minimap2 0.2.25.1 → 0.2.26.0

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Files changed (109) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +9 -0
  3. data/ext/Rakefile +2 -2
  4. data/ext/minimap2/NEWS.md +9 -0
  5. data/ext/minimap2/README.md +2 -2
  6. data/ext/minimap2/cookbook.md +2 -2
  7. data/ext/minimap2/minimap.h +1 -1
  8. data/ext/minimap2/minimap2.1 +1 -1
  9. data/ext/minimap2/misc/paftools.js +1 -1
  10. data/ext/minimap2/python/mappy.pyx +1 -1
  11. data/ext/minimap2/setup.py +22 -32
  12. data/lib/minimap2/version.rb +1 -1
  13. metadata +1 -97
  14. data/ext/minimap2/lib/simde/CONTRIBUTING.md +0 -114
  15. data/ext/minimap2/lib/simde/COPYING +0 -20
  16. data/ext/minimap2/lib/simde/README.md +0 -333
  17. data/ext/minimap2/lib/simde/amalgamate.py +0 -58
  18. data/ext/minimap2/lib/simde/meson.build +0 -33
  19. data/ext/minimap2/lib/simde/netlify.toml +0 -20
  20. data/ext/minimap2/lib/simde/simde/arm/neon/float32x2.h +0 -140
  21. data/ext/minimap2/lib/simde/simde/arm/neon/float32x4.h +0 -137
  22. data/ext/minimap2/lib/simde/simde/arm/neon/float64x1.h +0 -142
  23. data/ext/minimap2/lib/simde/simde/arm/neon/float64x2.h +0 -145
  24. data/ext/minimap2/lib/simde/simde/arm/neon/int16x4.h +0 -140
  25. data/ext/minimap2/lib/simde/simde/arm/neon/int16x8.h +0 -145
  26. data/ext/minimap2/lib/simde/simde/arm/neon/int32x2.h +0 -140
  27. data/ext/minimap2/lib/simde/simde/arm/neon/int32x4.h +0 -143
  28. data/ext/minimap2/lib/simde/simde/arm/neon/int64x1.h +0 -137
  29. data/ext/minimap2/lib/simde/simde/arm/neon/int64x2.h +0 -141
  30. data/ext/minimap2/lib/simde/simde/arm/neon/int8x16.h +0 -147
  31. data/ext/minimap2/lib/simde/simde/arm/neon/int8x8.h +0 -141
  32. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x4.h +0 -134
  33. data/ext/minimap2/lib/simde/simde/arm/neon/uint16x8.h +0 -138
  34. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x2.h +0 -134
  35. data/ext/minimap2/lib/simde/simde/arm/neon/uint32x4.h +0 -137
  36. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x1.h +0 -131
  37. data/ext/minimap2/lib/simde/simde/arm/neon/uint64x2.h +0 -135
  38. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x16.h +0 -141
  39. data/ext/minimap2/lib/simde/simde/arm/neon/uint8x8.h +0 -135
  40. data/ext/minimap2/lib/simde/simde/arm/neon.h +0 -97
  41. data/ext/minimap2/lib/simde/simde/check.h +0 -267
  42. data/ext/minimap2/lib/simde/simde/debug-trap.h +0 -83
  43. data/ext/minimap2/lib/simde/simde/hedley.h +0 -1899
  44. data/ext/minimap2/lib/simde/simde/simde-arch.h +0 -445
  45. data/ext/minimap2/lib/simde/simde/simde-common.h +0 -697
  46. data/ext/minimap2/lib/simde/simde/x86/avx.h +0 -5385
  47. data/ext/minimap2/lib/simde/simde/x86/avx2.h +0 -2402
  48. data/ext/minimap2/lib/simde/simde/x86/avx512bw.h +0 -391
  49. data/ext/minimap2/lib/simde/simde/x86/avx512f.h +0 -3389
  50. data/ext/minimap2/lib/simde/simde/x86/avx512vl.h +0 -112
  51. data/ext/minimap2/lib/simde/simde/x86/fma.h +0 -659
  52. data/ext/minimap2/lib/simde/simde/x86/mmx.h +0 -2210
  53. data/ext/minimap2/lib/simde/simde/x86/sse.h +0 -3696
  54. data/ext/minimap2/lib/simde/simde/x86/sse2.h +0 -5991
  55. data/ext/minimap2/lib/simde/simde/x86/sse3.h +0 -343
  56. data/ext/minimap2/lib/simde/simde/x86/sse4.1.h +0 -1783
  57. data/ext/minimap2/lib/simde/simde/x86/sse4.2.h +0 -105
  58. data/ext/minimap2/lib/simde/simde/x86/ssse3.h +0 -1053
  59. data/ext/minimap2/lib/simde/simde/x86/svml.h +0 -543
  60. data/ext/minimap2/lib/simde/test/CMakeLists.txt +0 -166
  61. data/ext/minimap2/lib/simde/test/arm/meson.build +0 -4
  62. data/ext/minimap2/lib/simde/test/arm/neon/meson.build +0 -23
  63. data/ext/minimap2/lib/simde/test/arm/neon/skel.c +0 -871
  64. data/ext/minimap2/lib/simde/test/arm/neon/test-neon-internal.h +0 -134
  65. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.c +0 -39
  66. data/ext/minimap2/lib/simde/test/arm/neon/test-neon.h +0 -10
  67. data/ext/minimap2/lib/simde/test/arm/neon/vadd.c +0 -1260
  68. data/ext/minimap2/lib/simde/test/arm/neon/vdup_n.c +0 -873
  69. data/ext/minimap2/lib/simde/test/arm/neon/vmul.c +0 -1084
