source: trunk/test/Makefile.am

Last change on this file was 4180, checked in by Peter, 3 weeks ago

refs #979. Add class for inference of Poissonian mixture models.

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1## $Id: Makefile.am 4180 2022-06-09 04:07:30Z 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, 2022 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/anova.test \
36  test/alignment.test \
37  test/alignment2.test \
38  test/averager.test \
39  test/averager1.test \
40  test/averager3.test \
41  test/averager4.test \
42  test/bam.test \
43  test/bam_pair.test \
44  test/bam_pair_analyse.test \
45  test/bam_pair_buffer.test \
46  test/bam_iterator.test \
47  test/bam_read_filter.test \
48  test/bam_region_iterator.test \
49  test/bam_header.test \
50  test/bam_header2.test \
51  test/bam_pair_iterator.test \
52  test/bam_pair_iterator2.test \
53  test/binary_read_write.test \
54  test/chi2.test \
55  test/cigar.test \
56  test/cigar2.test \
57  test/cigar_iterator.test \
58  test/codon.test test/commandline.test \
59  test/concept.test \
60  test/consensus_inputranker.test \
61  test/copy_k_of_n.test \
62  test/data_lookup_1d.test  \
63  test/data_weight.test test/data_weight_proxy.test \
64  test/deleter.test \
65  test/diagonal_matrix.test \
66  test/distance.test \
67  test/dna.test \
68  test/dna_reverse_complement.test \
69  test/ensemble.test \
70  test/fasta.test \
71  test/feature_selection.test \
72  test/fileutil.test \
73  test/fisher.test \
74  test/gaussian_mixture.test \
75  test/genomic_position.test test/getline_iterator.test \
76  test/getvector.test \
77  test/gff.test \
78  test/gsl_error_handler.test \
79  test/histogram.test \
80  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
81  test/iterator.test test/kendall.test test/kernel_lookup.test \
82  test/kernel_matrix.test \
83  test/kernel_pca.test test/kernel.test \
84  test/knn.test test/kolmogorov_smirnov.test \
85  test/large_file.test \
86  test/libbam.test \
87  test/likelihood_ratio_test_binomial.test \
88  test/matrix_lookup.test \
89  test/matrix_lookup_weighted.test test/matrix.test \
90  test/matrix_expression.test \
91  test/matrix_view.test \
92  test/matrix_weighted.test test/merge.test \
93  test/merge_iterator.test \
94  test/multiminimizer.test \
95  test/multiminimizerderivative.test \
96  test/multiprocess.test \
97  test/multivariate.test \
98  test/nbc.test \
99  test/ncc.test \
100  test/negative_binomial.test \
101  test/nni.test test/normalization.test \
102  test/ostream_iterator.test \
103  test/pca.test \
104  test/percentile_confidence_interval.test \
105  test/perceptron.test \
106  test/phred.test \
107  test/pileup.test \
108  test/print_what.test \
109  test/priority_queue.test \
110  test/poisson.test \
111  test/poisson_mixture.test \
112  test/queue.test test/queue2.test \
113  test/queue3.test \
114  test/range.test \
115  test/ranking.test \
116  test/regression.test test/rnd.test \
117  test/rng-mt.test \
118  test/round.test \
119  test/score.test \
120  test/scheduler.test \
121  test/scheduler2.test \
122  test/scheduler3.test \
123  test/scheduler4.test \
124  test/scheduler5.test \
125  test/scheduler6.test \
126  test/scheduler7.test \
127  test/scheduler8.test \
128  test/scheduler9.test \
129  test/segment.test test/smart_ptr.test \
130  test/smith_waterman.test \
131  test/smoother.test test/spearman.test \
132  test/split.test test/statistics.test test/stream_redirect.test \
133  test/subset_generator.test test/svd.test test/svm.test \
134  test/svm_multi_class.test test/target.test \
135  test/ttest.test test/tukey.test \
136  test/unity_scaler.test \
137  test/utility.test test/vector.test test/version.test \
138  test/weighted_iterator_archetype.test \
139  test/vcf.test \
140  test/vcf_compare.test \
141  test/vcf_file.test \
142  test/vcf_file2.test \
143  test/vcf_file3.test \
144  test/vcf_header.test \
145  test/vector_expression.test \
146  test/view.test
147
148EXTRA_PROGRAMS = $(CXX_TESTS)
149EXTRA_PROGRAMS += test/stdopt
150
151CLEANFILES += $(EXTRA_PROGRAMS)
152
153# tests not passing through yet
154XFAIL_TESTS =
155
156DISTRIBUTED_TESTS = \
157test/cmd_test.sh \
158test/doxygen_test.sh \
159test/help_test.sh \
160test/version_option_test.sh \
161test/yat_config_test.sh \
162test/yat_config_cblas_test.sh \
163test/yat_cpp_add_flag_test.sh \
164test/yat_cxx_add_flag_test.sh \
165test/yat_header_assert_test.sh \
166test/yat_ld_add_flag_test.sh \
167test/yat_have_svn_wc_test.sh \
168test/yat_lt_compile_ifelse_test.sh \
169test/yat_lt_link_ifelse_test.sh \
170test/yat_lt_link_la_ifelse_test.sh \
171test/yat_msg_error_test.sh \
172test/yat_msg_error_test2.sh \
173test/yat_m4_with_bam_test.sh \
174test/yat_m4_test.sh \
175test/yat_m4_test2.sh \
176test/yat_pc_test.sh \
