Merge pull request #181 from eseiler/infra/iwyu_clang

[INFRA] Run iwyu with libc++

.github/workflows/ci_iwyu.yml

@@ -67,7 +67,7 @@ jobs:
           mkdir build
           cd build
           cmake ../hibf/test/iwyu -DCMAKE_BUILD_TYPE=Release \
-                                  -DHIBF_NATIVE_BUILD=OFF \
+                                  -DCMAKE_CXX_FLAGS="-stdlib=libc++" \
                                   -DHIBF_VERBOSE_TESTS=OFF
 
       - name: Run Test

include/hibf/contrib/aligned_allocator.hpp

@@ -10,9 +10,12 @@
 
 #pragma once
 
-#include <limits>
-#include <memory>
-#include <type_traits>
+#include <algorithm>   // for max
+#include <cstddef>     // for size_t
+#include <limits>      // for numeric_limits
+#include <memory>      // for pointer_traits
+#include <new>         // for align_val_t, bad_alloc
+#include <type_traits> // for make_unsigned_t, true_type
 
 // __cpp_aligned_new is a C++17 feature that we use in this allocator and we require it.
 #if __cpp_aligned_new < 201606

include/hibf/hierarchical_interleaved_bloom_filter.hpp

@@ -4,15 +4,15 @@
 
 #pragma once
 
-#include <algorithm>  // for max, __sort_fn, fill, sort
+#include <algorithm>  // for __fn, fill, sort
 #include <cassert>    // for assert
 #include <cinttypes>  // for int64_t, uint16_t
 #include <concepts>   // for integral, unsigned_integral
 #include <cstddef>    // for size_t
-#include <functional> // for identity, less
+#include <functional> // for less, identity
+#include <memory>     // for addressof
 #include <ranges>     // for forward_range, range, range_value_t
-#include <utility>    // for addressof
-#include <vector>     // for vector
+#include <vector>     // for vector, operator==
 
 #include <hibf/cereal/concepts.hpp>          // for cereal_archive
 #include <hibf/config.hpp>                   // for config

include/hibf/interleaved_bloom_filter.hpp

@@ -15,9 +15,9 @@
 #include <cinttypes>   // for uint16_t, uint64_t
 #include <concepts>    // for integral, same_as, unsigned_integral
 #include <cstring>     // for size_t
-#include <ranges>      // for range, forward_range, input_range, range_reference_t, range_value_t
+#include <memory>      // for addressof
+#include <ranges>      // for range, forward_range, input_range, range_reference_t, range_va...
 #include <type_traits> // for remove_cvref_t
-#include <utility>     // for addressof
 #include <vector>      // for operator==, vector
 
 #include <hibf/cereal/concepts.hpp>           // for cereal_archive

include/hibf/layout/data_store.hpp

@@ -4,7 +4,6 @@
 
 #pragma once
 
-#include <algorithm> // for copy, fill_n, max
 #include <cassert>   // for assert
 #include <cinttypes> // for uint64_t
 #include <cstddef>   // for size_t
@@ -13,7 +12,7 @@
 #include <vector>    // for vector
 
 #include <hibf/layout/layout.hpp>      // for layout
-#include <hibf/misc/timer.hpp>         // for concurrent, timer
+#include <hibf/misc/timer.hpp>         // for concurrent_timer
 #include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 
 namespace seqan::hibf::layout

include/hibf/layout/graph.hpp

@@ -9,10 +9,9 @@
 
 #pragma once
 
-#include <algorithm> // for copy
-#include <cstddef>   // for size_t
-#include <optional>  // for nullopt, optional
-#include <vector>    // for vector
+#include <cstddef>  // for size_t
+#include <optional> // for nullopt, optional
+#include <vector>   // for vector
 
 #include <hibf/layout/layout.hpp> // for layout
 

include/hibf/layout/hierarchical_binning.hpp

@@ -6,7 +6,8 @@
 
 #include <cassert> // for assert
 #include <cstddef> // for size_t
-#include <utility> // for addressof, pair
+#include <memory>  // for addressof
+#include <utility> // for pair
 #include <vector>  // for vector
 
