Merge pull request #511 from manoelmarques/stable-0.5.0

Stable 0.5.0

Author: manoelmarques

.github/CONTRIBUTING.rst

@@ -166,17 +166,46 @@ you need to have some libraries, which can be installed in this way:
     pip install -r requirements.txt
     pip install -r requirements-dev.txt
 
-To install Qiskit Aqua locally, execute the following command from the `qiskit-aqua` root
-directory on your machine:
+To better contribute to Qiskit Aqua, we recommend that you clone the Qiskit Aqua repository
+and then install Qiskit Aqua from source.  This will give you the ability to inspect and extend
+the latest version of the Aqua code more efficiently.  The version of Qiskit Aqua in the repository's ``master``
+branch is typically ahead of the version in the Python Package Index (PyPI) repository, and
+we strive to always keep Aqua in sync with the development versions of the Qiskit elements,
+each available in the ``master`` branch of the corresponding repository.  Therefore,
+all the Qiskit elements and relevant components should be installed from source.  This can be
+correctly achieved by first uninstalling them from the Python environment in which you
+have Qiskit (if they were previously installed),
+using the ``pip uninstall`` command for each of them.  Next, clone the
+`Qiskit Terra <https://github.com/Qiskit/qiskit-terra>`__, `Qiskit Aer <https://github.com/Qiskit/qiskit-aer>`__,
+`Qiskit IBMQ Provider <https://github.com/Qiskit/qiskit-ibmq-provider>`__,
+`Qiskit Ignis <https://github.com/Qiskit/qiskit-ignis>`__ and
+`Qiskit Aqua <https://github.com/Qiskit/qiskit-aqua>`__ repositories and
+install them in this order from source in the same Python environment.
+Qiskit Terra, Qiskit IBMQ Provider and Qiskit Aqua can be installed by issuing the following commands 
+in the root directories of the repositoriy clones:
 
 .. code:: sh
 
+    $ pip install -r requirements.txt
+    $ pip install -r requirements-dev.txt
     $ pip install -e .
 
-Installing Aqua will automatically install `Terra <https://github.com/Qiskit/qiskit-terra>`__
-as one of its dependencies.  We recommend that you also set up
-`Aer <https://github.com/Qiskit/qiskit-aer>`__ to get more advanced simulators.
-Refer to the installation instructions of both Terra and Aer for more details.
+To install Qiskit Aer use:
+
+.. code:: sh
+
+    $ pip install -r requirements-dev.txt
+    $ python3 setup.py bdist_wheel
+    $ cd dist
+    $ pip install qiskit_aer-<...>.whl
+
+See the 
+`contribution guidelines of Qiskit Aer <https://github.com/Qiskit/qiskit-aer/blob/master/.github/CONTRIBUTING.md>`__
+for more precise instructions.
+
+Make sure to respect the order specified above: Qiskit Terra, Qiskit Aer, Qiskit IBMQ Provider, and Qiskit Aqua.
+All the other dependencies will be installed automatically.  This process may have to be repeated often
+as the ``master`` branch of Aqua is updated frequently.
 
