Merge branch 'beta' into 'master' to become PyGSTi version 0.9.4

.gitignore

@@ -6,18 +6,28 @@
 *.out
 *.coverage*
 *.serial
+*.cache
 .ipynb_checkpoints
 test/test_packages/temp_test_files/*
 jupyter_notebooks/Tutorials/tutorial_files
+jupyter_notebooks/Tutorials/offline
+jupyter_notebooks/Examples/example_files
+test/test_packages/offline
 hooks/etc/permissions.yml
 *comm_output*.txt
+**offline/
+**tutorial_files
+*.lprof
+*.cache
 
 # Test Metadata #
 #################
 test/output/*
 test/output/pylint/*
 test/output/individual_coverage/*/*
-test/test_packages/.noseids # Used in running failed tests
+test/test_packages/.noseids
+test/test_packages/cmp_chk_files/Fake_Dataset_none.txt.cache
+**tutorial_files
 
 # Compiled source #
 ###################
@@ -66,3 +76,18 @@ HighImpactPaper1/texFiles/.DS_Store
 doc/html/*
 doc/build/*.rst
 doc/build/_build/*
+
+# Customer Data #
+#################
+scripts/profiling/report/*.ipynb
+scripts/profiling/report/Analyze+2Q+data.py
+scripts/profiling/report/*.html
+scripts/profiling/*.html
+scripts/profiling/report/standard_report.py
+scripts/profiling/report/tp_report.py
+scripts/profiling/report/rigetti_nocache.py
+
+# Profiling data #
+scripts/profiling/output
+scripts/profiling/data
+

.travis.yml

@@ -1,3 +1,4 @@
+dist: precise
 language: python
 
 python:
@@ -11,15 +12,17 @@ branches:
     - develop
 
 env:
-    - Drivers=True  # All of drivers (Tends to take longer, put it first in the mx)
-    - Default=True  # construction, io, objects, tools, optimize, algorithms
-    - ReportA=True  # Only testReport.py (none of the other reports tests)
-    - ReportB=True  # test the other reports tests
-    - MPI=True  # All of MPI
-
+    - Drivers=True    # First in build mx because long duration
+    - Algorithms=True 
+    - AlgorithmsB=True
+    - Default=True    # construction, io, objects, tools, optimize
+    - Report=True      
+    - ReportB=True
+    - MPI=True        
+
 before_install:
   - sudo apt-get -qq update
-  - sudo apt-get -qq install gfortran libblas-dev liblapack-dev >/dev/null
+  - 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
   - "export DISPLAY=:99.0"
@@ -29,36 +32,28 @@ before_install:
 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 python-pptx mpi4py zmq coverage >/dev/null
+  - pip install ipython mpi4py zmq coverage msgpack-python cython psutil >/dev/null
   - pip install -e . >/dev/null
 
 cache:
   pip: true
   timeout: 1000
 
+#Script For default "test" stage
 script:
   - cd test
   - travis_wait 50 python travisTests.py # Tests may take some time!
   - cd ..
 
-after_script:
-    - |
-        declare exitCode
-        
-        curl -sSL https://raw.githubusercontent.com/alrra/travis-after-all/1.4.4/lib/travis-after-all.js | node
-        exitCode=$?
-
-        if [ $exitCode -eq 0 ]; then
-            python CI/deploy
-        fi
-
-        if [ $exitCode -eq 1 ]; then
-            echo "Build failed - not deploying!!!!!!"
-        fi
+jobs:
+  include:
+    - stage: deploy
+      python: 3.5
+      env: Drivers=False Algorithms=False AlgorithmsB=False Default=False Report=False ReportB=False MPI=False
+      script: python CI/deploy
 
 notifications:
     email:
         on_success: change
         on_failure: always
 