  70. data/ext/minimap2/lib/simde/test/arm/neon/vsub.c +0 -1260
  71. data/ext/minimap2/lib/simde/test/arm/test-arm-internal.h +0 -18
  72. data/ext/minimap2/lib/simde/test/arm/test-arm.c +0 -20
  73. data/ext/minimap2/lib/simde/test/arm/test-arm.h +0 -8
  74. data/ext/minimap2/lib/simde/test/cmake/AddCompilerFlags.cmake +0 -171
  75. data/ext/minimap2/lib/simde/test/cmake/ExtraWarningFlags.cmake +0 -68
  76. data/ext/minimap2/lib/simde/test/meson.build +0 -64
  77. data/ext/minimap2/lib/simde/test/munit/COPYING +0 -21
  78. data/ext/minimap2/lib/simde/test/munit/Makefile +0 -55
  79. data/ext/minimap2/lib/simde/test/munit/README.md +0 -54
  80. data/ext/minimap2/lib/simde/test/munit/example.c +0 -351
  81. data/ext/minimap2/lib/simde/test/munit/meson.build +0 -37
  82. data/ext/minimap2/lib/simde/test/munit/munit.c +0 -2055
  83. data/ext/minimap2/lib/simde/test/munit/munit.h +0 -535
  84. data/ext/minimap2/lib/simde/test/run-tests.c +0 -20
  85. data/ext/minimap2/lib/simde/test/run-tests.h +0 -260
  86. data/ext/minimap2/lib/simde/test/x86/avx.c +0 -13752
  87. data/ext/minimap2/lib/simde/test/x86/avx2.c +0 -9977
  88. data/ext/minimap2/lib/simde/test/x86/avx512bw.c +0 -2664
  89. data/ext/minimap2/lib/simde/test/x86/avx512f.c +0 -10416
  90. data/ext/minimap2/lib/simde/test/x86/avx512vl.c +0 -210
  91. data/ext/minimap2/lib/simde/test/x86/fma.c +0 -2557
  92. data/ext/minimap2/lib/simde/test/x86/meson.build +0 -33
  93. data/ext/minimap2/lib/simde/test/x86/mmx.c +0 -2878
  94. data/ext/minimap2/lib/simde/test/x86/skel.c +0 -2984
  95. data/ext/minimap2/lib/simde/test/x86/sse.c +0 -5121
  96. data/ext/minimap2/lib/simde/test/x86/sse2.c +0 -9860
  97. data/ext/minimap2/lib/simde/test/x86/sse3.c +0 -486
  98. data/ext/minimap2/lib/simde/test/x86/sse4.1.c +0 -3446
  99. data/ext/minimap2/lib/simde/test/x86/sse4.2.c +0 -101
  100. data/ext/minimap2/lib/simde/test/x86/ssse3.c +0 -2084
  101. data/ext/minimap2/lib/simde/test/x86/svml.c +0 -1545
  102. data/ext/minimap2/lib/simde/test/x86/test-avx.h +0 -16
  103. data/ext/minimap2/lib/simde/test/x86/test-avx512.h +0 -25
  104. data/ext/minimap2/lib/simde/test/x86/test-mmx.h +0 -13
  105. data/ext/minimap2/lib/simde/test/x86/test-sse.h +0 -13
  106. data/ext/minimap2/lib/simde/test/x86/test-sse2.h +0 -13
  107. data/ext/minimap2/lib/simde/test/x86/test-x86-internal.h +0 -196
  108. data/ext/minimap2/lib/simde/test/x86/test-x86.c +0 -48
  109. data/ext/minimap2/lib/simde/test/x86/test-x86.h +0 -8
@@ -1,134 +0,0 @@
1
- #if !defined(SIMDE_TESTS_NEON_INTERNAL_H)
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- #define SIMDE_TESTS_CURRENT_ARCH arm
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- #define SIMDE_TESTS_CURRENT_ISAX neon
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-
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- #include "../../run-tests.h"
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- #include "../../../simde/arm/neon.h"
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-
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- HEDLEY_BEGIN_C_DECLS
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-
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- #define SIMDE_TESTS_GENERATE_SUITE_GETTERS(op) \
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- MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (void); \
12
- MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, cpp)(void); \
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- MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) (void); \
14
- MunitSuite* SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, cpp)(void)
15
-
16
- #define SIMDE_TESTS_NEON_GENERATE_INTRIN_FULL(vtype, variant) HEDLEY_CONCAT(v, SIMDE_TESTS_CONCAT3(HEDLEY_CONCAT(SIMDE_TESTS_CURRENT_NEON_OP, vtype), _, variant))
17
- #define SIMDE_TESTS_NEON_GENERATE_INTRIN(vtype, variant) HEDLEY_CONCAT(v, SIMDE_TESTS_CONCAT3(SIMDE_TESTS_CURRENT_NEON_OP, _, variant))
18
-
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- #define SIMDE_TESTS_NEON_DEFINE_TEST_FULL(vtype, variant) \
20
