Merge branch 'pybind11' into vmc

.gitattributes

+*.py  filter=tabspace
+*.cpp  filter=tabspace

.gitconfig

+.git/config
\ No newline at end of file

.gitignore

-# Ignore everything
-*
-
-# But not these files...
-!.gitignore
-!*.h
-!*.hpp
-!*.hxx
-
-!*.c
-!*.cpp
-!*.cxx
-
-!*.mk
-!Makefile
-
-!Dockerfile
-
-!*.sh
-
-!*.rb
-!*.py
-!.config.mk.*
-
-!*.md
-!*.xml
-!*.dox
-!*.css
-!*.js
-!*.yml
-
-# ...even if they are in subdirectories
-!*/
-
-# However we really want to ignore
-lapacke/*
-build/*
-doc/html/*
+.cache
+__pycache__
+*.sw[pon]
+*.np[yz]
+*.xrs
+lapacke
+build
+doc/html
+doc/findDoxytag
+doc/parseDoxytags
+doc/xerus.tagfile
+doc/xerus.tags
 config.mk
+XerusTest

.gitlab-ci-configs/.config.mk.ci.gcc.python

@@ -5,13 +5,10 @@ CXX = g++
 COMPATIBILITY = -std=c++11
 PYTHON2_CONFIG = `python2-config --cflags --ldflags`
 PYTHON3_CONFIG = `python3-config --cflags --ldflags`
-PYTEST2 = pytest
-PYTEST3 = pytest-3
+PYTEST2 = python2 -m pytest
+PYTEST3 = python3 -m pytest
 
-STRICT_WARNINGS = TRUE
-# DEBUG += -D XERUS_TEST_COVERAGE                 # Enable coverage tests
-
- DEBUG += -g                # Adds debug symbols
+DEBUG += -g                # Adds debug symbols
 
 #=================================================================================================
 # External libraries
@@ -23,6 +20,6 @@ BOOST_LIBS = -lboost_filesystem
 
 OTHER += -I /usr/include/python2.7/ -lboost_python -I/usr/lib64/python2.7/site-packages/numpy/core/include/ -lpython2.7 -fno-var-tracking-assignments
 
-BOOST_PYTHON2 = -lboost_python-py27
-BOOST_PYTHON3 = -lboost_python-py35
+# BOOST_PYTHON2 = -lboost_python-py27
+# BOOST_PYTHON3 = -lboost_python-py35
 

.gitlab-ci.yml

@@ -14,7 +14,7 @@ job_build_homepage:
   stage: build_homepage
   script: "cp .gitlab-ci-configs/.config.mk.ci.cc config.mk; make -C doc doc && scp -r doc/html xerusweb:libxerus.org-443"
   when: always
-  only: 
+  only:
     - master
   allow_failure: true
 
@@ -46,21 +46,25 @@ job_build_python2:
   stage: build_python2
   script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make python2"
   when: always
+  variables:
+    GIT_SUBMODULE_STRATEGY: normal
 
 job_build_python3:
   stage: build_python3
   script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make python3"
   when: always
+  variables:
+    GIT_SUBMODULE_STRATEGY: normal
 
 job_test_python2:
   stage: test_python2
   script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make test_python2"
   when: always
 
-#job_test_python3:
-#  stage: test_python3
-#  script: "g++ --version; cp .config.mk.ci.gcc.python config.mk; make test_python3"
-#  when: always
+job_test_python3:
+  stage: test_python3
+  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make test_python3"
+  when: always
 
 job_make_clang:
   stage: build_clang

.gitmodules

+[submodule "src/pybind11"]
+	path = 3rdParty/pybind11
+	url = https://github.com/pybind/pybind11.git
+
 [submodule "3rdParty/measurement_utils"]
 	path = 3rdParty/measurement_utils
 	url = https://trunschk@bitbucket.org/trunschk/measurement_utils.git

.project

+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>xerus</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+	</buildSpec>
+	<natures>
+	</natures>
+</projectDescription>

pybind11 @ 25abf7ef

+Subproject commit 25abf7efba0b2990f5a6dfb0a31bc65c0f2f4d17

ChangeLog.md

@@ -11,7 +11,7 @@ Potentially breaking changes are marked with an exclamation point '!' at the beg
  * ! Support for GCC <= 4.8 was dropped. Update your compiler if this affects you.
  * (optional) support for arpack https://github.com/opencollab/arpack-ng
  * Fixed minor rank reduction bug in TensorNetwork soft thresholding.
- 
+ * Defining multiple UnitTests with the same name does not crash the execution of 'make test' anymore.
 
