Merge branch 'beta' (to become release 0.9.5)

Author: Erik Nielsen

.gitignore

@@ -41,6 +41,14 @@ test/test_packages/cmp_chk_files/Fake_Dataset_none.txt.cache
 *.aux
 *.dvi
 *.toc
+build/*
+dist/*
+packages/pygsti.egg-info
+packages/pygsti/baseobjs/parsetab_string.py
+packages/pygsti/objects/fastgatecalc.cpp
+packages/pygsti/objects/fastreplib.cpp
+packages/pygsti/tools/fastcalc.c
+
 
 # Packages #
 ############
@@ -88,6 +96,11 @@ scripts/profiling/report/tp_report.py
 scripts/profiling/report/rigetti_nocache.py
 
 # Profiling data #
+#################
 scripts/profiling/output
 scripts/profiling/data
 
+# Other Local-only Files #
+############################
+local
+

.travis.yml

@@ -23,17 +23,15 @@ env:
 before_install:
   - sudo apt-get -qq update
   - sudo apt-get -qq install gfortran libblas-dev liblapack-dev
-  - sudo apt-get -qq install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3 libopenmpi-dbg libopenmpi-dev >/dev/null
-  - sudo bash CI/install.sh # Only install texlive and extensions if we need them
+  - sudo apt-get -qq install openmpi-bin openmpi-common openssh-client openssh-server libopenmpi1.3 libopenmpi-dbg libopenmpi-dev > /dev/null
+  - travis_wait 30 "sudo bash CI/install.sh > /dev/null 2>&1"
   - "export DISPLAY=:99.0"
   - "sh -e /etc/init.d/xvfb start" #some tests require a display
   - sleep 3 # give xvfb some time to start
 
 install:
-  - travis_retry travis_wait pip install -r requirements.txt
-  - pip install --global-option=build_ext --global-option="-I/usr/include/suitesparse" cvxpy cvxopt >/dev/null
-  - pip install ipython mpi4py zmq coverage msgpack-python cython psutil >/dev/null
-  - pip install -e . >/dev/null
+  - pip install zmq coverage >/dev/null
+  - pip install -e .[travisci]
 
 cache:
   pip: true
@@ -42,8 +40,10 @@ cache:
 #Script For default "test" stage
 script:
   - cd test
-  - travis_wait 50 python travisTests.py # Tests may take some time!
-  - cd ..
+  - python travisTests.py # just produce test_packages/runTravisTests.sh
+  - cd test_packages
+  - source runTravisTests.sh # no need for travis_wait (always outputs every 9m)
+  - cd ../..
 
 jobs:
   include:

CI/install.sh

@@ -1,5 +1,6 @@
 #!/bin/bash
 # This script needs to be run as admin
+sudo apt-get update  > /dev/null 2>&1
 
 ##An example of how to search for a file in apt packages
 ## (useful for debugging TravisCI build errors)
@@ -16,49 +17,39 @@
 # lapack as this requested library, which allow the build to
 # proceed since it apparently doesn't actually require anything
 # in the non-existent library...
-apt-get install libsuitesparse-dev
-cp /usr/lib/liblapack.so /usr/lib/libsuitesparseconfig.so
+apt-get install libsuitesparse-dev  > /dev/null 2>&1
+cp /usr/lib/liblapack.so /usr/lib/libsuitesparseconfig.so  > /dev/null 2>&1
 
+sudo add-apt-repository ppa:ubuntu-toolchain-r/test  > /dev/null 2>&1
+sudo apt-get update  > /dev/null 2>&1
 
-#Latex is no longer needed!
-#echo "Checking if pdflatex install is needed"
-#
-#if [ "$ReportA" == "True" ]; then
-#    apt-get -qq install texlive-full
-#fi
-#
-#if [ "$Drivers" == "True" ]; then
-#    apt-get -qq install texlive-latex-base
-#fi
-#
-#if [ "$ReportA" == "True" ] || [ "$Drivers" == "True" ]; then
-#    echo "Installing pdflatex requirements"
-#    pushd /usr/share/texmf-texlive/
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/etoolbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/adjustbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/collectbox.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/pdfcomment.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/datetime2.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/generic/tracklang.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/bezos.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/hyperref.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/oberdiek.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/generic/ifxetex.tds.zip
-#    wget http://mirrors.ctan.org/install/macros/latex/contrib/standalone.tds.zip
-#    unzip -o etoolbox.tds.zip 
-#    unzip -o adjustbox.tds.zip 
-#    unzip -o collectbox.tds.zip 
-#    unzip -o pdfcomment.tds.zip 
-#    unzip -o datetime2.tds.zip 
-#    unzip -o tracklang.tds.zip 
-#    unzip -o bezos.tds.zip 
-#    unzip -o hyperref.tds.zip 
-#    unzip -o oberdiek.tds.zip 
-#    unzip -o ifxetex.tds.zip 
-#    unzip -o standalone.tds.zip 
-#    texhash  
-#    popd
-#else
-#    echo "pdflatex is not required for these tests (ReportA is not set to \"True\")"
-#fi
+sudo update-alternatives --remove-all gcc  > /dev/null 2>&1
+sudo update-alternatives --remove-all g++  > /dev/null 2>&1
+sudo apt-get install gcc-4.8  > /dev/null 2>&1
+sudo apt-get install g++-4.8  > /dev/null 2>&1
+sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.8 20  > /dev/null 2>&1
+sudo update-alternatives --install /usr/bin/g++ g++ /usr/bin/g++-4.8 20  > /dev/null 2>&1
+sudo update-alternatives --config gcc  > /dev/null 2>&1
+sudo update-alternatives --config g++  > /dev/null 2>&1
+sudo apt-get update  > /dev/null 2>&1
+sudo apt-get upgrade -y  > /dev/null 2>&1
+sudo apt-get dist-upgrade  > /dev/null 2>&1
 
+export CXX=g++  > /dev/null 2>&1
+
+sudo apt remove cmake  > /dev/null 2>&1
+
+# Install the following version of CMAKE
+version=3.11  > /dev/null 2>&1
+build=1  > /dev/null 2>&1
+mkdir ~/temp  > /dev/null 2>&1
+cd ~/temp  > /dev/null 2>&1
+wget https://cmake.org/files/v$version/cmake-$version.$build.tar.gz  > /dev/null 2>&1
+tar -xzvf cmake-$version.$build.tar.gz  > /dev/null 2>&1
+cd cmake-$version.$build/  > /dev/null 2>&1
+./bootstrap  > /dev/null 2>&1
+make -j4  > /dev/null 2>&1
+sudo make install  > /dev/null 2>&1
+cd ..  > /dev/null 2>&1
+rm -r temp  > /dev/null 2>&1
+cmake --version

MANIFEST.in

@@ -1,5 +1,7 @@
 include README COPYING license.txt
-include install_locally.py 
+include install_locally.py
+include requirements.txt
+include optional-requirements.txt
 include jupyter_notebooks/Tutorials/*.ipynb
 include jupyter_notebooks/Examples/*.ipynb
 include jupyter_notebooks/FAQ.ipynb

doc/build/requirements.txt

@@ -0,0 +1,3 @@
+sphinx
+numpydoc
+sphinx_rtd_theme