-

CI/deploy

@@ -98,35 +98,39 @@ if TRAVIS_BRANCH == "develop" and TRAVIS_PULL_REQUEST == "false":
                                       branchname]) # View merge tree between beta and (our) develop
     output = output.decode('utf-8', 'ignore')
     print('Done:')
-    # print(output)
+    #print(output)
 
     canMerge = ('<' * 5) not in output # '<' * 5 avoids git finding the expanded string in this file and thinking it is a merge conflict
 
     if canMerge:
         print('Merge of develop into beta is possible')
         # The below code is active, but only for testing
-        subprocess.call(['git', 'merge', '--no-ff', '--no-commit', 'develop']) #into beta
-        print('Merge command finished.')
-        print('Staging files..')
-        subprocess.call(['git', 'add', '-u'])
-        print('Committing..')
-        subprocess.call(['git', 'commit', '--no-verify', '-m', 
-                         'Auto-merged develop -> beta (No conflicts, CI passed)'])
-        print('Commit finished')
-
-        PUSHKEY  = os.environ['PUSHKEY']
-        push_uri = 'https://%s:%s@github.com/pyGSTio/pyGSTi.git' % (USER, PUSHKEY) # yikes
-        try:
-            print('Pushing to origin/beta. If this fails, there shouldn\'t be any useful output, since it would contain my access token')
-            with open(os.devnull, 'w') as FNULL:
-                result = subprocess.call(['git', 'push', '--no-verify', push_uri, 'beta'], stdout=FNULL, stderr=FNULL)
-                if result != 0:
-                    print('Secure push failed')
-                else:
-                    print('Secure push worked')
-        except:
-            print('Secure push failed')
-
+        merge_output = subprocess.check_output(['git', 'merge', '--no-ff', '--no-commit', 'develop']) #into beta
+        merge_output = merge_output.decode('utf-8', 'ignore')
+        if ("Automatic merge failed" in merge_output) or ("CONFLICT" in merge_output):
+            print('Merge command failed to automatically merge.  Exiting without committing!')
+        else:
+            print('Merge command automatically merged successfully.')
+
+            print('Staging files..')
+            subprocess.call(['git', 'add', '-u'])
+            print('Committing..')
+            subprocess.call(['git', 'commit', '--no-verify', '-m', 
+                             'Auto-merged develop -> beta (No conflicts, CI passed)'])
+            print('Commit finished')
+
+            PUSHKEY  = os.environ['PUSHKEY']
+            push_uri = 'https://%s:%s@github.com/pyGSTio/pyGSTi.git' % (USER, PUSHKEY) # yikes
+            try:
+                print('Pushing to origin/beta. If this fails, there shouldn\'t be any useful output, since it would contain my access token')
+                with open(os.devnull, 'w') as FNULL:
+                    result = subprocess.call(['git', 'push', '--no-verify', push_uri, 'beta'], stdout=FNULL, stderr=FNULL)
+                    if result != 0:
+                        print('Secure push failed')
+                    else:
+                        print('Secure push worked')
+            except:
+                print('Secure push failed')    
     else:
         print('Potential merge conflicts found! Cannot merge beta into develop')
 

CI/install.sh

@@ -20,44 +20,45 @@ apt-get install libsuitesparse-dev
 cp /usr/lib/liblapack.so /usr/lib/libsuitesparseconfig.so
 
 
-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
+#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
 

README.md

@@ -11,18 +11,46 @@ This is the root directory of the pyGSTi software, which is a Python
  under the GNU General Public License (GPL).  Copyright and license information
  can be found in ``license.txt``, and the GPL itself in ``COPYING``.
 
