Add support for PCH

.github/workflows/codecov.yml

@@ -131,6 +131,7 @@ jobs:
                 -DHICTK_ENABLE_TESTING=ON                     \
                 -DHICTK_DOWNLOAD_TEST_DATASET=OFF             \
                 -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF       \
+                -DHICTK_USE_PCH=ON                            \
                 -S .                                          \
                 -B build
 

.github/workflows/macos-ci.yml

@@ -193,6 +193,7 @@ jobs:
                 -DOPT_ENABLE_CPPCHECK=OFF                            \
                 -DHICTK_DOWNLOAD_TEST_DATASET=OFF                    \
                 -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF              \
+                -DHICTK_USE_PCH=ON                                   \
                 -DCMAKE_INSTALL_PREFIX=dest                          \
                 -S "${{ github.workspace }}"                         \
                 -B "${{ github.workspace }}/build"

.github/workflows/run-clang-tidy.yml

@@ -127,6 +127,7 @@ jobs:
                 -DHICTK_ENABLE_TESTING=ON                     \
                 -DHICTK_DOWNLOAD_TEST_DATASET=OFF             \
                 -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF       \
+                -DHICTK_USE_PCH=ON                            \
                 -S .                                          \
                 -B build
 

.github/workflows/ubuntu-ci.yml

@@ -256,6 +256,7 @@ jobs:
                 -DHICTK_DOWNLOAD_TEST_DATASET=OFF                    \
                 -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF              \
                 -DCMAKE_INSTALL_PREFIX=dest                          \
+                -DHICTK_USE_PCH=ON                                   \
                 -S .                                                 \
                 -B build
 

.github/workflows/windows-ci.yml

@@ -172,6 +172,7 @@ jobs:
                 -DHICTK_ENABLE_GIT_VERSION_TRACKING=OFF              \
                 -DOPT_ENABLE_CLANG_TIDY=OFF                          \
                 -DOPT_ENABLE_CPPCHECK=OFF                            \
+                -DHICTK_USE_PCH=OFF                                  \
                 -S .                                                 \
                 -B build
 

CMakeLists.txt

@@ -117,6 +117,8 @@ target_compile_features(hictk_project_options INTERFACE "cxx_std_${CMAKE_CXX_STA
 
 # Tweak fmt
 target_compile_definitions(hictk_project_options INTERFACE FMT_HEADER_ONLY FMT_ENFORCE_COMPILE_STRING)
+# Tweak spanlite
+target_compile_definitions(hictk_project_options INTERFACE span_FEATURE_MAKE_SPAN=1)
 # Tweak spdlog
 target_compile_definitions(hictk_project_options INTERFACE SPDLOG_FMT_EXTERNAL)
 #Tweak xxHash
@@ -136,6 +138,7 @@ option(HICTK_BUILD_EXAMPLES "Build examples" OFF)
 option(HICTK_BUILD_BENCHMARKS "Build benchmarks" OFF)
 option(HICTK_WITH_EIGEN "Build with Eigen3 support" ON)
 option(HICTK_BUILD_TOOLS "Build cli tools" ON)
+option(HICTK_USE_PCH "Build hictk using PCH" OFF)
 
 if(HICTK_WITH_EIGEN)
   target_compile_definitions(hictk_project_options INTERFACE HICTK_WITH_EIGEN)

src/hictk/CMakeLists.txt

@@ -36,6 +36,11 @@ target_sources(
           ${CMAKE_CURRENT_SOURCE_DIR}/zoomify/zoomify.cpp)
 
 target_include_directories(hictk PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/include")
+
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk PRIVATE [["hictk/tools/internal/pch.hpp"]])
+endif()
+
 target_link_libraries(hictk PRIVATE hictk_project_options hictk_project_warnings hictk::libhictk)
 