 * 2017-05-31 v3.0.1
  * Added TTNetwork::use_dense_representations() to convert all components to dense representation.

Makefile

@@ -58,9 +58,18 @@ XERUS_SOURCES = $(wildcard src/xerus/*.cpp)
 XERUS_SOURCES += $(wildcard src/xerus/algorithms/*.cpp)
 XERUS_SOURCES += $(wildcard src/xerus/applications/*.cpp)
 XERUS_SOURCES += $(wildcard src/xerus/examples/*.cpp)
+# XERUS_SOURCES = $(wildcard src/xerus/**/*.cpp)
+
+XERUS_INCLUDES =  $(wildcard include/xerus/*.h)
+XERUS_INCLUDES += $(wildcard include/xerus/algorithms/*.h)
+XERUS_INCLUDES += $(wildcard include/xerus/applications/*.h)
+XERUS_INCLUDES += $(wildcard include/xerus/examples/*.h)
+# XERUS_INCLUDES = $(wildcard include/xerus/**/*.h)
 
 MISC_SOURCES = $(wildcard src/xerus/misc/*.cpp)
 
+MISC_INCLUDES = $(wildcard include/xerus/misc/*.h)
+
 PYTHON_SOURCES = $(wildcard src/xerus/python/*.cpp)
 
 TEST_SOURCES = $(wildcard src/xerus/test/*.cpp)
@@ -202,14 +211,14 @@ shared: build/libxerus_misc.so build/libxerus.so
 .PHONY: libxerus_misc_dependencies
 libxerus_misc_dependencies:
 	@:$(call check_defined, BOOST_LIBS, include and link paths)
-build/libxerus_misc.so: libxerus_misc_dependencies $(MINIMAL_DEPS) $(MISC_SOURCES)
+build/libxerus_misc.so: $(MINIMAL_DEPS) $(MISC_SOURCES) $(MISC_INCLUDES) | libxerus_misc_dependencies
 	mkdir -p $(dir $@)
 	$(CXX) -shared -fPIC -Wl,-soname,libxerus_misc.so $(FLAGS) -I include $(MISC_SOURCES) -Wl,--as-needed $(CALLSTACK_LIBS) $(BOOST_LIBS) -o build/libxerus_misc.so
 
 .PHONY: libxerus_dependencies
 libxerus_dependencies:
 	@:$(call check_defined, SUITESPARSE LAPACK_LIBRARIES BLAS_LIBRARIES, include and link paths)
-build/libxerus.so: libxerus_dependencies $(MINIMAL_DEPS) $(XERUS_SOURCES) build/libxerus_misc.so
+build/libxerus.so: $(MINIMAL_DEPS) $(XERUS_SOURCES) $(XERUS_INCLUDES) build/libxerus_misc.so | libxerus_dependencies
 	mkdir -p $(dir $@)
 	$(CXX) -shared -fPIC -Wl,-soname,libxerus.so $(FLAGS) -I include $(XERUS_SOURCES) -L ./build/ -Wl,--as-needed -lxerus_misc $(SUITESPARSE) $(LAPACK_LIBRARIES) $(ARPACK_LIBRARIES) $(BLAS_LIBRARIES) -o build/libxerus.so
 
@@ -217,21 +226,20 @@ build/libxerus.so: libxerus_dependencies $(MINIMAL_DEPS) $(XERUS_SOURCES) build/
 python2: build/python2/xerus.so
 python3: build/python3/xerus.so
 
