Allow building against system libs instead of bundled dependencies

When DIP_BUILD_BUNDLED_DEPENDENCIES=OFF is passed to cmake, we
will rely on find_package to find Eigen3, zlib, jpeg, ics and tiff
libraries. The fftw_api.h header will always be used, as it's not
public API that's included in the fftw3 package on ArchLinux e.g.

The default for this option is still ON, i.e. this is an opt-in
feature.

To allow building against an externally provided doctest, the
includes are normalized to follow the suggested upstream format:

```
#include <doctest/doctest.h>
```

Change-Id: I4ed9095eefbfd889642d1c3d42b3d9af0dfc15ae

CMakeLists.txt

@@ -22,6 +22,9 @@ endif()
 set(DIP_SHARED_LIBRARY ON CACHE BOOL "Build a shared library (off for static library)")
 set(BUILD_SHARED_LIBS ${DIP_SHARED_LIBRARY})
 
+# build bundled dependencies or use find_package?
+set(DIP_BUILD_BUNDLED_DEPENDENCIES ON CACHE BOOL "Build the bundled dependencies or use find_package otherwise")
+
 # Installation path
 set(CMAKE_INSTALL_PREFIX "${CMAKE_BUILD_TYPE}" CACHE PATH "Installation directory")
 set(DOCUMENTATION_OUTPUT share/doc/DIPlib)

dependencies/libics/CMakeLists.txt

@@ -100,8 +100,8 @@ endif(UNIX)
 #endif()
 
 # DIPlib-specific zlib
-if(TARGET zlibstatic)
-   target_link_libraries(libics PRIVATE zlibstatic)
+if(TARGET ZLIB::ZLIB)
+   target_link_libraries(libics PRIVATE ZLIB::ZLIB)
    target_compile_definitions(libics PUBLIC -DICS_ZLIB)
 endif()
 

dependencies/libtiff/CMakeLists.txt

@@ -378,7 +378,7 @@ set(MDI_SUPPORT TRUE)
 
 # ZLIB
 set(ZLIB_SUPPORT FALSE)
-if(TARGET zlibstatic)
+if(TARGET ZLIB::ZLIB)
   set(ZLIB_SUPPORT TRUE)
 endif()
 set(ZIP_SUPPORT ${ZLIB_SUPPORT})
@@ -468,10 +468,10 @@ if(M_LIBRARY)
   list(APPEND TIFF_LIBRARY_DEPS ${M_LIBRARY})
 endif()
 if(ZLIB_SUPPORT)
-  list(APPEND TIFF_LIBRARY_DEPS zlibstatic)
+  list(APPEND TIFF_LIBRARY_DEPS ZLIB::ZLIB)
 endif()
 if(JPEG_SUPPORT)
-  list(APPEND TIFF_LIBRARY_DEPS jpeg)
+  list(APPEND TIFF_LIBRARY_DEPS JPEG::JPEG)
 endif()
 if(JPEG12_LIBRARIES)
   list(APPEND TIFF_LIBRARY_DEPS ${JPEG12_LIBRARIES})

pydip/CMakeLists.txt

@@ -1,5 +1,9 @@
 set(PYBIND11_PYTHON_VERSION ${PYTHON_VERSION}) # Avoid a warning message
-add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/pybind11" "${PROJECT_BINARY_DIR}/pybind11" EXCLUDE_FROM_ALL)
+if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+   add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/pybind11" "${PROJECT_BINARY_DIR}/pybind11" EXCLUDE_FROM_ALL)
+else()
+   find_package(pybind11 REQUIRED)
+endif()
 
