Rearragne directory structure and update symbol visibility

.github/workflows/publish_pypi.yml

@@ -40,7 +40,7 @@ jobs:
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.16.2 delvewheel wheel
+          python -m pip install cibuildwheel==2.16.2 delvewheel==1.7.1 wheel
 
       - name: Building wheels 
         run: |

.github/workflows/wheel_build.yml

@@ -38,7 +38,7 @@ jobs:
 
       - name: Install cibuildwheel
         run: |
-          python -m pip install cibuildwheel==2.16.2 delvewheel wheel
+          python -m pip install cibuildwheel==2.16.2 delvewheel==1.7.1 wheel
 
       - name: Building wheels 
         run: |

CMakeLists.txt

@@ -4,29 +4,35 @@ project(Argolid)
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
+if(NOT WIN32)
+  set(CMAKE_CXX_VISIBILITY_PRESET hidden)
+  set(CMAKE_VISIBILITY_INLINES_HIDDEN 1)
+endif()
+
 include(GNUInstallDirs)
 # this is a workaround for GitHub Action for wheelbuiling
 if(DEFINED ENV{ARGOLID_DEP_DIR})
 	set(CMAKE_PREFIX_PATH $ENV{ARGOLID_DEP_DIR})
 	link_directories($ENV{ARGOLID_DEP_DIR}/${CMAKE_INSTALL_LIBDIR})
 endif()
 message(STATUS "CMAKE_PREFIX_PATH ${CMAKE_PREFIX_PATH}")
+
 if(NOT CMAKE_BUILD_TYPE)
     set(CMAKE_BUILD_TYPE Release)
   endif()
 
 set(CMAKE_CXX_FLAGS_RELEASE "-O2")
 set(SOURCE 
-           src/ts_driver/tiled_tiff/omexml.cc
-           src/ts_driver/tiled_tiff/tiled_tiff_key_value_store.cc
-           src/ts_driver/ometiff/metadata.cc
-           src/ts_driver/ometiff/driver.cc
-           src/ome_tiff_to_chunked_converter.cpp
-           src/chunked_pyramid_assembler.cpp
-           src/chunked_base_to_pyr_gen.cpp
-           src/ome_tiff_to_chunked_pyramid.cpp
-           src/utilities.cpp
-           src/pyramid_view.cpp
+           src/cpp/ts_driver/tiled_tiff/omexml.cc
+           src/cpp/ts_driver/tiled_tiff/tiled_tiff_key_value_store.cc
+           src/cpp/ts_driver/ometiff/metadata.cc
+           src/cpp/ts_driver/ometiff/driver.cc
+           src/cpp/core/ome_tiff_to_chunked_converter.cpp
+           src/cpp/core/chunked_pyramid_assembler.cpp
+           src/cpp/core/chunked_base_to_pyr_gen.cpp
+           src/cpp/core/ome_tiff_to_chunked_pyramid.cpp
+           src/cpp/core/pyramid_view.cpp
+           src/cpp/utilities/utilities.cpp
 )
 
 include(FetchContent)
@@ -52,8 +58,10 @@ find_package(filepattern REQUIRED)
 find_package(Threads QUIET)
 if (Threads_FOUND)
     if (CMAKE_USE_PTHREADS_INIT)
-      if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
-		    SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+      if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU" OR CMAKE_CXX_COMPILER_ID STREQUAL "Clang")
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -pthread")
+      elseif(CMAKE_CXX_COMPILER_ID STREQUAL "MSVC")
+          set(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} /pthread")
       endif()
     endif (CMAKE_USE_PTHREADS_INIT)
     list(APPEND Build_LIBRARIES ${CMAKE_THREAD_LIBS_INIT})
@@ -66,7 +74,7 @@ find_package(pybind11 CONFIG REQUIRED)
 
 pybind11_add_module(libargolid 
   ${SOURCE}
-  src/python/pyramid_python_interface.cpp
+  src/cpp/interface/pyramid_python_interface.cpp
 )
 
 # VERSION_INFO is defined by setup.py and passed into the C++ code as a define (VERSION_INFO) here.
@@ -81,5 +89,9 @@ if(CMAKE_CXX_COMPILER_ID STREQUAL "GNU")
   target_link_libraries(libargolid PRIVATE stdc++fs)
 endif()
 
-target_link_libraries(libargolid PRIVATE tensorstore::tensorstore tensorstore::all_drivers filepattern::filepattern)
+target_link_libraries(libargolid PRIVATE 
+                      tensorstore::tensorstore 
+                      tensorstore::all_drivers
+                      filepattern::filepattern
+                      )
 target_link_libraries(libargolid PRIVATE ${Build_LIBRARIES})  

src/chunked_base_to_pyr_gen.cpp → src/cpp/core/chunked_base_to_pyr_gen.cpp

@@ -1,6 +1,6 @@
 #include "chunked_base_to_pyr_gen.h"
-#include "downsample.h"
-#include "utilities.h"
+#include "../utilities/downsample.h"
+#include "../utilities/utilities.h"
 #include <plog/Log.h>
 #include "plog/Initializers/RollingFileInitializer.h"
 

