removed warnings added clang-tidy

.clang-tidy

@@ -0,0 +1,42 @@
+
+---
+Checks:          '*, 
+                    -altera-*,
+                    -android-cloexec-fopen,
+                    -cppcoreguidelines-pro-bounds-array-to-pointer-decay, 
+                    -cppcoreguidelines-pro-bounds-pointer-arithmetic, 
+                    -fuchsia*,
+                    -readability-else-after-return,
+                    -readability-avoid-const-params-in-decls,
+                    -readability-identifier-length,
+                    -cppcoreguidelines-pro-bounds-constant-array-index,
+                    -cppcoreguidelines-pro-type-reinterpret-cast,
+                    -llvm-header-guard,
+                    -modernize-use-nodiscard,
+                    -misc-non-private-member-variables-in-classes,
+                    -readability-static-accessed-through-instance,
+                    -readability-braces-around-statements,
+                    -readability-isolate-declaration,
+                    -readability-implicit-bool-conversion,
+                    -readability-identifier-length,
+                    -readability-identifier-naming,
+                    -hicpp-signed-bitwise,
+                    -hicpp-no-array-decay, 
+                    -hicpp-braces-around-statements,
+                    -google-runtime-references, 
+                    -google-readability-todo, 
+                    -google-readability-braces-around-statements,
+                    -modernize-use-trailing-return-type,
+                    -llvmlibc-*'
+
+HeaderFilterRegex: \.hpp
+FormatStyle:     none
+CheckOptions:
+  - { key: readability-identifier-naming.NamespaceCase,       value: lower_case }
+ # - { key: readability-identifier-naming.FunctionCase,        value: lower_case }
+  - { key: readability-identifier-naming.ClassCase,           value: CamelCase  }
+ # - { key: readability-identifier-naming.MethodCase,          value: CamelCase  }
+ # - { key: readability-identifier-naming.StructCase,          value: CamelCase  }
+ # - { key: readability-identifier-naming.VariableCase,        value: lower_case }
+  - { key: readability-identifier-naming.GlobalConstantCase,  value: UPPER_CASE }
+...

CMakeLists.txt

@@ -60,6 +60,8 @@ if(AARE_SYSTEM_LIBRARIES)
     set(AARE_FETCH_CATCH OFF CACHE BOOL "Disabled FetchContent for catch2" FORCE)
     set(AARE_FETCH_JSON OFF CACHE BOOL "Disabled FetchContent for nlohmann::json" FORCE)
     set(AARE_FETCH_ZMQ OFF CACHE BOOL "Disabled FetchContent for libzmq" FORCE)
+    # Still fetch lmfit when setting AARE_SYSTEM_LIBRARIES since this is not available
+    # on conda-forge
 endif()
 
 if(AARE_VERBOSE)
@@ -78,6 +80,7 @@ endif()
 set(CMAKE_EXPORT_COMPILE_COMMANDS ON)
 
 if(AARE_FETCH_LMFIT)
+    #TODO! Should we fetch lmfit from the web or inlcude a tar.gz in the repo?
     set(lmfit_patch git apply ${CMAKE_CURRENT_SOURCE_DIR}/patches/lmfit.patch)
     FetchContent_Declare(
         lmfit

include/aare/NDArray.hpp

@@ -388,12 +388,12 @@ NDArray<T, Ndim> NDArray<T, Ndim>::operator*(const T &value) {
     result *= value;
     return result;
 }
-template <typename T, int64_t Ndim> void NDArray<T, Ndim>::Print() {
+// template <typename T, int64_t Ndim> void NDArray<T, Ndim>::Print() {
-    if (shape_[0] < 20 && shape_[1] < 20)
+//     if (shape_[0] < 20 && shape_[1] < 20)
-        Print_all();
+//         Print_all();
-    else
+//     else
-        Print_some();
+//         Print_some();
-}
+// }
 
 template <typename T, int64_t Ndim>
 std::ostream &operator<<(std::ostream &os, const NDArray<T, Ndim> &arr) {

include/aare/RawSubFile.hpp

@@ -64,7 +64,7 @@ class RawSubFile {
 
     size_t bytes_per_frame() const { return m_bytes_per_frame; }
     size_t pixels_per_frame() const { return m_rows * m_cols; }
-    size_t bytes_per_pixel() const { return m_bitdepth / 8; }
+    size_t bytes_per_pixel() const { return m_bitdepth / bits_per_byte; }
 
 private:
   template <typename T>

include/aare/defs.hpp

@@ -38,6 +38,8 @@
 
 namespace aare {
 
+inline constexpr size_t bits_per_byte = 8;
+
 void assert_failed(const std::string &msg);
 
