minimap2 0.2.25.1 → 0.2.26.0
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- checksums.yaml +4 -4
- data/README.md +9 -0
- data/ext/Rakefile +2 -2
- data/ext/minimap2/NEWS.md +9 -0
- data/ext/minimap2/README.md +2 -2
- data/ext/minimap2/cookbook.md +2 -2
- data/ext/minimap2/minimap.h +1 -1
- data/ext/minimap2/minimap2.1 +1 -1
- data/ext/minimap2/misc/paftools.js +1 -1
- data/ext/minimap2/python/mappy.pyx +1 -1
- data/ext/minimap2/setup.py +22 -32
- data/lib/minimap2/version.rb +1 -1
- metadata +1 -97
- data/ext/minimap2/lib/simde/CONTRIBUTING.md +0 -114
- data/ext/minimap2/lib/simde/COPYING +0 -20
- data/ext/minimap2/lib/simde/README.md +0 -333
- data/ext/minimap2/lib/simde/amalgamate.py +0 -58
- data/ext/minimap2/lib/simde/meson.build +0 -33
- data/ext/minimap2/lib/simde/netlify.toml +0 -20
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +0 -142
- data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +0 -145
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +0 -145
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +0 -140
- data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +0 -143
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +0 -147
- data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +0 -134
- data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +0 -138
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +0 -134
- data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +0 -137
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +0 -131
- data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +0 -135
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +0 -141
- data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +0 -135
- data/ext/minimap2/lib/simde/simde/arm/neon.h +0 -97
- data/ext/minimap2/lib/simde/simde/check.h +0 -267
- data/ext/minimap2/lib/simde/simde/debug-trap.h +0 -83
- data/ext/minimap2/lib/simde/simde/hedley.h +0 -1899
- data/ext/minimap2/lib/simde/simde/simde-arch.h +0 -445
- data/ext/minimap2/lib/simde/simde/simde-common.h +0 -697
- data/ext/minimap2/lib/simde/simde/x86/avx.h +0 -5385
- data/ext/minimap2/lib/simde/simde/x86/avx2.h +0 -2402
- data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +0 -391
- data/ext/minimap2/lib/simde/simde/x86/avx512f.h +0 -3389
- data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +0 -112
- data/ext/minimap2/lib/simde/simde/x86/fma.h +0 -659
- data/ext/minimap2/lib/simde/simde/x86/mmx.h +0 -2210
- data/ext/minimap2/lib/simde/simde/x86/sse.h +0 -3696
- data/ext/minimap2/lib/simde/simde/x86/sse2.h +0 -5991
- data/ext/minimap2/lib/simde/simde/x86/sse3.h +0 -343
- data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +0 -1783
- data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +0 -105
- data/ext/minimap2/lib/simde/simde/x86/ssse3.h +0 -1053
- data/ext/minimap2/lib/simde/simde/x86/svml.h +0 -543
- data/ext/minimap2/lib/simde/test/CMakeLists.txt +0 -166
- data/ext/minimap2/lib/simde/test/arm/meson.build +0 -4
- data/ext/minimap2/lib/simde/test/arm/neon/meson.build +0 -23
- data/ext/minimap2/lib/simde/test/arm/neon/skel.c +0 -871
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +0 -134
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +0 -39
- data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +0 -10
- data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +0 -1260
- data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +0 -873
- data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +0 -1084
- data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +0 -1260
- data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +0 -18
- data/ext/minimap2/lib/simde/test/arm/test-arm.c +0 -20
- data/ext/minimap2/lib/simde/test/arm/test-arm.h +0 -8
- data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +0 -171
- data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +0 -68
- data/ext/minimap2/lib/simde/test/meson.build +0 -64
- data/ext/minimap2/lib/simde/test/munit/COPYING +0 -21
- data/ext/minimap2/lib/simde/test/munit/Makefile +0 -55
- data/ext/minimap2/lib/simde/test/munit/README.md +0 -54
- data/ext/minimap2/lib/simde/test/munit/example.c +0 -351
- data/ext/minimap2/lib/simde/test/munit/meson.build +0 -37
- data/ext/minimap2/lib/simde/test/munit/munit.c +0 -2055
- data/ext/minimap2/lib/simde/test/munit/munit.h +0 -535
- data/ext/minimap2/lib/simde/test/run-tests.c +0 -20
- data/ext/minimap2/lib/simde/test/run-tests.h +0 -260
- data/ext/minimap2/lib/simde/test/x86/avx.c +0 -13752
- data/ext/minimap2/lib/simde/test/x86/avx2.c +0 -9977
- data/ext/minimap2/lib/simde/test/x86/avx512bw.c +0 -2664
- data/ext/minimap2/lib/simde/test/x86/avx512f.c +0 -10416
- data/ext/minimap2/lib/simde/test/x86/avx512vl.c +0 -210
- data/ext/minimap2/lib/simde/test/x86/fma.c +0 -2557
- data/ext/minimap2/lib/simde/test/x86/meson.build +0 -33
- data/ext/minimap2/lib/simde/test/x86/mmx.c +0 -2878
- data/ext/minimap2/lib/simde/test/x86/skel.c +0 -2984
- data/ext/minimap2/lib/simde/test/x86/sse.c +0 -5121
- data/ext/minimap2/lib/simde/test/x86/sse2.c +0 -9860
- data/ext/minimap2/lib/simde/test/x86/sse3.c +0 -486
- data/ext/minimap2/lib/simde/test/x86/sse4.1.c +0 -3446
- data/ext/minimap2/lib/simde/test/x86/sse4.2.c +0 -101
- data/ext/minimap2/lib/simde/test/x86/ssse3.c +0 -2084
- data/ext/minimap2/lib/simde/test/x86/svml.c +0 -1545
