Commit e28213ab authored by Fabian Klötzl's avatar Fabian Klötzl
Browse files

Imported Upstream version 0.12

parent 88a91de1

.gitignore

+1 −0
Original line number Diff line number Diff line
@@ -58,6 +58,7 @@ test-driver 
test_esa

test_seq

test_fasta

test_process

*.trs



# Coverage

.travis.yml

+10 −17
Original line number Diff line number Diff line 
language: cpp

os:

  - linux

  # - osx

compiler:

  - gcc

  - clang
@@ -13,9 +10,9 @@ addons: 
      - ubuntu-toolchain-r-test

    packages:

      - cmake

      - g++-4.8

      - libglib2.0-dev

      - libgsl0-dev



install:

  - export LIBDIVDIR="$HOME/libdivsufsort"

  - pip install --user cpp-coveralls
@@ -24,30 +21,26 @@ install: 
  - cd libdivsufsort-master && mkdir build && cd build

  - cmake -DCMAKE_BUILD_TYPE="Release" -DCMAKE_INSTALL_PREFIX="$LIBDIVDIR" ..

  - make && make install

  - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then brew install gsl; fi

  - if [ "${TRAVIS_OS_NAME}" = "osx" ]; then brew install glib; fi

before_install:

  - if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi



# - sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 90

script:

- export DYLD_LIBRARY_PATH="$DYLD_LIBRARY_PATH:$LIBDIVDIR/lib"

- CONFIGURE_FLAGS=""

- export LD_LIBRARY_PATH="$LIBDIVDIR:$LIBDIVDIR/lib"

- export LIBRARY_PATH="$LIBDIVDIR:$LIBRARY_PATH"

- cd $TRAVIS_BUILD_DIR

- autoreconf -fvi -Im4

- export MYFLAGS="-fprofile-arcs -ftest-coverage -I$LIBDIVDIR/include"

- ./configure --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"

- if [ "${CC}" = "clang" ]; then export CONFIGURE_FLAGS="--disable-openmp"; fi

- ./configure $CONFIGURE_FLAGS --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"

- make

- make check

- make check || cat ./test-suite.log || exit 1

- export MYFLAGS="-I$LIBDIVDIR/include"

- ./configure --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"

- make distcheck DISTCHECK_CONFIGURE_FLAGS="LDFLAGS=\"-L$LIBDIVDIR/lib\" CFLAGS=\"-I$LIBDIVDIR/include\" CXXFLAGS=\"-I$LIBDIVDIR/include\""

- ./configure $CONFIGURE_FLAGS --enable-unit-tests LDFLAGS="-L$LIBDIVDIR/lib" CFLAGS="$MYFLAGS" CXXFLAGS="$MYFLAGS"

- make distcheck DISTCHECK_CONFIGURE_FLAGS="LDFLAGS=\"-L$LIBDIVDIR/lib\" CFLAGS=\"-I$LIBDIVDIR/include\" CXXFLAGS=\"-I$LIBDIVDIR/include\" $CONFIGURE_FLAGS"

- tar xzvf andi-*.tar.gz

- cd andi-*

- ./configure --enable-unit-tests --without-libdivsufsort

- ./configure $CONFIGURE_FLAGS --enable-unit-tests --without-libdivsufsort

- make

- make check

- make check || cat ./test-suite.log || exit 1

- cd ..

after_success:

- if [ "${TRAVIS_OS_NAME}" = "linux" -a "$CXX" = "g++-4.8" ]; then coveralls --exclude libdivsufsort-master -E '^andi-.*' --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'; fi
 
- if [ "$CXX" = "g++" ]; then coveralls --exclude libdivsufsort-master -E '^andi-.*' --exclude libs --exclude test --gcov `which gcov-4.8` --gcov-options '\-lp'; fi

Makefile.am

+2 −1
Original line number Diff line number Diff line
@@ -18,7 +18,8 @@ SUBDIRS+= test 
AM_TESTS_ENVIRONMENT= \

	RANDOM_SEED='@SEED@' ; export RANDOM_SEED ;



TESTS = test/test_esa test/test_seq test/test_extra.sh test/test_random.sh test/test_join.sh

XFAIL_TESTS=

TESTS = $(XFAIL_TESTS) test/nan.sh test/low_homo.sh test/test_esa test/test_seq test/test_extra.sh test/test_random.sh test/test_join.sh test/test_process



$(TESTS): src/andi

andi-manual.pdf

+27 B (434 KiB)

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configure.ac

+4 −5
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AC_INIT([andi], [0.11])

AC_INIT([andi], [0.12])

AM_INIT_AUTOMAKE([-Wall foreign])



AC_CONFIG_MACRO_DIR([m4])
@@ -78,8 +78,7 @@ AC_ARG_WITH([seed], 


AC_SUBST([SEED])



if test "x${try_unit_tests}" = xyes; then



AS_IF([test "x${try_unit_tests}" = xyes], [

	have_glib=yes

	PKG_CHECK_MODULES([GLIB], [glib-2.0], [], [have_glib=no])
@@ -88,7 +87,7 @@ if test "x${try_unit_tests}" = xyes; then 
	fi



	AX_CXX_COMPILE_STDCXX_11([],[mandatory])

fi

])





# Check for various headers including those used by libdivsufsort.