Finish Release-2.3.1

No changes to the KAT tools themselves.  This release focuses on making an improved build process.  User's now have the option of disabling plotting completely, and requesting whether to link to boost in dynamic mode.  We also ensure that KAT only links to python3 rather than python2 if python2 is the default python installation on the system.

.travis.yml

@@ -20,7 +20,13 @@ matrix:
               env: COMPILER=GCC5 PLOT=python
             - os: osx
               compiler: clang
-
+
+# safelist
+branches:
+  only:
+  - master
+  - develop
+
 # Setup compiler
 before_install:
 - ./.travis/before_install.sh
@@ -34,8 +40,14 @@ install:
 
 # Make sure python's available at runtime (if necessary) and then build KAT and run tests
 script:
-- if [[ "$PLOT" == "python" ]] || [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH="$HOME/miniconda/bin:$PATH" && source activate test-environment && export LD_LIBRARY_PATH="$HOME/miniconda/envs/test-environment/lib:$LD_LIBRARY_PATH"; fi
-- ./configure --disable-silent-rules && make && make check && make distcheck
+- if [[ "$COMPILER" == "GCC5" ]]; then export CXX="g++-5" && export CC="gcc-5"; elif [[ "$TRAVIS_OS_NAME" == "linux" ]]; then export CXX="g++-4.9" && export CC="gcc-4.9"; fi     
+- if [[ "$PLOT" == "python" ]] || [[ "$TRAVIS_OS_NAME" == "osx" ]]; then export PATH="$HOME/miniconda/bin:$PATH" && source activate test-environment && export LD_LIBRARY_PATH="$LD_LIBRARY_PATH:$HOME/miniconda/envs/test-environment/lib"; fi
+- gcc --version
+- g++ --version
+- ./configure
+- make V=1
+- make V=1 check
+#- make V=1 distcheck
 
 
 

.travis/.gitignore

@@ -0,0 +1 @@
+/.install.sh.swp

.travis/before_install.sh

@@ -5,18 +5,21 @@ if [[ $TRAVIS_OS_NAME == 'osx' ]]; then
 else
     sudo add-apt-repository -y ppa:ubuntu-toolchain-r/test
     sudo apt-get update -qq
+    sudo apt-get install -qq libc6-dev
     if [ "$COMPILER" == "GCC5" ]; then 
-        sudo apt-get install -qq g++-5
+        sudo apt-get install -qq gcc-5 g++-5
         sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-5 100
         sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 100
         export CXX="g++-5"
-        export CC="gcc-5"        
+        export CC="gcc-5"
     else 
-        sudo apt-get install -qq g++-4.9
+        sudo apt-get install -qq gcc-4.9 g++-4.9
         sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.9 100
         sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 100
         export CXX="g++-4.9"
         export CC="gcc-4.9"
     fi
     gcc --version
+    g++ --version
+    gcc --print-search-dirs
 fi

.travis/install.sh

@@ -1,51 +1,54 @@
 #!/bin/bash
 
 if [[ $TRAVIS_OS_NAME == 'osx' ]]; then
+    # Install boost -- looks like boost 1.55.0_2 is already installed with brew
+    #brew install boost
 
-	# Install boost -- looks like boost 1.55.0_2 is already installed with brew
-	#brew install boost
 
-
-	# install anaconda
-	wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
-	bash miniconda.sh -b -p $HOME/miniconda;
-	export PATH="$HOME/miniconda/bin:$PATH";
-	hash -r; 
-	conda config --set always_yes yes --set changeps1 no; 
-	conda update -q conda;  
-	conda info -a
-	conda create -q -n test-environment python=3.5 anaconda; 
+    # install anaconda
+    wget https://repo.continuum.io/miniconda/Miniconda3-latest-MacOSX-x86_64.sh -O miniconda.sh;
+    bash miniconda.sh -b -p $HOME/miniconda;
+    export PATH="$HOME/miniconda/bin:$PATH";
+    hash -r; 
+    conda config --set always_yes yes --set changeps1 no; 
+    conda update -q conda;  
+    conda info -a
+    conda create -q -n test-environment python=3.5 anaconda; 
 