- { (char*) HEDLEY_STRINGIFY(vtype) "_" HEDLEY_STRINGIFY(variant) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_LANG), HEDLEY_CONCAT(test_simde_, SIMDE_TESTS_NEON_GENERATE_INTRIN_FULL(vtype, variant)), NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
21
- #define SIMDE_TESTS_NEON_DEFINE_TEST(variant) \
22
- { (char*) "_" HEDLEY_STRINGIFY(variant) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_NATIVE) "/" HEDLEY_STRINGIFY(SIMDE_TESTS_CURRENT_LANG), HEDLEY_CONCAT(test_simde_, SIMDE_TESTS_NEON_GENERATE_INTRIN(vtype, variant)), NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
23
-
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- SIMDE_TESTS_GENERATE_SUITE_GETTERS(add);
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- SIMDE_TESTS_GENERATE_SUITE_GETTERS(dup);
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- SIMDE_TESTS_GENERATE_SUITE_GETTERS(mul);
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- SIMDE_TESTS_GENERATE_SUITE_GETTERS(sub);
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-
29
- #define simde_neon_assert_int8x8(a, op, b) \
30
- simde_assert_typev(int8_t, PRId8, (sizeof(a) / sizeof(int8_t)), (const int8_t*) &(a), op, (const int8_t*) &(b))
31
- #define simde_neon_assert_int16x4(a, op, b) \
32
- simde_assert_typev(int16_t, PRId16, (sizeof(a) / sizeof(int16_t)), (const int16_t*) &(a), op, (const int16_t*) &(b))
33
- #define simde_neon_assert_int32x2(a, op, b) \
34
- simde_assert_typev(int32_t, PRId32, (sizeof(a) / sizeof(int32_t)), (const int32_t*) &(a), op, (const int32_t*) &(b))
35
- #define simde_neon_assert_int64x1(a, op, b) \
36
- simde_assert_typev(int64_t, PRId64, (sizeof(a) / sizeof(int64_t)), (const int64_t*) &(a), op, (const int64_t*) &(b))
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- #define simde_neon_assert_uint8x8(a, op, b) \
38
- simde_assert_typev(uint8_t, PRId8, (sizeof(a) / sizeof(uint8_t)), (const uint8_t*) &(a), op, (const uint8_t*) &(b))
39
- #define simde_neon_assert_uint16x4(a, op, b) \
40
- simde_assert_typev(uint16_t, PRId16, (sizeof(a) / sizeof(uint16_t)), (const uint16_t*) &(a), op, (const uint16_t*) &(b))
41
- #define simde_neon_assert_uint32x2(a, op, b) \
42
- simde_assert_typev(uint32_t, PRId32, (sizeof(a) / sizeof(uint32_t)), (const uint32_t*) &(a), op, (const uint32_t*) &(b))
43
- #define simde_neon_assert_uint64x1(a, op, b) \
44
- simde_assert_typev(uint64_t, PRId64, (sizeof(a) / sizeof(uint64_t)), (const uint64_t*) &(a), op, (const uint64_t*) &(b))
45
- #define simde_neon_assert_float32x2(a, op, b) \
46
- simde_assert_typev(simde_float32, "f", (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), op, (const simde_float32*) &(b))
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- #define simde_neon_assert_float32x2_equal(a, b, precision) \
48
- simde_assert_f32v_equal(simde_float32, (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), (const simde_float32*) &(b), precision)
49
- #define simde_neon_assert_float64x1(a, op, b) \
50
- simde_assert_typev(simde_float64, "f", (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), op, (const simde_float64*) &(b))
51
- #define simde_neon_assert_float64x1_equal(a, b, precision) \
52
- simde_assert_f32v_equal(simde_float64, (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), (const simde_float64*) &(b), precision)
53
-
54
- #define simde_neon_assert_int8x16(a, op, b) \
55
- simde_assert_typev(int8_t, PRId8, (sizeof(a) / sizeof(int8_t)), (const int8_t*) &(a), op, (const int8_t*) &(b))
56
- #define simde_neon_assert_int16x8(a, op, b) \
57
- simde_assert_typev(int16_t, PRId16, (sizeof(a) / sizeof(int16_t)), (const int16_t*) &(a), op, (const int16_t*) &(b))
58
- #define simde_neon_assert_int32x4(a, op, b) \
59
- simde_assert_typev(int32_t, PRId32, (sizeof(a) / sizeof(int32_t)), (const int32_t*) &(a), op, (const int32_t*) &(b))
60
- #define simde_neon_assert_int64x2(a, op, b) \
61
- simde_assert_typev(int64_t, PRId64, (sizeof(a) / sizeof(int64_t)), (const int64_t*) &(a), op, (const int64_t*) &(b))
62
- #define simde_neon_assert_uint8x16(a, op, b) \
63
- simde_assert_typev(uint8_t, PRId8, (sizeof(a) / sizeof(uint8_t)), (const uint8_t*) &(a), op, (const uint8_t*) &(b))