- data/ext/minimap2/lib/simde/test/x86/test-avx.h +0 -16
- data/ext/minimap2/lib/simde/test/x86/test-avx512.h +0 -25
- data/ext/minimap2/lib/simde/test/x86/test-mmx.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-sse.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-sse2.h +0 -13
- data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +0 -196
- data/ext/minimap2/lib/simde/test/x86/test-x86.c +0 -48
- data/ext/minimap2/lib/simde/test/x86/test-x86.h +0 -8
@@ -1,260 +0,0 @@
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#if !defined(SIMDE_RUN_TESTS_H)
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#define SIMDE_RUN_TESTS_H
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#include "../simde/hedley.h"
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#include "munit/munit.h"
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#include "../simde/simde-common.h"
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#include <stdio.h>
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#include <math.h>
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SIMDE_DISABLE_UNWANTED_DIAGNOSTICS
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#if defined(HEDLEY_MSVC_VERSION)
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/* Unused function(s) */
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#pragma warning(disable:4505)
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#endif
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HEDLEY_DIAGNOSTIC_PUSH
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#define SIMDE_TESTS_CONCAT3_EX(a, b, c) a##b##c
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#define SIMDE_TESTS_CONCAT3(a, b, c) SIMDE_TESTS_CONCAT3_EX(a, b, c)
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#if defined(__cplusplus)
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# define SIMDE_TESTS_CURRENT_LANG cpp
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#else
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# define SIMDE_TESTS_CURRENT_LANG c
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#endif
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#if defined(SIMDE_NO_NATIVE)
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# define SIMDE_TESTS_CURRENT_NATIVE emul
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#else
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# define SIMDE_TESTS_CURRENT_NATIVE native
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#endif
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#define SIMDE_TESTS_GENERATE_SYMBOL_FULL(sym, arch, isa, native, lang) \
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HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(HEDLEY_CONCAT(simde_tests_, HEDLEY_CONCAT(arch, _)), isa), _), native), _), lang),_),sym)
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#define SIMDE_TESTS_GENERATE_SYMBOL(sym) \
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SIMDE_TESTS_GENERATE_SYMBOL_FULL(sym, SIMDE_TESTS_CURRENT_ARCH, SIMDE_TESTS_CURRENT_ISAX, SIMDE_TESTS_CURRENT_NATIVE, SIMDE_TESTS_CURRENT_LANG)
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#if defined(SIMDE_BUILD_CPP_TESTS)
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#define SIMDE_TESTS_GENERATE_NAME(name) \
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"/" HEDLEY_STRINGIFY(name) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_LANG)
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#else
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#define SIMDE_TESTS_GENERATE_NAME(name) \
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"/" HEDLEY_STRINGIFY(name) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE)
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#endif
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#define SIMDE_TESTS_DEFINE_TEST(name) \
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{ (char*) SIMDE_TESTS_GENERATE_NAME(name), test_simde_##name, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
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HEDLEY_BEGIN_C_DECLS
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#if !defined(HEDLEY_PGI_VERSION)
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# define SIMDE_ALMOST_EQUAL_TO "≈"
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#else
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# define SIMDE_ALMOST_EQUAL_TO "~=~"
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#endif
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SIMDE__FUNCTION_POSSIBLY_UNUSED
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static int
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simde_check_double_close(double a, double b, int precision) {
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const double r = 1.0 * pow(10, HEDLEY_STATIC_CAST(double, precision));
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return
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HEDLEY_UNLIKELY(a < (b - r)) ||
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HEDLEY_UNLIKELY(a > (b + r));
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}
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#define SIMDE_TEST_DEFINE_ASSERT_VEC_CLOSE(VT, accessor) \
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HEDLEY_ALWAYS_INLINE \
