Refactor/clang tidy cleanup

stan/math/fwd/arr/fun/log_sum_exp.hpp

@@ -12,8 +12,9 @@ template <typename T>
 fvar<T> log_sum_exp(const std::vector<fvar<T> >& v) {
   using std::exp;
   std::vector<T> vals(v.size());
-  for (size_t i = 0; i < v.size(); ++i)
+  for (size_t i = 0; i < v.size(); ++i) {
     vals[i] = v[i].val_;
+  }
   T deriv(0.0);
   T denominator(0.0);
   for (size_t i = 0; i < v.size(); ++i) {

stan/math/fwd/arr/fun/sum.hpp

@@ -18,8 +18,9 @@ namespace math {
  */
 template <typename T>
 inline fvar<T> sum(const std::vector<fvar<T> >& m) {
-  if (m.size() == 0)
+  if (m.size() == 0) {
     return 0.0;
+  }
   std::vector<T> vals(m.size());
   std::vector<T> tans(m.size());
   for (size_t i = 0; i < m.size(); ++i) {

stan/math/fwd/arr/fun/to_fvar.hpp

@@ -11,17 +11,19 @@ namespace math {
 template <typename T>
 inline std::vector<fvar<T>> to_fvar(const std::vector<T>& v) {
   std::vector<fvar<T>> x(v.size());
-  for (size_t i = 0; i < v.size(); ++i)
+  for (size_t i = 0; i < v.size(); ++i) {
     x[i] = T(v[i]);
+  }
   return x;
 }
 
 template <typename T>
 inline std::vector<fvar<T>> to_fvar(const std::vector<T>& v,
                                     const std::vector<T>& d) {
   std::vector<fvar<T>> x(v.size());
-  for (size_t i = 0; i < v.size(); ++i)
+  for (size_t i = 0; i < v.size(); ++i) {
     x[i] = fvar<T>(v[i], d[i]);
+  }
   return x;
 }
 

stan/math/fwd/core/fvar.hpp

@@ -88,8 +88,9 @@ struct fvar {
    * @param[in] v value
    */
   fvar(const T& v) : val_(v), d_(0.0) {  // NOLINT(runtime/explicit)
-    if (unlikely(is_nan(v)))
+    if (unlikely(is_nan(v))) {
       d_ = v;
+    }
   }
 
   /**
@@ -104,10 +105,12 @@ struct fvar {
    */
   template <typename V>
   fvar(const V& v,
-       typename std::enable_if<ad_promotable<V, T>::value>::type* dummy = 0)
+       typename std::enable_if<ad_promotable<V, T>::value>::type* dummy
+       = nullptr)
       : val_(v), d_(0.0) {
-    if (unlikely(is_nan(v)))
+    if (unlikely(is_nan(v))) {
       d_ = v;
+    }
   }
 
   /**
@@ -123,8 +126,9 @@ struct fvar {
    */
   template <typename V, typename D>
   fvar(const V& v, const D& d) : val_(v), d_(d) {
-    if (unlikely(is_nan(v)))
+    if (unlikely(is_nan(v))) {
       d_ = v;
+    }
   }
 
   /**

stan/math/fwd/mat/fun/Eigen_NumTraits.hpp

@@ -58,7 +58,7 @@ struct NumTraits<stan::math::fvar<T>> : GenericNumTraits<stan::math::fvar<T>> {
  */
 template <typename T, typename BinaryOp>
 struct ScalarBinaryOpTraits<stan::math::fvar<T>, double, BinaryOp> {
-  typedef stan::math::fvar<T> ReturnType;
+  using ReturnType = stan::math::fvar<T>;
 };
 
 /**
@@ -67,7 +67,7 @@ struct ScalarBinaryOpTraits<stan::math::fvar<T>, double, BinaryOp> {
  */
 template <typename T, typename BinaryOp>
 struct ScalarBinaryOpTraits<double, stan::math::fvar<T>, BinaryOp> {
-  typedef stan::math::fvar<T> ReturnType;
+  using ReturnType = stan::math::fvar<T>;
 };
 
 }  // namespace Eigen

stan/math/fwd/mat/fun/crossprod.hpp

@@ -11,8 +11,9 @@ namespace math {
 template <typename T, int R, int C>
 inline Eigen::Matrix<fvar<T>, C, C> crossprod(
     const Eigen::Matrix<fvar<T>, R, C>& m) {
-  if (m.rows() == 0)
+  if (m.rows() == 0) {
     return Eigen::Matrix<fvar<T>, C, C>(0, 0);
+  }
   return multiply(transpose(m), m);
 }
 