 Style guide
 ~~~~~~~~~~~
@@ -197,22 +226,20 @@ your changes respect the style guidelines, run the next commands (all platforms)
 Documentation
 -------------
 
-The documentation for the project is in the ``doc`` directory. The
-documentation for the python SDK is auto-generated from python
-docstrings using `Sphinx <http://www.sphinx-doc.org>`_ for generating the
-documentation. Please follow `Google's Python Style
+The documentation source code for the project is located in the ``docs`` directory of the general
+`Qiskit repository <https://github.com/Qiskit/qiskit>`__ and automatically rendered on the
+`Qiskit documentation Web site <https://qiskit.org/documentation/>`__. The
+documentation for the Python SDK is auto-generated from Python
+docstrings using `Sphinx <http://www.sphinx-doc.org>`_. Please follow `Google's Python Style
 Guide <https://google.github.io/styleguide/pyguide.html?showone=Comments#Comments>`_
 for docstrings. A good example of the style can also be found with
-`sphinx's napolean converter
+`Sphinx's napolean converter
 documentation <http://sphinxcontrib-napoleon.readthedocs.io/en/latest/example_google.html>`_.
 
-To generate the documentation, we need to invoke CMake first in order to generate
+To generate the documentation, you need to invoke CMake first in order to generate
 all specific files for our current platform.
 See the `instructions <https://github.com/Qiskit/qiskit-terra/blob/master/.github/CONTRIBUTING.rst#dependencies>`__
 in the Terra repository for details on how to install and run CMake.
-The docunentation can then be built using the instructions available in the
-`docs folder's README file <../docs/README.md>`__.
-
 
 Development Cycle
 -----------------

.gitignore

@@ -92,33 +92,6 @@ instance/
 
 # Sphinx documentation
 docs/_build/
-docs/*.rst
-#Allow
-!docs/qiskit-aqua.rst
-!docs/index.rst
-!docs/aqua.rst
-!docs/library.rst
-!docs/overview.rst
-!docs/installation.rst
-!docs/execution.rst
-!docs/extending.rst
-!docs/algorithms.rst
-!docs/optimizers.rst
-!docs/variational_forms.rst
-!docs/oracles.rst
-!docs/iqfts.rst
-!docs/initial_states.rst
-!docs/feature_extractions.rst
-!docs/aqua_chemistry_*.rst
-!docs/aqua_ai.rst
-!docs/aqua_optimization.rst
-!docs/aqua_tutorials.rst
-!docs/aqua_finance.rst
-!docs/qiskit_aqua_chemistry.rst
-!docs/random_distributions.rst
-!docs/uncertainty_problems.rst
-!docs/multiclass_extensions.rst
-!docs/release_history.rst
 
 # PyBuilder
 target/

.travis.yml

@@ -1,7 +1,14 @@
-# Copyright 2018, IBM.
+# This code is part of Qiskit.
 #
-# This source code is licensed under the Apache License, Version 2.0 found in
-# the LICENSE.txt file in the root directory of this source tree.
+# (C) Copyright IBM 2018, 2019.
+#
+# This code is licensed under the Apache License, Version 2.0. You may
+# obtain a copy of this license in the LICENSE.txt file in the root directory
+# of this source tree or at http://www.apache.org/licenses/LICENSE-2.0.
+#
+# Any modifications or derivative works of this code must retain this
+# copyright notice, and modified files need to carry a notice indicating
+# that they have been altered from the originals.
 
 notifications:
     on_success: change
@@ -29,21 +36,34 @@ stage_dependencies: &stage_dependencies
         - g++-7    
 
   before_install:
+    - |
+      INIT_FILE="$TRAVIS_BUILD_DIR/qiskit/__init__.py"
+      if [ -f $INIT_FILE ]; then
+        # stops travis if __init__.py exists under qiskit
+        echo "File '$INIT_FILE' found. It should not exist, since this repo extends qiskit namespace.";
+        travis_terminate 1;
+      fi
+    - pip install --upgrade pip setuptools wheel
     # download Qiskit Terra master and unzip it only if forced from master or not stable branch, otherwise use the pypi version
     - |
