source: trunk/test/Makefile.am @ 3317

## $Id: Makefile.am 3317 2014-09-19 05:41:50Z peter $

# Copyright (C) 2003 Daniel Dalevi, Jari Häkkinen
# Copyright (C) 2004 Jari Häkkinen, Peter Johansson, Cecilia Ritz
# Copyright (C) 2005 Jari Häkkinen, Peter Johansson
# Copyright (C) 2006, 2007, 2008 Jari Häkkinen, Peter Johansson, Markus Ringnér
# Copyright (C) 2009, 2010, 2011, 2012, 2013, 2014 Peter Johansson
#
# This file is part of the yat library, http://dev.thep.lu.se/yat
#
# The yat library is free software; you can redistribute it
# and/or modify it under the terms of the GNU General Public License as
# published by the Free Software Foundation; either version 3 of the
# License, or (at your option) any later version.
#
# The yat library is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU
# General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with yat. If not, see <http://www.gnu.org/licenses/>.

## we use suffix .cc for all source
AM_DEFAULT_SOURCE_EXT = .cc

noinst_HEADERS = test/Suite.h test/weighted_iterator_archetype.h

check_LTLIBRARIES = test/libyattest.la

check_SCRIPTS = test/defs.sh

EXTRA_DIST += test/init.sh

EXTRA_PROGRAMS = test/alignment.test \
  test/alignment2.test \
  test/averager.test \
  test/averager1.test \
  test/averager3.test \
  test/averager4.test \
  test/bam.test \
  test/bam_pair_analyse.test \
  test/bam_iterator.test \
  test/bam_read_filter.test \
  test/bam_region_iterator.test \
  test/bam_header.test \
  test/bam_header2.test \
  test/bam_pair_iterator.test \
  test/cigar.test \
  test/codon.test test/commandline.test \
  test/concept.test \
  test/consensus_inputranker.test test/data_lookup_1d.test  \
  test/data_weight.test test/data_weight_proxy.test \
  test/deleter.test \
  test/distance.test \
  test/dna.test test/ensemble.test test/feature_selection.test \
  test/fileutil.test \
  test/fisher.test test/genomic_position.test test/getline_iterator.test \
  test/gff.test test/help.test test/histogram.test \
  test/igp.test test/index.test test/inputranker.test test/interpolation.test \
  test/iterator.test test/kendall.test test/kernel_lookup.test \
  test/kernel_matrix.test \
  test/kernel_pca.test test/kernel.test \
  test/knn.test test/kolmogorov_smirnov.test test/large_file.test \
  test/likelihood_ratio_test_binomial.test \
  test/matrix_lookup.test \
  test/matrix_lookup_weighted.test test/matrix.test \
  test/matrix_weighted.test test/merge.test \
  test/merge_iterator.test test/nbc.test \
  test/ncc.test test/nni.test test/normalization.test \
  test/ostream_iterator.test \
  test/pca.test \
  test/pileup.test \
  test/queue.test test/queue2.test \
  test/range.test test/regression.test test/rnd.test \
  test/rng-mt.test \
  test/roc.test \
  test/score.test test/segment.test test/smart_ptr.test   \
  test/smith_waterman.test \
  test/smoother.test test/spearman.test \
  test/split.test test/statistics.test test/stream_redirect.test \
  test/subset_generator.test test/svd.test test/svm.test \
  test/svm_multi_class.test test/target.test \
  test/ttest.test test/tukey.test \
  test/utility.test test/vector.test test/version.test \
  test/weighted_iterator_archetype.test \
  test/view.test

TESTS = $(EXTRA_PROGRAMS)
CLEANFILES += $(EXTRA_PROGRAMS)

# tests not passing through yet
XFAIL_TESTS =

DISTRIBUTED_TESTS = \
test/cmd_test.sh \
test/doxygen_test.sh \
test/help_test.sh \
test/static_test.sh \
test/yat_config_test.sh \
test/yat_config_cblas_test.sh \
test/yat_cpp_add_flag_test.sh \
test/yat_cxx_add_flag_test.sh \
test/yat_header_assert_test.sh \
test/yat_ld_add_flag_test.sh \
test/yat_have_svn_wc_test.sh \
test/yat_lt_compile_ifelse_test.sh \
test/yat_lt_link_ifelse_test.sh \
test/yat_lt_link_la_ifelse_test.sh \
test/yat_msg_error_test.sh \
test/yat_msg_error_test2.sh \
test/yat_m4_with_bam_test.sh \
test/yat_m4_test.sh \
test/yat_m4_test2.sh \
test/yat_pc_test.sh \
test/yat_prog_move_if_change_test.sh \
test/yat_revision_header_test.sh \
test/yat_svn_release_year_test.sh \
test/yat_svn_revision_test.sh \
test/yat_use_libtool_tag_test.sh

TESTS += $(DISTRIBUTED_TESTS)
EXTRA_DIST += $(DISTRIBUTED_TESTS)

TEST_EXTENSIONS = .sh .test

LDADD = yat/libyat.la test/libyattest.la $(YAT_LIBS)