+Gate Set Tomography is used to characterize the operations performed by
+hardware designed to implement a (small) system of quantum bits (qubits).
+Here's the basic idea:
+
+  1. you tell pyGSTi what quantum operations you'd like to perform
+  2. pyGSTi tells you what sequences of operations it want's data for
+  3. you perform the requested experiments and place the resulting
+     data (outcome counts) into a text file that looks something like:
+
+     ```
+     ## Columns = 0 count, 1 count
+     {} 0 100
+     Gx 10 90
+     GxGy 40 60
+     Gx^4 20 80
+     ```
+
+  4. pyGSTi takes the data file and outputs a "report" - currently a
+     HTML web page.
+
+There are numerous [Tutorial](https://github.com/pyGSTio/pyGSTi/tree/beta/jupyter_notebooks/Tutorials)
+and [Example](https://github.com/pyGSTio/pyGSTi/tree/beta/jupyter_notebooks/Examples)
+ipython notebooks (especially
+[Tutorial 0](https://github.com/pyGSTio/pyGSTi/blob/beta/jupyter_notebooks/Tutorials/00%20Getting%20Started.ipynb)
+) included in this repository that demonstrate pyGSTi's
+syntax and use, as well as a [FAQ](https://github.com/pyGSTio/pyGSTi/blob/beta/jupyter_notebooks/FAQ.ipynb).
+
 
 Getting Started:
 ---------------
-pyGSTi is written entirely in Python, and so there's no compiling necessary.
-The first step is to install Python (and
-[Jupyter notebook](http://jupyter.org/) is highly recommended) if you haven't
-already.  In order to use pyGSTi you need to tell your Python distribution
-where pyGSTi lives, which can be done in one of two ways:
+pyGSTi is written almost entirely in Python.  Apart from a single optional
+Cython module, there's no compiling necessary. The first step is to install
+Python (and [Jupyter notebook](http://jupyter.org/) is highly recommended)
+if you haven't already.  In order to use pyGSTi you need to tell your Python
+distribution where pyGSTi lives, which can be done in one of several ways:
 
 * User-Only Installation
 
-     To install pyGSTi for the current user, run ``python install_locally.py``
+    To install pyGSTi for the current user, you can run from the top-level
+    directory either ``pip install -e .`` or ``python install_locally.py``.
 
     This adds the current pyGSTi path to Python's list of search paths, and
     doesn't require administrative access.  Typically you want to do this if
@@ -31,6 +59,8 @@ where pyGSTi lives, which can be done in one of two ways:
     You'd also want to use this option if you'd like long-term access the
     tutorial notebook files in the ``jupyter_notebooks`` directory under this
     one, since this means you'll be keeping this directory around anyway.
+    The ``pip install -e .`` is slightly preferable since it will automatically
+    build the optional Cython extension.
 
 * System-Wide Installation
 
@@ -53,7 +83,7 @@ where pyGSTi lives, which can be done in one of two ways:
     to be the one Python uses when you ``import pygsti``.
 
 Using pyGSTi
-----------
+------------
 
 After you've installed pyGSTi, you should be able to import the 
 `pygsti` Python package.  The next thing to do is take a look at
@@ -66,13 +96,17 @@ the tutorials, which you do by:
   ``jupyter notebook``
 
 The Jupyter server should open up your web browser to the server root, from
-where you can start the first "00" tutorial notebook.  (Note that the key
+where you can start the first "0th" tutorial notebook.  (Note that the key
 command to execute a cell within the Jupyter notebook is ``Shift+Enter``, not
-just ``Enter``.)
+just ``Enter``.)  Example notebooks, found in the ``jupyter_notebooks/Examples/``
+directory, are focused on more specific tasks than the tutorials, and will be
+most useful for those looking to get a quick start using pyGSTi in a typical
+scenario.
 
 Congratulations!  You're up and running with pyGSTi!
 
 
+
 Documentation
 -------------
 Online documentation is hosted on [Read the Docs](http://pygsti.readthedocs.io).

doc/build/_templates/my_autosummary_class.rst

@@ -10,10 +10,9 @@
        :noindex:
 
    {% if methods %}
-   .. rubric:: Methods
-
    .. autosummary::
       :toctree:
+      :hidden:
    {% for item in methods %}
       ~{{ name }}.{{ item }}
    {%- endfor %}
@@ -22,12 +21,12 @@
 
    {% block attributes %}
    {% if attributes %}
-   .. rubric:: Attributes
-
    .. autosummary::
       :toctree:
+      :hidden:
    {% for item in attributes %}
       ~{{ name }}.{{ item }}
    {%- endfor %}
    {% endif %}
    {% endblock %}
+