src/chunked_base_to_pyr_gen.h → src/cpp/core/chunked_base_to_pyr_gen.h

@@ -2,8 +2,7 @@
 #include <string>
 #include <unordered_map>
 #include "BS_thread_pool.hpp"
-#include "utilities.h"
-
+#include "../utilities/utilities.h"
 namespace argolid{
 class ChunkedBaseToPyramid{
 public:

src/chunked_pyramid_assembler.cpp → src/cpp/core/chunked_pyramid_assembler.cpp

@@ -1,5 +1,5 @@
 #include "chunked_pyramid_assembler.h"
-#include "utilities.h"
+#include "../utilities/utilities.h"
 #include "pugixml.hpp"
 #include "tiffio.h"
 #include <plog/Log.h>

src/chunked_pyramid_assembler.h → src/cpp/core/chunked_pyramid_assembler.h

@@ -1,7 +1,7 @@
 #pragma once
 
 #include <string>
-#include "utilities.h"
+#include "../utilities/utilities.h"
 #include "BS_thread_pool.hpp"
 
 namespace argolid{

src/ome_tiff_to_chunked_converter.cpp → src/cpp/core/ome_tiff_to_chunked_converter.cpp

@@ -1,6 +1,5 @@
 #include "ome_tiff_to_chunked_converter.h"
-#include "utilities.h"
-
+#include "../utilities/utilities.h"
 #include <string>
 #include <stdint.h>
 #include <iostream>

src/ome_tiff_to_chunked_converter.h → src/cpp/core/ome_tiff_to_chunked_converter.h

@@ -2,7 +2,7 @@
 
 #include <string>
 #include "BS_thread_pool.hpp"
-#include "utilities.h"
+#include "../utilities/utilities.h"
 namespace argolid {
 class OmeTiffToChunkedConverter{
 

src/ome_tiff_to_chunked_pyramid.h → src/cpp/core/ome_tiff_to_chunked_pyramid.h

@@ -6,7 +6,7 @@
 #include "ome_tiff_to_chunked_converter.h"
 #include "chunked_pyramid_assembler.h"
 #include "chunked_base_to_pyr_gen.h"
-#include "utilities.h"
+#include "../utilities/utilities.h"
 #include "BS_thread_pool.hpp"
 #include <plog/Log.h>
 #include "plog/Initializers/RollingFileInitializer.h"

src/pyramid_view.cpp → src/cpp/core/pyramid_view.cpp

@@ -28,7 +28,7 @@
 
 #include "pyramid_view.h"
 #include "chunked_base_to_pyr_gen.h"
-#include "utilities.h"
+#include "../utilities/utilities.h"
 #include "pugixml.hpp"
 #include <plog/Log.h>
 #include "plog/Initializers/RollingFileInitializer.h"

src/pyramid_view.h → src/cpp/core/pyramid_view.h

@@ -3,7 +3,7 @@
 #include <tuple>
 #include <unordered_map>
 #include <optional>
-#include "utilities.h"
+#include "../utilities/utilities.h"
 #include "BS_thread_pool.hpp"
 namespace argolid{
 

src/python/pyramid_python_interface.cpp → src/cpp/interface/pyramid_python_interface.cpp

@@ -1,6 +1,6 @@
-#include "../ome_tiff_to_chunked_pyramid.h"
-#include "../pyramid_view.h"
-#include "../utilities.h"
+#include "../core/ome_tiff_to_chunked_pyramid.h"
+#include "../core/pyramid_view.h"
+#include "../utilities/utilities.h"
 #include <pybind11/pybind11.h>
 #include <pybind11/stl.h>
 namespace py = pybind11;

src/ts_driver/ometiff/driver.cc → src/cpp/ts_driver/ometiff/driver.cc

@@ -1,5 +1,5 @@
 
-#include "../../src/ts_driver/ometiff/metadata.h"
+#include "metadata.h"
 
 #include "tensorstore/driver/driver.h"
 #include "absl/status/status.h"

src/ts_driver/ometiff/metadata.cc → src/cpp/ts_driver/ometiff/metadata.cc

@@ -1,5 +1,5 @@
 
-#include "../../src/ts_driver/ometiff/metadata.h"
+#include "metadata.h"
 
 // ToDo - Clean up headers
 #include <iostream>

src/ts_driver/tiled_tiff/omexml.cc → src/cpp/ts_driver/tiled_tiff/omexml.cc

@@ -1,4 +1,4 @@
-#include "../../src/ts_driver/tiled_tiff/omexml.h"
+#include "omexml.h"
 #include <algorithm>
 #include <cctype>
 #include <iostream>

src/ts_driver/tiled_tiff/tiled_tiff_key_value_store.cc → src/cpp/ts_driver/tiled_tiff/tiled_tiff_key_value_store.cc

@@ -1,4 +1,4 @@
-#include "../../src/ts_driver/tiled_tiff/omexml.h"
+#include "omexml.h"
 #include <tiffio.h>
 #include <regex>
 #include <stddef.h>