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Merge pull request #236 from eseiler/infra/libc++
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[INFRA] libc++ CI
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@eseiler
eseiler authored Dec 5, 2023
2 parents 34b8c4f + 485576e commit 17d067b
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Showing 12 changed files with 260 additions and 55 deletions.
3 changes: 1 addition & 2 deletions .github/workflows/ci_coverage.yml
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Expand Up @@ -68,8 +68,7 @@ jobs:
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size" \
-DCHOPPER_NATIVE_BUILD=OFF
-DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size"
make -j2 gtest_build
- name: Build tests
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20 changes: 11 additions & 9 deletions .github/workflows/ci_linux.yml
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Expand Up @@ -35,21 +35,27 @@ jobs:
compiler: "clang-17"
build: unit
build_type: Release
cxx_flags: "-stdlib=libc++"

- name: "gcc13"
compiler: "gcc-13"
build_type: Release
cxx_flags: -Wno-interference-size
cxx_flags: "-Wno-interference-size"

- name: "gcc12"
compiler: "gcc-12"
build_type: Release
cxx_flags: -Wno-interference-size
cxx_flags: "-Wno-interference-size"

- name: "gcc11"
compiler: "gcc-11"
build_type: Release
cxx_flags: -Wno-interference-size
cxx_flags: "-Wno-interference-size"

- name: "IntelLLVM"
compiler: "intel"
build_type: Release
cxx_flags: "-fp-model=strict"

steps:
- name: Checkout
Expand All @@ -64,11 +70,8 @@ jobs:
compiler: ${{ matrix.compiler }}
ccache_size: 125M

- name: Install OpenMP
if: contains(matrix.name, 'clang')
run: install libomp-17-dev

- name: Install CMake
if: contains(matrix.compiler, 'intel') == false
uses: seqan/actions/setup-cmake@main
with:
cmake: 3.18.6
Expand All @@ -78,8 +81,7 @@ jobs:
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-DCMAKE_CXX_FLAGS="-Werror ${{ matrix.cxx_flags }}" \
-DCHOPPER_NATIVE_BUILD=OFF
-DCMAKE_CXX_FLAGS="-Werror ${{ matrix.cxx_flags }}"
make -j2 gtest_build
- name: Build tests
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11 changes: 9 additions & 2 deletions .github/workflows/ci_macos.yml
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Expand Up @@ -31,17 +31,25 @@ jobs:
fail-fast: true
matrix:
include:
- name: "clang17"
compiler: "clang-17"
build_type: Release
cxx_flags: "-stdlib=libc++" # For verbosity. This is already the default.

- name: "gcc13"
compiler: "gcc-13"
build_type: Release
cxx_flags: "-Wno-interference-size"

- name: "gcc12"
compiler: "gcc-12"
build_type: Release
cxx_flags: "-Wno-interference-size"

- name: "gcc11"
compiler: "gcc-11"
build_type: Release
cxx_flags: "-Wno-interference-size"

steps:
- name: Checkout
Expand All @@ -66,8 +74,7 @@ jobs:
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size" \
-DCHOPPER_NATIVE_BUILD=OFF
-DCMAKE_CXX_FLAGS="-Werror ${{ matrix.cxx_flags }}"
make -j3 gtest_build
- name: Build tests
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13 changes: 10 additions & 3 deletions .github/workflows/ci_misc.yml
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Expand Up @@ -29,17 +29,25 @@ jobs:
fail-fast: false
matrix:
include:
- name: "Header clang17"
compiler: "clang-17"
build_type: Release
cxx_flags: "-stdlib=libc++"

- name: "Header gcc13"
compiler: "gcc-13"
build_type: Release
cxx_flags: "-Wno-interference-size"

- name: "Header gcc12"
compiler: "gcc-12"
build_type: Release
cxx_flags: "-Wno-interference-size"

