Naming: "module" over "Qiskit Stack" (#935)

* use Qiskit module over application stack

* update readme

* chem renamings

* finance renamings

* ML renamings

* fix title line length

* Apply suggestions from code review

* found some more "stack"s

* fix copyright

Co-authored-by: Manoel Marques <[email protected]>

Author: Cryoris

CHANGELOG.md

@@ -24,11 +24,11 @@ Added
 -   NFT optimizer, part of a project of Qiskit Camp Asia 2019 (#729)
 -   Algorithm interface and result classes (#849)
 -   Chemistry FCIDump file driver (#859)
--   Chemistry stack automatic Z2 symmetry reduction (#870)
--   Ising Optimization: The 0-1 Knapsack problem (#878)
+-   Automatic Z2 symmetry reduction in the chemistry module (#870)
+-   Ising optimization: The 0-1 Knapsack problem (#878)
 -   VQE, VQC and QSVM accept `QuantumCircuit`s as variational forms/feature maps (#905)
 -   New `GSLS` (Gaussian Smoothing Line Search) optimizer for variational algorithms (#877)
--   Qiskit optimization, an application stack for solving quadratic programs (#877)
+-   Qiskit's optimization module: a full toolset for solving quadratic programs (#877)
     -   QuadraticProblem: A class representing quadratic programs with quadratic and linear objective and constraints
     -   OptimizationAlgorithm: A base class for optimization algorithm
     -   OptimizationResult: A base class for optimization results

README.md

@@ -17,7 +17,7 @@ Aqua includes domain application support for:
 * [Machine Learning](#machine-learning)
 * [Optimization](#optimization)
 
-_**Note**: the Chemistry application stack was the first domain worked on. At the time of writing
+_**Note**: the chemistry module was the first domain worked on. At the time of writing
 the other domains have some logic in them but are not as fully realised. Future work is expected to
 build out functionality in all application areas._
 
@@ -143,16 +143,16 @@ excited states and dipole moments of molecule, both open and closed-shell.
 The code comprises chemistry drivers, which when provided with a molecular
 configuration will return one and two-body integrals as well as other data that is efficiently
 computed classically. This output data from a driver can then be used as input to the chemistry
-application stack that contains logic which is able to translate this into a form that is suitable
+module that contains logic which is able to translate this into a form that is suitable
 for quantum algorithms. The conversion first creates a FermionicOperator which must then be mapped,
 e.g. by a Jordan Wigner mapping, to a qubit operator in readiness for the quantum computation.
 
 ### Optional Installs
 
-To run chemistry experiments using Qiskit Chemistry, it is recommended that you to install a
-classical computation chemistry software program/library interfaced by Qiskit Chemistry.
+To run chemistry experiments using Qiskit's chemistry module, it is recommended that you to install
+a classical computation chemistry software program/library interfaced by Qiskit.
 Several, as listed below, are supported, and while logic to interface these programs is supplied by
-Qiskit Chemistry via the above pip installation, the dependent programs/libraries themselves need
+the chemistry module via the above pip installation, the dependent programs/libraries themselves need
 to be installed separately.
 
 Note: As `PySCF` can be installed via pip the installation of Qiskit (Aqua) will install PySCF
@@ -166,8 +166,8 @@ whether this might be possible manually.
 
 ### HDF5 Driver
 
-A useful functionality integrated into Qiskit Chemistry is its ability to serialize a file in
-Hierarchical Data Format 5 (HDF5) format representing all the output data from a chemistry driver.
+A useful functionality integrated into Qiskit's chemistry module is its ability to serialize a file
+in hierarchical Data Format 5 (HDF5) format representing all the output data from a chemistry driver.
 
 The [HDF5 driver](qiskit/chemistry/drivers/hdf5d/hdf5driver.py#L25)
 accepts such such HDF5 files as input so molecular experiments can be run, albeit on the fixed data
@@ -182,9 +182,9 @@ repository. This
 [HDF5 Driver tutorial](https://github.com/Qiskit/qiskit-community-tutorials/blob/master/chemistry/hdf5_files_and_driver.ipynb)
 contains further information about creating and using such HDF5 files.
 
-### Creating Your First Qiskit Chemistry Programming Experiment
+### Creating Your First Chemistry Programming Experiment in Qiskit
 
-Now that Qiskit is installed, it's time to begin working with Chemistry.
+Now that Qiskit is installed, it's time to begin working with the chemistry module.
 Let's try a chemistry application experiment using VQE (Variational Quantum Eigensolver) algorithm
 to compute the ground-state (minimum) energy of a molecule.
 
