chore(cleanup): cleans up codebase (#376)

Clean up incorporates (amid others) the following:
- removes duplicate header includes
- adds missing header includes
- adds Closing namespace comments
- removes unnecessary semicolons

Author: krishnakumarg1984

cpp/examples/primal_dual/inpainting.cc

@@ -16,7 +16,6 @@
 #include "sopt/power_method.h"
 #include "sopt/relative_variation.h"
 #include "sopt/sampling.h"
-#include "sopt/types.h"
 #include "sopt/utilities.h"
 #include "sopt/wavelets.h"
 #include "sopt/wavelets/sara.h"

cpp/sopt/cppflow_utils.h

@@ -6,6 +6,7 @@
 #include <cppflow/cppflow.h>
 #include "cppflow/ops.h"
 #include <complex>
+#include <vector>
 
 namespace sopt::cppflowutils {
 

cpp/sopt/credible_region.h

@@ -2,8 +2,11 @@
 #define SOPT_CREDIBLE_REGION_H
 
 #include "sopt/config.h"
+#include <algorithm> // for std::min()
 #include <functional>
 #include <iostream>
+#include <memory> // for make_shared<>
+#include <tuple> // for tuple<>
 #include <type_traits>
 #include "sopt/bisection_method.h"
 #include "sopt/exception.h"

cpp/sopt/forward_backward.h

@@ -4,6 +4,8 @@
 #include "sopt/config.h"
 #include <functional>
 #include <limits>
+#include <tuple> // for tuple<>
+#include <utility> // for std::move<>
 #include "sopt/exception.h"
 #include "sopt/linear_transform.h"
 #include "sopt/logging.h"

cpp/sopt/imaging_forward_backward.h

@@ -2,6 +2,8 @@
 #define SOPT_IMAGING_FORWARD_BACKWARD_H
 
 #include "sopt/config.h"
+#include <limits> // for std::numeric_limits<>
+#include <memory> // for std::shared_ptr<>
 #include <numeric>
 #include <tuple>
 #include <utility>
@@ -141,7 +143,7 @@ class ImagingForwardBackward {
   //! Vector of target measurements
   t_Vector const &target() const { return target_; }
   //! Minimun of objective_function
-  Real objmin() const { return objmin_; };
+  Real objmin() const { return objmin_; }
   //! Sets the vector of target measurements
   template <class DERIVED>
   ImagingForwardBackward<Scalar> &target(Eigen::MatrixBase<DERIVED> const &target) {
@@ -293,7 +295,7 @@ bool ImagingForwardBackward<SCALAR>::residual_convergence(t_Vector const &x,
   auto const residual_norm = sopt::l2_norm(residual);
   SOPT_LOW_LOG("    - [FB] Residuals: {} <? {}", residual_norm, residual_tolerance());
   return residual_norm < residual_tolerance();
-};
+}
 
 template <class SCALAR>
 bool ImagingForwardBackward<SCALAR>::objective_convergence(ScalarRelativeVariation<Scalar> &scalvar,
@@ -304,7 +306,7 @@ bool ImagingForwardBackward<SCALAR>::objective_convergence(ScalarRelativeVariati
   auto const current = ((gamma() > 0) ? g_proximal_->proximal_norm(x)
 			* gamma() : 0) + std::pow(sopt::l2_norm(residual), 2) / (2 * sigma() * sigma());
   return scalvar(current);
-};
+}
 
 #ifdef SOPT_MPI
 template <class SCALAR>
@@ -318,7 +320,7 @@ bool ImagingForwardBackward<SCALAR>::objective_convergence(mpi::Communicator con
 	((gamma() > 0) ? g_proximal_->proximal_norm(x)
        * gamma() : 0) + std::pow(sopt::l2_norm(residual), 2) / (2 * sigma_ * sigma_));
   return scalvar(current);
-};
+}
 #endif
 
 template <class SCALAR>

cpp/sopt/imaging_padmm.h

@@ -2,6 +2,7 @@
 #define SOPT_L1_PROXIMAL_ADMM_H
 
 #include "sopt/config.h"
+#include <limits> // for std::numeric_limits<>
 #include <numeric>
 #include <tuple>
 #include <utility>
@@ -322,7 +323,7 @@ bool ImagingProximalADMM<SCALAR>::residual_convergence(t_Vector const &x,
   auto const residual_norm = sopt::l2_norm(residual, l2ball_proximal_weights());
   SOPT_LOW_LOG("    - [PADMM] Residuals: {} <? {}", residual_norm, residual_tolerance());
   return residual_norm < residual_tolerance();
-};
+}
 
