1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
|
pbcopper_test_cpp_sources = files([
# algorithm
'src/algorithm/test_Heteroduplex.cpp',
# align
'src/align/test_Alignment.cpp',
'src/align/test_BandedChainAlign.cpp',
'src/align/test_EdlibAlign.cpp',
'src/align/test_GlobalLocalAlignment.cpp',
'src/align/test_Seeds.cpp',
#cli2
'src/cli2/test_CLI.cpp',
'src/cli2/test_CommandLineParser.cpp',
'src/cli2/test_InterfaceHelpPrinter.cpp',
'src/cli2/test_MultiToolInterfaceHelpPrinter.cpp',
'src/cli2/test_OptionTranslator.cpp',
'src/cli2/test_OptionValue.cpp',
'src/cli2/test_PositionalArgumentTranslator.cpp',
'src/cli2/test_Results.cpp',
'src/cli2/test_VersionPrinter.cpp',
# data
'src/dagcon/test_Alignment.cpp',
'src/dagcon/test_AlignmentGraph.cpp',
# data
'src/data/test_Accuracy.cpp',
'src/data/test_Cigar.cpp',
'src/data/test_Frames.cpp',
'src/data/test_GenomicInterval.cpp',
'src/data/test_Interval.cpp',
'src/data/test_IntervalTree.cpp',
'src/data/test_MappedRead.cpp',
'src/data/test_MovieName.cpp',
'src/data/test_QualityValues.cpp',
'src/data/test_Read.cpp',
'src/data/test_ReadName.cpp',
'src/data/test_RSMovieName.cpp',
'src/data/test_RSReadName.cpp',
'src/data/test_SNR.cpp',
# JSON
'src/json/test_JSON.cpp',
# library
'src/library/test_Library.cpp',
# logging
'src/logging/test_Logging.cpp',
# math
'src/math/test_ConfusionMatrix.cpp',
'src/math/test_FishersExact.cpp',
# parallel
'src/parallel/test_WorkQueue.cpp',
'src/parallel/test_FireAndForget.cpp',
'src/parallel/test_FireAndForgetIndexed.cpp',
# pbmer
'src/pbmer/test_Dbg.cpp',
'src/pbmer/test_DbgNode.cpp',
'src/pbmer/test_DnaBit.cpp',
'src/pbmer/test_KFGraph.cpp',
'src/pbmer/test_Kmer.cpp',
'src/pbmer/test_Mers.cpp',
'src/pbmer/test_Parser.cpp',
# poa
'src/poa/test_PoaConsensus.cpp',
'src/poa/test_SparsePoa.cpp',
# qgram
'src/qgram/test_Index.cpp',
# reports
'src/reports/test_Report.cpp',
# utility
'src/utility/test_Alarm.cpp',
'src/utility/test_Base64.cpp',
'src/utility/test_FileUtils.cpp',
'src/utility/test_MinMax.cpp',
'src/utility/test_MoveAppend.cpp',
'src/utility/test_MoveInsert.cpp',
'src/utility/test_OStreamRedirect.cpp',
'src/utility/test_PartitionElements.cpp',
'src/utility/test_Shuffle.cpp',
'src/utility/test_Ssize.cpp',
'src/utility/test_Stopwatch.cpp',
'src/utility/test_StringUtils.cpp',
'src/utility/test_TimeReporter.cpp',
# sparc
'src/third-party/sparc/test_SparcConsensus.cpp',
])
# find GoogleTest
pbcopper_gtest_dep = dependency(
'gtest',
main : true,
fallback : ['gtest', 'gtest_main_dep'])
pbcopper_PbcopperTestData_h_config = configuration_data()
pbcopper_PbcopperTestData_h_config.set('Pbcopper_TestsDir', meson.current_source_dir())
pbcopper_PbcopperTestData_h_config.set('CMAKE_CURRENT_BINARY_DIR', meson.current_build_dir())
pbcopper_PbcopperTestData_h_config.set('GeneratedDir', meson.current_build_dir())
pbcopper_PbcopperTestData_h_config.set('GeneratedTestDataDir', meson.current_build_dir())
pbcopper_PbcopperTestData_h = configure_file(
input : files('include/PbcopperTestData.h.in'),
output : 'PbcopperTestData.h',
configuration : pbcopper_PbcopperTestData_h_config)
pbcopper_test_cpp_sources += pbcopper_PbcopperTestData_h
pbcopper_test = executable(
'pbcopper_test', [
pbcopper_test_cpp_sources],
dependencies : [pbcopper_gtest_dep, pbcopper_thread_dep, pbcopper_boost_dep],
include_directories : [pbcopper_include_directories, include_directories('include')],
link_with : [pbcopper_lib],
c_args : pbcopper_c_flags,
cpp_args : pbcopper_cpp_flags,
install : false)
#########
# tests #
#########
test(
'pbcopper formatting check',
pbcopper_clang_formatter,
args : [
'--all'],
workdir : meson.project_source_root())
test(
'pbcopper EOF check',
pbcopper_eof_check,
workdir : meson.project_source_root())
test(
'pbcopper gtest unittests',
pbcopper_test,
args : [
'--gtest_output=xml:' + join_paths(meson.project_build_root(), 'pbcopper-gtest-unittests.xml')],
env : [
'ARGS=-V',
'VERBOSE=1'],
timeout : 300) # debug unit tests on PoaConsensus can be *slow*
|
