Merge branch 'development' into update-lexci-models

Author: SJaffa

.gitignore

@@ -79,4 +79,54 @@ build/
 .settings
 python/tests/__pycache__
 *.h.gch
-*~
+*~
+
+### CMake ###
+CMakeLists.txt.user
+CMakeCache.txt
+CMakeFiles
+CMakeScripts
+Testing
+Makefile
+cmake_install.cmake
+install_manifest.txt
+compile_commands.json
+CTestTestfile.cmake
+_deps
+
+# CMake External projects (created by CMake fetchcontent module)
+*-prefix/
+
+### C++ ###
+# Prerequisites
+*.d
+
+# Compiled Object files
+*.slo
+*.lo
+*.o
+*.obj
+
+# Precompiled Headers
+*.gch
+*.pch
+
+# Compiled Dynamic libraries
+*.so
+*.dylib
+*.dll
+
+# Fortran module files
+*.mod
+*.smod
+
+# Compiled Static libraries
+*.lai
+*.la
+*.a
+*.lib
+
+# Executables
+*.exe
+*.out
+*.app

CMakeLists.txt

@@ -1,5 +1,23 @@
-cmake_minimum_required(VERSION 3.0)
-project(Sopt CXX)
+cmake_minimum_required(VERSION 3.13.4) # CMake 3.13.4 is the currently default in Debian 10 repositories
+project(Sopt
+        DESCRIPTION "Sparse OPTimisation using state-of-the-art convex optimisation algorithms."
+        HOMEPAGE_URL "http://astro-informatics.github.io/sopt/"
+        LANGUAGES CXX)
+
+set(CMAKE_CXX_STANDARD 17)
+set(CMAKE_CXX_STANDARD_REQUIRED ON)
+set(CMAKE_CXX_EXTENSIONS OFF)
+
+# https://cmake.org/cmake/help/latest/variable/CMAKE_EXPORT_COMPILE_COMMANDS.html
+# Enable output of compile commands during generation. If enabled, generates a compile_commands.json file containing the exact compiler calls for all translation units of the project in machine-readable form. This can be consumed by various IDEs and static analysers to provide smarter project diagnostics/completions etc.
+set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
+
+# https://stackoverflow.com/a/67410042
+# Create a symlink to compile_commands.json located in CMAKE_BINARY_DIR to the project root (works across filesystems)
+execute_process(
+  COMMAND ${CMAKE_COMMAND} -E create_symlink
+  ${CMAKE_BINARY_DIR}/compile_commands.json
+  ${CMAKE_SOURCE_DIR}/compile_commands.json)
 
 # Location of extra cmake includes for the project
 list(APPEND CMAKE_MODULE_PATH ${PROJECT_SOURCE_DIR}/cmake_files)
@@ -33,11 +51,7 @@ if(tests)
   enable_testing()
 endif()
 
-# Add c++11 stuff
-#include(AddCPP11Flags)
-set(CMAKE_CXX_STANDARD 17)
-include(CheckCXX11Features)
-cxx11_feature_check(REQUIRED unique_ptr override)
+
 include(compilations)
 
 # search/install dependencies

cpp/benchmarks/conjugate_gradient.cc

@@ -26,7 +26,7 @@ void function_cg(benchmark::State &state) {
 
   auto const AhA = A.matrix().transpose().conjugate() * A.matrix();
   auto const Ahb = A.matrix().transpose().conjugate() * b.matrix();
-  typedef sopt::Vector<TYPE> t_Vector;
+  using t_Vector = sopt::Vector<TYPE>;
   auto func = [&AhA](t_Vector &out, t_Vector const &input) { out = AhA * input; };
   auto output = sopt::Vector<TYPE>::Zero(N).eval();
   sopt::ConjugateGradient cg(0, epsilon);

cpp/benchmarks/l1_proximal.cc

@@ -6,7 +6,7 @@
 
 template <class TYPE>
 void function_l1p(benchmark::State &state) {
-  typedef typename sopt::real_type<TYPE>::type Real;
+  using Real = typename sopt::real_type<TYPE>::type;
   auto const N = state.range_x();
   auto const input = sopt::Vector<TYPE>::Random(N).eval();
   auto const Psi = sopt::Matrix<TYPE>::Random(input.size(), input.size() * 10).eval();

cpp/docs/Doxyfile.in

@@ -391,7 +391,7 @@ SUBGROUPING            = YES
 INLINE_GROUPED_CLASSES = NO
 
 # When the INLINE_SIMPLE_STRUCTS tag is set to YES, structs, classes, and unions
-# with only public data fields or simple typedef fields will be shown inline in
+# with only public data fields or simple type alias fields will be shown inline in
 # the documentation of the scope in which they are defined (i.e. file,
 # namespace, or group documentation), provided this scope is documented. If set
 # to NO, structs, classes, and unions are shown on a separate page (for HTML and
@@ -400,16 +400,16 @@ INLINE_GROUPED_CLASSES = NO
 
