run clang-tidy with readability-braces-around-statements (#2899)

* run clang-tidy with readability-braces-around-statements
clang-format the results
clean up all the parts that clang-tidy-8 broke

* fix problem on windows

Code/Numerics/Alignment/AlignPoints.cpp

@@ -172,7 +172,9 @@ unsigned int jacobi(double quad[4][4], double eigenVals[4],
 
   // initialize the eigen vector to Identity
   for (j = 0; j <= 3; j++) {
-    for (i = 0; i <= 3; i++) eigenVecs[i][j] = 0.0;
+    for (i = 0; i <= 3; i++) {
+      eigenVecs[i][j] = 0.0;
+    }
     eigenVecs[j][j] = 1.0;
     eigenVals[j] = quad[j][j];
   }
@@ -186,7 +188,9 @@ unsigned int jacobi(double quad[4][4], double eigenVals[4],
         offDiagNorm += fabs(quad[i][j]);
       }
     }
-    if ((offDiagNorm / diagNorm) <= TOLERANCE) goto Exit_now;
+    if ((offDiagNorm / diagNorm) <= TOLERANCE) {
+      goto Exit_now;
+    }
     for (j = 1; j <= 3; j++) {
       for (i = 0; i <= j - 1; i++) {
         b = quad[i][j];

Code/Numerics/Alignment/Wrap/rdAlignment.cpp

@@ -30,11 +30,13 @@ void GetPointsFromPythonSequence(python::object &points,
   double *data;
   if (PyArray_Check(pyObj)) {
     // get the dimensions of the array
-    PyArrayObject *ptsMat = reinterpret_cast<PyArrayObject *>(pyObj);
+    auto *ptsMat = reinterpret_cast<PyArrayObject *>(pyObj);
     nrows = PyArray_DIM(ptsMat, 0);
     ncols = PyArray_DIM(ptsMat, 1);
 
-    if (ncols != 3) throw_value_error("Wrong dimension for the points array");
+    if (ncols != 3) {
+      throw_value_error("Wrong dimension for the points array");
+    }
 
     data = reinterpret_cast<double *>(PyArray_DATA(ptsMat));
 
@@ -45,13 +47,16 @@ void GetPointsFromPythonSequence(python::object &points,
     }
   } else if (PySequence_Check(pyObj)) {
     nrows = PySequence_Size(pyObj);
-    if (nrows <= 0) throw_value_error("Empty sequence passed in");
+    if (nrows <= 0) {
+      throw_value_error("Empty sequence passed in");
+    }
     python::extract<RDGeom::Point3D> ptOk(points[0]);
     if (!ptOk.check()) {
       for (unsigned int i = 0; i < nrows; i++) {
         PySequenceHolder<double> row(points[i]);
-        if (row.size() != 3)
+        if (row.size() != 3) {
           throw_value_error("Wrong number of entries in the list of lists");
+        }
         auto *rpt = new RDGeom::Point3D(row[0], row[1], row[2]);
         pts.push_back(rpt);
       }
@@ -90,19 +95,21 @@ PyObject *AlignPointPairs(python::object refPoints, python::object probePoints,
   GetPointsFromPythonSequence(probePoints, probePts);
 
   unsigned int npt = refPts.size();
-  if (npt != probePts.size())
+  if (npt != probePts.size()) {
     throw_value_error("Mis-match in number of points");
+  }
 
   PyObject *weightsObj = weights.ptr();
   RDNumeric::DoubleVector *wtsVec;
   wtsVec = nullptr;
   double *data;
   if (PyArray_Check(weightsObj)) {
-    PyArrayObject *wtsMat = reinterpret_cast<PyArrayObject *>(weightsObj);
+    auto *wtsMat = reinterpret_cast<PyArrayObject *>(weightsObj);
     unsigned int nwts = PyArray_DIM(wtsMat, 0);
-    if (nwts != npt)
+    if (nwts != npt) {
       throw_value_error(
           "Number of weights supplied do not match the number of points");
+    }
     wtsVec = new RDNumeric::DoubleVector(nwts);
     data = reinterpret_cast<double *>(PyArray_DATA(wtsMat));
     for (unsigned int i = 0; i < nwts; i++) {
@@ -113,9 +120,10 @@ PyObject *AlignPointPairs(python::object refPoints, python::object probePoints,
     unsigned int nwts = wts.size();
 
     if (nwts > 0) {
-      if (nwts != npt)
+      if (nwts != npt) {
         throw_value_error(
             "Number of weights supplied do not match the number of points");
+      }
       wtsVec = new RDNumeric::DoubleVector(nwts);
       for (unsigned int i = 0; i < npt; i++) {
         wtsVec->setVal(i, wts[i]);
@@ -130,8 +138,8 @@ PyObject *AlignPointPairs(python::object refPoints, python::object probePoints,
   npy_intp dims[2];
   dims[0] = 4;
   dims[1] = 4;
-  PyArrayObject *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);
-  double *resData = reinterpret_cast<double *>(PyArray_DATA(res));
+  auto *res = (PyArrayObject *)PyArray_SimpleNew(2, dims, NPY_DOUBLE);
+  auto *resData = reinterpret_cast<double *>(PyArray_DATA(res));
   const double *tdata = trans.getData();
   for (unsigned int i = 0; i < trans.numRows(); ++i) {
     unsigned int itab = i * 4;

Code/Numerics/EigenSolvers/PowerEigenSolver.cpp

@@ -43,7 +43,9 @@ bool powerEigenSolver(unsigned int numEig, DoubleSymmMatrix &mat,
   unsigned int i, j, id, iter, evalId;
 
   DoubleVector v(N), z(N);
-  if (seed <= 0) seed = clock();
+  if (seed <= 0) {
+    seed = clock();
+  }
   for (ei = 0; ei < numEig; ei++) {
     eigVal = -HUGE_EIGVAL;
     seed += ei;

Code/Numerics/testConrec.cpp

@@ -24,7 +24,7 @@ TEST_CASE("Conrec basics", "[conrec]") {
   SECTION("basics") {
     std::vector<RDGeom::Point2D> pts = {{0., 0.}, {1., 0.}, {1., 1.}, {0., 1.}};
     const size_t gridSz = 100;
-    double *grid = new double[gridSz * gridSz];
+    auto *grid = new double[gridSz * gridSz];
     double xps[gridSz];
     double yps[gridSz];
     double x1 = -4, y1 = -4, x2 = 6, y2 = 6;
@@ -35,13 +35,17 @@ TEST_CASE("Conrec basics", "[conrec]") {
       xps[ix] = px;
       for (size_t iy = 0; iy < gridSz; ++iy) {
         auto py = y1 + iy * dy;
-        if (ix == 0) yps[iy] = py;
+        if (ix == 0) {
+          yps[iy] = py;
+        }
         RDGeom::Point2D loc(px, py);
         double val = 0.0;
         for (const auto &pt : pts) {
           auto dv = loc - pt;
           auto r = dv.length();
-          if (r > 0) val += 1 / r;
+          if (r > 0) {
+            val += 1 / r;
+          }
         }
         maxV = std::max(val, maxV);
         grid[ix * gridSz + iy] = val;