@@ -255,7 +255,7 @@ of the circuits. By passing in a backend as is done above it is internally wrapp
 
 ### Further examples
 
-Jupyter notebooks containing further examples, for Qiskit Chemistry, may be found in the
+Jupyter notebooks containing further chemistry examples may be found in the
 following Qiskit GitHub repositories at
 [qiskit-iqx-tutorials/qiskit/advanced/aqua/chemistry](https://github.com/Qiskit/qiskit-iqx-tutorials/tree/master/qiskit/advanced/aqua/chemistry)
 and
@@ -269,9 +269,9 @@ The `qiskit.finance` package contains uncertainty components for stock/securitie
 Ising translators for portfolio optimizations and data providers to source real or random data to
 finance experiments.
 
-### Creating Your First Qiskit Finance Programming Experiment
+### Creating Your First Finance Programming Experiment in Qiskit
 
-Now that Qiskit is installed, it's time to begin working with Finance.
+Now that Qiskit is installed, it's time to begin working with the finance module.
 Let's try a experiment using Amplitude Estimation algorithm to
 evaluate a fixed income asset with uncertain interest rates.
 
@@ -305,7 +305,7 @@ When running the above the estimated value result should be 2.46 and probability
 
 ### Further examples
 
-Jupyter notebooks containing further examples, for Qiskit Finance, may be found in the
+Jupyter notebooks containing further finance examples may be found in the
 following Qiskit GitHub repositories at
 [qiskit-iqx-tutorials/qiskit/advanced/aqua/finance](https://github.com/Qiskit/qiskit-iqx-tutorials/tree/master/qiskit/advanced/aqua/finance)
 and
@@ -320,7 +320,7 @@ classification algorithms such as QSVM and VQC (Variational Quantum Classifier),
 can be used for experiments, and there is also QGAN (Quantum Generative Adversarial Network)
 algorithm.
 
-### Creating Your First Qiskit Machine Learning Programming Experiment
+### Creating Your First Machine Learning Programming Experiment in Qiskit
 
 Now that Qiskit is installed, it's time to begin working with Machine Learning.
 Let's try a experiment using VQC (Variational Quantum Classified) algorithm to
@@ -359,7 +359,7 @@ print('Testing accuracy: {:0.2f}'.format(result['testing_accuracy']))
 
 ### Further examples
 
-Jupyter notebooks containing further examples, for Qiskit Machine Learning, may be found in the
+Jupyter notebooks containing further Machine Learning examples may be found in the
 following Qiskit GitHub repositories at
 [qiskit-iqx-tutorials/qiskit/advanced/aqua/machine_learning](https://github.com/Qiskit/qiskit-iqx-tutorials/tree/master/qiskit/advanced/aqua/machine_learning)
 and
@@ -376,9 +376,9 @@ as Max-Cut, Traveling Salesman and Vehicle Routing. It also has a has an automat
 generator for a problem model specified by the user as a model in
 [docplex](qiskit/optimization/ising/docplex.py#L16).
 
-### Creating Your First Qiskit Optimization Programming Experiment
+### Creating Your First Optimization Programming Experiment in Qiskit
 
-Now that Qiskit is installed, it's time to begin working with Optimization.
+Now that Qiskit is installed, it's time to begin working with the optimization module.
 Let's try a optimization experiment using QAOA (Quantum Approximate Optimization Algorithm)
 to compute the solution of a [Max-Cut](https://en.wikipedia.org/wiki/Maximum_cut) problem using
 a docplex model to create the Ising Hamiltonian operator for QAOA.
@@ -438,7 +438,7 @@ print('solution objective:', max_cut.max_cut_value(x, w))
 
 ### Further examples
 
-Jupyter notebooks containing further examples, for Qiskit Optimization, may be found in the
+Jupyter notebooks containing further examples, for the optimization module, may be found in the
 following Qiskit GitHub repositories at
 [qiskit-iqx-tutorials/qiskit/advanced/aqua/optimization](https://github.com/Qiskit/qiskit-iqx-tutorials/tree/master/qiskit/advanced/aqua/optimization)
 and

qiskit/chemistry/README.md

@@ -1,14 +1,15 @@
-# Qiskit Chemistry
+# Chemistry In Qiskit
 
-Qiskit Chemistry is a set of tools, algorithms and software for use with quantum computers
+Qiskit's chemistry module is a set of tools, algorithms and software for use with quantum computers
 to carry out research and investigate how to take advantage of quantum computing power to solve chemistry
 problems.
 
 If you need introductory material see the main [readme](../../README.md) which has
-[installation](../../README.md#installation) instructions and information on how to use Qiskit Chemistry for 
+[installation](../../README.md#installation) instructions and information on how to use the
+chemisty module for
 [running a chemistry experiment](../../README.md#running-a-chemistry-experiment).
 
