Merge branch 'main' into impl-stats

.gitignore

@@ -19,9 +19,10 @@ Testing/
 venv/
 
 # Ignored files
+*.bak
 gmon.out
 perf.*
 compile_commands.json
 CMakeUserPresets.json
-src/common/include/hictk/git.hpp
-src/common/include/hictk/version.hpp
+src/libhictk/common/include/hictk/git.hpp
+src/libhictk/common/include/hictk/version.hpp

CMakeLists.txt

@@ -26,14 +26,14 @@ include(cmake/Versioning.cmake)
 project(
   hictk
   LANGUAGES C CXX
-  VERSION ${HICTK_PROJECT_VERSION_MAJOR}.${HICTK_PROJECT_VERSION_MINOR}.${HICTK_PROJECT_VERSION_PATCH}
+  VERSION "${HICTK_PROJECT_VERSION_MAJOR}.${HICTK_PROJECT_VERSION_MINOR}.${HICTK_PROJECT_VERSION_PATCH}"
   HOMEPAGE_URL https://github.com/robomics/hictk
   DESCRIPTION "High-performance C++ library to read and write .cool files.")
 
 include(FetchContent)
 FetchContent_Declare(
   _hictk_project_options
-  URL ${CMAKE_CURRENT_SOURCE_DIR}/external/project_options-v0.29.0.tar.xz
+  URL "${CMAKE_CURRENT_SOURCE_DIR}/external/project_options-v0.29.0.tar.xz"
   URL_HASH SHA256=ee2836af616d42e22c61048f4aedafd104fbfd97cf52bdd122a212d98777304c
   SYSTEM)
 FetchContent_MakeAvailable(_hictk_project_options)
@@ -55,8 +55,8 @@ if(BUILDING_MULTI_CONFIG)
   endif()
 endif()
 
-include(${_hictk_project_options_SOURCE_DIR}/src/DynamicProjectOptions.cmake)
-include(${CMAKE_CURRENT_SOURCE_DIR}/cmake/CompilerWarnings.cmake)
+include("${_hictk_project_options_SOURCE_DIR}/src/DynamicProjectOptions.cmake")
+include("${CMAKE_CURRENT_SOURCE_DIR}/cmake/CompilerWarnings.cmake")
 
 # dynamic_project_options sets recommended defaults and provides user and developer modes and full GUI support for
 # choosing options at configure time
@@ -101,15 +101,15 @@ dynamic_project_options(
   --suppress=passedByValue
   --inconclusive
   MSVC_WARNINGS
-  ${MSVC_WARNINGS}
+  "${MSVC_WARNINGS}"
   CLANG_WARNINGS
-  ${CLANG_WARNINGS}
+  "${CLANG_WARNINGS}"
   GCC_WARNINGS
-  ${GCC_WARNINGS}
+  "${GCC_WARNINGS}"
   CUDA_WARNINGS
-  ${CUDA_WARNINGS})
+  "${CUDA_WARNINGS}")
 
-target_compile_features(hictk_project_options INTERFACE cxx_std_${CMAKE_CXX_STANDARD})
+target_compile_features(hictk_project_options INTERFACE "cxx_std_${CMAKE_CXX_STANDARD}")
 
 if(WIN32)
   target_compile_definitions(hictk_project_options INTERFACE NOMINMAX _CRT_SECURE_NO_WARNINGS)
@@ -131,8 +131,6 @@ if(HICTK_WITH_EIGEN)
   target_compile_definitions(hictk_project_options INTERFACE HICTK_WITH_EIGEN)
 endif()
 
-include(cmake/FetchExternalDeps.cmake)
-
 add_subdirectory(src)
 
 if(HICTK_ENABLE_TESTING)
@@ -156,3 +154,6 @@ if(HICTK_BUILD_PYTHON_BINDINGS)
   message(STATUS "Building Python bindings.")
   add_subdirectory(bindings/python)
 endif()
+
+
+include(cmake/Install.cmake)