-build/python2/xerus.so: $(MINIMAL_DEPS) $(PYTHON_SOURCES) build/libxerus.so
-	@:$(call check_defined, PYTHON2_CONFIG BOOST_PYTHON2, include and link paths)
+build/python2/xerus.so: $(MINIMAL_DEPS) $(PYTHON_SOURCES) src/xerus/python/misc.h build/libxerus.so
+	@:$(call check_defined, PYTHON2_CONFIG, include and link paths)
 	mkdir -p $(dir $@)
-	$(CXX) -shared -fPIC -Wl,-soname,xerus.so $(PYTHON2_CONFIG) $(PYTHON_FLAGS) -I include $(PYTHON_SOURCES) -L ./build/ -Wl,--as-needed -lxerus $(BOOST_PYTHON2) -o $@
+	$(CXX) -shared -fPIC -Wl,-soname,xerus.so $(PYTHON2_CONFIG) $(PYTHON_FLAGS) -I include -I 3rdParty/pybind11/include $(PYTHON_SOURCES) -L ./build/ -Wl,--as-needed -lxerus -o $@
 
-build/python3/xerus.so: $(MINIMAL_DEPS) $(PYTHON_SOURCES) build/libxerus.so
-	@:$(call check_defined, PYTHON3_CONFIG BOOST_PYTHON3, include and link paths)
+build/python3/xerus.so: $(MINIMAL_DEPS) $(PYTHON_SOURCES) src/xerus/python/misc.h build/libxerus.so
+	@:$(call check_defined, PYTHON3_CONFIG, include and link paths)
 	mkdir -p $(dir $@)
-	@# -fpermissive is needed because of a bug in the definition of BOOST_PYTHON_MODULE_INIT in <boost/python/module_init.h>
-	$(CXX) -shared -fPIC -Wl,-soname,xerus.so $(PYTHON3_CONFIG) $(PYTHON_FLAGS) -fpermissive -I include $(PYTHON_SOURCES) -L ./build/ -Wl,--as-needed -lxerus $(BOOST_PYTHON3) -o $@
+	$(CXX) -shared -fPIC -Wl,-soname,xerus.so $(PYTHON3_CONFIG) $(PYTHON_FLAGS) -I include -I 3rdParty/pybind11/include $(PYTHON_SOURCES) -L ./build/ -Wl,--as-needed -lxerus -o $@
 
 
 static: build/libxerus_misc.a build/libxerus.a
 
-build/libxerus_misc.a: libxerus_misc_dependencies $(MINIMAL_DEPS) $(MISC_OBJECTS)
+build/libxerus_misc.a: $(MINIMAL_DEPS) $(MISC_OBJECTS) | libxerus_misc_dependencies
 	mkdir -p $(dir $@)
 ifdef USE_LTO
 	gcc-ar rcs ./build/libxerus_misc.a $(MISC_OBJECTS)
@@ -239,7 +247,7 @@ else
 	ar rcs ./build/libxerus_misc.a $(MISC_OBJECTS)
 endif
 
-build/libxerus.a: libxerus_dependencies $(MINIMAL_DEPS) $(XERUS_OBJECTS)
+build/libxerus.a: $(MINIMAL_DEPS) $(XERUS_OBJECTS) | libxerus_dependencies
 	mkdir -p $(dir $@)
 ifdef USE_LTO
 	gcc-ar rcs ./build/libxerus.a $(XERUS_OBJECTS)
@@ -260,18 +268,22 @@ install: shared
 	test -d $(strip $(INSTALL_LIB_PATH));
 	test -d $(strip $(INSTALL_HEADER_PATH));
 	@printf "Installing libxerus.so to $(strip $(INSTALL_LIB_PATH)) and storing the header files in $(strip $(INSTALL_HEADER_PATH)).\n"
+ifdef INSTALL_PYTHON2_PATH
+	test -d $(strip $(INSTALL_PYTHON2_PATH));
+	@printf "Installing python2/xerus.so to $(strip $(INSTALL_PYTHON2_PATH)).\n"
+endif
+ifdef INSTALL_PYTHON3_PATH
+	test -d $(strip $(INSTALL_PYTHON3_PATH));
+	@printf "Installing python3/xerus.so to $(strip $(INSTALL_PYTHON3_PATH)).\n"
+endif
 	cp include/xerus.h $(INSTALL_HEADER_PATH)
 	cp -r include/xerus $(INSTALL_HEADER_PATH)
 	cp build/libxerus_misc.so $(INSTALL_LIB_PATH)
 	cp build/libxerus.so $(INSTALL_LIB_PATH)
 ifdef INSTALL_PYTHON2_PATH
-	test -d $(strip $(INSTALL_PYTHON2_PATH));
-	@printf "Installing xerus.so to $(strip $(INSTALL_PYTHON2_PATH)).\n"
 	cp build/python2/xerus.so $(INSTALL_PYTHON2_PATH)
 endif
 ifdef INSTALL_PYTHON3_PATH
-	test -d $(strip $(INSTALL_PYTHON3_PATH));
-	@printf "Installing xerus.so to $(strip $(INSTALL_PYTHON3_PATH)).\n"
 	cp build/python3/xerus.so $(INSTALL_PYTHON3_PATH)
 endif
 else
@@ -283,7 +295,7 @@ install:
 	@printf "Cannot install xerus: INSTALL_LIB_PATH not set.  Please set the path in config file.\n"
 endif
 