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static void \
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simde_assert_##VT##_##accessor##_close_ex(int line, const char* file, simde__##VT a, simde__##VT b, int precision) { \
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simde__##VT##_private \
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a_ = simde__##VT##_to_private(a), \
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b_ = simde__##VT##_to_private(b); \
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\
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for (int i = 0 ; i < HEDLEY_STATIC_CAST(int, sizeof(a_.accessor) / sizeof(a_.accessor[0])) ; i++) { \
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if (simde_check_double_close(HEDLEY_STATIC_CAST(double, a_.accessor[i]), HEDLEY_STATIC_CAST(double, b_.accessor[i]), precision)) { \
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fprintf(stderr, "%s:%d: assertion failed[%d]: %g " SIMDE_ALMOST_EQUAL_TO " %g (precision: 1e-%d)\n", file, line, i, a_.accessor[i], b_.accessor[i], precision); \
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abort(); \
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} \
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} \
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}
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SIMDE__FUNCTION_POSSIBLY_UNUSED
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static void random_f32v(size_t nmemb, simde_float32 v[HEDLEY_ARRAY_PARAM(nmemb)]) {
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for (size_t i = 0 ; i < nmemb ; i++) {
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do {
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munit_rand_memory(sizeof(v[i]), HEDLEY_REINTERPRET_CAST(uint8_t*, &(v[i])));
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} while (!isnormal(v[i]));
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}
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}
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static simde_float64 random_f64_range(simde_float64 min, simde_float64 max) {
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const simde_float64 range = max - min;
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simde_float64 x = HEDLEY_STATIC_CAST(simde_float64, munit_rand_uint32());
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x /= HEDLEY_STATIC_CAST(simde_float64, UINT32_MAX) / range;
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x += min;
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return x;
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}
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static simde_float32 random_f32_range(simde_float32 min, simde_float32 max) {
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return HEDLEY_STATIC_CAST(simde_float32, random_f64_range(HEDLEY_STATIC_CAST(double, min), HEDLEY_STATIC_CAST(double, max)));
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}
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static void random_f64v(size_t nmemb, simde_float64 v[HEDLEY_ARRAY_PARAM(nmemb)]) {
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for (size_t i = 0 ; i < nmemb ; i++) {
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do {
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munit_rand_memory(sizeof(v[i]), HEDLEY_REINTERPRET_CAST(uint8_t*, &(v[i])));
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} while (!isnormal(v[i]));
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}
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}
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#define random_intv_range(T, nmemb, v, min, max) \
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do { \
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for (size_t simde_tmp_i_ = 0 ; simde_tmp_i_ < nmemb ; simde_tmp_i_++) { \
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((T*) (v))[simde_tmp_i_] = munit_rand_int_range(min, max); \
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} \
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} while (0)
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#define TEST_PREFERRED_ITERATIONS (256)
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/* I'll probably move these into µnit, but I want to play around with
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them for a while first. */
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#define simde_assert_array_full(prefix, suffix, T, fmt, nmemb, a, op, b) \
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do { \
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const T* simde__tmp_a_ = (a); \
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const T* simde__tmp_b_ = (b); \
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for (size_t simde__i_ = 0 ; simde__i_ < nmemb ; simde__i_++) { \
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if (!(simde__tmp_a_[simde__i_] op simde__tmp_b_[simde__i_])) { \
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munit_errorf("assertion failed: (" #a ")[%" MUNIT_SIZE_MODIFIER "u] " #op " (" #b ")[%" MUNIT_SIZE_MODIFIER "u] (" prefix "%" fmt suffix " " #op " " prefix "%" fmt suffix ")", simde__i_, simde__i_, simde__tmp_a_[simde__i_], simde__tmp_b_[simde__i_]); \
