Merge branch 'dev'

Author: molpopgen

.travis.yml

@@ -1,10 +1,17 @@
 sudo: false
 language: cpp
-compiler:
-  - gcc
-  - clang
-install:
-- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
+
+matrix:
+    include:
+    - os: linux
+      dist: trusty
+    - os: osx 
+      osx_image: xcode8
+    - os: osx
+      osx_image: xcode7.2
+
+#install:
+#- if [ "$CXX" = "g++" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
 addons:
   apt:
     sources:
@@ -23,8 +30,16 @@ addons:
 notifications:
   email: false
 
+before_install:
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew update; fi
+  - if [[ "$TRAVIS_OS_NAME" == "osx" ]]; then brew install tbb   ; fi
 script:
  - export LD_LIBRARY_PATH=$HOME/lib
+ - if [ "$TRAVIS_OS_NAME" == "linux" ]; then export CXX="g++-4.8" CC="gcc-4.8"; fi
  - ./configure --prefix=$HOME && make  && make install
- - make test
+ - make check
+ - if [ "$TRAVIS_OS_NAME" == "linux" ]; then make check; fi
+ #For some reason, make check on OS X + conda fails to respect LD_LIBRARY_PATH,
+ #so we'll run the tests manually
+ - if [ "$TRAVIS_OS_NAME" == "osx" ]; then cd test; for i in $(find . -type f -perm +111);do $i -r detailed;cd .. ;done; fi
  - $HOME/bin/libsequenceConfig --version

README.md

@@ -57,21 +57,18 @@ The revision history of the library is [here](REVISION_HISTORY.md).  The documen
 
 ### Obtaining the master branch
 You have a few options:
-<ol>
-<li> Clone the repo (best option): git clone https://github.com/molpopgen/libsequence.git</li>
-<li> Click on "Download Zip" at https://github.com/molpopgen/libsequence </li>
-</ol>
+
+* Clone the repo (best option): git clone https://github.com/molpopgen/libsequence.git
+* Click on "Download Zip" at https://github.com/molpopgen/libsequence
+
 
 ### Obtaining a specific release
 Again, a few options:
-<ol>
-<li> Click on "Releases" at https://github.com/molpopgen/libsequence, then download the one you want </li>
-<li> Clone the repo (see previous section)</li>
-<ol>
-<li> Get a list of releases by saying "git tag -l" </li>
-<li> Checkout the release you want.  For example "git checkout 1.8.0"</li>
-</ol>
-</ol>
+
+* Click on "Releases" at https://github.com/molpopgen/libsequence, then download the one you want
+* Clone the repo (see previous section)
+* Get a list of releases by saying "git tag -l"
+* Checkout the release you want.  For example "git checkout 1.8.0"
 
