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
@@ -1,351 +0,0 @@
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- /* Example file for using µnit.
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- *
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- * µnit is MIT-licensed, but for this file and this file alone:
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- *
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- * To the extent possible under law, the author(s) of this file have
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- * waived all copyright and related or neighboring rights to this
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- * work. See <https://creativecommons.org/publicdomain/zero/1.0/> for
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- * details.
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- *********************************************************************/
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-
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- #include "munit.h"
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-
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- /* This is just to disable an MSVC warning about conditional
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- * expressions being constant, which you shouldn't have to do for your
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- * code. It's only here because we want to be able to do silly things
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- * like assert that 0 != 1 for our demo. */
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- #if defined(_MSC_VER)
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- #pragma warning(disable: 4127)
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- #endif
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-
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- /* Tests are functions that return void, and take a single void*
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- * parameter. We'll get to what that parameter is later. */
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- static MunitResult
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- test_compare(const MunitParameter params[], void* data) {
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- /* We'll use these later */
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- const unsigned char val_uchar = 'b';
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- const short val_short = 1729;
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- double pi = 3.141592654;
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- char* stewardesses = "stewardesses";
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- char* most_fun_word_to_type;
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-
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- /* These are just to silence compiler warnings about the parameters
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- * being unused. */
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- (void) params;
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- (void) data;
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-
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- /* Let's start with the basics. */
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- munit_assert(0 != 1);
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-
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- /* There is also the more verbose, though slightly more descriptive
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- munit_assert_true/false: */
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- munit_assert_false(0);
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-
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- /* You can also call munit_error and munit_errorf yourself. We
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- * won't do it is used to indicate a failure, but here is what it
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- * would look like: */
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- /* munit_error("FAIL"); */
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- /* munit_errorf("Goodbye, cruel %s", "world"); */
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-
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- /* There are macros for comparing lots of types. */
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- munit_assert_char('a', ==, 'a');
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-
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- /* Sure, you could just assert('a' == 'a'), but if you did that, a
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- * failed assertion would just say something like "assertion failed:
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- * val_uchar == 'b'". µnit will tell you the actual values, so a
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- * failure here would result in something like "assertion failed:
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- * val_uchar == 'b' ('X' == 'b')." */
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- munit_assert_uchar(val_uchar, ==, 'b');
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-
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- /* Obviously we can handle values larger than 'char' and 'uchar'.
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- * There are versions for char, short, int, long, long long,
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- * int8/16/32/64_t, as well as the unsigned versions of them all. */
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- munit_assert_short(42, <, val_short);
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-
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- /* There is also support for size_t.
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- *
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- * The longest word in English without repeating any letters is
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- * "uncopyrightables", which has uncopyrightable (and
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- * dermatoglyphics, which is the study of fingerprints) beat by a
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- * character */
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- munit_assert_size(strlen("uncopyrightables"), >, strlen("dermatoglyphics"));
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-
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- /* Of course there is also support for doubles and floats. */
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- munit_assert_double(pi, ==, 3.141592654);
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-
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- /* If you want to compare two doubles for equality, you might want
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- * to consider using munit_assert_double_equal. It compares two
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- * doubles for equality within a precison of 1.0 x 10^-(precision).
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- * Note that precision (the third argument to the macro) needs to be
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- * fully evaluated to an integer by the preprocessor so µnit doesn't
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- * have to depend pow, which is often in libm not libc. */
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- munit_assert_double_equal(3.141592654, 3.141592653589793, 9);
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-
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- /* And if you want to check strings for equality (or inequality),
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- * there is munit_assert_string_equal/not_equal.
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- *
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- * "stewardesses" is the longest word you can type on a QWERTY
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- * keyboard with only one hand, which makes it loads of fun to type.
