Merge branch 'pybind11' into development

.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
+*.so
+lapacke
+build
+doc/html
+doc/findDoxytag
+doc/parseDoxytags
+doc/xerus.tagfile
+doc/xerus.tags
 config.mk
+XerusTest

.gitlab-ci-configs/.config.mk.ci.cc

@@ -6,11 +6,10 @@ COMPATIBILITY = -std=c++14
 
 DEBUG_OPTIMIZATION = TRUE
 
-ACTIVATE_CODE_COVERAGE = TRUE                 # Enable coverage tests
-BROCKEN_CI = TRUE			# Enable workaround for brocken CI runner
-DEBUG += -D _GLIBCXX_ASSERTIONS        # Activate GLIBCXX assertions
-
-DEBUG += -g                # Adds debug symbols
+ACTIVATE_CODE_COVERAGE = TRUE       # Enable coverage tests
+BROCKEN_CI = TRUE                   # Enable workaround for brocken CI runner
+DEBUG += -D _GLIBCXX_ASSERTIONS     # Activate GLIBCXX assertions
+DEBUG += -g                         # Adds debug symbols
 
 #=================================================================================================
 # External libraries

.gitlab-ci-configs/.config.mk.ci.clang

 #=================================================================================================
 # Compiler Options
 #=================================================================================================
-CXX = clang++-3.9
+CXX = clang++
 COMPATIBILITY = -std=c++11
 
- DEBUG += -g                # Adds debug symbols
+DEBUG += -D XERUS_DISABLE_RUNTIME_CHECKS  # Disable all runtime checks
 
-LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour but might 
+DEBUG += -g                               # Adds debug symbols
+LOGGING += -D XERUS_LOG_INFO
 
 #=================================================================================================
 # External libraries
 #=================================================================================================
-STRICT_WARNINGS = TRUE
-
-# Uncomment or add the appropriate blas libraries 
-BLAS_LIBRARIES = -lopenblas -lgfortran                    # Openblas, serial
-
-# Uncomment or add the appropriate lapack libraries 
-LAPACK_LIBRARIES = -llapacke -llapack                     # Standard Lapack + Lapacke libraries
-
-# Uncomment or add the appropriate CXSparse library
+BLAS_LIBRARIES = -lopenblas -lgfortran    # Openblas, serial
+LAPACK_LIBRARIES = -llapacke -llapack     # Standard Lapack + Lapacke libraries
 SUITESPARSE = -lcholmod -lspqr
 BOOST_LIBS = -lboost_filesystem
-
-
-# custom include paths
-# OTHER += -I /path/to/include
-

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

@@ -6,19 +6,15 @@ COMPATIBILITY = -std=c++11
 
 STRICT_WARNINGS = TRUE
 
-DEBUG += -D XERUS_DISABLE_RUNTIME_CHECKS    # Disable all runtime checks
-DEBUG += -D XERUS_REPLACE_ALLOCATOR
+DEBUG += -D XERUS_DISABLE_RUNTIME_CHECKS  # Disable all runtime checks
 
-DEBUG += -g                # Adds debug symbols
-
-LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour bu
+DEBUG += -g                               # Adds debug symbols
+LOGGING += -D XERUS_LOG_INFO
 
 #=================================================================================================
 # External libraries
 #=================================================================================================
-BLAS_LIBRARIES = -lopenblas -lgfortran                    # Openblas, serial
-LAPACK_LIBRARIES = -llapacke -llapack                     # Standard Lapack + Lapacke libraries
+BLAS_LIBRARIES = -lopenblas -lgfortran    # Openblas, serial
+LAPACK_LIBRARIES = -llapacke -llapack     # Standard Lapack + Lapacke libraries
 SUITESPARSE = -lcholmod -lspqr
 BOOST_LIBS = -lboost_filesystem
-
-

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

@@ -3,15 +3,11 @@
 #=================================================================================================
 CXX = g++
 COMPATIBILITY = -std=c++11
-PYTHON2_CONFIG = `python2-config --cflags --ldflags`
 PYTHON3_CONFIG = `python3-config --cflags --ldflags`
-PYTEST2 = pytest
-PYTEST3 = pytest-3
+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
+LOGGING += -D XERUS_LOG_INFO                     # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
 