#test_large_file_test_LDADD = test/libyattest.la

test_libyattest_la_LIBADD = yat/libyat.la
test_libyattest_la_SOURCES = test/Suite.cc

lazycheck:; $(MAKE) $(AM_MAKEFLAGS) check RECHECK_LOGS=

shell_test_deps = $(srcdir)/test/init.sh test/defs.sh

# dependencies for lazycheck
test/bam.log: test/data/foo.sorted.bam
test/bam_header.log: test/data/foo.sorted.bam
test/bam_header2.log: test/data/foo.sorted.bam
test/bam_iterator.log: test/data/foo.sorted.bam
test/bam_pair_analyse.log: test/data/foo.sorted.bam
test/bam_pair_iterator.log: test/data/foo.sorted.bam
test/bam_read_filter.log: test/data/foo.sorted.bam
test/bam_region_iterator.log: test/data/foo.sorted.bam
test/cmd_test.log: test/help.test $(shell_test_deps)
test/help_test.log: test/help.test $(shell_test_deps)
test/pileup.log: test/data/foo.sorted.bam
test/static_test.log: $(srcdir)/m4/yat.m4 $(shell_test_deps)
test/yat_config_test.log: build_support/yat-config \
  build_support/for_installation/yat-config $(shell_test_deps)
test/yat_config_cblas_test.log: build_support/yat-config $(shell_test_deps)
test/yat_cpp_add_flag_test.log: $(srcdir)/m4/yat_add_flag.m4 \
  $(srcdir)/m4/ax_append_flag.m4 \
  $(srcdir)/m4/ax_check_preproc_flag.m4 \
  $(shell_test_deps)
test/yat_cxx_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
  $(top_srcdir)/m4/ax_append_compile_flags.m4 \
  $(top_srcdir)/m4/ax_append_flag.m4 \
  $(top_srcdir)/m4/ax_check_compile_flag.m4 \
  $(top_srcdir)/m4/ax_require_defined.m4 \
  $(shell_test_deps)
test/yat_have_svn_wc_test.log: $(srcdir)/m4/yat_am_macros.m4 $(shell_test_deps)
test/yat_ld_add_flag_test.log: $(top_srcdir)/m4/yat_add_flag.m4 \
  $(top_srcdir)/m4/ax_append_flag.m4 \
  $(top_srcdir)/m4/ax_append_link_flags.m4 \
  $(top_srcdir)/m4/ax_check_link_flag.m4 \
  $(top_srcdir)/m4/ax_require_defined.m4 \
  $(shell_test_deps)
test/yat_lt_compile_ifelse_test.log: $(shell_test_deps) \
  $(top_srcdir)/m4/yat_lt_link_ifelse.m4
test/yat_lt_link_ifelse_test.log: $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
  $(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
  $(top_builddir)/build_support/yat-config
test/yat_lt_link_la_ifelse_test.log: $(shell_test_deps) \
  test/lib/libmy-shared.la \
  $(top_srcdir)/m4/yat_lt_link_ifelse.m4 \
  $(top_srcdir)/m4/yat_common.m4
test/yat_m4_test.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps) \
  $(top_builddir)/build_support/yat-config
test/yat_m4_test2.log:$(top_srcdir)/m4/yat.m4 $(shell_test_deps)
test/yat_msg_error_test.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
test/yat_msg_error_test2.log:$(srcdir)/m4/yat_msg_error.m4 $(shell_test_deps)
test/yat_pc_test.log: $(shell_test_deps) build_support/yat.pc
test/yat_prog_move_if_change_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
  $(top_srcdir)/m4/ax_file_escapes.m4 \
  $(shell_test_deps)
test/yat_revision_header_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
  $(shell_test_deps) \
  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
  $(top_srcdir)/m4/ax_file_escapes.m4
test/yat_svn_release_year_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
  $(shell_test_deps) \
  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
  $(top_srcdir)/m4/ax_file_escapes.m4
test/yat_svn_revision_test.log: $(top_srcdir)/m4/yat_am_macros.m4 \
  $(shell_test_deps) \
  $(top_srcdir)/m4/ax_ac_append_to_file.m4 \
  $(top_srcdir)/m4/ax_ac_print_to_file.m4 \
  $(top_srcdir)/m4/ax_file_escapes.m4
test/yat_use_libtool_tag_test.log: $(shell_test_deps) \
  $(top_srcdir)/m4/yat_lt_link_ifelse.m4

if DX_ENABLE_HTML
test/doxygen_test.log: doc/$(DX_HTML_OUTPUT)/index.html
endif

# yat-hello is an example of a tiny package that uses yat
dist_noinst_DATA = $(srcdir)/test/yat-hello-1.0.tar.gz

# Directory yat-hello contains what a developer would check out
# from a VCS, i.e., no files generated by autotools.
yat_hello_sources  =
yat_hello_sources += $(srcdir)/test/yat-hello/configure.ac
yat_hello_sources += $(srcdir)/test/yat-hello/Makefile.am
yat_hello_sources += $(srcdir)/test/yat-hello/hello.cc