-$(TEST_NAME): libxerus_misc_dependencies libxerus_dependencies $(MINIMAL_DEPS) $(UNIT_TEST_OBJECTS) $(TEST_OBJECTS) build/libxerus.a build/libxerus_misc.a
+$(TEST_NAME): $(MINIMAL_DEPS) $(UNIT_TEST_OBJECTS) $(TEST_OBJECTS) build/libxerus.a build/libxerus_misc.a | libxerus_misc_dependencies libxerus_dependencies
 	$(CXX) -D XERUS_UNITTEST $(FLAGS) $(UNIT_TEST_OBJECTS) $(TEST_OBJECTS) build/libxerus.a build/libxerus_misc.a $(SUITESPARSE) $(LAPACK_LIBRARIES) $(ARPACK_LIBRARIES) $(BLAS_LIBRARIES) $(BOOST_LIBS) $(CALLSTACK_LIBS) -o $(TEST_NAME)
 
 build/print_boost_version: src/print_boost_version.cpp
@@ -319,13 +331,13 @@ endif
 .PHONY: test_python2_dependencies
 test_python2_dependencies:
 	@:$(call check_defined, PYTEST2, pytest executable)
-test_python2: test_python2_dependencies build/libxerus.so build/python2/xerus.so
+test_python2: build/libxerus.so build/python2/xerus.so | test_python2_dependencies
 	@PYTHONPATH=build/python2:${PYTHONPATH} LD_LIBRARY_PATH=build:${LD_LIBRARY_PATH} $(PYTEST2) src/pyTests
 
 .PHONY: test_python3_dependencies
 test_python3_dependencies:
 	@:$(call check_defined, PYTEST3, pytest executable)
-test_python3: test_python3_dependencies build/libxerus.so build/python3/xerus.so
+test_python3: build/libxerus.so build/python3/xerus.so | test_python3_dependencies
 	@PYTHONPATH=build/python3:${PYTHONPATH} LD_LIBRARY_PATH=build:${LD_LIBRARY_PATH} $(PYTEST3) src/pyTests
 
 

config.mk.default

@@ -14,8 +14,8 @@ CXX = g++
 # pytest executable(s). If you installed these system-wide you likely don't need to change anything.
 PYTHON2_CONFIG = `python2-config --cflags --ldflags`
 PYTHON3_CONFIG = `python3-config --cflags --ldflags`
-PYTEST2 = pytest2
-PYTEST3 = pytest3
+PYTEST2 = python2 -m pytest
+PYTEST3 = python3 -m pytest
 
 #=================================================================================================
 # C++ Version
@@ -140,9 +140,5 @@ BOOST_LIBS = -lboost_filesystem -lboost_system
 # ARPACK_LIBRARIES = -larpack
 # OTHER += -DARPACK_LIBRARIES
 
-# Uncomment or add the appropriate boost python library
-BOOST_PYTHON2 = -lboost_python-py27
-BOOST_PYTHON3 = -lboost_python-py35
-
 # Custom include paths
 # OTHER += -I /path/to/include

docker/base/Dockerfile

-FROM phusion/baseimage:0.9.22
+FROM phusion/baseimage:0.11
 USER root
 WORKDIR "/tmp/"
 
