source: trunk/test/Makefile.am @ 3615

Last change on this file since 3615 was 3615, checked in by Peter, 6 years ago

some trivial tests for regression::Poisson. refs #882

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1## $Id: Makefile.am 3615 2017-02-06 02:31:36Z 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 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
35EXTRA_PROGRAMS = 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_analyse.test \
43  test/bam_iterator.test \
44  test/bam_read_filter.test \
45  test/bam_region_iterator.test \
46  test/bam_header.test \
47  test/bam_header2.test \
48  test/bam_pair_iterator.test \
49  test/cigar.test \
50  test/cigar2.test \
51  test/cigar_iterator.test \
52  test/codon.test test/commandline.test \
53  test/concept.test \
54  test/consensus_inputranker.test \
55  test/copy_k_of_n.test \
56  test/data_lookup_1d.test  \
57  test/data_weight.test test/data_weight_proxy.test \
58  test/deleter.test \
59  test/distance.test \
60  test/dna.test \
61  test/dna_reverse_complement.test \
62  test/ensemble.test \
63  test/fasta.test \
64  test/feature_selection.test \
65  test/fileutil.test \
66  test/fisher.test test/genomic_position.test test/getline_iterator.test \
67  test/gff.test test/help.test test/histogram.test \
68  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
69  test/iterator.test test/kendall.test test/kernel_lookup.test \
70  test/kernel_matrix.test \
71  test/kernel_pca.test test/kernel.test \
72  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
73  test/likelihood_ratio_test_binomial.test \
74  test/matrix_lookup.test \
75  test/matrix_lookup_weighted.test test/matrix.test \
76  test/matrix_expression.test \
77  test/matrix_weighted.test test/merge.test \
78  test/merge_iterator.test test/nbc.test \
79  test/ncc.test test/nni.test test/normalization.test \
80  test/ostream_iterator.test \
81  test/pca.test \
82  test/phred.test \
83  test/pileup.test \
84  test/priority_queue.test \
85  test/poisson.test \
86  test/queue.test test/queue2.test \
87  test/range.test test/regression.test test/rnd.test \
88  test/rng-mt.test \
89  test/roc.test \
90  test/score.test \
91  test/scheduler.test \
92  test/scheduler2.test \
93  test/scheduler3.test \
94  test/segment.test test/smart_ptr.test \
95  test/smith_waterman.test \
96  test/smoother.test test/spearman.test \
97  test/split.test test/statistics.test test/stream_redirect.test \
98  test/subset_generator.test test/svd.test test/svm.test \
99  test/svm_multi_class.test test/target.test \
100  test/ttest.test test/tukey.test \
101  test/utility.test test/vector.test test/version.test \
102  test/weighted_iterator_archetype.test \
103  test/vector_expression.test \
104  test/view.test
105
106CLEANFILES += $(EXTRA_PROGRAMS)
107
108# tests not passing through yet
109XFAIL_TESTS =
110
111DISTRIBUTED_TESTS = \
112test/cmd_test.sh \
113test/doxygen_test.sh \
114test/help_test.sh \
115test/yat_config_test.sh \
116test/yat_config_cblas_test.sh \
117test/yat_cpp_add_flag_test.sh \
118test/yat_cxx_add_flag_test.sh \
119test/yat_header_assert_test.sh \
120test/yat_ld_add_flag_test.sh \
121test/yat_have_svn_wc_test.sh \
122test/yat_lt_compile_ifelse_test.sh \
123test/yat_lt_link_ifelse_test.sh \
124test/yat_lt_link_la_ifelse_test.sh \
125test/yat_msg_error_test.sh \
126test/yat_msg_error_test2.sh \
127test/yat_m4_with_bam_test.sh \
128test/yat_m4_test.sh \
129test/yat_m4_test2.sh \
130test/yat_pc_test.sh \
131test/yat_prog_move_if_change_test.sh \
132test/yat_revision_header_test.sh \
133test/yat_svn_release_year_test.sh \
134test/yat_svn_revision_test.sh \
135test/yat_use_libtool_tag_test.sh
136
137TESTS = $(DISTRIBUTED_TESTS) $(EXTRA_PROGRAMS)
138EXTRA_DIST += $(DISTRIBUTED_TESTS)
139
140TEST_EXTENSIONS = .sh .test
141
142LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)
143
144#test_large_file_test_LDADD = test/libyattest.la
145
146test_libyattest_la_LIBADD = yat/libyat.la
147test_libyattest_la_SOURCES = test/Suite.cc
148
149lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=
150
151shell_test_deps = $(srcdir)/test/init.sh test/defs.sh
152
153# dependencies for lazycheck
154test/bam.log: test/data/foo.sorted.bam
155test/bam_header.log: test/data/foo.sorted.bam
156test/bam_header2.log: test/data/foo.sorted.bam
157test/bam_iterator.log: test/data/foo.sorted.bam
158test/bam_pair_analyse.log: test/data/foo.sorted.bam
159test/bam_pair_iterator.log: test/data/foo.sorted.bam
160test/bam_read_filter.log: test/data/foo.sorted.bam
161test/bam_region_iterator.log: test/data/foo.sorted.bam
162test/cmd_test.log: test/help.test $(shell_test_deps)
163test/help_test.log: test/help.test $(shell_test_deps)
164test/pileup.log: test/data/foo.sorted.bam
165test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
166test/yat_config_test.log: build_support/yat-config \
167  build_support/for_installation/yat-config $(shell_test_deps)
168test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
169test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
170  $(srcdir)/m4/ax_append_flag.m4 \
171  $(srcdir)/m4/ax_check_preproc_flag.m4 \
172  $(shell_test_deps)
173test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
174  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
175  $(top_srcdir)/m4/ax_append_flag.m4 \
176  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
177  $(top_srcdir)/m4/ax_require_defined.m4 \
178  $(shell_test_deps)
179test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
180test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
181  $(top_srcdir)/m4/ax_append_flag.m4 \
182  $(top_srcdir)/m4/ax_append_link_flags.m4 \
183  $(top_srcdir)/m4/ax_check_link_flag.m4 \
184  $(top_srcdir)/m4/ax_require_defined.m4 \
185  $(shell_test_deps)
186test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
187  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
188test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
189  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
190  $(top_builddir)/build_support/yat-config
191test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
192  test/lib/libmy-shared.la \
193  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
194  $(top_srcdir)/m4/yat_common.m4
195test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
196  $(top_builddir)/build_support/yat-config
197test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
198test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
199test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
200test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
201test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
202  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
203  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
204  $(top_srcdir)/m4/ax_file_escapes.m4 \
205  $(shell_test_deps)
206test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
207  $(shell_test_deps) \
208  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
209  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
210  $(top_srcdir)/m4/ax_file_escapes.m4
211test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
212  $(shell_test_deps) \
213  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
214  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
215  $(top_srcdir)/m4/ax_file_escapes.m4
216test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
217  $(shell_test_deps) \
218  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
219  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
220  $(top_srcdir)/m4/ax_file_escapes.m4
221test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
222  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
223
224if DX_ENABLE_HTML
225test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
226endif
227
228# yat-hello is an example of a tiny package that uses yat
229dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz
230
231# Directory yat-hello contains what a developer would check out
232# from a VCS, i.e., no files generated by autotools.