 #include <hibf/build/bin_size_in_bits.hpp> // for bin_size_in_bits

include/hibf/layout/layout.hpp

@@ -4,13 +4,12 @@
 
 #pragma once
 
-#include <algorithm> // for copy
-#include <concepts>  // for derived_from
-#include <cstddef>   // for size_t
-#include <iosfwd>    // for ostream
-#include <vector>    // for vector, operator==
+#include <concepts> // for derived_from
+#include <cstddef>  // for size_t
+#include <iosfwd>   // for ostream, istream
+#include <vector>   // for operator==, vector
 
-#include <hibf/layout/prefixes.hpp> // for header, merged_bin
+#include <hibf/layout/prefixes.hpp> // for layout_fullest_technical_bin_idx, layout_header, layout_lower_level
 #include <hibf/platform.hpp>
 
 namespace seqan::hibf::layout

include/hibf/layout/simple_binning.hpp

@@ -6,8 +6,8 @@
 
 #include <cassert>   // for assert
 #include <cstddef>   // for size_t
+#include <memory>    // for addressof
 #include <stdexcept> // for runtime_error
-#include <utility>   // for addressof
 #include <vector>    // for vector
 
 #include <hibf/layout/data_store.hpp>        // for data_store

include/hibf/misc/counting_vector.hpp

@@ -9,6 +9,7 @@
 
 #pragma once
 
+#include <algorithm>   // for transform
 #include <bit>         // for countr_zero
 #include <cassert>     // for assert
 #include <cinttypes>   // for uint64_t

include/hibf/misc/insert_iterator.hpp

@@ -4,12 +4,11 @@
 
 #pragma once
 
-#include <algorithm> // for max
 #include <cassert>   // for assert
 #include <cinttypes> // for uint64_t
 #include <cstddef>   // for ptrdiff_t
 #include <iterator>  // for output_iterator_tag
-#include <utility>   // for addressof, move
+#include <memory>    // for addressof
 #include <vector>    // for vector
 
 #include <hibf/contrib/robin_hood.hpp> // for unordered_flat_set

include/hibf/platform.hpp

@@ -9,8 +9,6 @@
 
 #pragma once
 
-#include <memory> // for allocator
-
 // macro cruft
 //!\cond
 #define HIBF_STR_HELPER(x) #x
@@ -98,7 +96,7 @@
 // ============================================================================
 
 #if __has_include(<version>)
-#    include <version> // for _GLIBCXX_USE_CXX11_ABI, __cpp_lib_constexpr_vector
+#    include <version> // for __cpp_lib_constexpr_vector
 #endif
 
 // C++ standard [required]

include/hibf/sketch/estimate_kmer_counts.hpp

@@ -4,9 +4,8 @@
 
 #pragma once
 
-#include <algorithm> // for fill_n, max
-#include <cstddef>   // for size_t
-#include <vector>    // for vector
+#include <cstddef> // for size_t
+#include <vector>  // for vector
 
 #include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
 

include/hibf/sketch/hyperloglog.hpp

@@ -11,7 +11,6 @@
 
 #pragma once
 
-#include <algorithm> // for copy
 #include <array>     // for array
 #include <cinttypes> // for uint64_t, uint8_t
 #include <cstddef>   // for size_t

include/hibf/sketch/toolbox.hpp

@@ -4,7 +4,6 @@
 
 #pragma once
 
-#include <algorithm>  // for max
 #include <cinttypes>  // for uint64_t, int64_t
 #include <cstddef>    // for size_t
 #include <functional> // for greater

src/config.cpp

@@ -3,13 +3,12 @@
 // SPDX-License-Identifier: BSD-3-Clause
 
 #include <cassert>     // for assert
-#include <cmath>       // for ceil, sqrt
+#include <cmath>       // for sqrt, ceil
 #include <functional>  // for function
-#include <iostream>    // for basic_ostream, operator<<, basic_istream, stringstream, cerr, istream
-#include <sstream>     // for basic_stringstream
+#include <iostream>    // for operator<<, basic_ostream, basic_istream, getline, stringstream
 #include <stdexcept>   // for invalid_argument
-#include <string>      // for char_traits, getline, operator<<, string
-#include <string_view> // for operator<<, operator==, basic_string_view
+#include <string>      // for char_traits, string
+#include <string_view> // for operator==, basic_string_view
 