 # Find sources
 file(GLOB DIP_PYTHON_SRC "${CMAKE_CURRENT_LIST_DIR}/src/*.cpp" "${CMAKE_CURRENT_LIST_DIR}/src/*.h")

src/CMakeLists.txt

@@ -68,7 +68,15 @@ endif()
 # that uses DIPlib, hence we define a variable here that removes all of DocTest from the DIPlib sources.
 set(DIP_ENABLE_DOCTEST ON CACHE BOOL "Turn off to not include doctest.h in the library headers")
 if(DIP_ENABLE_DOCTEST)
-   target_include_directories(DIP PRIVATE "${PROJECT_SOURCE_DIR}/dependencies/doctest")
+   if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+      list(APPEND CMAKE_MODULE_PATH "${PROJECT_SOURCE_DIR}/dependencies/doctest")
+      add_library(doctest INTERFACE)
+      target_include_directories(doctest INTERFACE "${PROJECT_SOURCE_DIR}/dependencies")
+      add_library(doctest::doctest ALIAS doctest)
+   else()
+      find_package(doctest REQUIRED)
+   endif()
+   target_link_libraries(DIP PRIVATE doctest::doctest)
    target_compile_definitions(DIP PRIVATE
                               DIP_CONFIG_ENABLE_DOCTEST
                               DOCTEST_CONFIG_NO_SHORT_MACRO_NAMES
@@ -95,39 +103,64 @@ endif()
 set(HAS_128_INT ${HAS_128_INT} PARENT_SCOPE)
 
 # Eigen
-target_include_directories(DIP PRIVATE "${PROJECT_SOURCE_DIR}/dependencies/eigen3")
+if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+   target_include_directories(DIP PRIVATE "${PROJECT_SOURCE_DIR}/dependencies/eigen3")
+else()
+   find_package(Eigen3 REQUIRED)
+   target_include_directories(DIP PRIVATE ${EIGEN3_INCLUDE_DIR})
+endif()
 target_compile_definitions(DIP PRIVATE
                            EIGEN_MPL2_ONLY # This makes sure we only use parts of the Eigen library that use the MPL2 license or more permissive ones.
                            EIGEN_DONT_PARALLELIZE) # This to prevent Eigen algorithms trying to run in parallel -- we parallelize at a larger scale.
 
 # zlib (for use in libics and libtiff)
 set(DIP_ENABLE_ZLIB ON CACHE BOOL "Enable zlib compression in ICS and TIFF (deflate)")
 if(DIP_ENABLE_ZLIB)
-   add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/zlib" "${PROJECT_BINARY_DIR}/zlib" EXCLUDE_FROM_ALL)
+   if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+      add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/zlib" "${PROJECT_BINARY_DIR}/zlib" EXCLUDE_FROM_ALL)
+      add_library(ZLIB::ZLIB ALIAS zlibstatic)
+   else()
+      find_package(ZLIB REQUIRED)
+   endif()
 endif()
 
 # libjpeg (for use in libtiff)
 set(DIP_ENABLE_JPEG ON CACHE BOOL "Enable JPEG file support and compression in TIFF")
 if(DIP_ENABLE_JPEG)
-   add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libjpeg" "${PROJECT_BINARY_DIR}/libjpeg" EXCLUDE_FROM_ALL)
-   target_link_libraries(DIP PRIVATE jpeg)
+   if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+      add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libjpeg" "${PROJECT_BINARY_DIR}/libjpeg" EXCLUDE_FROM_ALL)
+      add_library(JPEG::JPEG ALIAS jpeg)
+   else()
+      find_package(JPEG REQUIRED)
+   endif()
+   target_link_libraries(DIP PRIVATE JPEG::JPEG)
    target_compile_definitions(DIP PRIVATE DIP_CONFIG_HAS_JPEG)
 endif()
 
 # libics
 set(DIP_ENABLE_ICS ON CACHE BOOL "Enable ICS file support")
 if(DIP_ENABLE_ICS)
-   set(LIBICS_INCLUDE_CPP Off) # TODO: we should start using the C++ interface
-   add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libics" "${PROJECT_BINARY_DIR}/libics" EXCLUDE_FROM_ALL)
-   target_link_libraries(DIP PRIVATE libics)
+   if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+      set(LIBICS_INCLUDE_CPP Off) # TODO: we should start using the C++ interface
+      add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libics" "${PROJECT_BINARY_DIR}/libics" EXCLUDE_FROM_ALL)
+      add_library(ICS::ICS ALIAS libics)
+   else()
+      find_package(ICS REQUIRED)
+   endif()
+   target_link_libraries(DIP PRIVATE ICS::ICS)
    target_compile_definitions(DIP PRIVATE DIP_CONFIG_HAS_ICS)
 endif()
 
