source: trunk/test/Makefile.am @ 4083

Last change on this file since 4083 was 4083, checked in by Peter, 10 months ago

merge kendall-score branch into trunk. refs #710

  • Property svn:eol-style set to native
  • Property svn:keywords set to Author Date Id Revision
File size: 13.8 KB
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1## $Id: Makefile.am 4083 2021-08-27 01:32:27Z peter $
2
3# Copyright (C) 2003 Daniel Dalevi, Jari Häkkinen
4# Copyright (C) 2004 Jari Häkkinen, Peter Johansson, Cecilia Ritz
5# Copyright (C) 2005 Jari Häkkinen, Peter Johansson
6# Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
7# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014, 2015, 2016, 2017, 2018, 2019, 2020, 2021 Peter Johansson
8#
9# This file is part of the yat library, http://dev.thep.lu.se/yat
10#
11# The yat library is free software; you can redistribute it
12# and/or modify it under the terms of the GNU General Public License as
13# published by the Free Software Foundation; either version 3 of the
14# License, or (at your option) any later version.
15#
16# The yat library is distributed in the hope that it will be useful,
17# but WITHOUT ANY WARRANTY; without even the implied warranty of
18# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
19# General Public License for more details.
20#
21# You should have received a copy of the GNU General Public License
22# along with yat. If not, see <http://www.gnu.org/licenses/>.
23
24## we use suffix .cc for all source
25AM_DEFAULT_SOURCE_EXT = .cc
26
27noinst_HEADERS = test/Suite.h
28
29check_LTLIBRARIES = test/libyattest.la
30
31check_SCRIPTS = test/defs.sh
32
33EXTRA_DIST += test/init.sh
34
35CXX_TESTS = test/alignment.test \
36  test/alignment2.test \
37  test/averager.test \
38  test/averager1.test \
39  test/averager3.test \
40  test/averager4.test \
41  test/bam.test \
42  test/bam_pair.test \
43  test/bam_pair_analyse.test \
44  test/bam_pair_buffer.test \
45  test/bam_iterator.test \
46  test/bam_read_filter.test \
47  test/bam_region_iterator.test \
48  test/bam_header.test \
49  test/bam_header2.test \
50  test/bam_pair_iterator.test \
51  test/bam_pair_iterator2.test \
52  test/binary_read_write.test \
53  test/chi2.test \
54  test/cigar.test \
55  test/cigar2.test \
56  test/cigar_iterator.test \
57  test/codon.test test/commandline.test \
58  test/concept.test \
59  test/consensus_inputranker.test \
60  test/copy_k_of_n.test \
61  test/data_lookup_1d.test  \
62  test/data_weight.test test/data_weight_proxy.test \
63  test/deleter.test \
64  test/diagonal_matrix.test \
65  test/distance.test \
66  test/dna.test \
67  test/dna_reverse_complement.test \
68  test/ensemble.test \
69  test/fasta.test \
70  test/feature_selection.test \
71  test/fileutil.test \
72  test/fisher.test \
73  test/gaussian_mixture.test \
74  test/genomic_position.test test/getline_iterator.test \
75  test/getvector.test \
76  test/gff.test \
77  test/gsl_error_handler.test \
78  test/help.test test/histogram.test \
79  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
80  test/iterator.test test/kendall.test test/kernel_lookup.test \
81  test/kernel_matrix.test \
82  test/kernel_pca.test test/kernel.test \
83  test/knn.test test/kolmogorov_smirnov.test \
84  test/large_file.test \
85  test/libbam.test \
86  test/likelihood_ratio_test_binomial.test \
87  test/matrix_lookup.test \
88  test/matrix_lookup_weighted.test test/matrix.test \
89  test/matrix_expression.test \
90  test/matrix_weighted.test test/merge.test \
91  test/merge_iterator.test \
92  test/multiprocess.test \
93  test/nbc.test \
94  test/ncc.test \
95  test/negative_binomial.test \
96  test/nni.test test/normalization.test \
97  test/ostream_iterator.test \
98  test/pca.test \
99  test/percentile_confidence_interval.test \
100  test/perceptron.test \
101  test/phred.test \
102  test/pileup.test \
103  test/print_what.test \
104  test/priority_queue.test \