 ## Installation
 
@@ -109,6 +106,24 @@ make
 sudo make install
 ~~~
 
+The build conditions can be adjusted via the usual environment variables.  To compile an optimized "release" build:
+
+~~~
+./configure CXXFLAGS="-O3 -DNDEBUG"
+~~~
+
+To compile a debugger-friendly build:
+
+~~~
+./configure CXXFLAGS="-O0 -g"
+~~~
+
+To change the compiler, set the C and C++ compiler variables:
+
+~~~
+./configure CC=gcc CXX=g++
+~~~
+
 #### Compiling unit tests and examples
 
 To compile unit testing suite and example programs
@@ -136,13 +151,15 @@ cd test && sh runTests.sh
 
 Some users may not have the dependent libraries installed in the standard locations on their systems.  Note that "standard" means wherever the compiler system looks for header files during compilation and libraries during linking.  This scenario is common on OS X systems where users have used some sort of "system" to install various libraries rather than installing from source directly.  In order to accomodate such situations, the user must provide the correct path to the include and lib directories.  For example, assume that the dependend libraries are in /opt on your system.  You would install libsequence as follows:
 
-CXXFLAGS=-I/opt/include LDFLAGS="$LDFLAGS -l/opt/lib" ./configure
+CPPFLAGS=-I/opt/include LDFLAGS="$LDFLAGS -l/opt/lib" ./configure
 
 make
 
+~~~
 sudo make install
+~~~
 
-Note that the modification of LDFLAGS prepends the current value of LDFLAGS if it exists.  This allows for scenarios where the system's search path for libraries may have been modified by the user or sysadmin via a modification of that shell variable.  (One could also do the same with CXXFLAGS, FYI.)
+Note that the modification of LDFLAGS prepends the current value of LDFLAGS if it exists.  This allows for scenarios where the system's search path for libraries may have been modified by the user or sysadmin via a modification of that shell variable.  (One could also do the same with CPPFLAGS, FYI.)
 
 ### Installing libsequence locally
 
@@ -152,15 +169,18 @@ If you do not have permission to "sudo make install", you can install the librar
 
 Then, when compiling any program using libsequence, you need to add
 
-> -I$HOME/include
-
+~~~
+-I$HOME/include
+~~~
 to any compilation commands and
 
-> -L$HOME/lib
+~~~
+-L$HOME/lib
+~~~
 
 to any linking commands.
 
-When running programs linking to any of the above run-time libraries, and depending on your system, you may also need to adjust variables like LD _ LIBRARY _ PATH to prepend $HOME/lib to them, etc., but you'll need to figure that out on case-by-case basis, as different systems can behave quite differently.
+When running programs linking to any of the above run-time libraries, and depending on your system, you may also need to adjust variables like LD_LIBRARY_PATH to prepend $HOME/lib to them, etc., but you'll need to figure that out on case-by-case basis, as different systems can behave quite differently.
 
 ### Another installation option (not supported by the libsequence author)
 

REVISION_HISTORY.md

@@ -4,7 +4,7 @@
 
 This document lists major changes between tags/releases of libsequence. The following caveat is important:
 
-If you see a section below referring to libseqeunce version X, and no version X exists as a release, then you must consider the info here inaccurate.  In such cases, the list of changes may refer to planned changes for a future release which may or may not be implemented yet in either the master or some development branch.
+If you see a section below referring to libsequence version X, and no version X exists as a release, then you must consider the info here inaccurate.  In such cases, the list of changes may refer to planned changes for a future release which may or may not be implemented yet in either the master or some development branch.
 
 ## Moving towards a "2.0" release: ABI compatibility in flux
 
@@ -30,6 +30,11 @@ However:
 
 1. Sequence/SeqRegexes.hpp -- not working.  This will not be fixed until GCC supports <regex>.  The function is now currently implemented in a non-regex manner, which is lame, but it works.
 
+## libsequence 1.9.1
+
+* Sequence::SeqException was removed.  Exceptions from namespace std are preferred, and are easier to wrap in other languages.
+* Sequence::PolySNP::ThetaL throws exception if outrgroup not present
+
 ## libsequence 1.9.0
 
 * Fixed issues with Sequence::Comeron95 that made it impossible to allocate on the stack.

Sequence/AlignStream.hpp

@@ -26,10 +26,10 @@ long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
 
 #include <Sequence/Alignment.hpp>
 #include <Sequence/Seq.hpp>
-#include <Sequence/SeqExceptions.hpp>
 #include <type_traits>
 #include <utility>
 #include <string>
+#include <stdexcept>
 
 /*! \file AlignStream.hpp
   @brief declaration of virtual base class for alignment streams (Sequence::AlignStream)
@@ -148,15 +148,15 @@ namespace Sequence
 	for these iterators evaluates to
 	std::vector<T>::const_iterator, any vector<T>
 	can be the data source
-	\exception Sequence::SeqException is thrown
+	\exception std::runtime_error is thrown
 	if all data elements in the range (beg,end]
 	are not of the same length
       */
       void assign(const_iterator beg,const_iterator end);
       /*!
 	Assign via a move operation
 
-	\exception Sequence::SeqException is thrown
+	\exception std::runtime_error is thrown
 	if all data elements are not of the same length
       */
       void assign( std::vector<T> && _data);

Sequence/Alignment.hpp

@@ -27,8 +27,7 @@ long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
 #include <fstream>
 #include <vector>
 #include <string>
-#include <Sequence/SeqExceptions.hpp>
-
+#include <stdexcept>
 /*! \file Alignment.hpp
   @brief Declaration of namespace Sequence::Alignment
 */

Sequence/Comparisons.hpp

@@ -37,7 +37,6 @@ long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
 #include <string>
 #include <algorithm>
 #include <type_traits>
-#include <Sequence/SeqExceptions.hpp>
 #include <Sequence/SeqEnums.hpp>
 
 namespace Sequence

Sequence/FST.hpp

@@ -28,7 +28,6 @@ long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
 #include <set>
 #include <memory>
 #include <Sequence/stateCounter.hpp>
-#include <Sequence/SeqExceptions.hpp>
 
 /*! \file FST.hpp
   @brief delcaration of a class (Sequence::FST) to analyze population structure

Sequence/Makefile.am

@@ -35,7 +35,6 @@ pkginclude_HEADERS = AlignStream.hpp\
 	Seq.hpp\
 	SeqConstants.hpp\
 	SeqEnums.hpp\
-	SeqExceptions.hpp\
 	SeqFunctors.hpp\
 	SeqProperties.hpp\
 	SeqRegexes.hpp\

Sequence/Makefile.in

@@ -369,7 +369,6 @@ pkginclude_HEADERS = AlignStream.hpp\
 	Seq.hpp\
 	SeqConstants.hpp\
 	SeqEnums.hpp\
-	SeqExceptions.hpp\
 	SeqFunctors.hpp\
 	SeqProperties.hpp\
 	SeqRegexes.hpp\

Sequence/PolyTable.hpp

@@ -53,7 +53,6 @@ long with libsequence.  If not, see <http://www.gnu.org/licenses/>.
 #include <type_traits>
 #include <functional>
 #include <memory>
-#include <Sequence/SeqExceptions.hpp>
 #include <Sequence/polySiteVector.hpp>
 /*! \example PolyTableIterators.cc */
 namespace Sequence