       if [ ${MASTER_BRANCH_DEPENDENCIES} = "true" ] || [ ${TRAVIS_BRANCH} != "stable" ]; then
+        # Download github Terra
         wget https://codeload.github.com/Qiskit/qiskit-terra/zip/master -O /tmp/qiskit-terra.zip
         unzip /tmp/qiskit-terra.zip -d /tmp/
         # Install Qiskit Terra requirements.
-        pip install -U -r /tmp/qiskit-terra-master/requirements.txt
-        pip install -U -r /tmp/qiskit-terra-master/requirements-dev.txt
+        pip install -U -r /tmp/qiskit-terra-master/requirements-dev.txt --progress-bar off
         # Install local Qiskit Terra
-        pip install -e /tmp/qiskit-terra-master
+        pip install -e /tmp/qiskit-terra-master --progress-bar off
+        # Download github Ignis
+        wget https://codeload.github.com/Qiskit/qiskit-ignis/zip/master -O /tmp/qiskit-ignis.zip
+        unzip /tmp/qiskit-ignis.zip -d /tmp/
+        # Install local Qiskit Ignis
+        pip install -e /tmp/qiskit-ignis-master --progress-bar off
       fi
   install:
-    # install Aqua and dev requirements
-    - pip install -e $TRAVIS_BUILD_DIR
-    - pip install -U -r requirements-dev.txt
+      # install Aqua and dev requirements
+      - pip install -e $TRAVIS_BUILD_DIR --progress-bar off
+      - pip install -U -r requirements-dev.txt --progress-bar off
 
 # Define the order of the stages.
 stages:
@@ -55,9 +75,9 @@ jobs:
     - stage: test first half
       <<: *stage_dependencies
       script:
-        - python test/customtests.py 0 -end 21
+        - python test/custom_tests.py 0 -end 34
 
     - stage: test second half
       <<: *stage_dependencies
       script:
-        - python test/customtests.py 21
+        - python test/custom_tests.py 34

CHANGELOG.rst

@@ -18,14 +18,80 @@ The format is based on `Keep a Changelog`_.
 `UNRELEASED`_
 =============
 
+`0.5.0`_ - 2019-05-02
+=====================
+
+Added
+-----
+
+- Implementation of the HHL algorithm supporting ``LinearSystemInput``.
+- Pluggable component ``Eigenvalues`` with variant ``EigQPE``.
+- Pluggable component ``Reciprocal`` with variants ``LookupRotation`` and ``LongDivision``.
+- Multiple-Controlled U1 and U3 operations ``mcu1`` and ``mcu3``.
+- Pluggable component ``QFT`` derived from component ``IQFT``.
+- Summarize the transpiled circuits at the DEBUG logging level.
+- ``QuantumInstance`` accepts ``basis_gates`` and ``coupling_map`` again.
+- Support to use ``cx`` gate for the entangement in ``RY`` and ``RYRZ`` variational form. (``cz`` is the default choice.)
+- Support to use arbitrary mixer Hamiltonian in ``QAOA``. This allows to use QAOA in constrained optimization problems [arXiv:1709.03489].
+- Added variational algorithm base class ``VQAlgorithm``, implemented by ``VQE`` and ``QSVMVariational``.
+- Added ``ising/docplex.py`` for automatically generating Ising Hamiltonian from optimization models of DOcplex.
+- Added ``'basic-dirty-ancilla'`` mode for ``mct``.
+- Added ``mcmt`` for Multi-Controlled, Multi-Target gate.
+- Exposed capabilities to generate circuits from logical AND, OR, DNF (disjunctive normal forms), and CNF (conjunctive normal forms) formulae.
+- Added the capability to generate circuits from ESOP (exclusive sum of products) formulae with optional optimization based on Quine-McCluskey and ExactCover.
+- Added ``LogicalExpressionOracle`` for generating oracle circuits from arbitrary boolean logic expressions (including DIMACS support) with optional optimization capability.
+- Added ``TruthTableOracle`` for generating oracle circuits from truth-tables with optional optimization capability.
+- Added ``CustomCircuitOracle`` for generating oracle from user specified circuits.
+- Added implementation of the Deutsch-Jozsa algorithm.
+- Added implementation of the Bernstein-Vazirani algorithm.
+- Added implementation of the Simon's algorithm.
+- Added implementation of the Shor's algorithm.
