Release 1.7.3 (#1096)

* STACK: update stack commit to revert zoltan changes as that was not the problem

* MAINT: update version number in .py files for release

* FIX/ADD: add back Doxyfile

* MAINT: update version number in Doxyfile from 1.7.2dev to 1.7.3

* FIX/ADD: add back .rst files for documentation

* FIX/ADD: add back proteus images for documentation

* TST: added decorator to dambreak_solver_options test to skip

* MAINT: remove xtensor script, update stack to get xtensor, remove xtensor script call in .travis.yaml

* STACK: test fix for travis failure regarding xtensor and numpy

* STACK: update to get xtensor-python compilation fixes

Author: zhang-alvin

.travis.yml

@@ -32,7 +32,6 @@ jobs:
     env: TEST_PROFILE="proteus-hashdist"
     install:
       - git lfs pull
-      - ./get_xtensor.sh
       - ./stack/hit/bin/hit init-home
       - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_src --objects="source"
       - ./stack/hit/bin/hit remote add http://levant.hrwallingford.com/hashdist_ubuntu_16_04 --objects="build"

docs/Doxyfile

@@ -0,0 +1,327 @@
+.. Proteus documentation master file. This file generates the Proteus homepage (index.html) and serves as the root of the toctree
+
+.. _intro-sec:
+
+Introduction
+============
+
+Proteus is a Python package for rapidly developing computer models and
+numerical methods. It is focused on models of continuum mechanical
+processes described by partial differential equations and on
+discretizations and solvers for computing approximate solutions to
+these equations. Proteus consists of a collection of Python modules
+and scripts. Proteus also uses several C, C++, and Fortran libraries,
+which are either external open source packages or part of Proteus, and
+several open source Python packages.
+
+The design of Proteus is organized around two goals:
+
+* Make it easy to solve new model equations with existing numerical methods
+* Make it easy to solve existing model equations with new numerical methods
+
+We want to improve the development process for models *and*
+methods. Proteus is not intended to be an expert system for solving
+partial differential equations. In fact, effective numerical methods
+are often physics-based. Nevertheless many physical models are
+mathematically represented by the same small set of differential
+operators, and effective numerical methods can be developed with minor
+adjustments to existing methods. The problem with much existing
+software is that the physics and numerics are completely intertwined,
+which makes it difficult to extend (and maintain). In Proteus the
+description of the physical model and initial-boundary value problems
+are nearly "method agnostic".  This approach has been used in the
+developement of a variety of mathematical models and numerical
+methods, both of which are described in more detail below
+(:ref:`capabilities-sec`).
+
+.. _obtaining-sec:
+
+Obtaining and Installing Proteus
+================================
+
+For learning and experimenting there is a
+`Docker image <https://cloud.docker.com/u/erdc/repository/docker/erdc/proteus>`_.
+Proteus can be installed through conda with:::
+
+  % conda install proteus -c conda-forge
+
+Proteus is available as source from our public
+`GitHub <https://github.com/erdc/proteus>`_
+repository. For a development installation, the installation of
+dependencies and the compilation of Proteus from source is done with:::
+
+  % git clone https://github.com/erdc/proteus
+  % cd proteus
+  % conda env create -f environment-dev.yml
+  % conda activate proteus-dev
+  % pip install -v -e .
+
+Alternatively, if you already have compilers (C,C++, and Fortran!)
+installed on your system, you can install Proteus through hashdist
+with the following commands:::
+
+  % git clone https://github.com/erdc/proteus
+  % cd proteus
+  % make develop
+  % make test
+
+More information is available on our `Wiki <https://github.com/erdc/proteus/wiki>`_, and you can ask for help on
+the `Developers' Mailing List <https://groups.google.com/forum/#!forum/proteus-dev>`_.
+
+.. _running-sec:
+
+Running
+=======
+
+If you have successfully compiled and tested Proteus then you should be able to do::
+
+   % cd $PROTEUS/tests/ci
+   % $PROTEUS_PREFIX/bin/parun poisson_3d_p.py poisson_3d_c0p1_n.py
+
+The solution will be saved in a file ending in .xmf, which can be
+opened with ParaView or Ensight.
+
+.. _capabilities-sec:
+
+Capabilities
+============
+
+Test problems and some analytical solutions have been implemented for
+
+* Poisson's equation
+* The heat equation
+* Linear advection-diffusion-reaction equations
+* Singly degenerate nonlinear advection-diffusion-reaction equations (including various forms of Burger's equation)
+* Doubly degenerate nonlinear advection-diffusion-reaction equations
+* The eikonal (signed distance) equation