233yat_hello_sources  =
234yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
235yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
236yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc
237
238EXTRA_DIST += $(yat_hello_sources)
239
240yat_hello_tmp_files =
241yat_hello_tmp_files += Makefile.in
242yat_hello_tmp_files += autom4te.cache
243yat_hello_tmp_files += aclocal.m4
244yat_hello_tmp_files += build-aux
245yat_hello_tmp_files += configure
246yat_hello_tmp_files += config.h.in
247yat_hello_tmp_files += m4
248
249
250yat_hello_deps = $(yat_hello_sources)
251yat_hello_deps += $(top_srcdir)/m4/yat.m4
252## We depend on version.m4 so tarball is updated at every release (at least)
253yat_hello_deps += $(top_srcdir)/m4/version.m4
254
255$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
256  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
257  && cd $(srcdir)/test/yat-hello \
258  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
259  && autoreconf -if $(yat_dev_null) \
260  && ./configure --without-yat $(yat_dev_null) \
261  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
262  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
263  && mv yat-hello-1.0.tar.gz .. \
264  && rm -rf $(yat_hello_tmp_files)
265
266INSTALL_CHECK_TARGETS += yat-hello-check
267
268yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
269  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
270  && cd yat-hello-1.0 \
271  && ./configure --with-yat=$(bindir) \
272  && $(MAKE) $(AM_MAKEFLAGS) all \
273  && ./hello \
274  && test x"`./hello`" = x"$(VERSION)" \
275  && cd .. \
276  && rm -rf yat-hello-1.0
277
278
279## test data
280EXTRA_DIST += \
281test/data/foo.sam \
282test/data/isoform.peaks \
283test/data/knni_matrix.data \
284test/data/knni_result.data \
285test/data/knni_weight.data \
286test/data/nm_alpha_linear_matlab.txt \
287test/data/nm_data_centralized.txt \
288test/data/nm_kernel.txt \
289test/data/nm_kernel2.txt \
290test/data/nm_kernel_gaussian.txt \
291test/data/nm_target_bin.txt \
292test/data/normalization_test.data \
293test/data/rank_data.txt \
294test/data/rank_target.txt \
295test/data/regression_gauss.data \
296test/data/small.gff2 \
297test/data/small.gff3 \
298test/data/sorlie_centroid_classes.txt \
299test/data/sorlie_centroid_data.txt  \
300test/data/sorlie_centroid_predictions.txt \
301test/data/sorlie_centroids.txt \
302test/data/vector1.data  \
303test/data/vector2.data \
304test/data/vector3.data \
305test/data/vector4.data \
306test/data/vector5.data \
307test/data/vector6.data  \
308test/data/vector7.data \
309test/data/wenni_result.data \
310test/data/wenni_weight.data
311
312CLEANFILES += test/data/.dirstamp
313CLEANFILES += test/data/foo.sorted.bam
314CLEANFILES += test/data/foo.sorted.bam.bai
315CLEANFILES += test/data/foo.fasta
316CLEANFILES += test/data/foo.fasta.fai
317
318check_DATA  = test/data/foo.sorted.bam
319check_DATA += test/data/foo.sorted.bam.bai
320check_DATA += test/data/foo.fasta
321check_DATA += test/data/foo.fasta.fai
322
323test/data/.dirstamp:
324  @$(MKDIR_P) test/data
325  @: > $@
326
327if HAVE_SAMTOOLS_EXECUTABLE
328# depend on config.h to ensure rule is triggered when
329# HAVE_SAMTOOLS_EXECUTABLE has changed and possible (empty) dummy bam
330# file is replaced with a proper one.
331test/data/foo.sorted.bam: test/data/.dirstamp test/data/foo.sam config.h
332  $(AM_V_GEN)
333  $(AM_V_at)$(SAMTOOLS) sort -T foo -o $@ $(srcdir)/test/data/foo.sam
334
335test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
336  $(AM_V_GEN)
337  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
338
339else
340test/data/foo.sorted.bam: test/data/.dirstamp
341  $(AM_V_at): > $@
342
343test/data/foo.sorted.bam.bai: test/data/.dirstamp
344  $(AM_V_at): > $@
345endif
346
347if HAVE_SAMTOOLS_FASTA_EXECUTABLE
348test/data/foo.fasta: test/data/foo.sorted.bam
349  $(AM_V_GEN)
350  $(AM_V_at)$(SAMTOOLS) fasta test/data/foo.sorted.bam > $@
351
352test/data/foo.fasta.fai: test/data/foo.fasta
353  $(AM_V_GEN)
354  $(AM_V_at)$(SAMTOOLS) faidx test/data/foo.fasta
355
356else
357test/data/foo.fasta: test/data/.dirstamp
358  $(AM_V_at): > $@
359
360test/data/foo.fasta.fai: test/data/.dirstamp
361  $(AM_V_at): > $@
362endif
363
364test/lib/.dirstamp:
365  @$(MKDIR_P) test/lib
366  @: > $@
367
368check_DATA += test/lib/libmy-static.a
369EXTRA_DIST += test/gen_libmy_static.sh
370
371test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
372test/defs.sh
373  $(AM_V_GEN)
374  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)
375
376check_DATA += test/lib/libmy-shared.la
377EXTRA_DIST += test/gen_libmy_shared.sh
378
379test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
380test/defs.sh
381  $(AM_V_GEN)
382  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)
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