 else
 
-	# Boost installation
-	wget -q http://sourceforge.net/projects/boost/files/boost/1.59.0/boost_1_59_0.tar.gz/download
-	mv download boost.tar.gz
-	tar -xf boost.tar.gz
-	cd boost_1_59_0
-	sudo ./bootstrap.sh --with-libraries=chrono,timer,program_options,filesystem,system
-	if [[ "$COMPILER" == "GCC5" ]]; then 
-		sudo ./b2 -d0 --toolset=gcc-5 install; 
-	else 
-		sudo ./b2 -d0 --toolset=gcc-4.9 install; 
-	fi
-	cd ..
-
-
-	# Plotting installation
-	if [[ "$PLOT" == "python" ]]; then 
-		wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
-		bash miniconda.sh -b -p $HOME/miniconda;
-		export PATH="$HOME/miniconda/bin:$PATH"; 
-		hash -r; 
-		conda config --set always_yes yes --set changeps1 no; 
-		conda update -q conda;	
-		conda info -a
-		conda create -q -n test-environment python=3.5 anaconda;	
-	elif [ "$PLOT" == "gnuplot" ]; then 
-		sudo apt-get install gnuplot
-		gnuplot --version; 
-	fi
+    # Boost installation
+    wget -q http://sourceforge.net/projects/boost/files/boost/1.59.0/boost_1_59_0.tar.gz/download
+    mv download boost.tar.gz
+    tar -xf boost.tar.gz
+    cd boost_1_59_0
+    sudo ./bootstrap.sh --with-libraries=chrono,timer,program_options,filesystem,system
+    if [[ "$COMPILER" == "GCC5" ]]; then 
+        export CXX="g++-5"
+        export CC="gcc-5"
+        sudo ./b2 -d0 --toolset=gcc-5 install; 
+    else 
+        export CXX="g++-4.9"
+        export CC="gcc-4.9"
+        sudo ./b2 -d0 --toolset=gcc-4.9 install; 
+    fi
+    cd ..
+
+
+    # Plotting installation
+    if [[ "$PLOT" == "python" ]]; then 
+        wget https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh;
+        bash miniconda.sh -b -p $HOME/miniconda;
+        export PATH="$HOME/miniconda/bin:$PATH"; 
+        hash -r; 
+        conda config --set always_yes yes --set changeps1 no; 
+        conda update -q conda;	
+        conda info -a
+        conda create -q -n test-environment python=3.5 anaconda;	
+    elif [ "$PLOT" == "gnuplot" ]; then 
+        sudo apt-get install gnuplot
+        gnuplot --version; 
+    fi
 
 fi
 

configure.ac

@@ -4,7 +4,7 @@
 
 # Autoconf initialistion.  Sets package name version and contact details
 AC_PREREQ([2.68])
-AC_INIT([kat],[2.3.0],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
+AC_INIT([kat],[2.3.1],[https://github.com/TGAC/KAT/issues],[kat],[https://github.com/TGAC/KAT])
 AC_CONFIG_SRCDIR([src/kat.cc])
 AC_CONFIG_AUX_DIR([build-aux])
 AC_CONFIG_MACRO_DIR([m4])
@@ -78,45 +78,48 @@ else
 fi
 