- name: "Header gcc11"
compiler: "gcc-11"
build_type: Release
cxx_flags: "-Wno-interference-size"

steps:
- name: Checkout
Expand All @@ -64,9 +72,8 @@ jobs:
mkdir build
cd build
cmake .. -DCMAKE_BUILD_TYPE=${{ matrix.build_type }} \
-DCMAKE_CXX_FLAGS="-Werror -Wno-interference-size" \
-DCHOPPER_HEADER_TEST_ONLY=ON \
-DCHOPPER_NATIVE_BUILD=OFF
-DCMAKE_CXX_FLAGS="-Werror ${{ matrix.cxx_flags }}" \
-DCHOPPER_HEADER_TEST_ONLY=ON
- name: Build tests
env:
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31 changes: 1 addition & 30 deletions CMakeLists.txt
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Expand Up @@ -11,7 +11,7 @@ cmake_minimum_required (VERSION 3.18)

# Define the application name and version.
project (chopper
LANGUAGES CXX C
LANGUAGES CXX
VERSION 1.0.0
)

Expand All @@ -28,40 +28,11 @@ if (NOT CMAKE_BUILD_TYPE)
)
endif ()

# Check CXX and C compiler versions.
string (REGEX MATCH "^[0-9]+" CHOPPER_CXX_MAJOR_VERSION "${CMAKE_CXX_COMPILER_VERSION}")
string (REGEX MATCH "^[0-9]+" CHOPPER_C_MAJOR_VERSION "${CMAKE_C_COMPILER_VERSION}")
if (NOT "${CHOPPER_CXX_MAJOR_VERSION}" STREQUAL "${CHOPPER_C_MAJOR_VERSION}")
message (FATAL_ERROR "CXX and C compiler major versions differ (${CHOPPER_CXX_MAJOR_VERSION} and\
${CHOPPER_C_MAJOR_VERSION})! This will likely result in linker errors. Please set both\
-DCMAKE_CXX_COMPILER and -DCMAKE_C_COMPILER to use the same major version, and/or set the\
environment variables CXX and CC accordingly."
)
endif ()

set (CHOPPER_SUBMODULES_DIR
"${CMAKE_CURRENT_LIST_DIR}/lib"
CACHE STRING "Directory containing submodules."
)

# Flag checks
include (CheckCXXCompilerFlag)

check_cxx_compiler_flag ("-fopenmp" CHOPPER_HAS_OPENMP)
if (CHOPPER_HAS_OPENMP)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp")
endif ()

check_cxx_compiler_flag ("-fopenmp-simd" CHOPPER_HAS_OPENMP_SIMD)
if (CHOPPER_HAS_OPENMP_SIMD)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fopenmp-simd -DSIMDE_ENABLE_OPENMP")
endif ()

check_cxx_compiler_flag ("-fopenmp-simd" CHOPPER_SUPPRESS_GCC4_ABI)
if (CHOPPER_SUPPRESS_GCC4_ABI)
set (CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -Wno-psabi")
endif ()