 target_link_system_libraries(

src/hictk/include/hictk/tools/internal/pch.hpp

@@ -0,0 +1,39 @@
+// Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
+//
+// SPDX-License-Identifier: MIT
+
+#pragma once
+
+#include <fmt/format.h>
+
+#include <algorithm>
+#include <cassert>
+#include <cstddef>
+#include <cstdint>
+#include <exception>
+#include <filesystem>
+#include <functional>
+#include <highfive/H5File.hpp>
+#include <iterator>
+#include <limits>
+#include <memory>
+#include <stdexcept>
+#include <string>
+#include <string_view>
+#include <type_traits>
+#include <utility>
+#include <variant>
+#include <vector>
+
+#include "hictk/balancing/methods.hpp"
+#include "hictk/bin_table.hpp"
+#include "hictk/chromosome.hpp"
+#include "hictk/common.hpp"
+#include "hictk/cooler/cooler.hpp"
+#include "hictk/cooler/dataset.hpp"
+#include "hictk/cooler/group.hpp"
+#include "hictk/hic/common.hpp"
+#include "hictk/pixel.hpp"
+#include "hictk/reference.hpp"
+#include "hictk/suppress_warnings.hpp"
+#include "hictk/type_traits.hpp"

src/libhictk/balancing/CMakeLists.txt

@@ -30,5 +30,3 @@ target_link_system_libraries(
   phmap
   xxHash::xxhash
   "zstd::libzstd_$<IF:$<BOOL:${BUILD_SHARED_LIBS}>,shared,static>")
-
-target_compile_definitions(balancing INTERFACE span_FEATURE_MAKE_SPAN=1)

test/units/CMakeLists.txt

@@ -4,6 +4,8 @@
 
 include_directories(include)
 
+add_subdirectory(pch)
+
 add_subdirectory(balancing)
 add_subdirectory(bin_table)
 add_subdirectory(chromosome)

test/units/balancing/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_balancing_tests)
 
 target_sources(hictk_balancing_tests PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/balancing_test.cpp)
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_balancing_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_balancing_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/bin_table/CMakeLists.txt

@@ -7,17 +7,21 @@ find_package(Filesystem REQUIRED)
 include(CTest)
 include(Catch)
 
-add_executable(bin_table_tests)
+add_executable(hictk_bin_table_tests)
 
-target_sources(bin_table_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/bin_table_test.cpp")
+target_sources(hictk_bin_table_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/bin_table_test.cpp")
+
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_bin_table_tests REUSE_FROM hictk_test_pch)
+endif()
 
 target_link_libraries(
-  bin_table_tests
+  hictk_bin_table_tests
   PRIVATE hictk_project_warnings hictk_project_options
   PUBLIC hictk::bin_table hictk::format)
 
 target_link_system_libraries(
-  bin_table_tests
+  hictk_bin_table_tests
   PUBLIC
   Catch2::Catch2WithMain
   std::filesystem)
@@ -27,7 +31,7 @@ file(MAKE_DIRECTORY "${CMAKE_CURRENT_BINARY_DIR}/Testing/")
 # automatically discover tests that are defined in catch based test files you can modify the unittests. TEST_PREFIX to
 # whatever you want, or use different for different binaries
 catch_discover_tests(
-  bin_table_tests
+  hictk_bin_table_tests
   TEST_SPEC
   "[short]"
   TEST_SUFFIX
@@ -41,7 +45,7 @@ catch_discover_tests(
   --skip-benchmarks)
 
 catch_discover_tests(
-  bin_table_tests
+  hictk_bin_table_tests
   TEST_SPEC
   "[medium]"
   TEST_SUFFIX
@@ -53,7 +57,7 @@ catch_discover_tests(
   --skip-benchmarks)
 
 catch_discover_tests(
-  bin_table_tests
+  hictk_bin_table_tests
   TEST_SPEC
   "[long]"
   TEST_SUFFIX

test/units/cooler/CMakeLists.txt

@@ -39,6 +39,10 @@ target_sources(
           "${CMAKE_CURRENT_SOURCE_DIR}/utils_merge_test.cpp"
           "${CMAKE_CURRENT_SOURCE_DIR}/utils_validation_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_cooler_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_cooler_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/file/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_file_tests)
 
 target_sources(hictk_file_tests PRIVATE ${CMAKE_CURRENT_SOURCE_DIR}/file_test.cpp)
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_file_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_file_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/hic/CMakeLists.txt