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} \
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} \
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} while (0)
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#define simde_assert_typev(T, fmt, nmemb, a, op, b) \
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simde_assert_array_full("", "", T, fmt, nmemb, a, op, b)
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#define simde_assert_f32v(nmemb, a, op, b) \
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simde_assert_typev(simde_float32, "g", nmemb, a, op, b)
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#define simde_assert_intv(nmemb, a, op, b) \
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simde_assert_typev(int, "d", nmemb, a, op, b)
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#define simde_assert_uintv(nmemb, a, op, b) \
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simde_assert_typev(int, "u", nmemb, a, op, b)
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#define simde_assert_int8v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_int8_t, PRId8, nmemb, a, op, b)
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#define simde_assert_uint8v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_uint8_t, PRIu8, nmemb, a, op, b)
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#define simde_assert_int16v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_int16_t, PRId16, nmemb, a, op, b)
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#define simde_assert_uint16v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_uint16_t, PRIu16, nmemb, a, op, b)
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#define simde_assert_int32v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_int32_t, PRId32, nmemb, a, op, b)
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#define simde_assert_uint32v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_uint32_t, PRIu32, nmemb, a, op, b)
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#define simde_assert_int64v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_int64_t, PRId64, nmemb, a, op, b)
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#define simde_assert_uint64v(nmemb, a, op, b) \
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simde_assert_array_full("", "", munit_uint64_t, PRIu64, nmemb, a, op, b)
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#define simde_assert_f32v_equal(T, nmemb, a, b, precision) \
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do { \
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const T* simde_tmp_a_ = (a); \
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const T* simde_tmp_b_ = (b); \
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for (size_t simde_i_ = 0 ; simde_i_ < nmemb ; simde_i_++) { \
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const T simde_tmp_diff_ = ((simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]) < 0) ? \
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175
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(simde_tmp_b_[simde_i_] - simde_tmp_a_[simde_i_]) : \
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176
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(simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]); \
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if (MUNIT_UNLIKELY(simde_tmp_diff_ > 1e-##precision)) { \
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munit_errorf("assertion failed: (" #a ")[%" MUNIT_SIZE_MODIFIER "u] == (" #b ")[%" MUNIT_SIZE_MODIFIER "u] (%." #precision "f == %." #precision "f)", simde_i_, simde_i_, simde_tmp_a_[simde_i_], simde_tmp_b_[simde_i_]); \
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} \
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} \
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181
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} while (0)
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182
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-
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183
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#define simde_assert_f32v_close(T, nmemb, a, b, precision) \
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184
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do { \
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185
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const T* simde_tmp_a_ = (a); \
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186
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const T* simde_tmp_b_ = (b); \
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187
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for (size_t simde_i_ = 0 ; simde_i_ < nmemb ; simde_i_++) { \
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188
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const T simde_tmp_diff_ = ((simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]) < 0) ? \
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189
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(simde_tmp_b_[simde_i_] - simde_tmp_a_[simde_i_]) : \
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190
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(simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]); \