177test/yat_prog_move_if_change_test.sh \
178test/yat_revision_header_test.sh \
179test/yat_svn_release_year_test.sh \
180test/yat_svn_revision_test.sh \
181test/yat_use_libtool_tag_test.sh
182
183TESTS = $(DISTRIBUTED_TESTS) $(CXX_TESTS)
184EXTRA_DIST += $(DISTRIBUTED_TESTS)
185
186TEST_EXTENSIONS = .sh .test
187
188LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
189
190#test_large_file_test_LDADD = test/libyattest.la
191
192test_libyattest_la_LIBADD = yat/libyat.la
193test_libyattest_la_SOURCES = test/Suite.cc
194
195lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
196
197shell_test_deps = $(srcdir)/test/init.sh test/defs.sh
198
199# dependencies for lazycheck
200test/anova.log: test/data/anova.txt
201test/bam.log: test/data/foo.sorted.bam
202test/bam_header.log: test/data/foo.sorted.bam
203test/bam_header2.log: test/data/foo.sorted.bam
204test/bam_iterator.log: test/data/foo.sorted.bam
205test/bam_pair_analyse.log: test/data/foo.sorted.bam
206test/bam_pair_iterator.log: test/data/foo.sorted.bam
207test/bam_read_filter.log: test/data/foo.sorted.bam
208test/bam_region_iterator.log: test/data/foo.sorted.bam
209test/cmd_test.log: test/stdopt $(shell_test_deps)
210test/help_test.log: test/stdopt $(shell_test_deps)
211test/kendall.log: $(top_srcdir)/test/data/kendall.txt
212test/pileup.log: test/data/foo.sorted.bam
213test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
214
215test/vcf_file.log: $(srcdir)/test/data/foo.vcf
216test/vcf_file2.log: test/data/foo.vcf.gz
217
218test/version_option_test.log: test/stdopt $(shell_test_deps)
219
220test/yat_config_test.log: build_support/yat-config \
221  build_support/for_installation/yat-config $(shell_test_deps)
222test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
223test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
224  $(srcdir)/m4/ax_append_flag.m4 \
225  $(srcdir)/m4/ax_check_preproc_flag.m4 \
226  $(shell_test_deps)
227test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
228  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
229  $(top_srcdir)/m4/ax_append_flag.m4 \
230  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
231  $(top_srcdir)/m4/ax_require_defined.m4 \
232  $(shell_test_deps)
233test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
234test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
235  $(top_srcdir)/m4/ax_append_flag.m4 \
236  $(top_srcdir)/m4/ax_append_link_flags.m4 \
237  $(top_srcdir)/m4/ax_check_link_flag.m4 \
238  $(top_srcdir)/m4/ax_require_defined.m4 \
239  $(shell_test_deps)
240test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
241  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
242test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
243  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
244  $(top_builddir)/build_support/yat-config
245test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
246  test/lib/libmy-shared.la \
247  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
248  $(top_srcdir)/m4/yat_common.m4
249test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
250  $(top_builddir)/build_support/yat-config
251test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
252test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
253test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
254test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
255test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
256  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
257  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
258  $(top_srcdir)/m4/ax_file_escapes.m4 \
259  $(shell_test_deps)
260test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
261  $(shell_test_deps) \
262  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
263  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
264  $(top_srcdir)/m4/ax_file_escapes.m4
265test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
266  $(shell_test_deps) \
267  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
268  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
269  $(top_srcdir)/m4/ax_file_escapes.m4
270test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
271  $(shell_test_deps) \
272  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
273  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
274  $(top_srcdir)/m4/ax_file_escapes.m4
275test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
276  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
277
278if DX_ENABLE_HTML
279test/doxygen_test.log: doc/html/index.html
280endif
281
282# yat-hello is an example of a tiny package that uses yat
283dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
284
285# Directory yat-hello contains what a developer would check out
286# from a VCS, i.e., no files generated by autotools.