105  test/poisson.test \
106  test/queue.test test/queue2.test \
107  test/queue3.test \
108  test/range.test \
109  test/ranking.test \
110  test/regression.test test/rnd.test \
111  test/rng-mt.test \
112  test/round.test \
113  test/score.test \
114  test/scheduler.test \
115  test/scheduler2.test \
116  test/scheduler3.test \
117  test/scheduler4.test \
118  test/scheduler5.test \
119  test/scheduler6.test \
120  test/scheduler7.test \
121  test/segment.test test/smart_ptr.test \
122  test/smith_waterman.test \
123  test/smoother.test test/spearman.test \
124  test/split.test test/statistics.test test/stream_redirect.test \
125  test/subset_generator.test test/svd.test test/svm.test \
126  test/svm_multi_class.test test/target.test \
127  test/ttest.test test/tukey.test \
128  test/utility.test test/vector.test test/version.test \
129  test/weighted_iterator_archetype.test \
130  test/vcf.test \
131  test/vcf_compare.test \
132  test/vcf_file.test \
133  test/vcf_file2.test \
134  test/vcf_file3.test \
135  test/vcf_header.test \
136  test/vector_expression.test \
137  test/view.test
138
139EXTRA_PROGRAMS = $(CXX_TESTS)
140
141CLEANFILES += $(EXTRA_PROGRAMS)
142
143# tests not passing through yet
144XFAIL_TESTS =
145
146DISTRIBUTED_TESTS = \
147test/cmd_test.sh \
148test/doxygen_test.sh \
149test/help_test.sh \
150test/yat_config_test.sh \
151test/yat_config_cblas_test.sh \
152test/yat_cpp_add_flag_test.sh \
153test/yat_cxx_add_flag_test.sh \
154test/yat_header_assert_test.sh \
155test/yat_ld_add_flag_test.sh \
156test/yat_have_svn_wc_test.sh \
157test/yat_lt_compile_ifelse_test.sh \
158test/yat_lt_link_ifelse_test.sh \
159test/yat_lt_link_la_ifelse_test.sh \
160test/yat_msg_error_test.sh \
161test/yat_msg_error_test2.sh \
162test/yat_m4_with_bam_test.sh \
163test/yat_m4_test.sh \
164test/yat_m4_test2.sh \
165test/yat_pc_test.sh \
166test/yat_prog_move_if_change_test.sh \
167test/yat_revision_header_test.sh \
168test/yat_svn_release_year_test.sh \
169test/yat_svn_revision_test.sh \
170test/yat_use_libtool_tag_test.sh
171
172TESTS = $(DISTRIBUTED_TESTS) $(CXX_TESTS)
173EXTRA_DIST += $(DISTRIBUTED_TESTS)
174
175TEST_EXTENSIONS = .sh .test
176
177LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
178
179#test_large_file_test_LDADD = test/libyattest.la
180
181test_libyattest_la_LIBADD = yat/libyat.la
182test_libyattest_la_SOURCES = test/Suite.cc
183
184lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
185
186shell_test_deps = $(srcdir)/test/init.sh test/defs.sh
187
188# dependencies for lazycheck
189test/bam.log: test/data/foo.sorted.bam
190test/bam_header.log: test/data/foo.sorted.bam
191test/bam_header2.log: test/data/foo.sorted.bam
192test/bam_iterator.log: test/data/foo.sorted.bam
193test/bam_pair_analyse.log: test/data/foo.sorted.bam
194test/bam_pair_iterator.log: test/data/foo.sorted.bam
195test/bam_read_filter.log: test/data/foo.sorted.bam
196test/bam_region_iterator.log: test/data/foo.sorted.bam
197test/cmd_test.log: test/help.test $(shell_test_deps)
198test/help_test.log: test/help.test $(shell_test_deps)
199test/kendall.log: $(top_srcdir)/test/data/kendall.txt
200test/pileup.log: test/data/foo.sorted.bam
201test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
202
203test/vcf_file.log: $(srcdir)/test/data/foo.vcf
204test/vcf_file2.log: test/data/foo.vcf.gz
205
206test/yat_config_test.log: build_support/yat-config \
207  build_support/for_installation/yat-config $(shell_test_deps)
208test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
209test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
210  $(srcdir)/m4/ax_append_flag.m4 \
211  $(srcdir)/m4/ax_check_preproc_flag.m4 \
212  $(shell_test_deps)
213test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
214  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
215  $(top_srcdir)/m4/ax_append_flag.m4 \
216  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
217  $(top_srcdir)/m4/ax_require_defined.m4 \