64
- #define simde_neon_assert_uint16x8(a, op, b) \
65
- simde_assert_typev(uint16_t, PRId16, (sizeof(a) / sizeof(uint16_t)), (const uint16_t*) &(a), op, (const uint16_t*) &(b))
66
- #define simde_neon_assert_uint32x4(a, op, b) \
67
- simde_assert_typev(uint32_t, PRId32, (sizeof(a) / sizeof(uint32_t)), (const uint32_t*) &(a), op, (const uint32_t*) &(b))
68
- #define simde_neon_assert_uint64x2(a, op, b) \
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- simde_assert_typev(uint64_t, PRId64, (sizeof(a) / sizeof(uint64_t)), (const uint64_t*) &(a), op, (const uint64_t*) &(b))
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- #define simde_neon_assert_float32x4(a, op, b) \
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- simde_assert_typev(simde_float32, "f", (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), op, (const simde_float32*) &(b))
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- #define simde_neon_assert_float32x4_equal(a, b, precision) \
73
- simde_assert_f32v_equal(simde_float32, (sizeof(a) / sizeof(simde_float32)), (const simde_float32*) &(a), (const simde_float32*) &(b), precision)
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- #define simde_neon_assert_float64x2(a, op, b) \
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- simde_assert_typev(simde_float64, "f", (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), op, (const simde_float64*) &(b))
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- #define simde_neon_assert_float64x2_equal(a, b, precision) \
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- simde_assert_f32v_equal(simde_float64, (sizeof(a) / sizeof(simde_float64)), (const simde_float64*) &(a), (const simde_float64*) &(b), precision)
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-
79
- #include <math.h>
80
-
81
- #define SIMDE_NEON_GEN_RAND_ARRAY_FUNC(L, N, V) \
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- SIMDE__FUNCTION_ATTRIBUTES \
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- simde_float##L##x##N##_t \
84
- simde_neon_random_float##L##x##N(void) { \
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- simde_float##L v[sizeof(simde_float##L##x##N##_t) / sizeof(simde_float##L)]; \
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- for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) { \
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- v[i] = (simde_float##L) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0); \
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- } \
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- return simde_vld1##V##_f##L(v); \
90
- }
91
-
92
- SIMDE__FUNCTION_ATTRIBUTES
93
- simde_float32x2_t
94
- simde_neon_random_float32x2(void) {
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- simde_float32 v[sizeof(simde_float32x2_t) / sizeof(simde_float32)];
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- for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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- v[i] = (simde_float32) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
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- }
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- return simde_vld1_f32(v);
100
- }
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-
102
- SIMDE__FUNCTION_ATTRIBUTES
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- simde_float64x1_t
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- simde_neon_random_float64x1(void) {
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- simde_float64 v[sizeof(simde_float64x1_t) / sizeof(simde_float64)];
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- for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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- v[i] = (simde_float64) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
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- }
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- return simde_vld1_f64(v);
110
- }
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-
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- SIMDE__FUNCTION_ATTRIBUTES