 #=================================================================================================
 # External libraries
@@ -21,8 +17,8 @@ LAPACK_LIBRARIES = -llapacke -llapack                     # Standard Lapack + La
 SUITESPARSE = -lcholmod  -lspqr
 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
+# 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

 stages:
-- build_homepage
-- build_gcc_nocheck
-- test_gcc_nocheck
-- code_coverage
-- build_python2
-- build_python3
-- test_python2
-- test_python3
-- build_clang
-- test_clang
+  - build_homepage
+  - build_gcc_nocheck
+  - test_gcc_nocheck
+  - build_clang
+  - test_clang
+  - code_coverage
+  - build_python
+  - test_python
 
 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
 
-job_make_gcc_nocheck:
+job_build_gcc_nocheck:
   stage: build_gcc_nocheck
-  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.nocheck config.mk; make XerusTest"
+  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.nocheck config.mk; make XerusTest_static"
+  when: always
   artifacts:
     expire_in: 1h30min
     paths:
-      - XerusTest
+      - XerusTest_static
 
 job_test_gcc_nocheck:
   stage: test_gcc_nocheck
-  script: "echo $CI_COMMIT_SHA; ./XerusTest all"
+  script: "echo $CI_COMMIT_SHA; ./XerusTest_static all"
+  when: on_success
   dependencies:
-    - job_make_gcc_nocheck
+    - job_build_gcc_nocheck
 
+job_build_clang:
+  stage: build_clang
+  script: "clang++ --version; cp .gitlab-ci-configs/.config.mk.ci.clang config.mk; make XerusTest_static"
+  when: always
+  artifacts:
+    expire_in: 1h30min
+    paths:
+      - XerusTest_static
+
+job_test_clang:
+  stage: test_clang
+  script: "echo $CI_COMMIT_SHA; ./XerusTest_static all"
+  when: on_success
+  dependencies:
+    - job_build_clang
 
 job_code_coverage:
   stage: code_coverage
-  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.cc config.mk; mkdir -p build; make test &> build/build_output.txt || { tail -n 500 build/build_output.txt && readelf -S XerusTest && objdump -s -j .cc_loc XerusTest && false; }; tail -n 500 build/build_output.txt"
-  when: always
+  script: "clang++ --version; cp .gitlab-ci-configs/.config.mk.ci.cc config.mk; mkdir -p build; make test &> build/build_output.txt || { tail -n 500 build/build_output.txt && readelf -S XerusTest_static && objdump -s -j .cc_loc XerusTest_static && false; }; tail -n 500 build/build_output.txt"
+  when: on_success
   artifacts:
     expire_in: 3h
     paths:
       - build/build_output.txt
 
-job_build_python2:
-  stage: build_python2
-  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make python2"
-  when: always
-
-job_build_python3:
-  stage: build_python3
-  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make python3"
-  when: always
-
-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_make_clang:
-  stage: build_clang
-  script: "clang++ --version; cp .gitlab-ci-configs/.config.mk.ci.clang config.mk; make XerusTest"
+job_build_python:
+  stage: build_python
+  script: "g++ --version; cp .gitlab-ci-configs/.config.mk.ci.gcc.python config.mk; make python"
   when: always
+  variables:
+    GIT_SUBMODULE_STRATEGY: normal
   artifacts:
     expire_in: 1h30min
     paths:
-      - XerusTest
+      - xerus
 
-job_test_clang:
-  stage: test_clang
-  script: "echo $CI_COMMIT_SHA; ./XerusTest all"
+job_test_python:
+  stage: test_python
+  script: 'python3 -c "import xerus; assert xerus.__version__ == \"$(cat VERSION)\""'
+  when: on_success
   dependencies:
-    - job_make_clang
-
+    - job_build_python

.gitmodules

+[submodule "src/pybind11"]
+	path = 3rdParty/pybind11
+	url = https://github.com/pybind/pybind11.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

README.md

@@ -28,10 +28,14 @@ Test whether everything works correctly with
 
 build (and optionally install) the library with
 > make all -j4
-
 > sudo make install
 
-and you should be ready to use the library. For more details see <a href="https://www.libxerus.org/building_xerus/">the "Building Xerus" page in the documentation</a>.
+and you should be ready to use the library.
+To install the python bindings run
+> make python3
+> pip install .
+
+For more details see <a href="https://www.libxerus.org/building_xerus/">the "Building Xerus" page in the documentation</a>.
 