# Specify the directories where to store the built archives, libraries and executables
set (CMAKE_ARCHIVE_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
set (CMAKE_LIBRARY_OUTPUT_DIRECTORY "${CMAKE_BINARY_DIR}/lib")
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2 changes: 1 addition & 1 deletion lib/hibf
Submodule hibf updated 25 files
+0 −1 .github/workflows/ci_coverage.yml
+2 −6 .github/workflows/ci_linux.yml
+5 −1 .github/workflows/ci_macos.yml
+22 −1 .github/workflows/ci_misc.yml
+110 −0 .github/workflows/ci_sanitizer.yml
+1 −2 .github/workflows/ci_util.yml
+37 −17 cmake/configuration.cmake
+1 −0 cmake/hibf-config.cmake.in
+2 −0 include/hibf/layout/layout.hpp
+46 −5 include/hibf/misc/bit_vector.hpp
+1 −0 include/hibf/sketch/hyperloglog.hpp
+1 −1 src/CMakeLists.txt
+7 −4 src/layout/graph.cpp
+7 −0 src/layout/layout.cpp
+54 −18 src/sketch/hyperloglog.cpp
+12 −0 test/all/CMakeLists.txt
+6 −3 test/header/CMakeLists.txt
+1 −0 test/hibf-test.cmake
+5 −0 test/performance/sketch/CMakeLists.txt
+65 −0 test/performance/sketch/hyperloglog_benchmark.cpp
+1 −1 test/snippet/CMakeLists.txt
+1 −0 test/snippet/compare_snippet_output.cmake
+31 −20 test/unit/hibf/layout/layout_test.cpp
+4 −0 test/unit/hibf/sketch/toolbox_test.cpp
+8 −0 test/unit/test/expect_same_type_test.cpp
2 changes: 1 addition & 1 deletion lib/seqan3
Submodule seqan3 updated 62 files
+6 −0 .github/workflows/ci_linux.yml
+6 −0 .github/workflows/ci_macos.yml
+21 −0 .github/workflows/ci_misc.yml
+1 −1 doc/cookbook/simd_dna4.cpp
+0 −17 doc/tutorial/04_alphabet/alphabet_main.cpp
+1 −1 doc/tutorial/06_minimisers/minimisers_snippets.cpp
+0 −8 doc/tutorial/08_pairwise_alignment/configurations.cpp
+4 −2 doc/tutorial/11_read_mapper/read_mapper_step2.cpp
+2 −1 doc/tutorial/11_read_mapper/read_mapper_step3.cpp
+2 −2 include/seqan3/alignment/aligned_sequence/aligned_sequence_concept.hpp
+53 −25 include/seqan3/alignment/pairwise/alignment_result.hpp
+3 −0 include/seqan3/core/debug_stream.hpp
+6 −1 include/seqan3/core/debug_stream/debug_stream_type.hpp
+2 −2 include/seqan3/io/sam_file/format_bam.hpp
+8 −8 include/seqan3/io/sequence_file/format_embl.hpp
+4 −2 include/seqan3/io/sequence_file/format_fasta.hpp
+5 −1 include/seqan3/io/sequence_file/format_fastq.hpp
+10 −7 include/seqan3/io/sequence_file/format_genbank.hpp
+1 −0 include/seqan3/io/stream/detail/fast_istreambuf_iterator.hpp
+1 −1 include/seqan3/io/views/detail/take_until_view.hpp
+2 −2 include/seqan3/search/configuration/parallel.hpp
+14 −17 include/seqan3/search/detail/search_configurator.hpp
+24 −0 include/seqan3/std/new
+16 −1 include/seqan3/utility/char_operations/predicate_detail.hpp
+1 −1 include/seqan3/utility/simd/detail/builtin_simd.hpp
+12 −3 include/seqan3/utility/tuple/pod_tuple.hpp
+31 −0 test/api_stability/3.3.0/0001-FIX-take_until_view_test.patch
+25 −0 test/api_stability/3.3.0/0002-FIX-Change-constexpr-test.patch
+2 −2 test/api_stability/CMakeLists.txt
+4 −4 test/documentation/DoxygenLayout.xml
+1 −0 test/documentation/doc_dev/CMakeLists.txt
+2 −1 test/documentation/doc_usr/CMakeLists.txt
+2 −2 test/documentation/seqan3_doxygen_cfg.in
+5 −2 test/header/CMakeLists.txt
+3 −1 test/include/seqan3/test/performance/units.hpp
+1 −0 test/include/seqan3/test/pretty_printing.hpp