Dockerfile

@@ -69,8 +69,9 @@ RUN cmake -DCMAKE_BUILD_TYPE=Release            \
           -B "$build_dir"
 
 # Build and install project
-RUN cmake --build "$build_dir" -t hictk_tools -j "$(nproc)"  \
-&& cmake --install "$build_dir"
+RUN cmake --build "$build_dir" -t hictk -j "$(nproc)"  \
+&& cmake --install "$build_dir" \
+&& rm -rf "$build_dir/include" "$build_dir/lib"
 
 ARG FINAL_BASE_IMAGE
 ARG FINAL_BASE_IMAGE_DIGEST

benchmark/fetch_and_sum/CMakeLists.txt

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
+find_package(CLI11 CONFIG REQUIRED)
 find_package(Filesystem REQUIRED)
 
 add_executable(hictk_fetch_and_sum_bench fetch_and_sum.cpp)

benchmark/hic/CMakeLists.txt

@@ -2,6 +2,7 @@
 #
 # SPDX-License-Identifier: MIT
 
+find_package(CLI11 CONFIG REQUIRED)
 find_package(Filesystem REQUIRED)
 
 add_executable(hictk_hic_dump_bench dump.cpp)

cmake/FetchTestDataset.cmake

@@ -6,12 +6,12 @@
 file(
   DOWNLOAD https://zenodo.org/record/8143316/files/hictk_test_data.tar.xz?download=1
   EXPECTED_HASH SHA256=c36249596d429a3d0b1b4a32802ac505ab2eba550b19ca093706922155f2d333
-  ${PROJECT_SOURCE_DIR}/test/data/hictk_test_data.tar.xz)
+  "${PROJECT_SOURCE_DIR}/test/data/hictk_test_data.tar.xz")
 # cmake-format: on
 
 file(
   ARCHIVE_EXTRACT
   INPUT
-  ${PROJECT_SOURCE_DIR}/test/data/hictk_test_data.tar.xz
+  "${PROJECT_SOURCE_DIR}/test/data/hictk_test_data.tar.xz"
   DESTINATION
-  ${PROJECT_SOURCE_DIR})
+  "${PROJECT_SOURCE_DIR}")

cmake/Install.cmake

@@ -0,0 +1,51 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+set(targets
+    balancing;bin_table;chromosome;common;cooler;formatting;genomic_interval;hic;numeric;pixel;reference;transformers;variant
+)
+
+include(GNUInstallDirs)
+foreach(tgt ${targets})
+  install(DIRECTORY "${PROJECT_SOURCE_DIR}/src/libhictk/${tgt}/include/hictk" DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
+endforeach()
+
+install(
+  TARGETS libhictk
+          balancing
+          bin_table
+          chromosome
+          common
+          cooler
+          formatting
+          genomic_interval
+          hic
+          numeric
+          pixel
+          reference
+          transformers
+          variant
+  EXPORT libhictk-targets
+  FILE_SET HEADERS
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+  RUNTIME DESTINATION "${CMAKE_INSTALL_BINDIR}"
+  LIBRARY DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+  ARCHIVE DESTINATION "${CMAKE_INSTALL_LIBDIR}"
+  PUBLIC_HEADER DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+  PRIVATE_HEADER DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}"
+  INCLUDES
+  DESTINATION "${CMAKE_INSTALL_INCLUDEDIR}")
+
+install(
+  EXPORT libhictk-targets
+  FILE hictkTargets.cmake
+  NAMESPACE hictk::
+  DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/hictk/")
+
+include(CMakePackageConfigHelpers)
+configure_package_config_file(
+  "${PROJECT_SOURCE_DIR}/cmake/hictkConfig.cmake.in" "${CMAKE_CURRENT_BINARY_DIR}/hictkConfig.cmake"
+  INSTALL_DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/hictk/")
+
+install(FILES "${CMAKE_CURRENT_BINARY_DIR}/hictkConfig.cmake" DESTINATION "${CMAKE_INSTALL_LIBDIR}/cmake/hictk")