-This readme contains the following sections: 
+This readme contains the following sections:
 
 * [Developers](#developers)
 * [Additional reading](#additional-reading)
@@ -29,32 +30,32 @@ The dictionary contains the following fields of note:
 * *energies*
 
   An array of energies comprising the ground state energy and any excited states if they were computed
-  
+
 * *nuclear_repulsion_energy*
 
-  The nuclear repulsion energy 
-  
+  The nuclear repulsion energy
+
 * *hf_energy*
 
   The Hartree-Fock ground state energy as computed by the driver
-  
+
 * *nuclear_dipole_moment*, *electronic_dipole_moment*, *dipole_moment*
 
   Nuclear, electronic and combined dipole moments for x, y and z
-  
+
 * *total_dipole_moment*
 
-  Total dipole moment 
- 
-* *algorithm_retvals* 
+  Total dipole moment
+
+* *algorithm_retvals*
 
-  The result dictionary of the algorithm that ran for the above values. See the algorithm for any further information.  
+  The result dictionary of the algorithm that ran for the above values. See the algorithm for any further information.
 
 ### For writers of algorithms and other utilities such as optimizers and variational forms:
 
-Qiskit Aqua is the library of cross-domain algorithms and utilities. Please refer to the documentation 
+Qiskit Aqua is the library of cross-domain algorithms and utilities. Please refer to the documentation
 there for more information on how to write and contribute such objects to Qiskit Aqua. Such objects are then available
-to be used by Qiskit Chemistry.  
+to be used by Qiskit's chemistry module.
 
 ### For unit test writers:
 

qiskit/chemistry/__init__.py

@@ -12,19 +12,19 @@
 # copyright notice, and modified files need to carry a notice indicating
 # that they have been altered from the originals.
 r"""
-==============================================================
-Chemistry application stack for Aqua (:mod:`qiskit.chemistry`)
-==============================================================
+===================================================
+Qiskit's chemistry module (:mod:`qiskit.chemistry`)
+===================================================
 
 .. currentmodule:: qiskit.chemistry
 
-This is the chemistry application stack for Aqua that provides for experimentation with chemistry
+This is Qiskit's chemistry module that provides for experimentation with chemistry
 domain problems such as ground state energy and excited state energies of molecules.
 
 Overview
 ========
 
-This is an overview of the workings of the chemistry stack and how it may be used. There
+This is an overview of the workings of the chemistry module and how it may be used. There
 are different levels of exposure to its functionality, allowing for experimentation at different
 abstractions. The outline below starts with the flow that provides the most control of the
 process.
@@ -78,7 +78,8 @@
 
 Mappings
 ++++++++
-To map the FermionicOperator to a qubit operator Qiskit Chemistry supports the following mappings:
+To map the FermionicOperator to a qubit operator the chemistry module supports the following
+mappings:
 
 Jordan Wigner
     The `Jordan-Wigner transformation <https://rd.springer.com/article/10.1007%2FBF01331938>`__,

qiskit/chemistry/_logging.py

@@ -21,8 +21,7 @@
 
 
 def get_qiskit_chemistry_logging() -> int:
-    """
-    Returns the current Qiskit Chemistry logging level
+    """Returns the current Qiskit chemistry logging level
 
     Returns:
         int: logging level
@@ -31,8 +30,7 @@ def get_qiskit_chemistry_logging() -> int:
 
 
 def set_qiskit_chemistry_logging(level: int, filepath: Optional[str] = None) -> None:
-    """
-    Updates the Qiskit Chemistry logging with the appropriate logging level
+    """Updates the Qiskit chemistry logging with the appropriate logging level
 
     Args:
         level: minimum severity of the messages that are displayed.

qiskit/chemistry/drivers/__init__.py

@@ -17,13 +17,13 @@
 =========================================================
 .. currentmodule:: qiskit.chemistry.drivers
 
-Qiskit Chemistry requires a computational chemistry program or library, accessed via a chemistry
-*driver*, to be installed on the system for the electronic-structure computation of a given
-molecule. A driver is created with a molecular configuration, passed in the format compatible with
-that particular driver. This allows custom configuration specific to each computational chemistry
-program or library to be passed.
+Qiskit's chemistry module requires a computational chemistry program or library, accessed via a
+chemistry *driver*, to be installed on the system for the electronic-structure computation of a
+given molecule. A driver is created with a molecular configuration, passed in the format compatible
+with that particular driver. This allows custom configuration specific to each computational
+chemistry program or library to be passed.
 
-Qiskit Chemistry thus allows the user to configure a chemistry problem in a way that a chemist
+The chemistry module thus allows the user to configure a chemistry problem in a way that a chemist
 already using the underlying chemistry program or library will be familiar with. The driver is
 used to compute some intermediate data, which later will be used to form the input to an Aqua
 algorithm.  Such intermediate data, is populated into a :class:`~qiskit.chemistry.QMolecule`
@@ -39,8 +39,8 @@
 used to compute it.  However the values and level of accuracy of such data will depend on the
 underlying chemistry program or library used by the specific driver.
 