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- * If I'm going to have to type a string repeatedly, let's make it a
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- * good one! */
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- munit_assert_string_equal(stewardesses, "stewardesses");
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-
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- /* A personal favorite macro which is fantastic if you're working
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- * with binary data, is the one which naïvely checks two blobs of
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- * memory for equality. If this fails it will tell you the offset
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- * of the first differing byte. */
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- munit_assert_memory_equal(7, stewardesses, "steward");
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-
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- /* You can also make sure that two blobs differ *somewhere*: */
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- munit_assert_memory_not_equal(8, stewardesses, "steward");
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-
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- /* There are equal/not_equal macros for pointers, too: */
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- most_fun_word_to_type = stewardesses;
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- munit_assert_ptr_equal(most_fun_word_to_type, stewardesses);
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-
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- /* And null/not_null */
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- munit_assert_null(NULL);
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- munit_assert_not_null(most_fun_word_to_type);
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-
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- /* Lets verify that the data parameter is what we expected. We'll
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- * see where this comes from in a bit.
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- *
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- * Note that the casting isn't usually required; if you give this
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- * function a real pointer (instead of a number like 0xdeadbeef) it
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- * would work as expected. */
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- munit_assert_ptr_equal(data, (void*)(uintptr_t)0xdeadbeef);
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-
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- return MUNIT_OK;
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- }
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-
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- static MunitResult
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- test_rand(const MunitParameter params[], void* user_data) {
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- int random_int;
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- double random_dbl;
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- munit_uint8_t data[5];
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-
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- (void) params;
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- (void) user_data;
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-
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- /* One thing missing from a lot of unit testing frameworks is a
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- * random number generator. You can't just use srand/rand because
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- * the implementation varies across different platforms, and it's
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- * important to be able to look at the seed used in a failing test
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- * to see if you can reproduce it. Some randomness is a fantastic
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- * thing to have in your tests, I don't know why more people don't
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- * do it...
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- *
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- * µnit's PRNG is re-seeded with the same value for each iteration
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- * of each test. The seed is retrieved from the MUNIT_SEED
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- * envirnment variable or, if none is provided, one will be
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- * (pseudo-)randomly generated. */
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-
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- /* If you need an integer in a given range */
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- random_int = munit_rand_int_range(128, 4096);
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- munit_assert_int(random_int, >=, 128);
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- munit_assert_int(random_int, <=, 4096);
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-
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- /* Or maybe you want a double, between 0 and 1: */
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- random_dbl = munit_rand_double();
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- munit_assert_double(random_dbl, >=, 0.0);
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- munit_assert_double(random_dbl, <=, 1.0);
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-
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- /* Of course, you want to be able to reproduce bugs discovered
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- * during testing, so every time the tests are run they print the
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- * random seed used. When you want to reproduce a result, just put
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- * that random seed in the MUNIT_SEED environment variable; it even
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- * works on different platforms.
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- *
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- * If you want this to pass, use 0xdeadbeef as the random seed and
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- * uncomment the next line of code. Note that the PRNG is not
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- * re-seeded between iterations of the same test, so this will only
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- * work on the first iteration. */
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- /* munit_assert_uint32(munit_rand_uint32(), ==, 1306447409); */
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-
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- /* You can also get blobs of random memory: */
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- munit_rand_memory(sizeof(data), data);
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-
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- return MUNIT_OK;
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- }
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-
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- /* This test case shows how to accept parameters. We'll see how to
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- * specify them soon.
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- *
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- * By default, every possible variation of a parameterized test is
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- * run, but you can specify parameters manually if you want to only
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- * run specific test(s), or you can pass the --single argument to the
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- * CLI to have the harness simply choose one variation at random
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- * instead of running them all. */
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- static MunitResult
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- test_parameters(const MunitParameter params[], void* user_data) {
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- const char* foo;
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- const char* bar;
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-
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- (void) user_data;
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-
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- /* The "foo" parameter is specified as one of the following values:
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- * "one", "two", or "three". */
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- foo = munit_parameters_get(params, "foo");
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- /* Similarly, "bar" is one of "four", "five", or "six". */
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- bar = munit_parameters_get(params, "bar");
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- /* "baz" is a bit more complicated. We don't actually specify a
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- * list of valid values, so by default NULL is passed. However, the
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- * CLI will accept any value. This is a good way to have a value
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- * that is usually selected randomly by the test, but can be
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- * overridden on the command line if desired. */
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- /* const char* baz = munit_parameters_get(params, "baz"); */
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-
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- /* Notice that we're returning MUNIT_FAIL instead of writing an
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- * error message. Error messages are generally preferable, since
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- * they make it easier to diagnose the issue, but this is an
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- * option.