287yat_hello_sources  =
288yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
289yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
290yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
291
292EXTRA_DIST += $(yat_hello_sources)
293
294yat_hello_tmp_files =
295yat_hello_tmp_files += Makefile.in
296yat_hello_tmp_files += autom4te.cache
297yat_hello_tmp_files += aclocal.m4
298yat_hello_tmp_files += build-aux
299yat_hello_tmp_files += configure
300yat_hello_tmp_files += config.h.in
301yat_hello_tmp_files += m4
302
303
304yat_hello_deps = $(yat_hello_sources)
305yat_hello_deps += $(top_srcdir)/m4/yat.m4
306## We depend on version.m4 so tarball is updated at every release (at least)
307yat_hello_deps += $(top_srcdir)/m4/version.m4
308
309$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
310  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
311  && cd $(srcdir)/test/yat-hello \
312  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
313  && autoreconf -if $(yat_dev_null) \
314  && ./configure --without-yat $(yat_dev_null) \
315  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
316  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
317  && mv yat-hello-1.0.tar.gz .. \
318  && rm -rf $(yat_hello_tmp_files)
319
320INSTALL_CHECK_TARGETS += yat-hello-check
321
322yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
323  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
324  && cd yat-hello-1.0 \
325  && ./configure --with-yat=$(bindir) \
326  && $(MAKE) $(AM_MAKEFLAGS) all \
327  && ./hello \
328  && test x"`./hello`" = x"$(VERSION)" \
329  && cd .. \
330  && rm -rf yat-hello-1.0
331
332
333## test data
334EXTRA_DIST += \
335test/data/anova.txt \
336test/data/foo.sam \
337test/data/foo.vcf \
338test/data/isoform.peaks \
339test/data/kendall.txt \
340test/data/knni_matrix.data \
341test/data/knni_result.data \
342test/data/knni_weight.data \
343test/data/nm_alpha_linear_matlab.txt \
344test/data/nm_data_centralized.txt \
345test/data/nm_kernel.txt \
346test/data/nm_kernel2.txt \
347test/data/nm_kernel_gaussian.txt \
348test/data/nm_target_bin.txt \
349test/data/normalization_test.data \
350test/data/rank_data.txt \
351test/data/rank_target.txt \
352test/data/regression_gauss.data \
353test/data/small.gff2 \
354test/data/small.gff3 \
355test/data/sorlie_centroid_classes.txt \
356test/data/sorlie_centroid_data.txt  \
357test/data/sorlie_centroid_predictions.txt \
358test/data/sorlie_centroids.txt \
359test/data/vector1.data  \
360test/data/vector2.data \
361test/data/vector3.data \
362test/data/vector4.data \
363test/data/vector5.data \
364test/data/vector6.data  \
365test/data/vector7.data \
366test/data/wenni_result.data \
367test/data/wenni_weight.data
368
369CLEANFILES += test/data/.dirstamp
370CLEANFILES += test/data/foo.sorted.bam
371CLEANFILES += test/data/foo.sorted.bam.bai
372CLEANFILES += test/data/foo.fasta
373CLEANFILES += test/data/foo.fasta.fai
374CLEANFILES += test/data/foo.vcf.gz
375
376check_DATA  = test/data/foo.sorted.bam
377check_DATA += test/data/foo.sorted.bam.bai
378check_DATA += test/data/foo.fasta
379check_DATA += test/data/foo.fasta.fai
380check_DATA += test/data/foo.vcf.gz
381
382test/data/.dirstamp:
383  @$(MKDIR_P) test/data
384  @: > $@
385
386if HAVE_SAMTOOLS_EXECUTABLE
387# depend on config.h to ensure rule is triggered when
388# HAVE_SAMTOOLS_EXECUTABLE has changed and possible (empty) dummy bam
389# file is replaced with a proper one.
390test/data/foo.sorted.bam: test/data/.dirstamp test/data/foo.sam config.h
391  $(AM_V_GEN)
392  $(AM_V_at)$(SAMTOOLS) sort -T foo -o $@ $(srcdir)/test/data/foo.sam
393
394test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
395  $(AM_V_GEN)
396  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
397
398else
399test/data/foo.sorted.bam: test/data/.dirstamp
400  $(AM_V_at): > $@
401
402test/data/foo.sorted.bam.bai: test/data/.dirstamp
403  $(AM_V_at): > $@
404endif
405
406if HAVE_SAMTOOLS_FASTA_EXECUTABLE
407test/data/foo.fasta: test/data/foo.sorted.bam
408  $(AM_V_GEN)
409  $(AM_V_at)$(SAMTOOLS) fasta test/data/foo.sorted.bam > $@
410
411test/data/foo.fasta.fai: test/data/foo.fasta
412  $(AM_V_GEN)
413  $(AM_V_at)$(SAMTOOLS) faidx test/data/foo.fasta
414
415else
416test/data/foo.fasta: test/data/.dirstamp
417  $(AM_V_at): > $@
418
419test/data/foo.fasta.fai: test/data/.dirstamp
420  $(AM_V_at): > $@
421endif
422
423if HAVE_BCFTOOLS_EXECUTABLE
424test/data/foo.vcf.gz: test/data/.dirstamp test/data/foo.vcf
425  $(AM_V_GEN)
426  $(AM_V_at)$(BCFTOOLS) view $(srcdir)/test/data/foo.vcf -O z > $@
427else
428test/data/foo.vcf.gz: test/data/.dirstamp
429  $(AM_V_at): > $@
430endif
431
432test/lib/.dirstamp:
433  @$(MKDIR_P) test/lib
434  @: > $@
435
436check_DATA += test/lib/libmy-static.a
437EXTRA_DIST += test/gen_libmy_static.sh
438
439test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
440test/defs.sh
441  $(AM_V_GEN)
442  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)
443
444check_DATA += test/lib/libmy-shared.la
445EXTRA_DIST += test/gen_libmy_shared.sh
446
447test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
448test/defs.sh
449  $(AM_V_GEN)
450  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)
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