+- Added optional capability for ``Grover``'s algorithm to take a custom initial state (as opposed to the default uniform superposition)
+- Added capability to create a ``Custom`` initial state using existing circuit.
+- Added the ADAM (and AMSGRAD) optimization algorithm
+- Multivariate distributions added, so uncertainty models now have univariate and multivariate distribution components.
+- Added option to include or skip the swaps operations for qft and iqft circuit constructions.
+- Added classical linear system solver ``ExactLSsolver``.
+- Added parameters ``auto_hermitian`` and ``auto_resize`` to ``HHL`` algorithm to support non-hermititan and non 2**n sized matrices by default.
+- Added another feature map, ``RawFeatureVector``, that directly maps feature vectors to qubits' states for classification.
+- ``SVM_Classical`` can now load models trained by ``QSVM``.
+- Added CompleteMeasFitter for mitigating measurement error when jobs are run on a real device or noise simulation.
+
+Removed
+-------
+
+- ``QuantumInstance`` does not take ``memory`` anymore.
+- Moved Command line and GUI interfaces to separate repo (qiskit_aqua_uis).
+- Removed the ``SAT``-specific oracle (now supported by ``LogicalExpressionOracle``).
+
+
+Changed
+-------
+
+- Changed the type of ``entanger_map`` used in ``FeatureMap`` and ``VariationalForm`` to list of list.
+- Fixed package setup to correctly identify namespace packages using ``setuptools.find_namespace_packages``.
+- Changed ``advanced`` mode implementation of ``mct``: using simple ``h`` gates instead of ``ch``, and fixing the old recursion step in ``_multicx``.
+- Components ``random_distributions`` renamed to ``uncertainty_models``.
+- Reorganized the constructions of various common gates (``ch``, ``cry``, ``mcry``, ``mct``, ``mcu1``, ``mcu3``, ``mcmt``, ``logic_and``, and ``logic_or``) and circuits (``PhaseEstimationCircuit``, ``BooleanLogicCircuits``, ``FourierTransformCircuits``, and ``StateVectorCircuits``) under the ``circuits`` directory.
+- Renamed the algorithm ``QSVMVariational`` to ``VQC``, which stands for Variational Quantum Classifier.
+- Renamed the algorithm ``QSVMKernel`` to ``QSVM``.
+- Renamed the class ``SVMInput`` to ``ClassificationInput``.
+- Renamed problem type ``'svm_classification'`` to ``'classification'``
+
+Fixed
+-----
+
+- Fixed ``ising/docplex.py`` to correctly multiply constant values in constraints
+
+
 `0.4.1`_ - 2019-01-09
 =====================
 
 Added
 -----
 
 - Optimizers now have most relevant options on constructor for ease of programming. Options may still be set via set_options.
-- Provider is now explicilty named and the named backend is created from that named provider. Backend being selected from the first of the internally known set of providers is deprecated.
+- Provider is now explicitly named and the named backend is created from that named provider. Backend being selected from the first of the internally known set of providers is deprecated.
 - Improve operation with Aer provider/backends.
 - Registration to Aqua of externally provided pluggable algorithms and components altered to setuptools entry point support for plugins. The prior registration mechanism has been removed.
 - A flag ``before_04`` in the ``load_from_dict(file)`` method is added to support to load operator in the old format. We encourage to save the operator in the new format from now on.
@@ -44,11 +110,11 @@ Added
 - Transparent parallelization for gradient-based optimizers
 - Multiple-Controlled-NOT (cnx) operation
 - Pluggable algorithmic component ``RandomDistribution``
-- Concrete implementations of ``RandomDistribution``: ``BernoulliDistribution``, ``LogNormalDistribution``, 
+- Concrete implementations of ``RandomDistribution``: ``BernoulliDistribution``, ``LogNormalDistribution``,
