Merge pull request #76 from BackofenLab/intarna-2

prepare Intarna 2.0.3 release

.travis.yml

@@ -15,19 +15,18 @@ addons:
     sources:
     - ubuntu-toolchain-r-test
     packages:
-    - gcc-4.9
-    - g++-4.9
-    - doxygen
-
-
+    #- gcc-4.9
+    #- g++-4.9
+    # - doxygen
+
 before_install:
     - wget http://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh -O miniconda.sh
     - chmod +x miniconda.sh
     - "./miniconda.sh -b"
     - export CONDA_PATH=$HOME/miniconda3
     - export PATH=$CONDA_PATH/bin:$PATH
     - conda update --yes conda
-    - conda install --yes automake pkgconfig viennarna boost -c conda-forge -c bioconda
+    - conda install --yes gcc automake pkgconfig viennarna boost=1.61.* -c conda-forge -c bioconda
     #    - export CONDA_PATH=/home/travis/miniconda2/
     - export CONDA_LIB_PATH=$CONDA_PATH/lib
     #    - ls $CONDA_LIB_PATH
@@ -40,9 +39,12 @@ script:
     - cd $TRAVIS_BUILD_DIR 
     # generate autotools's files 
     - bash autotools-init.sh 
-    - CC=gcc-4.9 CXX=g++-4.9 ./configure --with-boost=$CONDA_PATH --with-vrna=$CONDA_PATH --prefix=$HOME/IntaRNA
+    #- CC=gcc-4.9 CXX=g++-4.9 ./configure --with-boost=$CONDA_PATH --with-vrna=$CONDA_PATH --prefix=$HOME/IntaRNA
+    - ./configure --with-boost=$CONDA_PATH --with-vrna=$CONDA_PATH --prefix=$HOME/IntaRNA
+    # compile documentation
+    # - make doxygen-doc
     # compile, test and install IntaRNA
-    - make && make tests && make install
+    - make -j 2 && make tests -j 2 && make install
     ##### check IntaRNA build #####
     # run IntaRNA with help output
     - $HOME/IntaRNA/bin/IntaRNA -h

ChangeLog

@@ -1,4 +1,41 @@
 
+170503 Martin Mann :
+ * README.md :
+   + OS X install instructions (thanks to Lars Barquist)
+ + IntaRNA/NussinovHandler : (thanks to Mostafa Mahmoud) implementation of
+   intramolecular structure prediction, partition function and probability
+   computation using a variant of the Nussinov-Jacobson model
+ * IntaRNA/AccessibilityBasePair :
+   * uses NussinovHandler for computation
+ * IntaRNA/InteractionEnergyBasePair :
+   * uses NussinovHandler for computation
+   + computeES() : fill a given ES value container
+   * getES*() : enabled
+ + tests for NussinovHandler 
+ + tests for InteractionEnergyBasePair
+
+170413 Martin Mann :
+ * doc/* 
+   + added to distribution build
+
+170412 Martin Mann :
+ * configure.ac :
+   * doxygen docu generation now truely optional
+   * pkgconfig usage now truely optional (check for m4 functions)
+ * Makefile.am :
+   * doxygen docu generation now truely optional
+   - include of doc/doxygen.am obsolete
+   + @DX_RULES@ : doxygen rules generated by configure
+ - doc/doxygen.am : obsolete
+
+170411 Martin Mann :
+ * PredictorHeuristicSeed :
+   * predict() :
+     * bugfix : reinit was not overwriting all hybridE_seed entries 
+       (thanks to Alex Gawronski)
+
+version 2.0.2
+
 170328 Martin Mann :
  * PredictorHeuristic* :
    * predict() :

Makefile.am

@@ -2,16 +2,17 @@
 # ACLOCAL_AMFLAGS=-I m4
 
 # sub directories to check for Makefiles
-SUBDIRS = src perl tests .
+SUBDIRS = src perl tests doc .
 
 ################################################################
 # doxygen
 ################################################################
 
 if enable_doxygen
 ## doxygen documentation make target
-include $(top_srcdir)/doc/doxygen.am
+@DX_RULES@
 else
+## generate mandatory targets otherwise generated by doxygen.m4
 DX_PHONY =
 endif
 

README.md

@@ -61,6 +61,7 @@ The following topics are covered by this documentation:
   - [Cloning from github](#instgithub)
   - [Source code distribution](#instsource)
   - [Microsoft Windows installation](#instwin)
+  - [OS X installation with homebrew](#instosx)
 - [Usage and Parameters](#usage)
   - [Just run ...](#defaultRun)
   - [Prediction modes, their features and emulated tools](#predModes)
@@ -120,10 +121,10 @@ dependencies:
 - compiler supporting C++11 standard and OpenMP
 - [boost C++ library](http://www.boost.org/) version >= 1.50.0 
   (ensure the following libraries are installed; or install all e.g. in Ubuntu via package `libboost-all-dev`)
-  - libboost_regex
-  - libboost_program_options
-  - libboost_filesystem
-  - libboost_system
+    - libboost_regex
+    - libboost_program_options
+    - libboost_filesystem
+    - libboost_system
 - [Vienna RNA package](http://www.tbi.univie.ac.at/RNA/) version >= 2.3.0
 - if [cloning from github](#instgithub): GNU autotools (automake, autoconf, ..)
 