 # Plotting
-AC_ARG_ENABLE([gnuplot], AS_HELP_STRING([--enable-gnuplot], [Enable gnuplot plotting even if python matplotlib is available]), enable_gnuplot="yes", enable_gnuplot="no")
-
-#AM_PATH_PYTHON([], [], AC_MSG_ERROR([Python interpreter not found.]))
-
-AX_PYTHON_DEVEL([>= '3.1'])
-
-pybin=python${PYTHON_VERSION}
 pymod_good="no"
-if [[ -n "${PYTHON_VERSION}" ]]; then
-    if [[ -z "${PYTHON_EXTRA_LIBS}" ]]; then
-        pymod_good="no"
-        AC_MSG_WARN([Python3 detected but Python3 development library was not found.  If you wish to use python plotting please install python3 library.  e.g. "sudo apt-get install python3-dev" on debian systems.])
-    fi
-    pymod_good="yes"
-    AX_PYTHON_MODULE(numpy, ,${pybin})
-    if [[ "${PYMOD}" == "no" ]]; then 
-            pymod_good="no" 
-    fi
-    AX_PYTHON_MODULE(matplotlib, ,${pybin})
-    if [[ "${PYMOD}" == "no" ]]; then 
-            pymod_good="no" 
-    fi
-    AX_PYTHON_MODULE(scipy, ,${pybin})
-    if [[ "${PYMOD}" == "no" ]]; then 
-            pymod_good="no"
+AC_ARG_ENABLE([noplotting], AS_HELP_STRING([--disable-plotting], [This will disable plotting even if python matplotlib or gnuplot are available]), do_plotting="no", do_plotting="yes")
+AC_ARG_ENABLE([gnuplot], AS_HELP_STRING([--enable-gnuplot], [Enable gnuplot plotting even if python matplotlib is available]), use_gnuplot="yes", use_gnuplot="no")
+
+if [[ "${do_plotting}" == "yes" ]]; then
+    if [[ "${use_gnuplot}" == "no" ]]; then
+        AX_PYTHON_DEVEL([>= '3.1'])
+
+        pybin=python${PYTHON_VERSION}
+        if [[ -n "${PYTHON_VERSION}" ]]; then
+            if [[ -z "${PYTHON_EXTRA_LIBS}" ]]; then
+                pymod_good="no"
+                AC_MSG_WARN([Python3 detected but Python3 development library was not found.  If you wish to use python plotting please install python3 library.  e.g. "sudo apt-get install python3-dev" on debian systems.])
+            fi
+            pymod_good="yes"
+            AX_PYTHON_MODULE(numpy, ,${pybin})
+            if [[ "${PYMOD}" == "no" ]]; then 
+                    pymod_good="no" 
+            fi
+            AX_PYTHON_MODULE(matplotlib, ,${pybin})
+            if [[ "${PYMOD}" == "no" ]]; then 
+                    pymod_good="no" 
+            fi
+            AX_PYTHON_MODULE(scipy, ,${pybin})
+            if [[ "${PYMOD}" == "no" ]]; then 
+                    pymod_good="no"
+            fi
+        fi
     fi
-fi
 
-# Check for gnuplot on path.  Just emit a warning if not present
-if [[ "${pymod_good}" == "no" ]] || [[ "${enable_gnuplot}" == "yes" ]]; then
-    AC_DEFINE([HAVE_PYTHON], [0], [Python not present])
-    AC_CHECK_PROG([gnuplot_found], [gnuplot], [yes], [no])
-    if [[ "${gnuplot_found}" == "no" ]] ; then
-        AC_DEFINE([HAVE_GNUPLOT], [0], [Gnuplot not present])
+    # Check for gnuplot on path.  Just emit a warning if not present
+    if [[ "${pymod_good}" == "no" ]] || [[ "${use_gnuplot}" == "yes" ]]; then
+        AC_DEFINE([HAVE_PYTHON], [0], [Python not present])
+        AC_CHECK_PROG([gnuplot_found], [gnuplot], [yes], [no])
+        if [[ "${gnuplot_found}" == "no" ]] ; then
+            AC_DEFINE([HAVE_GNUPLOT], [0], [Gnuplot not present])
+        else
+            AC_DEFINE([HAVE_GNUPLOT], [1], [Gnuplot present])
+        fi
     else
-        AC_DEFINE([HAVE_GNUPLOT], [1], [Gnuplot present])
+        AC_DEFINE([HAVE_PYTHON], [1], [Python present])
     fi
-else
-    AC_DEFINE([HAVE_PYTHON], [1], [Python present])
 fi
 
 # Check for sphinx to build documentation (optional)
@@ -141,7 +144,11 @@ AM_CONDITIONAL([MAKE_DOCS], [test x$sphinx = xyes])
 AC_SUBST([MAKE_DOCS])
 
 
+
 ## Check for boost
+
+AC_ARG_ENABLE([dynamic-boost], AS_HELP_STRING([--enable-dynamic-boost], [Boost is statically linked by default.  Use this option if you would prefer to dynamically link boost]), dynboost="yes", dynboost="no")
+
 AX_BOOST_BASE([1.52],, [AC_MSG_ERROR([Boost not found.  Please ensure that boost is properly built and the BOOST_ROOT environment variable is set.  Alternatively you can override BOOST_ROOT with the --with-boost option.])])
 AX_BOOST_FILESYSTEM
 AX_BOOST_SYSTEM
@@ -154,20 +161,37 @@ define([PC_FILE], lib/kat-2.2.pc)
 