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191
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if (MUNIT_UNLIKELY(simde_tmp_diff_ > precision)) { \
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192
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munit_errorf("assertion failed: (" #a ")[%" MUNIT_SIZE_MODIFIER "u] == (" #b ")[%" MUNIT_SIZE_MODIFIER "u] (%" #precision ".1f == %" #precision ".1f)", simde_i_, simde_i_, simde_tmp_a_[simde_i_], simde_tmp_b_[simde_i_]); \
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193
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} \
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194
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} \
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195
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} while (0)
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196
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-
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197
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#define simde_assert_f64v_close(T, nmemb, a, b, precision) \
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198
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do { \
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199
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const T* simde_tmp_a_ = (a); \
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200
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const T* simde_tmp_b_ = (b); \
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201
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for (size_t simde_i_ = 0 ; simde_i_ < nmemb ; simde_i_++) { \
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202
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const T simde_tmp_diff_ = ((simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]) < 0) ? \
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203
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(simde_tmp_b_[simde_i_] - simde_tmp_a_[simde_i_]) : \
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204
|
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(simde_tmp_a_[simde_i_] - simde_tmp_b_[simde_i_]); \
|
205
|
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if (MUNIT_UNLIKELY(simde_tmp_diff_ > precision)) { \
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206
|
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munit_errorf("assertion failed: (" #a ")[%" MUNIT_SIZE_MODIFIER "u] == (" #b ")[%" MUNIT_SIZE_MODIFIER "u] (%" #precision ".1f == %" #precision ".1f)", simde_i_, simde_i_, simde_tmp_a_[simde_i_], simde_tmp_b_[simde_i_]); \
|
207
|
-
} \
|
208
|
-
} \
|
209
|
-
} while (0)
|
210
|
-
|
211
|
-
/* These probably won't go into µnit; they're similar to the
|
212
|
-
simde_assert_*v macros above, but print in hex. */
|
213
|
-
|
214
|
-
#define simde_assert_int8vx(nmemb, a, op, b) \
|
215
|
-
simde_assert_array_full("0x", "", munit_int8_t, "02" PRIx8, nmemb, a, op, b)
|
216
|
-
#define simde_assert_uint8vx(nmemb, a, op, b) \
|
217
|
-
simde_assert_array_full("0x", "", munit_uint8_t, "02" PRIx8, nmemb, a, op, b)
|
218
|
-
#define simde_assert_int16vx(nmemb, a, op, b) \
|
219
|
-
simde_assert_array_full("0x", "", munit_int16_t, "04" PRIx16, nmemb, a, op, b)
|
220
|
-
#define simde_assert_uint16vx(nmemb, a, op, b) \
|
221
|
-
simde_assert_array_full("0x", "", munit_uint16_t, "04" PRIx16, nmemb, a, op, b)
|
222
|
-
#define simde_assert_int32vx(nmemb, a, op, b) \
|
223
|
-
simde_assert_array_full("0x", "", munit_int32_t, "08" PRIx32, nmemb, a, op, b)
|
224
|
-
#define simde_assert_uint32vx(nmemb, a, op, b) \
|
225
|
-
simde_assert_array_full("0x", "", munit_uint32_t, "08" PRIx32, nmemb, a, op, b)
|
226
|
-
#define simde_assert_int64vx(nmemb, a, op, b) \
|
227
|
-
simde_assert_array_full("0x", "", munit_int64_t, "016" PRIx64, nmemb, a, op, b)
|
228
|
-
#define simde_assert_uint64vx(nmemb, a, op, b) \
|
229
|
-
simde_assert_array_full("0x", "", munit_uint64_t, "016" PRIx64, nmemb, a, op, b)
|
230
|
-
|
231
|
-
#define simde_assert_int32_close(value, target) \
|
232
|
-
do { \
|
233
|
-
if (value != target && value != target + 1 && value != target - 1) \
|
234
|
-
munit_errorf("assertion failed: %s == %s (%" PRId32 " == %" PRId32 ")", #value, #target, value, target); \
|
235
|
-
} while (0)
|
236
|
-
|
237
|
-
#define simde_assert_int64_close(value, target) \
|
238
|
-
do { \
|
239
|
-
if (value != target && value != target + 1 && value != target - 1) \
|
240
|
-
munit_errorf("assertion failed: %s == %s (%" PRId64 " == %" PRId64 ")", #value, #target, value, target); \
|
241
|
-
} while (0)
|
242
|
-
|
243
|
-
HEDLEY_END_C_DECLS
|
244
|
-
|
245
|
-
HEDLEY_DIAGNOSTIC_POP
|
246
|
-
|
247
|
-
#if HEDLEY_HAS_WARNING("-Wpadded")
|
248
|
-
# pragma clang diagnostic ignored "-Wpadded"
|
249
|
-
#elif defined(HEDLEY_MSVC_VERSION)
|
250
|
-
# pragma warning(disable:4324)
|
251
|
-
#endif
|
252
|
-
|
253
|
-
#if defined(HEDLEY_MSVC_VERSION)
|
254
|
-
/* nonstandard extension used : non-lvalue array converted to pointer */
|
255
|
-
#pragma warning(disable:4223)
|
256
|
-
/* Conditional expression is a constant */
|
257
|
-
#pragma warning(disable:4127)
|
258
|
-
#endif
|
259
|
-
|
260
|
-
#endif /* !defined(SIMDE_RUN_TESTS_H) */
|