stan/math/fwd/mat/fun/divide.hpp

@@ -12,8 +12,9 @@ inline Eigen::Matrix<fvar<T>, R, C> divide(
     const Eigen::Matrix<fvar<T>, R, C>& v, const fvar<T>& c) {
   Eigen::Matrix<fvar<T>, R, C> res(v.rows(), v.cols());
   for (int i = 0; i < v.rows(); i++) {
-    for (int j = 0; j < v.cols(); j++)
+    for (int j = 0; j < v.cols(); j++) {
       res(i, j) = v(i, j) / c;
+    }
   }
   return res;
 }
@@ -23,8 +24,9 @@ inline Eigen::Matrix<fvar<T>, R, C> divide(
     const Eigen::Matrix<fvar<T>, R, C>& v, double c) {
   Eigen::Matrix<fvar<T>, R, C> res(v.rows(), v.cols());
   for (int i = 0; i < v.rows(); i++) {
-    for (int j = 0; j < v.cols(); j++)
+    for (int j = 0; j < v.cols(); j++) {
       res(i, j) = v(i, j) / c;
+    }
   }
   return res;
 }
@@ -34,8 +36,9 @@ inline Eigen::Matrix<fvar<T>, R, C> divide(const Eigen::Matrix<double, R, C>& v,
                                            const fvar<T>& c) {
   Eigen::Matrix<fvar<T>, R, C> res(v.rows(), v.cols());
   for (int i = 0; i < v.rows(); i++) {
-    for (int j = 0; j < v.cols(); j++)
+    for (int j = 0; j < v.cols(); j++) {
       res(i, j) = v(i, j) / c;
+    }
   }
   return res;
 }

stan/math/fwd/mat/fun/dot_product.hpp

@@ -18,8 +18,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<fvar<T>, R1, C1>& v1,
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < v1.size(); i++)
+  for (size_type i = 0; i < v1.size(); i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -31,8 +32,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<fvar<T>, R1, C1>& v1,
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < v1.size(); i++)
+  for (size_type i = 0; i < v1.size(); i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -44,8 +46,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<double, R1, C1>& v1,
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < v1.size(); i++)
+  for (size_type i = 0; i < v1.size(); i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -57,8 +60,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<fvar<T>, R1, C1>& v1,
   check_vector("dot_product", "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -70,8 +74,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<fvar<T>, R1, C1>& v1,
   check_vector("dot_product", "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -83,8 +88,9 @@ inline fvar<T> dot_product(const Eigen::Matrix<double, R1, C1>& v1,
   check_vector("dot_product", "v2", v2);
 
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1(i) * v2(i);
+  }
   return ret;
 }
 
@@ -93,8 +99,9 @@ inline fvar<T> dot_product(const std::vector<fvar<T> >& v1,
                            const std::vector<fvar<T> >& v2) {
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
   fvar<T> ret(0, 0);
-  for (size_t i = 0; i < v1.size(); i++)
+  for (size_t i = 0; i < v1.size(); i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 
@@ -103,8 +110,9 @@ inline fvar<T> dot_product(const std::vector<double>& v1,
                            const std::vector<fvar<T> >& v2) {
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
   fvar<T> ret(0, 0);
-  for (size_t i = 0; i < v1.size(); i++)
+  for (size_t i = 0; i < v1.size(); i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 
@@ -113,35 +121,39 @@ inline fvar<T> dot_product(const std::vector<fvar<T> >& v1,
                            const std::vector<double>& v2) {
   check_matching_sizes("dot_product", "v1", v1, "v2", v2);
   fvar<T> ret(0, 0);
-  for (size_t i = 0; i < v1.size(); i++)
+  for (size_t i = 0; i < v1.size(); i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 
 template <typename T>
 inline fvar<T> dot_product(const std::vector<fvar<T> >& v1,
                            const std::vector<fvar<T> >& v2, size_type& length) {
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 
 template <typename T>
 inline fvar<T> dot_product(const std::vector<double>& v1,
                            const std::vector<fvar<T> >& v2, size_type& length) {
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 
 template <typename T>
 inline fvar<T> dot_product(const std::vector<fvar<T> >& v1,
                            const std::vector<double>& v2, size_type& length) {
   fvar<T> ret(0, 0);
-  for (size_type i = 0; i < length; i++)
+  for (size_type i = 0; i < length; i++) {
     ret += v1.at(i) * v2.at(i);
+  }
   return ret;
 }
 

stan/math/fwd/mat/fun/log_softmax.hpp

@@ -17,8 +17,9 @@ inline Eigen::Matrix<fvar<T>, Eigen::Dynamic, 1> log_softmax(
   using Eigen::Matrix;
 
   Matrix<T, Dynamic, 1> alpha_t(alpha.size());
-  for (int k = 0; k < alpha.size(); ++k)
+  for (int k = 0; k < alpha.size(); ++k) {
     alpha_t(k) = alpha(k).val_;
+  }
 