EXTRA_DIST += $(yat_hello_sources)

yat_hello_tmp_files =
yat_hello_tmp_files += Makefile.in
yat_hello_tmp_files += autom4te.cache
yat_hello_tmp_files += aclocal.m4
yat_hello_tmp_files += build-aux
yat_hello_tmp_files += configure
yat_hello_tmp_files += config.h.in
yat_hello_tmp_files += m4


yat_hello_deps = $(yat_hello_sources)
yat_hello_deps += $(top_srcdir)/m4/yat.m4
## We depend on version.m4 so tarball is updated at every release (at least)
yat_hello_deps += $(top_srcdir)/m4/version.m4

$(srcdir)/test/yat-hello-1.0.tar.gz: $(yat_hello_deps)
  $(AM_V_GEN)$(MKDIR_P) $(srcdir)/test/yat-hello/m4 \
  && cd $(srcdir)/test/yat-hello \
  && cp $(abs_top_srcdir)/m4/yat.m4 m4/ \
  && autoreconf -if $(yat_dev_null) \
  && ./configure --without-yat $(yat_dev_null) \
  && $(MAKE) $(AM_MAKEFLAGS) dist $(yat_dev_null) \
  && $(MAKE) $(AM_MAKEFLAGS) distclean $(yat_dev_null) \
  && mv yat-hello-1.0.tar.gz .. \
  && rm -rf $(yat_hello_tmp_files)

INSTALL_CHECK_TARGETS += yat-hello-check

yat-hello-check: $(srcdir)/test/yat-hello-1.0.tar.gz
  GZIP=$(GZIP_ENV) gzip -dc $(srcdir)/test/yat-hello-1.0.tar.gz | $(am__untar)\
  && cd yat-hello-1.0 \
  && ./configure --with-yat=$(bindir) \
  && $(MAKE) $(AM_MAKEFLAGS) all \
  && ./hello \
  && test x"`./hello`" = x"$(VERSION)" \
  && cd .. \
  && rm -rf yat-hello-1.0


## test data
EXTRA_DIST += \
test/data/foo.sam \
test/data/isoform.peaks \
test/data/knni_matrix.data \
test/data/knni_result.data \
test/data/knni_weight.data \
test/data/nm_alpha_linear_matlab.txt \
test/data/nm_data_centralized.txt \
test/data/nm_kernel.txt \
test/data/nm_kernel2.txt \
test/data/nm_kernel_gaussian.txt \
test/data/nm_target_bin.txt \
test/data/normalization_test.data \
test/data/rank_data.txt \
test/data/rank_target.txt \
test/data/regression_gauss.data \
test/data/small.gff2 \
test/data/small.gff3 \
test/data/sorlie_centroid_classes.txt \
test/data/sorlie_centroid_data.txt  \
test/data/sorlie_centroid_predictions.txt \
test/data/sorlie_centroids.txt \
test/data/vector1.data  \
test/data/vector2.data \
test/data/vector3.data \
test/data/vector4.data \
test/data/vector5.data \
test/data/vector6.data  \
test/data/vector7.data \
test/data/wenni_result.data \
test/data/wenni_weight.data

CLEANFILES += test/data/.dirstamp
CLEANFILES += test/data/foo.bam
CLEANFILES += test/data/foo.sorted.bam
CLEANFILES += test/data/foo.sorted.bam.bai

check_DATA  = test/data/foo.sorted.bam
check_DATA += test/data/foo.sorted.bam.bai

test/data/.dirstamp:
  @$(MKDIR_P) test/data
  @: > $@

if HAVE_SAMTOOLS
test/data/foo.bam: test/data/foo.sam test/data/.dirstamp Makefile
  $(AM_V_GEN)
  $(AM_V_at)$(SAMTOOLS) view -Sb $(srcdir)/test/data/foo.sam \
  > $@-t && mv $@-t $@

test/data/foo.sorted.bam: test/data/foo.bam
  $(AM_V_GEN)
  $(AM_V_at)$(SAMTOOLS) sort test/data/foo.bam test/data/foo.sorted

test/data/foo.sorted.bam.bai: test/data/foo.sorted.bam
  $(AM_V_GEN)
  $(AM_V_at)$(SAMTOOLS) index test/data/foo.sorted.bam
else
test/data/foo.sorted.bam: test/data/.dirstamp
  $(AM_V_at): > $@

test/data/foo.sorted.bam.bai: test/data/.dirstamp
  $(AM_V_at): > $@
endif

test/lib/.dirstamp:
  @$(MKDIR_P) test/lib
  @: > $@

check_DATA += test/lib/libmy-static.a
EXTRA_DIST += test/gen_libmy_static.sh

test/lib/libmy-static.a: test/lib/.dirstamp test/gen_libmy_static.sh \
test/defs.sh
  $(AM_V_GEN)
  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_static.sh $(yat_dev_null)

check_DATA += test/lib/libmy-shared.la
EXTRA_DIST += test/gen_libmy_shared.sh

test/lib/libmy-shared.la: test/lib/.dirstamp test/gen_libmy_shared.sh \
test/defs.sh
  $(AM_V_GEN)
  $(AM_V_at)$(SHELL) $(srcdir)/test/gen_libmy_shared.sh $(yat_dev_null)