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- *
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- * Possible values are:
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- * - MUNIT_OK: Sucess
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- * - MUNIT_FAIL: Failure
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- * - MUNIT_SKIP: The test was skipped; usually this happens when a
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- * particular feature isn't in use. For example, if you're
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- * writing a test which uses a Wayland-only feature, but your
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- * application is running on X11.
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- * - MUNIT_ERROR: The test failed, but not because of anything you
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- * wanted to test. For example, maybe your test downloads a
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- * remote resource and tries to parse it, but the network was
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- * down.
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- */
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-
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- if (strcmp(foo, "one") != 0 &&
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- strcmp(foo, "two") != 0 &&
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- strcmp(foo, "three") != 0)
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- return MUNIT_FAIL;
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-
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- if (strcmp(bar, "red") != 0 &&
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- strcmp(bar, "green") != 0 &&
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- strcmp(bar, "blue") != 0)
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- return MUNIT_FAIL;
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-
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- return MUNIT_OK;
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- }
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-
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- /* The setup function, if you provide one, for a test will be run
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- * before the test, and the return value will be passed as the sole
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- * parameter to the test function. */
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- static void*
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- test_compare_setup(const MunitParameter params[], void* user_data) {
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- (void) params;
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-
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- munit_assert_string_equal(user_data, "µnit");
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- return (void*) (uintptr_t) 0xdeadbeef;
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- }
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-
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- /* To clean up after a test, you can use a tear down function. The
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- * fixture argument is the value returned by the setup function
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- * above. */
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- static void
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- test_compare_tear_down(void* fixture) {
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- munit_assert_ptr_equal(fixture, (void*)(uintptr_t)0xdeadbeef);
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- }
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-
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- static char* foo_params[] = {
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- (char*) "one", (char*) "two", (char*) "three", NULL
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- };
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-
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- static char* bar_params[] = {
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- (char*) "red", (char*) "green", (char*) "blue", NULL
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- };
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-
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- static MunitParameterEnum test_params[] = {
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- { (char*) "foo", foo_params },
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- { (char*) "bar", bar_params },
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- { (char*) "baz", NULL },
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- { NULL, NULL },
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- };
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-
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- /* Creating a test suite is pretty simple. First, you'll need an
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- * array of tests: */
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- static MunitTest test_suite_tests[] = {
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- {
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- /* The name is just a unique human-readable way to identify the
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- * test. You can use it to run a specific test if you want, but
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- * usually it's mostly decorative. */
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- (char*) "/example/compare",
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- /* You probably won't be surprised to learn that the tests are
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- * functions. */
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- test_compare,
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- /* If you want, you can supply a function to set up a fixture. If
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- * you supply NULL, the user_data parameter from munit_suite_main
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- * will be used directly. If, however, you provide a callback
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- * here the user_data parameter will be passed to this callback,
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- * and the return value from this callback will be passed to the
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- * test function.