 
 # Issues #

VERSION

-3.0.1
+4.0.1

conda/VERSION

+4.0.1

conda/build.sh

+#!/bin/bash
+
+set -x -e
+
+cd xerus
+
+cat <<EOF >config.mk
+CXX = ${CXX}
+COMPATIBILITY = -std=c++17
+COMPILE_THREADS = 8                       # Number of threads to use during link time optimization.
+HIGH_OPTIMIZATION = TRUE                  # Activates -O3 -march=native and some others
+OTHER += -fopenmp
+
+PYTHON3_CONFIG = \`python3-config --cflags --ldflags\`
+
+LOGGING += -D XERUS_LOG_INFO              # Information that is not linked to any unexpected behaviour but might nevertheless be of interest.
+LOGGING += -D XERUS_LOGFILE               # Use 'error.log' file instead of cerr
+LOGGING += -D XERUS_LOG_ABSOLUTE_TIME     # Print absolute times instead of relative to program time
+XERUS_NO_FANCY_CALLSTACK = TRUE           # Show simple callstacks only
+
+BLAS_LIBRARIES = -lopenblas -lgfortran    # Openblas, serial
+LAPACK_LIBRARIES = -llapacke -llapack     # Standard Lapack + Lapacke libraries
+SUITESPARSE = -lcholmod -lspqr
+BOOST_LIBS = -lboost_filesystem
+
+OTHER += -I${PREFIX}/include -I${PREFIX}/lib/python${PY_VER}/site-packages/numpy/core/include/
+OTHER += -L${PREFIX}/lib
+EOF
+
+ln -s ${PREFIX}/include/ ${PREFIX}/include/suitesparse
+make python
+${PYTHON} -m pip install . --no-deps -vv
+
+# INCLUDE_PATH="${PREFIX}/include"
+# mkdir -p ${INCLUDE_PATH}
+# cp include/xerus.h ${INCLUDE_PATH}
+# cp -r include/xerus ${INCLUDE_PATH}
+
+# LIBRARY_PATH="${PREFIX}/lib"
+# mkdir -p ${LIBRARY_PATH}
+# cp build/libxerus.so ${LIBRARY_PATH}
+# cp build/libxerus_misc.so ${LIBRARY_PATH}
+
+rm config.mk

conda/meta.yaml

+{% set name = "Xerus" %}
+{% set version = "4.0.1" %}
+{% set branch = "v4.0.1_conda" %}
+
+package:
+  name: {{ name|lower }}
+  version: {{ version }}
+
+source:
+  - git_url: https://github.com/libxerus/xerus.git
+    git_tag: {{ branch }}
+    folder: xerus
+
+build:
+  number: 1
+  skip: true       # [py<34 or win]
+
+requirements:
+  build:
+    - {{ compiler('cxx') }}
+    - make
+    - pip >=18.1
+  host:
+    - python
+    - numpy
+    - openblas
+    - suitesparse
+    - lapack
+    - boost-cpp >=1.69.0  # boost-cpp: boost without python
+    - llvm-openmp  # [osx]
+    - libgomp      # [linux]
+    #- gdb           # bfd
+    #- backward-cpp  # option for better python-like backtraces
+  run:
+    - {{ pin_compatible('python', max_pin='x.x') }}
+    - {{ pin_compatible('numpy') }}
+    - {{ pin_compatible('openblas', max_pin='x.x') }}
+    - {{ pin_compatible('suitesparse', max_pin='x.x') }}
+    - {{ pin_compatible('lapack') }}
+    - {{ pin_compatible('boost-cpp', max_pin='x.x.x') }}
+    - {{ pin_compatible('llvm-openmp') }}  # [osx]
+    - {{ pin_compatible('libgomp') }}      # [linux]
+
+test:
+  files:
+    - VERSION
+  source_files:
+    - xerus/src/pyTests
+
+about:
+  home: https://git.hemio.de/xerus/xerus.git
+  license: "AGPL 3.0"
+  license_file: LICENSE
+  summary: "A c++ library for numerical calculations with higher order tensors"
+  description: |
+    The Xerus library is a general purpose library for numerical calculations with higher order tensors, Tensor-Train Decompositions / Matrix Product States and other Tensor Networks.
+    The focus of development was the simple usability and adaptibility to any setting that requires higher order tensors or decompositions thereof.
+  doc_url: https://www.libxerus.org/
+  dev_url: https://git.hemio.de/xerus/xerus
+
+extra:
+  recipe-maintainers:
+    - trunschk

