorse.
 */
-void GaussMaster(n, alpha, beta, conflag, abscis, weight)
-int n;
-double alpha, beta;
-int conflag;
-double abscis[], weight[];
+void GaussMaster(int n, double alpha, double beta, int conflag,
+		 double abscis[], double weight[])
 {
 #define FALSE 0
 #define  TRUE 1

exputil/GaussCore.h

@@ -12,8 +12,10 @@
 #define   CONFLUENT 1
 #define NOCONFLUENT 0
 
-extern void GaussMaster();
-extern void GaussCheck();
+extern void GaussMaster(int n, double alpha, double beta, int conflag,
+			double abscis[], double weight[]);
+
+extern void GaussCheck(double value);
 
 /* ARGUMENT LISTS:
 

exputil/Hermite.c

@@ -23,9 +23,8 @@
 */
 #define odd(n) ((unsigned)(n) & 01)
 
-void Odd_Hermite(n, alpha, abscis, weight, w0)
-int n;
-double alpha, abscis[], weight[], *w0;
+void Odd_Hermite(int n, double alpha, double abscis[], double weight[],
+		 double* w0)
 {
     int k;
 
@@ -41,9 +40,7 @@ double alpha, abscis[], weight[], *w0;
 };
 
 
-void Even_Hermite(n, alpha, abscis, weight)
-int n;
-double alpha, abscis[], weight[];
+void Even_Hermite(int n, double alpha, double abscis[], double weight[])
 {
     int k;
 
@@ -59,9 +56,7 @@ double alpha, abscis[], weight[];
 };
 
 
-void Hermite(n, alpha, abscis, weight)
-int n;
-double alpha, abscis[], weight[];
+void Hermite(int n, double alpha, double abscis[], double weight[])
 {
     int n1, k;
 

exputil/Hermite.h

@@ -15,9 +15,12 @@
    Translation of module Hermite (export).
 */
 
-extern void Odd_Hermite();
-extern void Even_Hermite();
-extern void Hermite();
+extern void Odd_Hermite(int n, double alpha, double abscis[], double weight[],
+			double* w0);
+
+extern void Even_Hermite(int n, double alpha, double abscis[], double weight[]);
+
+extern void Hermite(int n, double alpha, double abscis[], double weight[]);
 
 /* ARGUMENT LISTS:
 

exputil/Jacobi.c

@@ -20,10 +20,7 @@
 
 #define sqr(x) ((x)*(x))
 
-void Jacobi(n, alpha, beta, abscis, weight)
-int n;
-double alpha, beta;
-double abscis[], weight[];
+void Jacobi(int n, double alpha, double beta, double abscis[], double weight[])
 {
     int k;
 
@@ -34,10 +31,8 @@ double abscis[], weight[];
 }
 
 
-void Radau_Jacobi(n, alpha, beta, abscis, weight, leftw)
-int n;
-double alpha, beta;
-double abscis[], weight[], *leftw;
+void Radau_Jacobi(int n, double alpha, double beta,
+		  double abscis[], double weight[], double *leftw)
 {
     int k;
     double temp;
@@ -62,10 +57,9 @@ double abscis[], weight[], *leftw;
 };
 
 
-void Lobatto_Jacobi(n, alpha, beta, abscis, weight, leftw, rightw)
-int n;
-double alpha, beta;
-double abscis[], weight[], *leftw, *rightw;
+void Lobatto_Jacobi(int n, double alpha, double beta,
+		    double abscis[], double weight[],
+		    double* leftw, double* rightw)
 {
     int k;
     double temp1, temp2;

exputil/Jacobi.h

@@ -15,10 +15,15 @@
    Translation of module Jacobi (export).
 */
 
+extern void Jacobi(int n, double alpha, double beta,
+		   double abscis[], double weight[]);
 
-extern void Jacobi();
-extern void Radau_Jacobi();
-extern void Lobatto_Jacobi();
+extern void Radau_Jacobi(int n, double alpha, double beta,
+			 double abscis[], double weight[], double *leftw);
+
+extern void Lobatto_Jacobi(int n, double alpha, double beta,
+			   double abscis[], double weight[],
+			   double* leftw, double* rightw);
 
 /* ARGUMENT LISTS:
    void Jacobi(n, alpha, beta, abscis, weight)

exputil/Laguerre.c

@@ -15,18 +15,15 @@
 #include "GaussCore.h"
 #include "Laguerre.h"
 
-void Laguerre(n, alpha, abscis, weight)
-int n;
-double alpha, abscis[], weight[];
+void Laguerre(int n, double alpha, double abscis[], double weight[])
 {
     GaussCheck(alpha);
     GaussMaster(n, alpha, 0.0, CONFLUENT, abscis, weight);
 };
 
 
-void Radau_Laguerre(n, alpha, abscis, weight, leftw)
-int n;
-double alpha, abscis[], weight[], *leftw;
+void Radau_Laguerre(int n, double alpha, double abscis[], double weight[],
+		    double* leftw)
 {
     int k;
     double temp;

exputil/Laguerre.h

@@ -15,8 +15,10 @@
    Translation of module Laguerre (export).
 */
 
-extern void Laguerre();
-extern void Radau_Laguerre();
+extern void Laguerre(int n, double alpha, double abscis[], double weight[]);
+
+extern void Radau_Laguerre(int n, double alpha,
+			   double abscis[], double weight[], double* leftw);
 
 /* 
    ARGUMENT LISTS:

exputil/ParticleReader.cc

@@ -3,6 +3,7 @@
 #include <iomanip>
 #include <fstream>
 #include <sstream>
+#include <memory>
 #include <numeric>
 #include <string>
 #include <vector>
@@ -530,11 +531,11 @@ namespace PR {
 
 	    int rank = dataspace.getSimpleExtentNdims();
 
-	    hsize_t dims[rank];
+	    auto dims = std::make_unique<hsize_t[]>(rank);
 
-	    int ndims = dataspace.getSimpleExtentDims(dims, NULL);
+	    int ndims = dataspace.getSimpleExtentDims(dims.get(), NULL);
 
-	    H5::DataSpace mspace(rank, dims);
+	    H5::DataSpace mspace(rank, dims.get());
 
 	    std::vector<float> masses(dims[0]);
 	    dataset.read(&masses[0], H5::PredType::NATIVE_FLOAT, mspace, dataspace );
@@ -569,11 +570,11 @@ namespace PR {
 
 	  int rank = dataspace.getSimpleExtentNdims();
 
-	  hsize_t dims[rank];
+	  auto dims = std::make_unique<hsize_t[]>(rank);
 
-	  int ndims = dataspace.getSimpleExtentDims( dims, NULL);
+	  int ndims = dataspace.getSimpleExtentDims( dims.get(), NULL);
 
-	  H5::DataSpace mspace(rank, dims);
+	  H5::DataSpace mspace(rank, dims.get());
 
 	  std::vector<unsigned> seq(dims[0]);
 	  dataset.read(&seq[0], H5::PredType::NATIVE_UINT32, mspace, dataspace );