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- *
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- * For our example we don't really need a fixture, but lets
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- * provide one anyways. */
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- test_compare_setup,
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- /* If you passed a callback for the fixture setup function, you
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- * may want to pass a corresponding callback here to reverse the
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- * operation. */
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- test_compare_tear_down,
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- /* Finally, there is a bitmask for options you can pass here. You
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- * can provide either MUNIT_TEST_OPTION_NONE or 0 here to use the
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- * defaults. */
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- MUNIT_TEST_OPTION_NONE,
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- NULL
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- },
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- /* Usually this is written in a much more compact format; all these
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- * comments kind of ruin that, though. Here is how you'll usually
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- * see entries written: */
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- { (char*) "/example/rand", test_rand, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL },
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- /* To tell the test runner when the array is over, just add a NULL
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- * entry at the end. */
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- { (char*) "/example/parameters", test_parameters, NULL, NULL, MUNIT_TEST_OPTION_NONE, test_params },
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- { NULL, NULL, NULL, NULL, MUNIT_TEST_OPTION_NONE, NULL }
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- };
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-
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- /* If you wanted to have your test suite run other test suites you
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- * could declare an array of them. Of course each sub-suite can
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- * contain more suites, etc. */
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- /* static const MunitSuite other_suites[] = { */
308
- /* { "/second", test_suite_tests, NULL, 1, MUNIT_SUITE_OPTION_NONE }, */
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- /* { NULL, NULL, NULL, 0, MUNIT_SUITE_OPTION_NONE } */
310
- /* }; */
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-
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- /* Now we'll actually declare the test suite. You could do this in
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- * the main function, or on the heap, or whatever you want. */
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- static const MunitSuite test_suite = {
315
- /* This string will be prepended to all test names in this suite;
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- * for example, "/example/rand" will become "/µnit/example/rand".
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- * Note that, while it doesn't really matter for the top-level
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- * suite, NULL signal the end of an array of tests; you should use
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- * an empty string ("") instead. */
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- (char*) "",
321
- /* The first parameter is the array of test suites. */
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- test_suite_tests,
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- /* In addition to containing test cases, suites can contain other
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- * test suites. This isn't necessary in this example, but it can be
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- * a great help to projects with lots of tests by making it easier
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- * to spread the tests across many files. This is where you would
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- * put "other_suites" (which is commented out above). */
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- NULL,
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- /* An interesting feature of µnit is that it supports automatically
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- * running multiple iterations of the tests. This is usually only
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- * interesting if you make use of the PRNG to randomize your tests
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- * cases a bit, or if you are doing performance testing and want to
333
- * average multiple runs. 0 is an alias for 1. */
334
- 1,
335
- /* Just like MUNIT_TEST_OPTION_NONE, you can provide
336
- * MUNIT_SUITE_OPTION_NONE or 0 to use the default settings. */
337
- MUNIT_SUITE_OPTION_NONE
338
- };
339
-
340
- /* This is only necessary for EXIT_SUCCESS and EXIT_FAILURE, which you
341
- * *should* be using but probably aren't (no, zero and non-zero don't
342
- * always mean success and failure). I guess my point is that nothing
343
- * about µnit requires it. */
344
- #include <stdlib.h>
345
-
346
- int main(int argc, char* argv[MUNIT_ARRAY_PARAM(argc + 1)]) {
347
- /* Finally, we'll actually run our test suite! That second argument
348
- * is the user_data parameter which will be passed either to the
349
- * test or (if provided) the fixture setup function. */
350
- return munit_suite_main(&test_suite, (void*) "µnit", argc, argv);
351
- }
@@ -1,37 +0,0 @@
1
- project('munit', 'c')
2
-
3
- conf_data = configuration_data()
4
- conf_data.set('version', '0.2.0')
5
-
6
- add_project_arguments('-std=c99', language : 'c')
7
-
8
- cc = meson.get_compiler('c')
9
-
10
- root_include = include_directories('.')
11
-
12
- munit = library('munit',
13
- ['munit.c'],
14
- install: meson.is_subproject())
15
-
16
- if meson.is_subproject()
17
- munit_dep = declare_dependency(
18
- include_directories : root_include,
19
- link_with : munit)
20
- else
21
- # standalone install
22
- install_headers('munit.h')
23
-
24
- pkg = import('pkgconfig')
25
- pkg.generate(name: 'munit',
26
- description: 'µnit Testing Library for C',
27
- version: conf_data.get('version'),
28
- libraries: munit)
29
-
30
- # compile the demo project
31
- munit_example_src = files('example.c')
32
- munit_example = executable('munit_example', munit_example_src,
33
- include_directories: root_include,
34
- link_with: munit)
35
-
36
- test('munit example test', munit_example)
37
- endif