 # Get Ubuntu updates
-RUN apt-get -qq update && \
-    apt-get -y --with-new-pkgs -o Dpkg::Options::="--force-confold" upgrade
+RUN apt-get update && \
+    apt-get upgrade -y -o Dpkg::Options::="--force-confold"
 
 # Set locale environment
 RUN apt-get -y install locales sudo && \
@@ -14,10 +14,6 @@ ENV LC_ALL=C.UTF-8 \
     LANG=C.UTF-8 \
     LANGUAGE=C.UTF-8
 
-# Turn off forwarding of syslog messages to stdout
-# https://github.com/phusion/baseimage-docker/issues/186
-RUN touch /etc/service/syslog-forwarder/down
-
 # Non-Python utilities and libraries
 RUN apt-get -y install \
     cmake \
@@ -32,7 +28,12 @@ RUN apt-get -y install \
     libopenblas-dev \
     libiberty-dev \
     binutils-dev \
-    zlib1g-dev
+    zlib1g-dev \
+    libdpkg-perl
+
+# Check Python versions
+RUN python  -c'from __future__ import print_function; import sys; version = "{0}.{1}".format(*sys.version_info); print("python2-version:", version)'
+RUN python3 -c'import sys; version = "{0}.{1}".format(*sys.version_info); print("python3-version:", version)'
 
 # Install Python2 based environment
 RUN apt-get -y install \

docker/build.sh

 #!/bin/bash
 DIRNAME=$(dirname $0)
-docker build "$@" -t firemarmot/base $DIRNAME/base
-docker build "$@" -t firemarmot/suitesparse $DIRNAME/suitesparse
-docker build "$@" -t firemarmot/xerus $DIRNAME/xerus
+docker build "$@" -t firemarmot/base $DIRNAME/base && \
+docker build "$@" -t firemarmot/suitesparse $DIRNAME/suitesparse && \
+docker build "$@" -t firemarmot/xerus $DIRNAME/xerus && \
 # docker build "$@" -t firemarmot/interactive $DIRNAME/interactive
 docker build "$@" -t firemarmot/interactive_fenics $DIRNAME/interactive_fenics

docker/interactive_fenics/Dockerfile

 FROM firemarmot/xerus AS xerus
 
-FROM quay.io/fenicsproject/stable:2017.1.0
+FROM quay.io/fenicsproject/stable:2019.1.0.r3
 USER root
 WORKDIR "/tmp/"
 
@@ -27,8 +27,8 @@ RUN apt-get -y install \
     python3-numpy
 
 # Check Python versions
-RUN python -c'import sys; raise SystemExit("{0}.{1}".format(*sys.version_info) != "2.7")'
-RUN python3 -c'import sys; raise SystemExit("{0}.{1}".format(*sys.version_info) != "3.5")'
+RUN python  -c'from __future__ import print_function; import sys; version = "{0}.{1}".format(*sys.version_info); print("python2-version:", version)'
+RUN python3 -c'import sys; version = "{0}.{1}".format(*sys.version_info); print("python3-version:", version)'
 
 # Clean apt
 RUN apt-get clean && \
@@ -38,7 +38,7 @@ RUN apt-get clean && \
 RUN mkdir -p /usr/local/lib && \
 	mkdir -p /usr/local/include && \
 	mkdir -p /usr/local/lib/python2.7/site-packages && \
-	mkdir -p /usr/local/lib/python3.5/site-packages
+	mkdir -p /usr/local/lib/python3.6/site-packages
 
 COPY --from=xerus /usr/local/include/suitesparse /usr/local/include/suitesparse
 COPY --from=xerus /usr/local/lib/suitesparse /usr/local/lib/suitesparse
@@ -47,7 +47,7 @@ COPY --from=xerus /usr/local/include/xerus /usr/local/include
 COPY --from=xerus /usr/local/lib/libxerus_misc.so /usr/local/lib
 COPY --from=xerus /usr/local/lib/libxerus.so /usr/local/lib
 COPY --from=xerus /usr/local/lib/python2.7/site-packages/xerus.so /usr/local/lib/python2.7/site-packages
-COPY --from=xerus /usr/local/lib/python3.5/site-packages/xerus.so /usr/local/lib/python3.5/site-packages
+COPY --from=xerus /usr/local/lib/python3.6/site-packages/xerus.so /usr/local/lib/python3.6/site-packages
 
