Commit 9908b637 authored by Andreas Tille's avatar Andreas Tille
Browse files

New upstream version 1.6.0+dfsg

parent 664a4f84

.bumpversion.cfg

+2 −2
Original line number Diff line number Diff line 
[bumpversion]

current_version = 1.5.0

current_version = 1.6.0

parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<stage>(dev|rc)))?(\.(?P<again>\d+))?

serialize = 

	{major}.{minor}.{patch}-{stage}.{again}
@@ -18,5 +18,5 @@ values = 


[bumpversion:file:configure.ac]



[bumpversion:file:doc/sina.tex]

[bumpversion:file:doc/source/install.rst]

.circleci/config.yml

+6 −0
Original line number Diff line number Diff line
@@ -79,6 +79,7 @@ jobs: 
            make code-coverage-capture

            bash <(curl -s https://codecov.io/bash) -X gcov -F unittest \

              -R ~/project -n Unit-Linux-CircleCI

          no_output_timeout: 20m # kmer_search_test is slow

      - run:

          <<: *configure

          environment:
@@ -95,6 +96,11 @@ jobs: 
            make code-coverage-capture

            bash <(curl -s https://codecov.io/bash) -X gcov -F integration \

              -R ~/project -n Integration-Linux-CircleCI

      - run:

          name: Collecting binaries

          when: on_fail

          command: |

            tar -C ~/build -czvf $ARTIFACT_PATH/build_src.tgz src

      - run:

          name: Copying logs

          when: always

.gitignore

+20 −17
Original line number Diff line number Diff line
@@ -29,27 +29,30 @@ 
*.app



# Automake/Autoconf stuff

build-aux/*

m4/libtool.m4

m4/ltoptions.m4

m4/ltsugar.m4

m4/ltversion.m4

m4/lt~obsolete.m4

Makefile.in

aclocal.m4

config.h

config.h.in

config.log

config.status

configure

autom4te.cache

libtool

/build-aux/*

/m4/libtool.m4

/m4/ltoptions.m4

/m4/ltsugar.m4

/m4/ltversion.m4

/m4/lt~obsolete.m4

/Makefile.in

/aclocal.m4

/config.h

/config.h.in

/config.log

/config.status

/configure

/autom4te.cache

/libtool

.deps

.dirstamp

Makefile

/Makefile

stamp-h1



# temp files

*~

\#*\#

.\#*



# build dirs

/build*/
 
 No newline at end of file

.travis.yml

+0 −1
Original line number Diff line number Diff line
@@ -14,7 +14,6 @@ env: 
  global:

    MINICONDA: $HOME/miniconda

    BASH_ENV: $HOME/.bashrc

    MAKEFLAGS: -j2



install:

  - ./ci_scripts/install_conda.sh

Makefile.am

+13 −6
Original line number Diff line number Diff line
@@ -80,6 +80,8 @@ src_libsina_la_SOURCES = \ 
    src/aligned_base.h \

    src/alignment_stats.cpp \

    src/alignment_stats.h \

    src/buffer.h \

    src/cache.h \

    src/cseq.cpp \

    src/cseq.h \

    src/cseq_impl.h \
@@ -94,6 +96,7 @@ src_libsina_la_SOURCES = \ 
    src/mesh_debug.h \

    src/mseq.cpp \

    src/mseq.h \

    src/progress.h \

    src/pseq.cpp \

    src/pseq.h \

    src/query_arb.cpp \
@@ -108,6 +111,7 @@ src_libsina_la_SOURCES = \ 
    src/log.h \

    src/scoring_schemes.h \

    src/search.h \

    src/search.cpp \

    src/search_filter.cpp \

    src/search_filter.h \

    src/timer.h \
@@ -180,12 +184,12 @@ man1_MANS = doc/man/sina.1 


$(doc_DATA): doc/build.stamp

doc/build.stamp: $(DOC_SOURCE)

	sphinx-build -M text $$(dirname $<) doc

	$(SPHINX_BUILD) -M text $$(dirname $<) doc

	touch $@

CLEANFILES += doc/build.stamp



$(man1_MANS): $(DOC_SOURCE)

	sphinx-build -M man $$(dirname $<) doc

	$(SPHINX_BUILD) -M man $$(dirname $<) doc



%: doc/text/%.txt

	cp $< $@
@@ -225,7 +229,7 @@ bindistdir: all 
          cp -fpR $(top_builddir)/$$f $(bindistdir)/$$f; done; \

	find $(bindistdir) -depth -type d -empty -exec rmdir {} \;

	binaries=$$(find $(bindistdir) -type f -exec file --mime {} \; | \

                grep -E "application/x-.*(mach|executable|sharedlib)" | cut -d: -f1); \

                $(GREP) -E "application/x-.*(mach|executable|sharedlib)" | cut -d: -f1); \

	export LDPATHS="$(subst -L,,$(filter -L%, $(BOOST_LDFLAGS)))"; \

        for binary in $$binaries; do $(top_srcdir)/tools/fix_libpaths.sh "$$binary"; done; \

	find $(bindistdir) \( -name \*.la -or -name \*.a \) -delete
@@ -252,7 +256,7 @@ test_libs = \ 
LOG_COMPILER = $(top_srcdir)/tools/test_driver.sh



TEST_LOG_DRIVER = env AM_TAP_AWK='$(AWK)' $(SHELL) \

                  $(top_srcdir)/build-aux/tap-driver.sh

                  $(top_srcdir)/build-aux/tap-driver.sh --comments



check_PROGRAMS = \

    src/unit_tests/cseq_test \
@@ -260,7 +264,8 @@ check_PROGRAMS = \ 
    src/unit_tests/idset_test \

    src/unit_tests/kmer_test \

    src/unit_tests/kmer_search_test \

    src/unit_tests/famfinder_test

    src/unit_tests/famfinder_test \

    src/unit_tests/progress_test



src_unit_tests_cseq_test_LDADD = $(test_libs)

src_unit_tests_cseq_test_LDFLAGS = $(ARB_LDFLAGS)
@@ -274,12 +279,14 @@ src_unit_tests_kmer_search_test_LDADD = $(test_libs) 
src_unit_tests_kmer_search_test_LDFLAGS = $(ARB_LDFLAGS)

src_unit_tests_famfinder_test_LDADD = $(test_libs)

src_unit_tests_famfinder_test_LDFLAGS = $(ARB_LDFLAGS)

src_unit_tests_progress_test_LDADD = $(BOOST_UNIT_TEST_FRAMEWORK_LIB)



test_scripts = \

    tests/readwrite.test \

    tests/align.test \

    tests/search.test \

    tests/infocommands.test \

    tests/accuracy_kmer.test \

    tests/accuracy.test
@@ -305,7 +312,7 @@ check-filtered: 
## pass ARGS to tests

TEST_ARGS := $(check_DATA) $(TEST_EXTRA_ARGS)

export TEST_ARGS

$(test_scripts): $(bin_PROGRAMS) $(check_DATA)

$(test_scripts): $(bin_PROGRAMS) $(check_DATA) tests/test_helper.sh



## unzip source test data into build folder

test_data/%: test_data/%.xz