 # libtiff
 set(DIP_ENABLE_TIFF ON CACHE BOOL "Enable TIFF file support")
 if(DIP_ENABLE_TIFF)
-   add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libtiff" "${PROJECT_BINARY_DIR}/libtiff" EXCLUDE_FROM_ALL)
-   target_link_libraries(DIP PRIVATE tiff)
+   if(DIP_BUILD_BUNDLED_DEPENDENCIES)
+      add_subdirectory("${PROJECT_SOURCE_DIR}/dependencies/libtiff" "${PROJECT_BINARY_DIR}/libtiff" EXCLUDE_FROM_ALL)
+      add_library(TIFF::TIFF ALIAS tiff)
+   else()
+      find_package(TIFF REQUIRED)
+   endif()
+   target_link_libraries(DIP PRIVATE TIFF::TIFF)
    target_compile_definitions(DIP PRIVATE DIP_CONFIG_HAS_TIFF)
 endif()
 
@@ -157,8 +190,7 @@ install(DIRECTORY "${PROJECT_SOURCE_DIR}/include/" DESTINATION include
 # DIPlib unit tests
 if(DIP_ENABLE_DOCTEST)
    add_executable(unit_tests EXCLUDE_FROM_ALL "${CMAKE_CURRENT_LIST_DIR}/library/unit_tests.cpp")
-   target_include_directories(unit_tests PRIVATE "${PROJECT_SOURCE_DIR}/dependencies/doctest")
-   target_link_libraries(unit_tests PRIVATE DIP)
+   target_link_libraries(unit_tests PRIVATE DIP doctest::doctest)
    target_compile_definitions(unit_tests PRIVATE
                               DIP_IMPLEMENT_UNIT_TESTS
                               DIP_CONFIG_ENABLE_DOCTEST
@@ -171,7 +203,7 @@ if(DIP_ENABLE_DOCTEST)
          set_target_properties(unit_tests PROPERTIES INSTALL_RPATH "$ORIGIN")
       endif()
    else()
-      include("${PROJECT_SOURCE_DIR}/dependencies/doctest/doctest_force_link_static_lib_in_target.cmake")
+      include(doctest_force_link_static_lib_in_target.cmake)
       doctest_force_link_static_lib_in_target(unit_tests DIP) # This pulls in all object files from the static DIP library
    endif()
    add_custom_target(check COMMAND unit_tests)

src/analysis/findshift.cpp

@@ -426,7 +426,7 @@ FloatArray FindShift(
 } // namespace dip
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/generation.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing the FindShift function") {

src/binary/binary_basic.cpp

@@ -225,7 +225,7 @@ void BinaryAreaOpening(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/statistics.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing the binary morphological filters") {

src/binary/sup_inf_generator.cpp

@@ -620,7 +620,7 @@ IntervalArray ConvexHullInterval2D() {
 }
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/testing.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing private function RotateBy45Degrees") {

src/color/color.cpp

@@ -395,7 +395,7 @@ void ColorSpaceManager::SetWhitePoint( dip::XYZ whitePoint ) {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/math.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing the ColorSpaceManager class") {

src/detection/hough.cpp

@@ -325,7 +325,7 @@ FloatCoordinateArray FindHoughCircles(
 } // namespace dip
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/linear.h"
 #include "diplib/segmentation.h"
 #include "diplib/math.h"

src/distance/separable_dt.cpp

@@ -216,7 +216,7 @@ void SeparableDistanceTransform(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/math.h"
 #include "diplib/statistics.h"
 #include "diplib/generation.h"

src/file_io/ics.cpp

@@ -816,7 +816,7 @@ void ImageWriteICS(
 } // namespace dip
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/testing.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing ICS file reading and writing" ) {

src/file_io/tiff_write.cpp

@@ -374,7 +374,7 @@ void ImageWriteTIFF(
 } // namespace dip
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/testing.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing TIFF file reading and writing" ) {

src/geometry/interpolation.cpp

@@ -654,7 +654,7 @@ void Rotation(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/generation.h"
 #include "diplib/transform.h"
 #include "diplib/testing.h"

src/histogram/distribution.cpp

@@ -244,7 +244,7 @@ void Distribution::SetSampling(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/random.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing dip::Distribution" ) {

src/histogram/histogram.cpp

@@ -593,7 +593,7 @@ Histogram& Histogram::Smooth( FloatArray sigma ) {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/random.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing dip::Histogram" ) {

src/library/copy_buffer.cpp

@@ -758,7 +758,7 @@ void ExpandBuffer(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include <numeric>
 