@@ -16,6 +16,10 @@ target_sources(
           "${CMAKE_CURRENT_SOURCE_DIR}/hic_file_test.cpp"
           "${CMAKE_CURRENT_SOURCE_DIR}/pixel_selector_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_hic_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_hic_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/pch/CMakeLists.txt

@@ -0,0 +1,17 @@
+# Copyright (C) 2022 Roberto Rossini <roberros@uio.no>
+#
+# SPDX-License-Identifier: MIT
+
+find_package(fmt REQUIRED)
+
+if(HICTK_USE_PCH)
+  add_library(hictk_test_pch)
+  target_sources(hictk_test_pch PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/lib.cpp")
+  target_precompile_headers(hictk_test_pch PUBLIC "${CMAKE_CURRENT_SOURCE_DIR}/pch.hpp")
+  target_link_libraries(
+    hictk_test_pch
+    PRIVATE hictk_project_options hictk_project_warnings
+    PUBLIC hictk::libhictk
+           Catch2::Catch2WithMain
+           fmt::fmt-header-only)
+endif()

test/units/pch/lib.cpp

@@ -0,0 +1,3 @@
+// Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
+//
+// SPDX-License-Identifier: MIT

test/units/pch/pch.hpp

@@ -0,0 +1,42 @@
+// Copyright (C) 2023 Roberto Rossini <roberros@uio.no>
+//
+// SPDX-License-Identifier: MIT
+
+#pragma once
+
+#include <fmt/format.h>
+
+#include <algorithm>
+#include <cassert>
+#include <catch2/catch_test_macros.hpp>
+#include <catch2/matchers/catch_matchers_floating_point.hpp>
+#include <catch2/matchers/catch_matchers_string.hpp>
+#include <cstddef>
+#include <cstdint>
+#include <exception>
+#include <filesystem>
+#include <functional>
+// #include <highfive/H5File.hpp>
+#include <iterator>
+#include <limits>
+#include <memory>
+#include <stdexcept>
+#include <string>
+#include <string_view>
+#include <type_traits>
+#include <utility>
+#include <variant>
+#include <vector>
+
+#include "hictk/balancing/methods.hpp"
+#include "hictk/bin_table.hpp"
+#include "hictk/chromosome.hpp"
+#include "hictk/common.hpp"
+#include "hictk/cooler/cooler.hpp"
+#include "hictk/cooler/dataset.hpp"
+#include "hictk/cooler/group.hpp"
+#include "hictk/hic/common.hpp"
+#include "hictk/pixel.hpp"
+#include "hictk/reference.hpp"
+#include "hictk/suppress_warnings.hpp"
+#include "hictk/type_traits.hpp"

test/units/pixel/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_pixel_tests)
 
 target_sources(hictk_pixel_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/pixel_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_pixel_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_pixel_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/reference/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_reference_tests)
 
 target_sources(hictk_reference_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/reference_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_reference_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_reference_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/transformers/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_transformers_tests)
 
 target_sources(hictk_transformers_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/transformers_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_transformers_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_transformers_tests
   PRIVATE hictk_project_warnings hictk_project_options

test/units/variant/CMakeLists.txt

@@ -11,6 +11,10 @@ add_executable(hictk_variant_tests)
 
 target_sources(hictk_variant_tests PRIVATE "${CMAKE_CURRENT_SOURCE_DIR}/variant_test.cpp")
 
+if(HICTK_USE_PCH)
+  target_precompile_headers(hictk_variant_tests REUSE_FROM hictk_test_pch)
+endif()
+
 target_link_libraries(
   hictk_variant_tests
   PRIVATE hictk_project_warnings hictk_project_options