 INLINE_SIMPLE_STRUCTS  = NO
 
-# When TYPEDEF_HIDES_STRUCT tag is enabled, a typedef of a struct, union, or
-# enum is documented as struct, union, or enum with the name of the typedef. So
-# typedef struct TypeS {} TypeT, will appear in the documentation as a struct
-# with name TypeT. When disabled the typedef will appear as a member of a file,
+# When TYPEALIAS_HIDES_STRUCT tag is enabled, a type alias of a struct, union, or
+# enum is documented as struct, union, or enum with the name of the type alias. So
+# using TypeT = struct TypeS {}; will appear in the documentation as a struct
+# with name TypeT. When disabled the type alias will appear as a member of a file,
 # namespace, or class. And the struct will be named TypeS. This can typically be
 # useful for C code in case the coding convention dictates that all compound
-# types are typedef'ed and only the typedef is referenced, never the tag name.
+# types are type aliases and only the alias is referenced, never the tag name.
 # The default value is: NO.
 
-TYPEDEF_HIDES_STRUCT   = NO
+TYPEALIAS_HIDES_STRUCT   = NO
 
 # The size of the symbol lookup cache can be set using LOOKUP_CACHE_SIZE. This
 # cache is used to resolve symbols given their name and scope. Since this can be
@@ -874,7 +874,7 @@ RECURSIVE              = YES
 # Note that relative paths are relative to the directory from which doxygen is
 # run.
 
-EXCLUDE                = 
+EXCLUDE                =
 
 # The EXCLUDE_SYMLINKS tag can be used to select whether or not files or
 # directories that are symbolic links (a Unix file system feature) are excluded

cpp/examples/conjugate_gradient.cc

@@ -8,8 +8,8 @@ int main(int, char const **) {
   // Lets try both approaches.
 
   // Creates the input.
-  typedef sopt::Vector<sopt::t_complex> t_Vector;
-  typedef sopt::Matrix<sopt::t_complex> t_Matrix;
+  using t_Vector = sopt::Vector<sopt::t_complex>;
+  using t_Matrix = sopt::Matrix<sopt::t_complex>;
   t_Vector const b = t_Vector::Random(8);
   t_Matrix const A = t_Matrix::Random(b.size(), b.size());
 

cpp/examples/forward_backward/inpainting.cc

@@ -22,17 +22,17 @@
 
 // \min_{x} ||\Psi^Tx||_1 \quad \mbox{s.t.} \quad ||y - Ax||_2 < \epsilon and x \geq 0
 int main(int argc, char const **argv) {
-  // Some typedefs for simplicity
-  typedef double Scalar;
+  // Some type aliases for simplicity
+  using Scalar = double;
   // Column vector - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Vector<Scalar> Vector;
+  using Vector = sopt::Vector<Scalar>;
   // Matrix - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Matrix<Scalar> Matrix;
+  using Matrix = sopt::Matrix<Scalar>;
   // Image - 2D array - A * x is a coefficient-wise multiplication
   // Type expected by wavelets and image write/read functions
-  typedef sopt::Image<Scalar> Image;
+  using Image = sopt::Image<Scalar>;
 
   std::string const input = argc >= 2 ? argv[1] : "cameraman256";
   std::string const output = argc == 3 ? argv[2] : "none";
@@ -46,9 +46,9 @@ int main(int argc, char const **argv) {
     exit(0);
   }
   // Set up random numbers for C and C++
-  auto const seed = std::time(0);
-  std::srand((unsigned int)seed);
-  std::mt19937 mersenne(std::time(0));
+  auto const seed = std::time(nullptr);
+  std::srand(static_cast<unsigned int>(seed));
+  std::mt19937 mersenne(std::time(nullptr));
 
   // Initializes and sets logger (if compiled with logging)
   // See set_level function for levels.