@@ -191,15 +192,15 @@ e.g. using [Cygwin](https://www.cygwin.com/) as 'linux emulator'. Just install
 Cygwin with the following packages:
 
 - *Devel*:
- - make
- - gcc-g++
- - autoconf
- - automake
- - pkg-config
+   - make
+   - gcc-g++
+   - autoconf
+   - automake
+   - pkg-config
 - *Libs*:
- - libboost-devel
+   - libboost-devel
 - *Perl*:
- - perl
+   - perl
 
 and follow either [install from github](#instgithub) or 
 [install from package](#instsource).
@@ -224,6 +225,61 @@ directory to your [`Path` System variable](http://www.computerhope.com/issues/ch
 
 
 
+<br /><br />
+<a name="instosx" />
+## OS X installation with homebrew (thanks to Lars Barquist)
+
+If you do not want to or can use the pre-compiled binaries for OS X available from 
+[bioconda](https://anaconda.org/bioconda/intarna), you can compile `IntaRNA` 
+locally.
+
+The following wraps up how to build `IntaRNA-2.0.2` under OS X (Sierra 10.12.4) using homebrew.
+
+First, install homebrew! :)
+
+```[bash]
+brew install gcc --without-multilib
+```
+
+`--without-multilib` is necessary for OpenMP multithreading support -- note 
+OS X default `gcc`/`clang` doesn't support OpenMP, so we need to install standard 
+`gcc`/`g++`
+
+```[bash]
+brew install boost --cc=gcc-6
+```
+
+`--cc=gcc-6` is necessary to build `boost` with standard `gcc`, rather than the 
+default bottle which appears to have been built with the system `clang`. 
+Brew installs `gcc`/`g++` as `/usr/local/bin/gcc-VERSION` by default to avoid 
+clashing with the system's `gcc`/`clang`. `6` is the current version as of 
+writing, but may change.
+
+```[bash]
+brew install viennarna
+brew install doxygen
+```
+
+Download and extract the IntaRNA source code package (e.g. `intaRNA-2.0.2.tar.gz`) from the [release page](releases/).
+
+```[bash]
+./configure CC=gcc-6 CXX=g++-6
+```
+
+This sets up makefiles to use standard `gcc`/`g++` from brew, which will 
+need an update to the appropriate compiler version if not still `6`. 
+You might also want to
+set `--prefix=INSTALLPATH` if you dont want to install IntaRNA globally.
+
+
+```[bash]
+Make
+make tests
+make install
+```
+
+
+
 
 <br /><br /><br /><br />
 <a name="usage" />

configure.ac

@@ -2,7 +2,7 @@
 
 AC_PREREQ([2.65])
 # 5 argument version only available with aclocal >= 2.64
-AC_INIT( [IntaRNA], [2.0.2], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
+AC_INIT( [IntaRNA], [2.0.3], [], [intaRNA], [http://www.bioinf.uni-freiburg.de] )
 
 
 # minimal required version of the boost library 
@@ -16,7 +16,10 @@ AC_CONFIG_AUX_DIR([.])
 AC_CONFIG_SRCDIR([src/easylogging++.h])
 AC_CONFIG_HEADERS([src/config.h])
 
-AC_CONFIG_MACRO_DIR([m4])
+# AC_CONFIG_MACRO_DIR([m4])
+m4_include([m4/m4_ax_cxx_compile_stdcxx.m4])
+m4_include([m4/m4_ax_openmp.m4])
+m4_include([m4/m4_ax_boost_base.m4])
 
 lt_enable_auto_import=""
 case "$host_os" in 
@@ -67,6 +70,16 @@ AC_MSG_RESULT([$pkgconfigEnabled])
 AS_IF([test x"$pkgconfigEnabled" = x"yes"], [
 	# Checks for pkg-config
 	AC_CHECK_PROG([HAVE_PKG_CONFIG],[pkg-config],[yes],[no])
+	AS_IF([test "HAVE_PKG_CONFIG" == "yes"], [
+		dnl Testing presence of pkg-config
+		AC_MSG_CHECKING([pkg-config m4 macros])
+		AS_IF([test m4_ifdef([PKG_CHECK_MODULES], [yes], [no]) == yes], [
+			AC_MSG_RESULT([yes]);
+		], [
+			AC_MSG_RESULT([no]);
+			HAVE_PKG_CONFIG=no
+		])
+	])
 ], [
 	HAVE_PKG_CONFIG=no
 ])
@@ -146,6 +159,8 @@ dnl generate doxygen documentation in Doxy
 AC_CHECK_PROG([HAVE_DOXYGEN],[doxygen],[yes],[no])
 
 AS_IF([test "x$HAVE_DOXYGEN" = "xyes"], [
+	# loading m4 macro
+	m4_include([m4/doxygen.m4])
 	# setup doxygen documentation to build
 	DX_HTML_FEATURE(ON)
 	DX_CHM_FEATURE(OFF)
@@ -156,7 +171,7 @@ AS_IF([test "x$HAVE_DOXYGEN" = "xyes"], [
 	DX_PDF_FEATURE(ON)
 	DX_PS_FEATURE(OFF)
 	# generate according options etc.
-	DX_INIT_DOXYGEN($PACKAGE_NAME, ["doc/doxygen.cfg"], ["doxygen-doc"])
+	DX_INIT_DOXYGEN($PACKAGE_NAME, [doc/doxygen.cfg], [doxygen-doc])
 ])
 
 ###############################################################################
@@ -298,6 +313,7 @@ AC_CONFIG_FILES([src/IntaRNA/intarna_config.h])
 AC_CONFIG_FILES([src/bin/Makefile])
 AC_CONFIG_FILES([perl/Makefile])
 AC_CONFIG_FILES([tests/Makefile])
+AC_CONFIG_FILES([doc/Makefile])
 AC_CONFIG_FILES([IntaRNA.pc])
 
 # generate the final Makefile etc.

doc/Makefile.am

@@ -0,0 +1,10 @@
+
+################################################################
+# extra files to be added to distribution
+################################################################
+
+EXTRA_DIST =	\
+			conda.txt \
+			doxygen.cfg
+
+