 template <class SCALAR>
 bool ImagingProximalADMM<SCALAR>::objective_convergence(ScalarRelativeVariation<Scalar> &scalvar,
@@ -333,7 +334,7 @@ bool ImagingProximalADMM<SCALAR>::objective_convergence(ScalarRelativeVariation<
   auto const current =
       sopt::l1_norm(static_cast<t_Vector>(Psi().adjoint() * x), l1_proximal_weights());
   return scalvar(current);
-};
+}
 
 template <class SCALAR>
 bool ImagingProximalADMM<SCALAR>::is_converged(ScalarRelativeVariation<Scalar> &scalvar,

cpp/sopt/imaging_primal_dual.h

@@ -2,6 +2,7 @@
 #define SOPT_L1_PRIMAL_DUAL_H
 
 #include "sopt/config.h"
+#include <limits> // for std::numeric_limits<>
 #include <numeric>
 #include <tuple>
 #include <utility>
@@ -296,7 +297,7 @@ class ImagingPrimalDual {
     no_weights(output, 1, x);
     with_weights(outputw, Vector<Real>::Ones(this->l1_proximal_weights().size()), x);
     return output.isApprox(outputw);
-  };
+  }
 };
 
 template <class SCALAR>
@@ -370,7 +371,7 @@ bool ImagingPrimalDual<SCALAR>::residual_convergence(t_Vector const &x,
   auto const residual_norm = sopt::l2_norm(residual, l2ball_proximal_weights());
   SOPT_LOW_LOG("    - [Primal Dual] Residuals: {} <? {}", residual_norm, residual_tolerance());
   return residual_norm < residual_tolerance();
-};
+}
 
 template <class SCALAR>
 bool ImagingPrimalDual<SCALAR>::objective_convergence(ScalarRelativeVariation<Scalar> &scalvar,
@@ -381,7 +382,7 @@ bool ImagingPrimalDual<SCALAR>::objective_convergence(ScalarRelativeVariation<Sc
   auto const current =
       sopt::l1_norm(static_cast<t_Vector>(Psi().adjoint() * x), l1_proximal_weights());
   return scalvar(current);
-};
+}
 
 template <class SCALAR>
 bool ImagingPrimalDual<SCALAR>::is_converged(ScalarRelativeVariation<Scalar> &scalvar,

cpp/sopt/joint_map.h

@@ -4,6 +4,8 @@
 #include "sopt/config.h"
 #include <functional>
 #include <limits>
+#include <memory> // for std::shared_ptr<>
+#include <utility> // for std::forward<>
 #include "sopt/exception.h"
 #include "sopt/forward_backward.h"
 #include "sopt/imaging_forward_backward.h"
@@ -42,7 +44,7 @@ class JointMAP {
         is_converged_([](t_Vector const &, t_Vector const &, t_real const) { return true; }),
         relative_variation_(1e-3),
         objective_variation_(1e-3),
-        itermax_(std::numeric_limits<t_uint>::max()){};
+        itermax_(std::numeric_limits<t_uint>::max()){}
 
 #define SOPT_MACRO(NAME, TYPE)                  \
   TYPE const &NAME() const { return NAME##_; }  \
@@ -131,7 +133,7 @@ class JointMAP {
     diagnostic.reg_niters = niters;
     diagnostic.reg_term = gamma;
     return diagnostic;
-  };
+  }
 };
 
 } // namespace sopt::algorithm

cpp/sopt/l1_g_proximal.h

@@ -41,7 +41,7 @@ class L1GProximal : public GProximal<SCALAR> {
   L1GProximal(bool tight_frame = false)
     : tight_frame_ (tight_frame),
       l1_proximal_() {}
-  ~L1GProximal() {};
+  ~L1GProximal() {}
 
 // Implements the interface in GProximal
 

cpp/sopt/l1_proximal.h

@@ -4,6 +4,7 @@
 #include "sopt/config.h"
 #include <array>
 #include <type_traits>
+#include <utility> // for std::forward<>
 #include <Eigen/Core>
 #include "sopt/linear_transform.h"
 #include "sopt/maths.h"