 # Install custom Python2 packages
 RUN pip install cython && pip install ttpy matplotlib2tikz joblib
@@ -57,7 +57,7 @@ USER fenics
 RUN mkdir -p $(python -m site --user-site) && \
 	echo /usr/local/lib/python2.7/site-packages/ >$(python -m site --user-site)/xerus.pth && \
 	mkdir -p $(python3 -m site --user-site) && \
-	echo /usr/local/lib/python3.5/site-packages/ >$(python3 -m site --user-site)/xerus.pth
+	echo /usr/local/lib/python3.6/site-packages/ >$(python3 -m site --user-site)/xerus.pth
 ENV LD_LIBRARY_PATH "/usr/local/lib/:/usr/local/lib/suitesparse:$LD_LIBRARY_PATH"
 
 WORKDIR "/home/fenics/"

docker/xerus/Dockerfile

@@ -3,23 +3,26 @@ USER root
 WORKDIR "/tmp/"
 
 # Check Python versions
-RUN python -c'import sys; raise SystemExit("{0}.{1}".format(*sys.version_info) != "2.7")'
-RUN python3 -c'import sys; raise SystemExit("{0}.{1}".format(*sys.version_info) != "3.5")'
+RUN python  -c'from __future__ import print_function; import sys; version = "{0}.{1}".format(*sys.version_info); print("python2-version:", version); raise SystemExit(version != "2.7")'
+RUN python3 -c'import sys; version = "{0}.{1}".format(*sys.version_info); print("python3-version:", version); raise SystemExit(version != "3.6")'
 
 # Install Xerus
 RUN git clone https://git.hemio.de/xerus/xerus.git
 WORKDIR "/tmp/xerus/"
 RUN git checkout vmc && \
 	git pull && \
-	cp ./docker/xerus/config.mk . && \
+	git submodule update --init --recursive
+RUN cp ./docker/xerus/config.mk . && \
 	mkdir -p /usr/local/lib && \
 	mkdir -p /usr/local/include && \
 	mkdir -p /usr/local/lib/python2.7/site-packages && \
-	mkdir -p /usr/local/lib/python3.5/site-packages && \
+	mkdir -p /usr/local/lib/python3.6/site-packages && \
+	make python2 python3 -j $(cat /tmp/NCORES_1)
+RUN ls /usr/local/lib/python3.6/ && \
 	make install -j $(cat /tmp/NCORES_1)
 
 RUN mkdir -p $(python -m site --user-site) && \
 	echo /usr/local/lib/python2.7/site-packages/ >$(python -m site --user-site)/xerus.pth && \
 	mkdir -p $(python3 -m site --user-site) && \
-	echo /usr/local/lib/python3.5/site-packages/ >$(python3 -m site --user-site)/xerus.pth
+	echo /usr/local/lib/python3.6/site-packages/ >$(python3 -m site --user-site)/xerus.pth
 ENV LD_LIBRARY_PATH "/usr/local/lib/:$LD_LIBRARY_PATH"

docker/xerus/config.mk

 CXX = g++
+
+PYTHON2_CONFIG = `python-config --cflags --ldflags`
+PYTHON3_CONFIG = `python3-config --cflags --ldflags`
+
 COMPATIBILITY = -std=c++17
 COMPILE_THREADS = 8                       # Number of threads to use during link time optimization.
 HIGH_OPTIMIZATION = TRUE                  # Activates -O3 -march=native and some others
 OTHER += -fopenmp
 