conda/run_test.sh

+#!/bin/bash
+
+set -e
+
+VERSION=$(cat VERSION)
+
+export PYTHONPATH=''
+
+${PYTHON} <<EOF
+print("="*80)
+print("\trun_test.sh for Xerus ${VERSION}")
+print("="*80)
+import xerus
+assert xerus.__version__ == '${VERSION}', xerus.__version__+" != ${VERSION}"
+EOF
+
+exit 0

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

@@ -3,22 +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 development && \
-	cp ./docker/xerus/config.mk . && \
+RUN git checkout vmc && \
+	git pull && \
+	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/applications/uqAdf.h

@@ -50,7 +50,17 @@ namespace xerus { namespace uq {
 	 */
     TTTensor uq_ra_adf(const std::vector<std::vector<Tensor>>& _positions, const std::vector<Tensor>& _solutions, const std::vector<size_t>& _dimensions, const double _targetEps = 1e-8, const size_t _maxItr = 0);
 
-	
+	/**
+	 * @brief Rank adaptive ADF to calculate the UQ solution for given measurements.
+	 * @param _x Initial value.
+	 * @param _positions The positions of the measurements.
+	 * @param _solutions The measured solutions corresponding to the @a _positions.
+	 * @param _dimensions The dimensions of the final solution tensor.
+	 * @param _targetEps TODO describe effect
+	 * @param _maxItr Maximal number of iterations to perform.
+	 */
+    TTTensor uq_ra_adf(const TTTensor& _x, const std::vector<std::vector<Tensor>>& _positions, const std::vector<Tensor>& _solutions, const std::vector<size_t>& _dimensions, const double _targetEps = 1e-8, const size_t _maxItr = 0);
+
 	/**
 	 * @brief Rank adaptive ADF to calculate the UQ solution for given weighted measurements.
 	 * @param _positions The positions of the measurements.
@@ -63,6 +73,5 @@ namespace xerus { namespace uq {
     TTTensor uq_ra_adf(const std::vector<std::vector<Tensor>>& _positions, const std::vector<Tensor>& _solutions, const std::vector<double>& _weights, const std::vector<size_t>& _dimensions, const double _targetEps = 1e-8, const size_t _maxItr = 0);
 
 	
-	// TODO How is this different to the inplace variant? Also very confusing that it changes _x inplace AND returns it.
-    TTTensor uq_ra_adf_iv(TTTensor& _x, const UQMeasurementSet& _measurements, const PolynomBasis _basisType, const double _targetEps = 1e-8, const size_t _maxItr = 0);
+    TTTensor uq_ra_adf(const TTTensor& _x, const UQMeasurementSet& _measurements, const PolynomBasis _basisType, const double _targetEps = 1e-8, const size_t _maxItr = 0);
 }}

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/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/tensorNetwork.h

@@ -529,11 +529,11 @@ namespace xerus {
         void draw(const std::string& _filename) const;
     };
 
-    TensorNetwork operator*(TensorNetwork &_lhs, value_t _factor);