cpp/examples/forward_backward/inpainting_credible_interval.cc

@@ -23,17 +23,17 @@
 
 // \min_{x} ||\Psi^Tx||_1 \quad \mbox{s.t.} \quad ||y - Ax||_2 < \epsilon and x \geq 0
 int main(int argc, char const **argv) {
-  // Some typedefs for simplicity
-  typedef sopt::t_real Scalar;
+  // Some type aliases for simplicity
+  using Scalar = sopt::t_real;
   // Column vector - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Vector<Scalar> Vector;
+  using Vector = sopt::Vector<Scalar>;
   // Matrix - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Matrix<Scalar> Matrix;
+  using Matrix = sopt::Matrix<Scalar>;
   // Image - 2D array - A * x is a coefficient-wise multiplication
   // Type expected by wavelets and image write/read functions
-  typedef sopt::Image<Scalar> Image;
+  using Image = sopt::Image<Scalar>;
 
   std::string const input = argc >= 2 ? argv[1] : "cameraman256";
   std::string const output = argc == 3 ? argv[2] : "none";
@@ -47,9 +47,9 @@ int main(int argc, char const **argv) {
     exit(0);
   }
   // Set up random numbers for C and C++
-  auto const seed = std::time(0);
-  std::srand((unsigned int)seed);
-  std::mt19937 mersenne(std::time(0));
+  auto const seed = std::time(nullptr);
+  std::srand(static_cast<unsigned int>(seed));
+  std::mt19937 mersenne(std::time(nullptr));
 
   // Initializes and sets logger (if compiled with logging)
   // See set_level function for levels.

cpp/examples/forward_backward/inpainting_joint_map.cc

@@ -23,17 +23,17 @@
 
 // \min_{x} ||\Psi^Tx||_1 \quad \mbox{s.t.} \quad ||y - Ax||_2 < \epsilon and x \geq 0
 int main(int argc, char const **argv) {
-  // Some typedefs for simplicity
-  typedef double Scalar;
+  // Some type aliases for simplicity
+  using Scalar = double;
   // Column vector - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Vector<Scalar> Vector;
+  using Vector = sopt::Vector<Scalar>;
   // Matrix - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Matrix<Scalar> Matrix;
+  using Matrix = sopt::Matrix<Scalar>;
   // Image - 2D array - A * x is a coefficient-wise multiplication
   // Type expected by wavelets and image write/read functions
-  typedef sopt::Image<Scalar> Image;
+  using Image = sopt::Image<Scalar>;
 
   std::string const input = argc >= 2 ? argv[1] : "cameraman256";
   std::string const output = argc == 3 ? argv[2] : "none";
@@ -47,9 +47,9 @@ int main(int argc, char const **argv) {
     exit(0);
   }
   // Set up random numbers for C and C++
-  auto const seed = std::time(0);
-  std::srand((unsigned int)seed);
-  std::mt19937 mersenne(std::time(0));
+  auto const seed = std::time(nullptr);
+  std::srand(static_cast<unsigned int>(seed));
+  std::mt19937 mersenne(std::time(nullptr));
 
   // Initializes and sets logger (if compiled with logging)
   // See set_level function for levels.

cpp/examples/forward_backward/l2_inpainting.cc

@@ -20,17 +20,17 @@
 
 // \min_{x} ||\Psi^Tx||_1 \quad \mbox{s.t.} \quad ||y - Ax||_2 < \epsilon and x \geq 0
 int main(int argc, char const **argv) {
-  // Some typedefs for simplicity
-  typedef double Scalar;
+  // Some type aliases for simplicity
+  using Scalar = double;
   // Column vector - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Vector<Scalar> Vector;
+  using Vector = sopt::Vector<Scalar>;
   // Matrix - linear algebra - A * x is a matrix-vector multiplication
   // type expected by Forward Backward
-  typedef sopt::Matrix<Scalar> Matrix;
+  using Matrix = sopt::Matrix<Scalar>;
   // Image - 2D array - A * x is a coefficient-wise multiplication
   // Type expected by wavelets and image write/read functions
-  typedef sopt::Image<Scalar> Image;
+  using Image = sopt::Image<Scalar>;
 
   std::string const input = argc >= 2 ? argv[1] : "cameraman256";
   std::string const output = argc == 3 ? argv[2] : "none";
@@ -44,9 +44,9 @@ int main(int argc, char const **argv) {
     exit(0);
   }
   // Set up random numbers for C and C++
-  auto const seed = std::time(0);
-  std::srand((unsigned int)seed);
-  std::mt19937 mersenne(std::time(0));
+  auto const seed = std::time(nullptr);
+  std::srand(static_cast<unsigned int>(seed));
+  std::mt19937 mersenne(std::time(nullptr));
 
   // Initializes and sets logger (if compiled with logging)
   // See set_level function for levels.