 
 # Combine BOOST variables (apart for BOOST_TEST)
-BOOST_LIBS="${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} ${BOOST_SYSTEM_LIB} ${BOOST_TIMER_LIB}"
-BOOST_STATIC_LIBS="${BOOST_TIMER_STATIC_LIB} ${BOOST_CHRONO_STATIC_LIB} ${RT_LIB} ${BOOST_FILESYSTEM_STATIC_LIB} ${BOOST_PROGRAM_OPTIONS_STATIC_LIB} ${BOOST_SYSTEM_STATIC_LIB} "
+BOOST_DYN_LIBS="${BOOST_TIMER_LIB} ${BOOST_CHRONO_LIB} ${BOOST_FILESYSTEM_LIB} ${BOOST_PROGRAM_OPTIONS_LIB} ${BOOST_SYSTEM_LIB}"
+AC_SUBST([BOOST_DYN_LIBS])
+
+BOOST_STATIC_LIBS="${BOOST_TIMER_STATIC_LIB} ${BOOST_CHRONO_STATIC_LIB} ${BOOST_FILESYSTEM_STATIC_LIB} ${BOOST_PROGRAM_OPTIONS_STATIC_LIB} ${BOOST_SYSTEM_STATIC_LIB} "
 AC_SUBST([BOOST_STATIC_LIBS])
 
+# Prefer static linking of boost.  If one or more static libs are not present 
+# (this happens with some default boost installations on some environments) then
+# use dynamic libs instead.
+if [[ "${dynboost}" == "yes" ]]; then
+    BOOST_LIBS="${BOOST_DYN_LIBS}"
+else
+    if [[ -z "${BOOST_TIMER_STATIC_LIB}" ]] || [[ -z "${BOOST_CHRONO_STATIC_LIB}" ]] || [[ -z "${BOOST_FILESYSTEM_STATIC_LIB}" ]] || [[ -z "${BOOST_PROGRAM_OPTIONS_STATIC_LIB}" ]] || [[ -z "${BOOST_SYSTEM_STATIC_LIB}" ]]; then
+        AC_MSG_WARN([Not all static boost libraries could be found.  Will use dynamic libraries instead.])
+        BOOST_LIBS="${BOOST_DYN_LIBS}"
+    else
+        BOOST_LIBS="${BOOST_STATIC_LIBS}"
+    fi
+fi
+AC_SUBST([BOOST_LIBS])
+
 AM_CXXFLAGS="-DCPLUSPLUS"
 AC_SUBST([AM_CXXFLAGS])
 
 if [[ "${pymod_good}" == "yes" ]]; then 
     AM_CPPFLAGS="${BOOST_CPPFLAGS} ${PYTHON_CPPFLAGS}"
-    AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_STATIC_LIBS} ${PYTHON_EXTRA_LIBS} ${PYTHON_LIBS}"
+    AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_LIBS} ${RT_LIB} ${PYTHON_EXTRA_LIBS} ${PYTHON_LIBS}"
     AM_LDFLAGS="${BOOST_LDFLAGS} ${PYTHON_EXTRA_LDFLAGS}"
 else
     AM_CPPFLAGS="${BOOST_CPPFLAGS}"
-    AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_STATIC_LIBS}"
+    AM_LIBS="${PTHREAD_CFLAGS} ${BOOST_LIBS} ${RT_LIB}"
     AM_LDFLAGS="${BOOST_LDFLAGS}"
 fi
 
@@ -181,24 +205,34 @@ AC_CONFIG_FILES([Makefile doc/Makefile doc/source/conf.py lib/kat.pc lib/Makefil
 AC_CONFIG_SUBDIRS([deps/jellyfish-2.2.0])
 AC_OUTPUT
 