cmake/Versioning.cmake

@@ -25,12 +25,12 @@ function(ConfigureVersioning input_config_folder output_config_folder)
     include(FetchContent)
     FetchContent_Declare(
       _hictk_cmake-git-version-tracking
-      URL ${CMAKE_CURRENT_SOURCE_DIR}/external/cmake-git-version-tracking.20221027.tar.xz
+      URL "${CMAKE_CURRENT_SOURCE_DIR}/external/cmake-git-version-tracking.20221027.tar.xz"
       URL_HASH SHA256=f2d407c9b45bf8874e5f2126147fbb4e7d2872d586f43d6a2c45d09f60f04365)
     FetchContent_MakeAvailable(_hictk_cmake-git-version-tracking)
 
     set(GIT_IGNORE_UNTRACKED ON)
-    include(${_hictk_cmake-git-version-tracking_SOURCE_DIR}/git_watcher.cmake)
+    include("${_hictk_cmake-git-version-tracking_SOURCE_DIR}/git_watcher.cmake")
   else()
     # Add dummy target
     add_custom_target(_hictk_check_git)
@@ -69,14 +69,15 @@ function(ConfigureVersioning input_config_folder output_config_folder)
       set(GIT_TAG "unknown")
     endif()
 
-    configure_file(${PRE_CONFIGURE_FILE} ${POST_CONFIGURE_FILE} @ONLY)
+    configure_file("${PRE_CONFIGURE_FILE}" "${POST_CONFIGURE_FILE}" @ONLY)
   endif()
 
   set(PRE_CONFIGURE_FILE "${input_config_folder}/version.hpp.in")
   set(POST_CONFIGURE_FILE "${output_config_folder}/version.hpp")
 
-  file(TOUCH ${POST_CONFIGURE_FILE})
-  configure_file(${PRE_CONFIGURE_FILE} ${POST_CONFIGURE_FILE} @ONLY)
+  file(TOUCH "${POST_CONFIGURE_FILE}")
+  configure_file("${PRE_CONFIGURE_FILE}" "${POST_CONFIGURE_FILE}" @ONLY)
 endfunction()
 
-configureversioning("${CMAKE_CURRENT_SOURCE_DIR}/src/config" "${CMAKE_CURRENT_SOURCE_DIR}/src/common/include/hictk")
+configureversioning("${CMAKE_CURRENT_SOURCE_DIR}/src/libhictk/config"
+                    "${CMAKE_CURRENT_SOURCE_DIR}/src/libhictk/common/include/hictk")

cmake/hictkConfig.cmake.in

@@ -0,0 +1,58 @@
+# Copyright (C) 2023 Roberto Rossini <[email protected]>
+#
+# SPDX-License-Identifier: MIT
+
+@PACKAGE_INIT@
+
+set(HICTK_WITH_EIGEN @HICTK_WITH_EIGEN@)
+
+include(CMakeFindDependencyMacro)
+if(HICTK_WITH_EIGEN)
+  find_dependency(
+    Eigen3
+    CONFIG
+    QUIET
+    REQUIRED)
+endif()
+
+find_dependency(
+  FastFloat
+  CONFIG
+  QUIET
+  REQUIRED)
+find_dependency(
+  FMT
+  CONFIG
+  QUIET
+  REQUIRED)
+find_dependency(
+  HDF5
+  CONFIG
+  QUIET
+  REQUIRED
+  COMPONENTS
+  C)
+find_dependency(
+  HighFive
+  CONFIG
+  QUIET
+  REQUIRED)
+find_dependency(
+  libdeflate
+  CONFIG
+  QUIET
+  REQUIRED)
+find_dependency(
+  phmap
+  CONFIG
+  QUIET
+  REQUIRED)
+find_dependency(
+  spdlog
+  CONFIG
+  QUIET
+  REQUIRED)
+
+include("${CMAKE_CURRENT_LIST_DIR}/hictkTargets.cmake")
+
+check_required_components(hictk)