 DOCTEST_TEST_CASE("[DIPlib] testing the CopyBuffer function") {

src/library/graph.cpp

@@ -520,7 +520,7 @@ LowestCommonAncestorSolver::LowestCommonAncestorSolver( Graph const& graph )
 } // namespace dip
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing dip::Graph") {
    dip::Image img( { 4, 5 }, 1, dip::DT_UINT8 );

src/library/image_copy.cpp

@@ -642,7 +642,7 @@ void Image::Fill( Image::Sample const& sample ) {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE( "[DIPlib] testing dip::Image::SwapBytesInSample" ) {
    dip::Image img( { 5, 8 }, 3, dip::DT_SINT16 );

src/library/image_data.cpp

@@ -746,7 +746,7 @@ CoordinatesComputer Image::IndexToCoordinatesComputer() const {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/random.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing dip::Image::Forge" ) {

src/library/image_indexing.cpp

@@ -160,7 +160,7 @@ void DefineROI(
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing image indexing") {
    // Note that this also tests parts of dip::Image::View and dip::Image::Pixel functionality, which is

src/library/image_manip.cpp

@@ -626,7 +626,7 @@ RangeArray Image::CropWindow( UnsignedArray const& sizes, String const& cropLoca
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing dip::Image dimension manipulation functions") {
    dip::Image src( { 5, 10, 15 }, 3 );

src/library/image_views.cpp

@@ -430,7 +430,7 @@ Image::View::Iterator Image::View::end() const {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/testing.h"
 
 DOCTEST_TEST_CASE( "[DIPlib] testing dip::Image::Pixel and related classes" ) {

src/library/iterators.cpp

@@ -19,7 +19,7 @@
  */
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/generic_iterators.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing ImageIterator and GenericImageIterator") {

src/library/neighborhood.cpp

@@ -485,7 +485,7 @@ NeighborList NeighborList::SelectForward( dip::uint procDim ) const {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing the NeighborList class") {
    dip::dfloat x = 1.2;

src/library/physical_dimensions.cpp

@@ -518,7 +518,7 @@ dip::String Units::StringRepresentation( bool unicode ) const {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing the dip::Units class") {
    // Note: further tested at the same time as dip::PhysicalQuantity below

src/library/pixel_table.cpp

@@ -461,7 +461,7 @@ void PixelTable::AddDistanceToOriginAsWeights() {
 
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 DOCTEST_TEST_CASE("[DIPlib] testing the PixelTable class") {
    dip::PixelTable pt( "elliptic", dip::FloatArray{ 10.1, 12.7, 5.3 }, 1 );

src/library/types.cpp

@@ -19,7 +19,7 @@
  */
 
 #ifdef DIP_CONFIG_ENABLE_DOCTEST
-#include "doctest.h"
+#include <doctest/doctest.h>
 #include "diplib/library/types.h"
 
 DOCTEST_TEST_CASE("[DIPlib] testing the dip::bin class") {

src/library/unit_tests.cpp

@@ -26,7 +26,7 @@
 #ifdef DIP_CONFIG_DOCTEST_IN_SHARED_LIB
 
 #define DOCTEST_CONFIG_IMPLEMENTATION_IN_DLL
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 #include "diplib.h"
 #include "diplib/linear.h"
@@ -51,7 +51,7 @@ int main( int argc, const char* const* argv ) {
 #else // !DIP_CONFIG_DOCTEST_IN_SHARED_LIB
 
 #define DOCTEST_CONFIG_IMPLEMENT_WITH_MAIN
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 #endif // DIP_CONFIG_DOCTEST_IN_SHARED_LIB
 
@@ -61,7 +61,7 @@ int main( int argc, const char* const* argv ) {
 
 #define DOCTEST_CONFIG_IMPLEMENTATION_IN_DLL
 #define DOCTEST_CONFIG_IMPLEMENT
-#include "doctest.h"
+#include <doctest/doctest.h>
 
 #endif // DIP_CONFIG_DOCTEST_IN_SHARED_LIB