 #include <hibf/config.hpp>                   // for config
 #include <hibf/layout/prefixes.hpp>          // for meta_header, meta_hibf_config_end, meta_hibf_config_start

src/layout/compute_layout.cpp

@@ -2,11 +2,11 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <algorithm>  // for __sort_fn, sort
+#include <algorithm>  // for __fn, sort
 #include <cstddef>    // for size_t
 #include <functional> // for identity
-#include <sstream>    // for basic_stringstream, stringstream
-#include <utility>    // for addressof
+#include <memory>     // for addressof
+#include <sstream>    // for stringstream
 #include <vector>     // for vector
 
 #include <hibf/config.hpp>                        // for config

src/layout/graph.cpp

@@ -2,12 +2,12 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <algorithm>        // for max, copy
+#include <algorithm>        // for max
 #include <cassert>          // for assert
 #include <cstddef>          // for size_t
 #include <initializer_list> // for initializer_list
+#include <iterator>         // for __fn, prev
 #include <optional>         // for optional, nullopt
-#include <ranges>           // for __prev_fn, prev
 #include <vector>           // for vector
 
 #include <hibf/layout/graph.hpp>  // for graph

src/sketch/compute_sketches.cpp

@@ -2,7 +2,6 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <algorithm>  // for max, fill_n
 #include <cinttypes>  // for uint64_t
 #include <cstddef>    // for size_t
 #include <functional> // for function

src/sketch/hyperloglog.cpp

@@ -3,16 +3,17 @@
 // SPDX-FileCopyrightText: 2013 Hideaki Ohno <hide.o.j55{at}gmail.com>
 // SPDX-License-Identifier: BSD-3-Clause AND MIT
 
-#include <algorithm> // for max, __fill_fn, fill
+#include <algorithm> // for max, __fn, fill
 #include <array>     // for array
 #include <bit>       // for countl_zero
 #include <cassert>   // for assert
 #include <cinttypes> // for uint64_t, uint8_t, uint32_t
 #include <cmath>     // for log
 #include <cstddef>   // for size_t
-#include <iostream>  // for basic_ostream, basic_istream, basic_istream::read, basic_ostre...
+#include <iostream>  // for basic_ostream, basic_istream, istream, ostream
+#include <memory>    // for addressof
 #include <stdexcept> // for runtime_error, invalid_argument
-#include <utility>   // for addressof, swap
+#include <utility>   // for swap
 #include <vector>    // for vector
 
 #include <hibf/contrib/aligned_allocator.hpp> // for aligned_allocator

src/sketch/toolbox.cpp

@@ -2,21 +2,20 @@
 // SPDX-FileCopyrightText: 2016-2023, Knut Reinert & MPI für molekulare Genetik
 // SPDX-License-Identifier: BSD-3-Clause
 
-#include <algorithm>  // for max, fill_n, sort
-#include <cassert>    // for assert
-#include <cinttypes>  // for uint64_t, int64_t
-#include <cmath>      // for floor, sqrt
-#include <cstddef>    // for size_t
-#include <functional> // for greater
-#include <limits>     // for numeric_limits
-#include <omp.h>      // for omp_get_thread_num
-#include <random>     // for uniform_int_distribution, mt19937_64
-#include <utility>    // for swap, move
-#include <vector>     // for vector
+#include <algorithm> // for sort
+#include <cassert>   // for assert
+#include <cinttypes> // for uint64_t, int64_t
+#include <cmath>     // for sqrt, floor
+#include <cstddef>   // for size_t
+#include <limits>    // for numeric_limits
+#include <omp.h>     // for omp_get_thread_num
+#include <random>    // for uniform_int_distribution, mt19937_64
+#include <utility>   // for swap, move
+#include <vector>    // for vector
 
 #include <hibf/contrib/robin_hood.hpp> // for unordered_flat_map, pair
 #include <hibf/sketch/hyperloglog.hpp> // for hyperloglog
-#include <hibf/sketch/toolbox.hpp>     // for clustering_node, entry, neighbor, prio_queue, distance_matrix
+#include <hibf/sketch/toolbox.hpp>     // for clustering_node, entry, neighbor, prio_queue, distance_matrix, cluste...
 
 namespace seqan::hibf::sketch::toolbox
 {

test/include/hibf/test/sandboxed_path.hpp

@@ -10,8 +10,8 @@
 #pragma once
 
 #include <filesystem>   // for path, filesystem_error, operator/
-#include <memory>       // for allocator
-#include <system_error> // for make_error_code, errc
+#include <system_error> // for errc, make_error_code
+#include <type_traits>  // for __libcpp_remove_reference_t
 #include <utility>      // for move, forward
 