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- simde_float32x4_t
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- simde_neon_random_float32x4(void) {
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- simde_float32 v[sizeof(simde_float32x4_t) / sizeof(simde_float32)];
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- for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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- v[i] = (simde_float32) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
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- }
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- return simde_vld1q_f32(v);
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- }
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-
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- SIMDE__FUNCTION_ATTRIBUTES
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- simde_float64x2_t
124
- simde_neon_random_float64x2(void) {
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- simde_float64 v[sizeof(simde_float64x2_t) / sizeof(simde_float64)];
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- for (size_t i = 0 ; i < sizeof(v) / sizeof(v[0]) ; i++) {
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- v[i] = (simde_float64) (round(random_f64_range(-1000.0, 1000.0) * 100.0) / 100.0);
128
- }
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- return simde_vld1q_f64(v);
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- }
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-
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- HEDLEY_END_C_DECLS
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-
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- #endif /* !defined(SIMDE_TESTS_NEON_INTERNAL_H) */
@@ -1,39 +0,0 @@
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- #include "test-neon.h"
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- #include "test-neon-internal.h"
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-
4
- #include <stdio.h>
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-
6
- #if defined(SIMDE_BUILD_CPP_TESTS)
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- #define CHILD_GROUP_LEN 4
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- #define SET_CHILDREN_FOR_OP(op) \
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- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (); \
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- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) (); \
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- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, cpp)(); \
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- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, cpp)()
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- #else
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- #define CHILD_GROUP_LEN 2
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- #define SET_CHILDREN_FOR_OP(op) \
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- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, native, c) (); \
17
- children[i++] = *SIMDE_TESTS_GENERATE_SYMBOL_FULL(op, SIMDE_TESTS_CURRENT_ARCH, neon, emul, c) ()
18
-
19
- #endif
20
-
21
- MunitSuite*
22
- simde_tests_arm_neon_get_suite(void) {
23
- static MunitSuite children[(4 * CHILD_GROUP_LEN) + 1];
24
- static MunitSuite suite = { "/neon", NULL, children, 1, MUNIT_SUITE_OPTION_NONE };
25
- static const MunitSuite empty = { NULL, NULL, NULL, 1, MUNIT_SUITE_OPTION_NONE };
26
-
27
- size_t i = 0;
28
-
29
- SET_CHILDREN_FOR_OP(add);
30
- SET_CHILDREN_FOR_OP(dup);
31
- SET_CHILDREN_FOR_OP(mul);
32
- SET_CHILDREN_FOR_OP(sub);
33
-
34
- children[i++] = empty;
35
-
36
- munit_assert_size(i, ==, sizeof(children) / sizeof(children[0]));
37
-
38
- return &suite;
39
- }
@@ -1,10 +0,0 @@
1
- #include "../../../simde/hedley.h"
2
- #include "../../munit/munit.h"
3
-
4
- #define SIMDE_TESTS_CURRENT_ISAX neon
5
-
6
- HEDLEY_BEGIN_C_DECLS
7
-
8
- MunitSuite* simde_tests_arm_neon_get_suite(void);
9
-
10
- HEDLEY_END_C_DECLS