-PYTHON2_CONFIG = `python-config --cflags --ldflags`
-PYTHON3_CONFIG = `python3-config --cflags --ldflags`
-
 LOGGING += -D XERUS_LOG_INFO              # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
 LOGGING += -D XERUS_LOGFILE               # Use 'error.log' file instead of cerr
 LOGGING += -D XERUS_LOG_ABSOLUTE_TIME     # Print absolute times instead of relative to program time
@@ -14,12 +15,9 @@ LOGGING += -D XERUS_LOG_ABSOLUTE_TIME     # Print absolute times instead of rela
 INSTALL_LIB_PATH = /usr/local/lib         # Path where to install the libxerus.so shared library.
 INSTALL_HEADER_PATH = /usr/local/include  # Path where to install the xerus header files.
 INSTALL_PYTHON2_PATH = /usr/local/lib/python2.7/site-packages
-INSTALL_PYTHON3_PATH = /usr/local/lib/python3.5/site-packages
+INSTALL_PYTHON3_PATH = /usr/local/lib/python3.6/site-packages
 
 BLAS_LIBRARIES = -lopenblas -lgfortran    # Openblas, serial
 LAPACK_LIBRARIES = -llapacke -llapack     # Standard Lapack + Lapacke libraries
 SUITESPARSE = -L/usr/local/lib/suitesparse -lcholmod -lspqr
 BOOST_LIBS = -lboost_filesystem
-
-BOOST_PYTHON2 = -lboost_python-py27
-BOOST_PYTHON3 = -lboost_python-py35

include/xerus/indexedTensor_tensor_factorisations.h

@@ -60,13 +60,13 @@ namespace xerus {
 		const size_t maxRank;
 		const bool preventZero;
 		
-		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input) : 
+		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input) :
 			input(&_input), epsilon(EPSILON), softThreshold(0.0), maxRank(std::numeric_limits<size_t>::max()), preventZero(false) { }
 			
 		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input, const double _softTreshold, const bool _preventZero = false) : 
 			input(&_input), epsilon(0.0), softThreshold(_softTreshold), maxRank(std::numeric_limits<size_t>::max()), preventZero(_preventZero) { }
 			
-		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input, const size_t _maxRank, const double _epsilon = EPSILON) : 
+		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input, const size_t _maxRank, const double _epsilon = EPSILON) :
 			input(&_input), epsilon(_epsilon), softThreshold(0.0), maxRank(_maxRank), preventZero(false) { }
 			
 		SVD(internal::IndexedTensorReadOnly<Tensor>&& _input, const size_t _maxRank, const double _epsilon, const double _softTreshold, const bool _preventZero) : 

include/xerus/misc/containerOutput.h

@@ -86,11 +86,11 @@ namespace xerus { namespace misc {
 	
 	
 	///@brief Allow to pipe std::maps to ostreams.
-	template<class T, class U>
-	std::ostream& operator<<(std::ostream& _out, const std::map<T,U>& _set) {
-		if(_set.size() == 0) { _out << "{ }"; return _out; }
+	template<class T, class U, class... rest_t>
+	std::ostream& operator<<(std::ostream& _out, const std::map<T, U, rest_t...>& _map) {
+		if(_map.size() == 0) { _out << "{ }"; return _out; }
 		_out << "{ ";
-		for(const auto& item : _set) {  _out << "(" << item.first << ", " << item.second << "), "; }
+		for(const auto& item : _map) {  _out << "(" << item.first << ", " << item.second << "), "; }
 		_out << "\b\b }";
 		return _out;
 	}

include/xerus/misc/containerSupport.h

@@ -63,7 +63,6 @@ namespace xerus { namespace misc {
 			return count;
 		}
 		
-		
 		///@brief: Checks whether an arbitary container contains a certain element.
 		template<template<class, class...> class container_t, class item_t, class... rest_t,
 			typename std::enable_if<sfinae::has_find<container_t<item_t, rest_t...>, item_t>::value, int>::type = 0>
@@ -195,7 +194,16 @@ namespace xerus { namespace misc {
 	inline void erase(container_t<item_t, rest_t...>& _container, const rule_t& _rule) {
 		_container.erase(std::remove_if(_container.begin(), _container.end(), _rule), _container.end());
 	}
-} } // namespaces xerus::misc
-
-
+	
+	///@brief: Erases a single element specified by @a _rule from the vector @a _vector by swaping with the last item (destroying the order).
+	template<class rule_t, class item_t, class... rest_t>
+	inline void swap_erase_single(std::vector<item_t, rest_t...>& _vector, const rule_t& _rule) {
+		const auto foundItr = std::find_if(_vector.begin(), _vector.end(), _rule);
+		if(foundItr != _vector.end()) {
+			if(foundItr+1 != _vector.end()) { std::iter_swap(foundItr, _vector.rbegin()); }
+			_vector.pop_back();
+		}
+	}
+	
+}} // namespaces xerus::misc
 