218  $(shell_test_deps)
219test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
220test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
221  $(top_srcdir)/m4/ax_append_flag.m4 \
222  $(top_srcdir)/m4/ax_append_link_flags.m4 \
223  $(top_srcdir)/m4/ax_check_link_flag.m4 \
224  $(top_srcdir)/m4/ax_require_defined.m4 \
225  $(shell_test_deps)
226test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
227  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
228test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
229  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
230  $(top_builddir)/build_support/yat-config
231test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
232  test/lib/libmy-shared.la \
233  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
234  $(top_srcdir)/m4/yat_common.m4
235test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
236  $(top_builddir)/build_support/yat-config
237test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
238test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
239test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
240test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
241test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
242  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
243  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
244  $(top_srcdir)/m4/ax_file_escapes.m4 \
245  $(shell_test_deps)
246test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
247  $(shell_test_deps) \
248  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
249  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
250  $(top_srcdir)/m4/ax_file_escapes.m4
251test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
252  $(shell_test_deps) \
253  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
254  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
255  $(top_srcdir)/m4/ax_file_escapes.m4
256test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
257  $(shell_test_deps) \
258  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
259  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
260  $(top_srcdir)/m4/ax_file_escapes.m4
261test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
262  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
263
264if DX_ENABLE_HTML
265test/doxygen_test.log: doc/html/index.html
266endif
267
268# yat-hello is an example of a tiny package that uses yat
269dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
270
271# Directory yat-hello contains what a developer would check out
272# from a VCS, i.e., no files generated by autotools.
273yat_hello_sources  =
274yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
275yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
276yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
277
278EXTRA_DIST += $(yat_hello_sources)
279
280yat_hello_tmp_files =
281yat_hello_tmp_files += Makefile.in
282yat_hello_tmp_files += autom4te.cache
283yat_hello_tmp_files += aclocal.m4
284yat_hello_tmp_files += build-aux
285yat_hello_tmp_files += configure
286yat_hello_tmp_files += config.h.in
287yat_hello_tmp_files += m4
288
289
290yat_hello_deps = $(yat_hello_sources)
291yat_hello_deps += $(top_srcdir)/m4/yat.m4
292## We depend on version.m4 so tarball is updated at every release (at least)
293yat_hello_deps += $(top_srcdir)/m4/version.m4
294
295$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
296  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
297  && cd $(srcdir)/test/yat-hello \
298  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
299  && autoreconf -if $(yat_dev_null) \
300  && ./configure --without-yat $(yat_dev_null) \
301  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
302  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
303  && mv yat-hello-1.0.tar.gz .. \
304  && rm -rf $(yat_hello_tmp_files)
305
306INSTALL_CHECK_TARGETS += yat-hello-check
307
308yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
309  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
310  && cd yat-hello-1.0 \
311  && ./configure --with-yat=$(bindir) \
312  && $(MAKE) $(AM_MAKEFLAGS) all \
313  && ./hello \
314  && test x"`./hello`" = x"$(VERSION)" \
315  && cd .. \
316  && rm -rf yat-hello-1.0
317
318
319## test data
320EXTRA_DIST += \
321test/data/foo.sam \
322test/data/foo.vcf \
323test/data/isoform.peaks \
324test/data/kendall.txt \
325test/data/knni_matrix.data \
326test/data/knni_result.data \
327test/data/knni_weight.data \
328test/data/nm_alpha_linear_matlab.txt \
329test/data/nm_data_centralized.txt \
330test/data/nm_kernel.txt \
331test/data/nm_kernel2.txt \
332test/data/nm_kernel_gaussian.txt \
333test/data/nm_target_bin.txt \
334test/data/normalization_test.data \
335test/data/rank_data.txt \
336test/data/rank_target.txt \
337test/data/regression_gauss.data \
338test/data/small.gff2 \
339test/data/small.gff3 \
340test/data/sorlie_centroid_classes.txt \
341test/data/sorlie_centroid_data.txt  \
342test/data/sorlie_centroid_predictions.txt \
343test/data/sorlie_centroids.txt \
344test/data/vector1.data  \
345test/data/vector2.data \
346test/data/vector3.data \
347test/data/vector4.data \
348test/data/vector5.data \
349test/data/vector6.data  \
350test/data/vector7.data \
351test/data/wenni_result.data \
352test/data/wenni_weight.data
353
354CLEANFILES += test/data/.dirstamp
355CLEANFILES += test/data/foo.sorted.bam
356CLEANFILES += test/data/foo.sorted.bam.bai
357CLEANFILES += test/data/foo.fasta
358CLEANFILES += test/data/foo.fasta.fai
359CLEANFILES += test/data/foo.vcf.gz
360
361check_DATA  = test/data/foo.sorted.bam
362check_DATA += test/data/foo.sorted.bam.bai
363check_DATA += test/data/foo.fasta
364check_DATA += test/data/foo.fasta.fai
365check_DATA += test/data/foo.vcf.gz
366
367test/data/.dirstamp:
368  @$(MKDIR_P) test/data
369  @: > $@
370
371if HAVE_SAMTOOLS_EXECUTABLE
372# depend on config.h to ensure rule is triggered when
373# HAVE_SAMTOOLS_EXECUTABLE has changed and possible (empty) dummy bam
374# file is replaced with a proper one.
375test/data/foo.sorted.bam: test/data/.dirstamp test/data/foo.sam config.h
376  $(AM_V_GEN)
377  $(AM_V_at)$(SAMTOOLS) sort -T foo -o $@ $(srcdir)/test/data/foo.sam
378
379test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
380  $(AM_V_GEN)
381  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
382
383else
384test/data/foo.sorted.bam: test/data/.dirstamp
385  $(AM_V_at): > $@
386
387test/data/foo.sorted.bam.bai: test/data/.dirstamp
388  $(AM_V_at): > $@
389endif
390
391if HAVE_SAMTOOLS_FASTA_EXECUTABLE
392test/data/foo.fasta: test/data/foo.sorted.bam
393  $(AM_V_GEN)
394  $(AM_V_at)$(SAMTOOLS) fasta test/data/foo.sorted.bam > $@
395
396test/data/foo.fasta.fai: test/data/foo.fasta
397  $(AM_V_GEN)
398  $(AM_V_at)$(SAMTOOLS) faidx test/data/foo.fasta
399
400else
401test/data/foo.fasta: test/data/.dirstamp
402  $(AM_V_at): > $@
403
404test/data/foo.fasta.fai: test/data/.dirstamp
405  $(AM_V_at): > $@
406endif
407
408if HAVE_BCFTOOLS_EXECUTABLE
409test/data/foo.vcf.gz: test/data/.dirstamp test/data/foo.vcf
410  $(AM_V_GEN)
411  $(AM_V_at)$(BCFTOOLS) view $(srcdir)/test/data/foo.vcf -O z > $@
412else
413test/data/foo.vcf.gz: test/data/.dirstamp
414  $(AM_V_at): > $@
415endif
416
417test/lib/.dirstamp:
418  @$(MKDIR_P) test/lib
419  @: > $@
420
421check_DATA += test/lib/libmy-static.a
422EXTRA_DIST += test/gen_libmy_static.sh
423
424test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
425test/defs.sh
426  $(AM_V_GEN)
427  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)
428
429check_DATA += test/lib/libmy-shared.la
430EXTRA_DIST += test/gen_libmy_shared.sh
431
432test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
433test/defs.sh
434  $(AM_V_GEN)
435  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)
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