   Matrix<T, Dynamic, 1> softmax_alpha_t = softmax(alpha_t);
   Matrix<T, Dynamic, 1> log_softmax_alpha_t = log_softmax(alpha_t);
@@ -33,11 +34,12 @@ inline Eigen::Matrix<fvar<T>, Eigen::Dynamic, 1> log_softmax(
     T negative_alpha_m_d_times_softmax_alpha_t_m
         = -alpha(m).d_ * softmax_alpha_t(m);
     for (int k = 0; k < alpha.size(); ++k) {
-      if (m == k)
+      if (m == k) {
         log_softmax_alpha(k).d_
             += alpha(m).d_ + negative_alpha_m_d_times_softmax_alpha_t_m;
-      else
+      } else {
         log_softmax_alpha(k).d_ += negative_alpha_m_d_times_softmax_alpha_t_m;
+      }
     }
   }
 

stan/math/fwd/mat/fun/mdivide_left_ldlt.hpp

@@ -26,11 +26,12 @@ inline Eigen::Matrix<fvar<T2>, R1, C2> mdivide_left_ldlt(
 
   Eigen::Matrix<T2, R2, C2> b_val(b.rows(), b.cols());
   Eigen::Matrix<T2, R2, C2> b_der(b.rows(), b.cols());
-  for (int i = 0; i < b.rows(); i++)
+  for (int i = 0; i < b.rows(); i++) {
     for (int j = 0; j < b.cols(); j++) {
       b_val(i, j) = b(i, j).val_;
       b_der(i, j) = b(i, j).d_;
     }
+  }
 
   return to_fvar(mdivide_left_ldlt(A, b_val), mdivide_left_ldlt(A, b_der));
 }

stan/math/fwd/mat/fun/multiply.hpp

@@ -15,8 +15,9 @@ inline Eigen::Matrix<fvar<T>, R1, C1> multiply(
     const Eigen::Matrix<fvar<T>, R1, C1>& m, const fvar<T>& c) {
   Eigen::Matrix<fvar<T>, R1, C1> res(m.rows(), m.cols());
   for (int i = 0; i < m.rows(); i++) {
-    for (int j = 0; j < m.cols(); j++)
+    for (int j = 0; j < m.cols(); j++) {
       res(i, j) = c * m(i, j);
+    }
   }
   return res;
 }
@@ -26,8 +27,9 @@ inline Eigen::Matrix<fvar<T>, R2, C2> multiply(
     const Eigen::Matrix<fvar<T>, R2, C2>& m, double c) {
   Eigen::Matrix<fvar<T>, R2, C2> res(m.rows(), m.cols());
   for (int i = 0; i < m.rows(); i++) {
-    for (int j = 0; j < m.cols(); j++)
+    for (int j = 0; j < m.cols(); j++) {
       res(i, j) = c * m(i, j);
+    }
   }
   return res;
 }
@@ -37,8 +39,9 @@ inline Eigen::Matrix<fvar<T>, R1, C1> multiply(
     const Eigen::Matrix<double, R1, C1>& m, const fvar<T>& c) {
   Eigen::Matrix<fvar<T>, R1, C1> res(m.rows(), m.cols());
   for (int i = 0; i < m.rows(); i++) {
-    for (int j = 0; j < m.cols(); j++)
+    for (int j = 0; j < m.cols(); j++) {
       res(i, j) = c * m(i, j);
+    }
   }
   return res;
 }

stan/math/fwd/mat/fun/multiply_lower_tri_self_transpose.hpp

@@ -12,14 +12,16 @@ namespace math {
 template <typename T, int R, int C>
 inline Eigen::Matrix<fvar<T>, R, R> multiply_lower_tri_self_transpose(
     const Eigen::Matrix<fvar<T>, R, C>& m) {
-  if (m.rows() == 0)
+  if (m.rows() == 0) {
     return Eigen::Matrix<fvar<T>, R, R>(0, 0);
+  }
   Eigen::Matrix<fvar<T>, R, C> L(m.rows(), m.cols());
   L.setZero();
 
   for (size_type i = 0; i < m.rows(); i++) {
-    for (size_type j = 0; (j < i + 1) && (j < m.cols()); j++)
+    for (size_type j = 0; (j < i + 1) && (j < m.cols()); j++) {
       L(i, j) = m(i, j);
+    }
   }
   return multiply(L, transpose(L));
 }

stan/math/fwd/mat/fun/qr_Q.hpp

@@ -12,15 +12,17 @@ namespace math {
 template <typename T>
 Eigen::Matrix<fvar<T>, Eigen::Dynamic, Eigen::Dynamic> qr_Q(
     const Eigen::Matrix<fvar<T>, Eigen::Dynamic, Eigen::Dynamic>& m) {
-  typedef Eigen::Matrix<fvar<T>, Eigen::Dynamic, Eigen::Dynamic> matrix_fwd_t;
+  using matrix_fwd_t = Eigen::Matrix<fvar<T>, Eigen::Dynamic, Eigen::Dynamic>;
   check_nonzero_size("qr_Q", "m", m);
   check_greater_or_equal("qr_Q", "m.rows()", m.rows(), m.cols());
   Eigen::HouseholderQR<matrix_fwd_t> qr(m.rows(), m.cols());
   qr.compute(m);
   matrix_fwd_t Q = qr.householderQ();
-  for (int i = 0; i < m.cols(); i++)
-    if (qr.matrixQR()(i, i) < 0.0)
+  for (int i = 0; i < m.cols(); i++) {
+    if (qr.matrixQR()(i, i) < 0.0) {
       Q.col(i) *= -1.0;
+    }
+  }
   return Q;
 }