 #include <hibf/platform.hpp>

test/include/hibf/test/tmp_directory.hpp

@@ -21,10 +21,9 @@
 #endif
 
 #include <cassert>      // for assert
-#include <filesystem>   // for exists, is_empty, path, remove_all, temp_directory_path, filesystem_...
-#include <memory>       // for allocator
+#include <filesystem>   // for path, exists, is_empty, remove_all, temp_directory_path, filesystem_...
 #include <optional>     // for optional, nullopt
-#include <system_error> // for make_error_code, errc
+#include <system_error> // for errc, make_error_code
 #include <utility>      // for exchange
 
 #include <hibf/platform.hpp>

test/include/hibf/test/type_name_as_string.hpp

@@ -10,16 +10,15 @@
 #pragma once
 
 #if defined(__GNUC__) || defined(__clang__)
-#    include <cxxabi.h> // for __cxa_demangle
+#    include <cxxabi.h> // for __cxa_demangle, abi
 #endif                  // defined(__GNUC__) || defined(__clang__)
 
 #include <cstdlib>     // for free
 #include <functional>  // for function
-#include <memory>      // for allocator, unique_ptr
-#include <string>      // for operator+, char_traits, string, to_string
+#include <memory>      // for allocator, addressof, unique_ptr
+#include <string>      // for char_traits, operator+, string, to_string
 #include <type_traits> // for remove_reference_t
 #include <typeinfo>    // for type_info
-#include <utility>     // for addressof
 
 #include <hibf/platform.hpp>
 

test/iwyu/mappings/gcc.stl.headers.imp

@@ -25,7 +25,6 @@
   { include: ["<bits/c++0x_warning.h>", private, "<iosfwd>", public ] },
   { include: ["<bits/charconv.h>", private, "<charconv>", public ] },
   { include: ["<bits/char_traits.h>", private, "<string>", public ] },
-  { include: ["<bits/chrono.h>", private, "<chrono>", public ] },
   { include: ["<bits/codecvt.h>", private, "<locale>", public ] },
   { include: ["<bits/concept_check.h>", private, "<iterator>", public ] },
   { include: ["<bits/cpp_type_traits.h>", private, "<ext/type_traits>", public ] },
@@ -298,24 +297,6 @@
   { include: ["<hashtable.h>", private, "<hash_set>", public ] },
   # (This one should perhaps be found automatically somehow.)
   { include: ["<ext/sso_string_base.h>", private, "<string>", public ] },
-  # The iostream .h files are confusing.  Lots of private headers,
-  # which are handled above, but we also have public headers
-  # #including each other (eg <iostream> //includes <istream>).  We
-  # are pretty forgiving: if a user specifies any public header, we
-  # generally don't require the others.
-  # ( cd /usr/crosstool/v12/gcc-4.3.1-glibc-2.3.6-grte/x86_64-unknown-linux-gnu/x86_64-unknown-linux-gnu/include/c++/4.3.1 && egrep '^ *# *include <(istream|ostream|iostream|fstream|sstream|streambuf|ios|iosfwd)>' *stream* ios | perl -nle 'm/^([^:]+).*[<"]([^>"]+)[>"]/ and print qq@    { include: ["<$2>", public, "<$1>", public ] },@' | sort -u )
-  { include: ["<ios>", public, "<istream>", public ] },
-  { include: ["<ios>", public, "<ostream>", public ] },
-  { include: ["<iosfwd>", public, "<ios>", public ] },
-  { include: ["<iosfwd>", public, "<streambuf>", public ] },
-  { include: ["<istream>", public, "<fstream>", public ] },
-  { include: ["<istream>", public, "<iostream>", public ] },
-  { include: ["<istream>", public, "<sstream>", public ] },
-  { include: ["<ostream>", public, "<fstream>", public ] },
-  { include: ["<ostream>", public, "<iostream>", public ] },
-  { include: ["<ostream>", public, "<istream>", public ] },
-  { include: ["<ostream>", public, "<sstream>", public ] },
-  { include: ["<streambuf>", public, "<ios>", public ] },
   # The location of exception_defines.h varies by GCC version.  It should
   # never be included directly.
   { include: ["<exception_defines.h>", private, "<exception>", public ] },