-if [[ "${pymod_good}" == "yes" ]] && [[ "$enable_gnuplot" == "no" ]] ; then
-    AC_MSG_NOTICE([Using python plotting])
+if [[ "${do_plotting}" == "no" ]]; then
+    AC_MSG_NOTICE([Plotting disabled])
 else
-    if [[ "${gnuplot_found}" == "yes" ]]; then
-        if [[ "$enable_gnuplot" == "no" ]]; then
-            AC_MSG_WARN([Python3, or some required python modules where not found.  Python via matplotlib is the preferred plotting method in KAT.  If you want to use python plotting (the preferred option) then we suggest you install anaconda3 (or python3 with numpy, scipy and matplotlib separately).  However, gnuplot was detected so KAT plots will be generated via gnuplot instead.])
+    if [[ "${pymod_good}" == "yes" ]] && [[ "$use_gnuplot" == "no" ]] ; then
+        AC_MSG_NOTICE([Using python plotting])
+    else
+        if [[ "${gnuplot_found}" == "yes" ]]; then
+            if [[ "${use_gnuplot}" == "no" ]]; then
+                AC_MSG_WARN([Python3, or some required python modules where not found.  Python via matplotlib is the preferred plotting method in KAT.  If you want to use python plotting (the preferred option) then we suggest you install anaconda3 (or python3 with numpy, scipy and matplotlib separately).  However, gnuplot was detected so KAT plots will be generated via gnuplot instead.])
+            else
+                AC_MSG_NOTICE([Using gnuplot plotting])
+            fi
         else
-            AC_MSG_NOTICE([Using gnuplot plotting])
+            AC_MSG_WARN([Neither python (with plotting modules present) or Gnuplot not detected.  KAT will still work (minus plots). Should you require plotting functionality, you must install either anaconda3 (or python3 with numpy, scipy and matplotlib) or gnuplot, and then reconfigure and compile to enable plotting in KAT.])
         fi
-    else
-        AC_MSG_WARN([Neither python (with plotting modules present) or Gnuplot not detected.  KAT will still work (minus plots). Should you require plotting functionality, you must install either anaconda3 (or python3 with numpy, scipy and matplotlib) or gnuplot, and then reconfigure and compile to enable plotting in KAT.])
     fi
-fi 
+fi
 
 if [[ "${sphinx}" == "no" ]]; then
     AC_MSG_WARN([Sphinx not detected, or version is too old.  Wont create documentation.  You can still find the documentation online at: https://kat.readthedocs.org/en/latest/])    
 else
     AC_MSG_NOTICE([Building documentation with sphinx])
 fi
 
+if [[ "${dynboost}" == "yes" ]]; then
+    AC_MSG_NOTICE([Boost will be dynamically linked to your executable])
+else
+    AC_MSG_NOTICE([Boost will be statically linked to your executable])
+fi
+
 

deps/jellyfish-2.2.0/tests/.gitignore

@@ -18,3 +18,4 @@
 /multi_file_fail_cmds
 /bloom_counter_commands
 *.timing
+merge_m40*

doc/Makefile

@@ -66,6 +66,7 @@ DISTFILES = $(DPS)/index.rst \
 	    $(DPI)/kmer_spectra1.png \
 	    $(DPI)/kmer_spectra_breakdown.png \
 	    $(DPI)/pe_v_asm_clean.png \
+	    $(DPI)/pe_v_asm_wrong.png \
 	    $(DPI)/pe_v_mp_after_density.png \
 	    $(DPI)/pe_v_mp_after_shared.png \
 	    $(DPI)/pe_v_mp_before_density.png \

doc/Makefile.in

@@ -66,6 +66,7 @@ DISTFILES = $(DPS)/index.rst \
 	    $(DPI)/kmer_spectra1.png \
 	    $(DPI)/kmer_spectra_breakdown.png \
 	    $(DPI)/pe_v_asm_clean.png \
+	    $(DPI)/pe_v_asm_wrong.png \
 	    $(DPI)/pe_v_mp_after_density.png \
 	    $(DPI)/pe_v_mp_after_shared.png \
 	    $(DPI)/pe_v_mp_before_density.png \

doc/source/conf.py

@@ -52,9 +52,9 @@
 # built documents.
 #
 # The short X.Y version.
-version = '2.3.0'
+version = '2.3.1'
 # The full version, including alpha/beta/rc tags.
-release = '2.3.0'
+release = '2.3.1'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.