include/xerus/misc/fileIO.h

@@ -110,7 +110,7 @@ namespace xerus { namespace misc {
     T deserialize(const std::string& _bytes) {
         T obj;
         std::string header = _bytes.substr(0, _bytes.find("\n"));
-        XERUS_REQUIRE(header == std::string("Xerus ") + misc::demangle_cxa(typeid(T).name()) + " serialized object.", "Invalid binary input. DBG: " << header);
+        XERUS_REQUIRE(header == std::string("Xerus ") + misc::demangle_cxa(typeid(T).name()) + " serialized object.", "Invalid binary input. \nExpected: \"" << std::string("Xerus ") + misc::demangle_cxa(typeid(T).name()) + " serialized object.\"\nGot: \"" << header << "\"");
         std::stringstream stream(_bytes.substr(_bytes.find("\n")+1));  // +1 because of the last \n
         XERUS_REQUIRE(stream, "Unexpected end of stream in load_from_file().");
         stream_reader(stream, obj, FileFormat::BINARY);

include/xerus/misc/fileUtilities.h

@@ -27,6 +27,7 @@
 #include <set>
 #include <string>
 #include <fstream>
+#include <vector>
 
 // #include "standard.h"
 
@@ -35,18 +36,27 @@ namespace xerus { namespace misc {
 	///@brief Creates all directories in the @a _path of the file, if needed.
 	void create_directories_for_file(const std::string& _path);
 	
-	///@brief Returns a set containing all regular files at the given @a _path.
+	///@brief Returns a set containing all regular files present at the given @a _path.
 	std::set<std::string> get_files(const std::string& _path);
+	
+	///@brief Returns a set containing all directories present at the given @a _path.
+	std::set<std::string> get_directories(const std::string& _path);
 
 	///@brief Checks whether a file at the given @a _path exists.
 	bool file_exists(const std::string& _path);
 	
+	///@brief Checks whether a directory at the given @a _path exists.
+	bool directory_exists(const std::string& _path);
+	
 	///@brief Checks whether a file at the given @a _path is empty.
 	bool file_is_empty(const std::string& _path);
 	
 	///@brief Reads the complete content of the file at the given @a _path into a string.
 	std::string read_file(const std::string& _path);
 	
+	///@brief Reads all lines of the file at the given @a _path into a vector of strings.
+	std::vector<std::string> read_file_lines(const std::string& _path);
+	
 	
 	/// @brief Resolves 'folder/..' occurences in pathnames.
 	std::string /*XERUS_warn_unused*/ normalize_pathname(const std::string& _name);

include/xerus/misc/math.h

@@ -37,6 +37,12 @@ namespace xerus {
 			return (T(0) < _value) - (_value < T(0));
 		}
 		
+		///@brief: Calculates the absolute value of _value.
+		template<class T> 
+		constexpr T abs(const T _value) noexcept {
+			return (_value < 0 ) ? -_value : _value;
+		}
+		
 		
 		///@brief: Calculates _a*_a.
 		template<class T>

include/xerus/misc/namedLogger.h

@@ -57,14 +57,14 @@ namespace xerus {
 			
 			// If the LOG_BUFFER is active there is the additional option only to print the log if an error occurs.
 			#ifdef XERUS_LOG_BUFFER
-				enum {
+				enum LogLvl {
 					NOT_LOGGING = 0,
 					LOGGING_ON_ERROR = 1,
 					LOGGING_FULL = 2,
 					LOGGING_EXCEPTION = 3
 				};
 			#else
-				enum {
+				enum LogLvl {
 					NOT_LOGGING = 0,