+3 −2 test/performance/alignment/global_affine_alignment_parallel_benchmark.cpp
+5 −5 test/performance/io/format_vienna_benchmark.cpp
+12 −1 test/performance/io/lowlevel_stream_input_benchmark.cpp
+3 −3 test/performance/range/container_assignment_benchmark.cpp
+2 −2 test/performance/range/container_push_back_benchmark.cpp
+8 −5 test/performance/range/container_seq_read_benchmark.cpp
+3 −3 test/performance/range/container_seq_write_benchmark.cpp
+3 −3 test/performance/search/views/view_minimiser_hash_benchmark.cpp
+1 −1 test/performance/utility/simd/views/iota_simd_benchmark.cpp
+4 −0 test/seqan3-test.cmake
+2 −1 test/snippet/CMakeLists.txt
+1 −1 test/snippet/alphabet/nucleotide/@target_alphabet@_implicit_conversion_from_@source_alphabet@_views.cpp.in
+1 −1 test/snippet/io/views/detail/take_line_view_adaptor_def.cpp
+14 −14 test/snippet/utility/char_operations/char_predicate.cpp
+1 −1 test/snippet/utility/type_pack/detail/type_pack_algorithm_all_of.cpp
+2 −1 test/unit/alignment/matrix/detail/debug_matrix_test.cpp
+9 −3 test/unit/alignment/pairwise/edit_distance/proxy_reference_test.cpp
+1 −1 test/unit/alphabet/views/char_strictly_to_test.cpp
+1 −1 test/unit/alphabet/views/validate_char_for_test.cpp
+11 −0 test/unit/core/debug_stream_test.cpp
+1 −2 test/unit/io/sequence_file/sequence_file_format_genbank_test.cpp
+8 −1 test/unit/test/expect_same_type_test.cpp
+21 −0 test/unit/test/sequence_generator_test.cpp
+4 −0 test/unit/utility/container/aligned_allocator_test.cpp
+4 −0 test/unit/utility/detail/type_name_as_string_test.cpp
+55 −50 test/unit/utility/tuple/pod_tuple_test.cpp
2 changes: 1 addition & 1 deletion lib/sharg-parser
Submodule sharg-parser updated 7 files
+8 −0 .github/workflows/ci_linux.yml
+6 −0 .github/workflows/ci_macos.yml
+15 −0 .github/workflows/ci_misc.yml
+1 −0 include/sharg/version.hpp
+5 −2 test/header/CMakeLists.txt
+1 −0 test/sharg-test.cmake
+4 −0 test/unit/detail/type_name_as_string_test.cpp
1 change: 1 addition & 0 deletions src/layout/hibf_statistics.cpp
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Expand Up @@ -24,6 +24,7 @@
#endif // CHOPPER_WORKAROUND_GCC_BOGUS_MEMCPY
#include <map>
#include <numeric>
#include <sstream>
#include <string>
#include <utility>
#include <vector>
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99 changes: 99 additions & 0 deletions test/api/layout/execute_layout_test.cpp
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Expand Up @@ -321,6 +321,104 @@ TEST(execute_test, many_ubs)
"#LOWER_LEVEL_IBF_26 fullest_technical_bin_idx:0\n"
"#LOWER_LEVEL_IBF_27 fullest_technical_bin_idx:0\n"
"#USER_BIN_IDX\tTECHNICAL_BIN_INDICES\tNUMBER_OF_TECHNICAL_BINS\n"
#ifdef _LIBCPP_VERSION // seqan::hibf::sketch::toolbox::sort_by_cardinalities is not stable
"5\t0;0\t1;14\n"
"4\t0;14\t1;10\n"
"3\t0;24\t1;10\n"
"2\t0;34\t1;10\n"
"1\t0;44\t1;10\n"
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"95\t63\t1\n"};
#else
"15\t0;0\t1;14\n"
"16\t0;14\t1;10\n"
"17\t0;24\t1;10\n"
Expand Down Expand Up @@ -417,6 +515,7 @@ TEST(execute_test, many_ubs)
"81\t61\t1\n"
"80\t62\t1\n"
"95\t63\t1\n"};
#endif
std::string const actual_file{string_from_file(layout_file)};

EXPECT_EQ(actual_file, expected_file) << actual_file << std::endl;
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