 

python/src/ctb_raw_file.hpp

@@ -32,7 +32,7 @@ m.def("adc_sar_05_decode64to16", [](py::array_t<uint8_t> input) {
     }
 
     //Create a 2D output array with the same shape as the input
-    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/8};
+    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/static_cast<int64_t>(bits_per_byte)};
     py::array_t<uint16_t> output(shape);
 
     //Create a view of the input and output arrays
@@ -53,7 +53,7 @@ m.def("adc_sar_04_decode64to16", [](py::array_t<uint8_t> input) {
     }
 
     //Create a 2D output array with the same shape as the input
-    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/8};
+    std::vector<ssize_t> shape{input.shape(0), input.shape(1)/static_cast<int64_t>(bits_per_byte)};
     py::array_t<uint16_t> output(shape);
 
     //Create a view of the input and output arrays

python/src/np_helper.hpp

@@ -40,25 +40,25 @@ template <typename T> py::array return_vector(std::vector<T> *vec) {
 }
 
 // todo rewrite generic
-template <class T, int Flags> auto get_shape_3d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto get_shape_3d(const py::array_t<T, Flags>& arr) {
     return aare::Shape<3>{arr.shape(0), arr.shape(1), arr.shape(2)};
 }
 
-template <class T, int Flags> auto make_view_3d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto make_view_3d(py::array_t<T, Flags>& arr) {
     return aare::NDView<T, 3>(arr.mutable_data(), get_shape_3d<T, Flags>(arr));
 }
 
-template <class T, int Flags> auto get_shape_2d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto get_shape_2d(const py::array_t<T, Flags>& arr) {
     return aare::Shape<2>{arr.shape(0), arr.shape(1)};
 }
 
-template <class T, int Flags> auto get_shape_1d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto get_shape_1d(const py::array_t<T, Flags>& arr) {
     return aare::Shape<1>{arr.shape(0)};
 }
 
-template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto make_view_2d(py::array_t<T, Flags>& arr) {
     return aare::NDView<T, 2>(arr.mutable_data(), get_shape_2d<T, Flags>(arr));
 }
-template <class T, int Flags> auto make_view_1d(py::array_t<T, Flags> arr) {
+template <class T, int Flags> auto make_view_1d(py::array_t<T, Flags>& arr) {
     return aare::NDView<T, 1>(arr.mutable_data(), get_shape_1d<T, Flags>(arr));
 }

python/src/var_cluster.hpp

@@ -25,7 +25,7 @@ void define_var_cluster_finder_bindings(py::module &m) {
         .def(py::init<Shape<2>, double>())
         .def("labeled",
              [](VarClusterFinder<double> &self) {
-                 auto ptr = new NDArray<int, 2>(self.labeled());
+                 auto *ptr = new NDArray<int, 2>(self.labeled());
                  return return_image_data(ptr);
              })
         .def("set_noiseMap",

src/Dtype.cpp

@@ -70,7 +70,7 @@ uint8_t Dtype::bitdepth() const {
 /**
  * @brief Get the number of bytes of the data type
  */
-size_t Dtype::bytes() const { return bitdepth() / 8; }
+size_t Dtype::bytes() const { return bitdepth() / bits_per_byte; }
 
 /**
  * @brief Construct a DType object from a TypeIndex

src/File.cpp

@@ -73,7 +73,7 @@ size_t File::tell() const { return file_impl->tell(); }
 size_t File::rows() const { return file_impl->rows(); }
 size_t File::cols() const { return file_impl->cols(); }
 size_t File::bitdepth() const { return file_impl->bitdepth(); }
-size_t File::bytes_per_pixel() const { return file_impl->bitdepth() / 8; }
+size_t File::bytes_per_pixel() const { return file_impl->bitdepth() / bits_per_byte; }
 
 DetectorType File::detector_type() const { return file_impl->detector_type(); }
 

src/RawFile.cpp

@@ -76,8 +76,7 @@ size_t RawFile::n_mod() const { return n_subfile_parts; }
 
 
 size_t RawFile::bytes_per_frame() {
-    // return m_rows * m_cols * m_master.bitdepth() / 8;
+    return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() / bits_per_byte;
-    return m_geometry.pixels_x * m_geometry.pixels_y * m_master.bitdepth() / 8;
 }
 size_t RawFile::pixels_per_frame() { 
     // return m_rows * m_cols;