Removed duplicated files from other repositories

CMakeLists.txt

@@ -1,5 +1,8 @@
 cmake_minimum_required(VERSION 3.18)
 
+set(XMIPP_CORE_REPO_REF "tags/v4.0.0" CACHE STRING "Xmipp Core's repository commit to be fetched")
+set(XMIPP3_REPO_REF "tags/v5.0.0-Beta-gal" CACHE STRING "Xmipp3's repository commit to be fetched")
+
 # Define the project
 file(READ ${CMAKE_CURRENT_SOURCE_DIR}/VERSION PROJECT_VERSION)
 string(STRIP "${PROJECT_VERSION}" PROJECT_VERSION)
@@ -16,9 +19,11 @@ include(GNUInstallDirs)
 # Set the module path
 list(APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake/modules)
 
+# Find system dependencies
 find_package(Threads REQUIRED)
 find_package(Python REQUIRED COMPONENTS Interpreter Development.Module NumPy)
 
+# Fetch dependencies
 include(fetch_hdf5)
 include(fetch_sqlite3)
 include(fetch_fftw3)
@@ -37,12 +42,111 @@ else()
 	set(PYTHON_INSTALL_DIR "${Python_SITEARCH}")
 endif()
 
+# Fetch main Xmipp repository
+cmake_policy(SET CMP0135 NEW) # To avoid warnings
+FetchContent_Declare(
+    xmipp_core_sources
+    URL https://github.com/I2PC/xmippCore/archive/refs/${XMIPP_CORE_REPO_REF}.tar.gz
+)	
+FetchContent_Declare(
+    xmipp3_sources
+	URL https://github.com/I2PC/xmipp3/archive/refs/${XMIPP3_REPO_REF}.tar.gz
+)
+FetchContent_Populate(xmipp_core_sources)
+FetchContent_Populate(xmipp3_sources)
+
 # Set project-wide compilation options
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_CXX_STANDARD_REQUIRED ON)
 
-# Add sources
-add_subdirectory(src)
+# Get FFTW include dir
+FetchContent_GetProperties(fftw3_double SOURCE_DIR FFTW_SOURCE_DIR)
+set(FFTW_INCLUDE_DIR ${FFTW_SOURCE_DIR}/api)
+
+# Register all source and header files
+set(XMIPP_CORE_DIR ${xmipp_core_sources_SOURCE_DIR})
+set(XMIPP3_LIBRARY_DIR ${xmipp3_sources_SOURCE_DIR}/src/xmipp/libraries)
+file(
+	GLOB_RECURSE 
+	SOURCES 
+        ${XMIPP_CORE_DIR}/core/*.cpp
+        ${XMIPP_CORE_DIR}/core/*.cc
+        ${XMIPP_CORE_DIR}/core/*.c
+		${CMAKE_CURRENT_SOURCE_DIR}/src/*.cpp 
+)
+list(
+    APPEND
+    SOURCES
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_enhance_psd.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_estimate_from_micrograph.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_estimate_from_psd_base.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_estimate_from_psd.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_estimate_from_psd_fast.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/ctf_estimate_psd_with_arma.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/fringe_processing.cpp
+        ${XMIPP3_LIBRARY_DIR}/reconstruction/psd_estimator.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/basic_pca.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/basis.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/blobs.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/cpu.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/ctf.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/fft_settings.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/fftwT.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/filters.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/fourier_filter.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/fourier_projection.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/grids.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/integration.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/mask.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/morphology.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/normalize.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/numerical_tools.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/polar.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/projection.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/splines.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/wavelet.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/xmipp_image_over.cpp
+        ${XMIPP3_LIBRARY_DIR}/data/xmipp_polynomials.cpp
+)
+
+# Create the shared library
+add_library(xmippLib MODULE ${SOURCES})
+target_link_libraries(
+    xmippLib 
+    PRIVATE 
+        Threads::Threads
+        Python::Module
+        Python::NumPy
+        sqlite3
+        HDF5::CXX
+        HDF5::HDF5
+        FFTW3::Double
+		FFTW3::Float
+		FFTW3::DoubleThreads
+		FFTW3::FloatThreads
+        JPEG::JPEG
+        TIFF::tiff
+)
+target_include_directories(
+    xmippLib 
+    PRIVATE 
+        ${XMIPP_CORE_DIR}
+        ${XMIPP3_LIBRARY_DIR}
+        ${CMAKE_CURRENT_SOURCE_DIR}/src
+        ${FFTW_INCLUDE_DIR}
+)
+set_target_properties(xmippLib 
+    PROPERTIES
+        PREFIX ""
+        OUTPUT_NAME "xmippLib"
+)
+
+# Install library's binary files and headers
+install(
+	TARGETS xmippLib
+	LIBRARY 
+	    DESTINATION "${PYTHON_INSTALL_DIR}"
+)
 
 # Install Python scripts
 install(DIRECTORY