-Qiskit Chemistry offers the option to serialize the Qmolecule data in a binary format known as
-`Hierarchical Data Format 5 (HDF5) <https://support.hdfgroup.org/HDF5/>`__.
+Qiskit's chemistry module offers the option to serialize the Qmolecule data in a binary format known
+as `Hierarchical Data Format 5 (HDF5) <https://support.hdfgroup.org/HDF5/>`__.
 This is done to allow chemists to reuse the same input data in the future and to enable researchers
 to exchange input data with each other --- which is especially useful to researchers who may not
 have particular computational chemistry drivers installed on their computers.
@@ -68,7 +68,7 @@
 
 Drivers
 =======
-Qiskit Chemistry drivers obtain their information from classical ab-initio programs
+The drivers in the chemistry module obtain their information from classical ab-initio programs
 or libraries. Several drivers, interfacing to common programs and libraries, are
 available. To use the driver its dependent program/library must be installed. See
 the relevant installation instructions below for your program/library that you intend

qiskit/chemistry/drivers/_basedriver.py

@@ -37,7 +37,7 @@ class HFMethodType(Enum):
 
 class BaseDriver(ABC):
     """
-    Base class for Qiskit Chemistry Drivers.
+    Base class for Qiskit's chemistry drivers.
     """
 
     @abstractmethod

qiskit/chemistry/drivers/gaussiand/__init__.py

@@ -2,7 +2,7 @@
 
 # This code is part of Qiskit.
 #
-# (C) Copyright IBM 2018, 2019.
+# (C) Copyright IBM 2018, 2020.
 #
 # 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
@@ -26,7 +26,7 @@
 `Gaussian product installation support <http://gaussian.com/techsupport/#install]>`__.
 
 Following the installation make sure the Gaussian™ 16 executable, `g16`, can be run from the
-command line environment where you will be running Python and Qiskit Chemistry. For example
+command line environment where you will be running Python and Qiskit. For example
 verifying that the `g16` executable is reachable via the system environment path,
 and appropriate exports, such as `GAUSS_EXEDIR`, have been configured as per
 `Gaussian product installation support <http://gaussian.com/techsupport/#install]>`__.
@@ -36,27 +36,27 @@
 
 
 In the :mod:`gauopen` folder the Python part of the above interfacing code,
-as needed by Qiskit Chemistry, has been made available. It is licensed under a
+as needed by Qiskit's chemistry modules, has been made available. It is licensed under a
 `Gaussian Open-Source Public License
 <https://github.com/Qiskit/qiskit-aqua/blob/master/qiskit/chemistry/drivers/gaussiand/gauopen/LICENSE.txt>`_.
 
 Part of this interfacing code --- specifically, the Fortran file `qcmatrixio.F` --- requires
-compilation to a Python native extension. However, Qiskit Chemistry comes with pre-built binaries
+compilation to a Python native extension. However, Qiskit comes with pre-built binaries
 for most common platforms. If there is no pre-built binary matching your platform, then it will be
 necessary to compile this file as per the instructions below.
 
 Compiling the Fortran Interfacing Code
 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
 
-If no prebuilt native extension binary, as supplied with Qiskit Chemistry, works for your
+If no prebuilt native extension binary, as supplied with Qiskit, works for your
 platform, then to use the Gaussian™ 16 driver on your machine, the Fortran file `qcmatrixio.F`
 must be compiled into object code that can be used by Python. This is accomplished using the
 `Fortran to Python Interface Generator (F2PY) <https://docs.scipy.org/doc/numpy/f2py/>`__,
 which is part of the `NumPy <http://www.numpy.org/>`__ Python library.
 Specifically, on your command prompt window, change directory to the
-`qiskit/chemistry/drivers/gaussiand/gauopen` directory inside the Qiskit Chemistry
-installation directory, and while in the Python environment created for Aqua and Qiskit Chemistry,
-invoke `f2py` on `qcmatrixio.F` as explained below.
+`qiskit/chemistry/drivers/gaussiand/gauopen` directory inside the Qiskit
+installation directory, and while in the Python environment created for Aqua and the chemistry
+module, invoke `f2py` on `qcmatrixio.F` as explained below.
 
 
 Apple macOS and Linux
@@ -93,7 +93,7 @@
     and that `~/.gaussian` is the full path to
     the selected scratch folder, where Gaussian™ 16 stores its temporary files.
 
-    Now, before Qiskit Chemistry can properly interface Gaussian™ 16, you will have to run the
+    Now, before Qiskit can properly interface Gaussian™ 16, you will have to run the
     `enable_gaussian` command defined above.  This, however, may generate the following error:
 
     .. code:: sh