   ``MultivariateDistribution``, ``MultivariateNormalDistribution``, ``MultivariateUniformDistribution``, ``NormalDistribution``,
   ``UniformDistribution``, and ``UnivariateDistribution``
 - Pluggable algorithmic component:
-- Concrete implementations of ``UncertaintyProblem``: ``FixedIncomeExpectedValue``, ``EuropeanCallExpectedValue``, and 
+- Concrete implementations of ``UncertaintyProblem``: ``FixedIncomeExpectedValue``, ``EuropeanCallExpectedValue``, and
   ``EuropeanCallDelta``
 - Amplitude Estimation algorithm
 - Qiskit Optimization: New Ising models for optimization problems exact cover, set packing, vertex cover, clique, and graph partition
@@ -187,7 +253,8 @@ Changed
 - Updated qiskit minimum version in setup.py.
 - Fixed links in readme.me.
 
-.. _UNRELEASED: https://github.com/Qiskit/qiskit-aqua/compare/0.4.1...HEAD
+.. _UNRELEASED: https://github.com/Qiskit/qiskit-aqua/compare/0.5.0...HEAD
+.. _0.5.0: https://github.com/Qiskit/qiskit-aqua/compare/0.4.1...0.5.0
 .. _0.4.1: https://github.com/Qiskit/qiskit-aqua/compare/0.4.0...0.4.1
 .. _0.4.0: https://github.com/Qiskit/qiskit-aqua/compare/0.3.1...0.4.0
 .. _0.3.1: https://github.com/Qiskit/qiskit-aqua/compare/0.3.0...0.3.1

CONTRIBUTORS.rst

@@ -10,27 +10,34 @@ levels:
 
 - `Panagiotis Barkoutsos <https://researcher.watson.ibm.com/researcher/view.php?person=zurich-BPA>`__
 - Sergey Bravyi
+- David Bucher
 - Chun-Fu (Richard) Chen
 - `Antonio Córcoles-Gonzalez <https://researcher.watson.ibm.com/researcher/view.php?person=us-adcorcol>`__
 - Albert Frisch
 - `Jay Gambetta <https://researcher.watson.ibm.com/researcher/view.php?person=us-jay.gambetta>`__
-- Jennifer Glick
 - `Donny Greenberg <https://researcher.watson.ibm.com/researcher/view.php?person=ibm-donny>`__
-- Tanvi Gujarati
+- Isabel Haide
 - `Shaohan Hu <https://researcher.watson.ibm.com/researcher/view.php?person=ibm-Shaohan.Hu>`__
 - `Takashi Imamichi <https://researcher.watson.ibm.com/researcher/view.php?person=jp-IMAMICHI>`__
 - Tal Kachman
+- `Gawel Kus <https://www.tudelft.nl/en/ae/organisation/departments/aerospace-structures-and-materials/novel-aerospace-materials/people/personal-pages-novam/students/g-kus-gawel/>`__
 - `Peng Liu <https://researcher.watson.ibm.com/researcher/view.php?person=us-liup>`__
+- `Jakub Marecek <http://researcher.ibm.com/person/ie-jakub.marecek>`__
 - Manoel Marques
+- `Martin Mevissen <https://researcher.watson.ibm.com/researcher/view.php?person=ie-MARTMEVI>`__
 - Antonio Mezzacapo
 - `Nikolaj Moll <https://researcher.watson.ibm.com/researcher/view.php?person=zurich-NIM>`__
+- Jan Müggenburg
 - `Giacomo Nannicini <https://researcher.watson.ibm.com/researcher/view.php?person=us-nannicini>`__
 - Pauline Ollitrault
 - `Anna Phan <https://researcher.watson.ibm.com/researcher/view.php?person=au1-anna.phan>`__
 - `Marco Pistoia <https://researcher.watson.ibm.com/researcher/view.php?person=us-pistoia>`__
 - `Julia Rice <https://researcher.watson.ibm.com/researcher/view.php?person=us-jrice>`__
 - `Raymond Harry Putra Rudy <https://researcher.watson.ibm.com/researcher/view.php?person=jp-RUDYHAR>`__
 - `Kanav Setia <https://physics.dartmouth.edu/people/kanav-setia>`__
+- `Andrea Simonetto <https://researcher.watson.ibm.com/researcher/view.php?person=ibm-Andrea.Simonetto>`__
+- Igor Sokolov
 - `Ivano Tavernelli <https://researcher.watson.ibm.com/researcher/view.php?person=zurich-ITA>`__
 - `Stephen Wood <https://researcher.watson.ibm.com/researcher/view.php?person=us-woodsp>`__
 - `Stefan Woerner <https://researcher.watson.ibm.com/researcher/view.php?person=zurich-wor>`__
+- `Christa Zoufal <https://researcher.watson.ibm.com/researcher/view.php?person=zurich-OUF>`__

MANIFEST.in

@@ -1,2 +1 @@
-recursive-include qiskit_aqua *.json
-recursive-include qiskit_aqua_ui *.json
+recursive-include qiskit/aqua *.json *.txt