+* The diffusive wave equations for overland flow
+* 1D and 2D Shallow Water Equations
+* 2D Dispersive Shallow Water Equations
+* Richards' equation (mass conservative head- and saturation-based)
+* Two-phase flow in porous media with diffuse interface (fully coupled  and IMPES formulations)
+* Two-phase flow in porous media with a sharp interface (level set formulation)
+* Stokes equations
+* Navier-Stokes equations
+* Reynolds-Averged Navier-Stokes equations
+* Two-phase Stokes/Navier-Stokes/RANS flow with a sharp interface (level set/VOF formulation)
+* Linear elasticity
+
+These problems are solved on unstructured simplicial meshes. Simple
+meshes can be generated with tools included with Proteus, and more
+complex meshes can by imported from other mesh generators. The finite
+elements implemented are
+
+Classical methods with various types of stabilization (entropy viscosity, variational multiscale, and algebraic methods)
+
+* :math:`C_0 P_1`
+* :math:`C_0 P_2`
+* :math:`C_0 Q_1`
+* :math:`C_0 Q_2`
+
+Discontinuous Galerkin methods
+
+* :math:`C_{-1} P_0`
+* :math:`C_{-1} P_1`  (Lagrange Basis)
+* :math:`C_{-1} P_2`  (Lagrange Basis)
+* :math:`C_{-1} P_k`  (Monomial Basis)
+
+Non-conforming and mixed methods
+
+* :math:`P_1` non-conforming
+* :math:`C_0 P_1 C_0 P_2` Taylor-Hood
+
+The time integration methods are
+
+* Backward Euler
+* Forward Euler
+* :math:`\Theta` Methods
+* Strong Stability Preserving Runge-Kutta Methods
+* Adaptive BDF Methods
+* Pseudo-transient continuation
+
+The linear solvers are
+
+* Jacobi
+* Gauss-Seidel
+* Alternating Schwarz
+* Full Multigrid
+* Wrappers to LAPACK, SuperLU, and PETSc
+
+The nonlinear solvers are
+
+* Jacobi
+* Gauss-Seidel
+* Alternating Schwarz
+* Newton's method
+* Nonlinear Multigrid (Full Approximation Scheme)
+* Fast Marching and Fast Sweeping
+
+Additional tools are included for pre- and post-processings meshes and
+solutions files generated by Proteus and other models, including methods for
+obtaining locally-conservative velocity fields from :math:`C_0` finite
+elements.
+
+.. _release-sec:
+
+Release Policy
+==============
+
+The releases are numbered major.minor.revision
+
+* A revision increment indicates a bug fix or extension that shouldn't break any models working with the same major.minor number.
+* A minor increment introduces significant new functionality but is mostly backward compatible
+* A major increment may require changes to input files and significantly change the underlying Proteus implementation.
+
+These are not hard and fast rules, and there is no time table for releases.
+
+References
+==========
+
+* `Robust explicit relaxation technique for solving the Green-Naghdi equations
+  <https://doi.org/10.1016/j.jcp.2019.108917>`_ (2019) J.-L. Guermond,
+  B. Popov, E. Tovar, C.E. Kees, *Journal of Computational Physics*
+* `An Unstructured Finite Element Model for Incompressible Two-Phase
+  Flow Based on a Monolithic Conservative Level Set Method
+  <https://arxiv.org/abs/1903.06919>`_
+  (2019) M. Quezada de Luna, J. H. Collins, and C.E. Kees.
+* Preconditioners for Two-Phase Incompressible Navier-Stokes
+  Flow (2019) N. Bootland, C.E. Kees, A. Wathen,
+  A. Bentley *SIAM Journal on Scientific Computing*, In Press.
+* `Modeling Sediment Transport in Three-Phase Surface Water Systems
+  <https://doi.org/10.1080/00221686.2019.1581673>`_ (2019)
+  C.T. Miller, W.G. Gray, C.E. Kees, I.V. Rybak, B.J. Shepherd,
+  *Journal of Hydraulic Engineering*
+* `Fast Random Wave Generation in Numerical Tanks
+  <https://doi.org/10.1680/jencm.17.00016>`_ (2019) A. Dimakopoulos, T. de
+  Lataillade, C.E. Kees, *Proceedings of the Institution of Civil
+  Engineers - Engineering and Computational Mechanics*, 1-29.
+* `A Partition of Unity Approach to Adaptivity and Limiting in
+  Continuous Finite Element Methods
+  <https://doi.org/10.1016/j.camwa.2019.03.021>`_ (2019) D. Kuzmin, M. Quezada
+  de Luna, C.E. Kees, *Computers and Mathematics with Applications*.
+* `Simulating Oscillatory and Sliding Displacements of Caisson
+  Breakwaters Using a Coupled Approach
+  <https://doi.org/10.1061/(ASCE)WW.1943-5460.0000504>`_ (2019) G. Cozzuto,
+  A. Dimakopoulos, T. de Lataillade, P.O. Morillas, and C.E. Kees,
+  *Journal of Waterway, Port, Coastal, and Ocean Engineering*.
+* `A Monolithic Conservative Level Set Method with Built-In
+  Redistancing
+  <https://doi.org/10.1016/j.jcp.2018.11.044>`_ (2019) M. Quezada de
+  Luna, D. Kuzmin, C.E. Kees, *Journal of Computational Physics*, 379,
+  262-278.
+* `Computational Model for Wave Attenuation by Flexible Vegetation
+  <https://doi.org/10.1061/(ASCE)WW.1943-5460.0000487>`_ (2018)
+  S.A. Mattis, C.E. Kees, M.V. Wei, A. Dimakopoulos, and C.N. Dawson,
+  *Journal of Waterway, Port, Coastal, and Ocean Engineering* 145(1),
+  p.04018033.
+* `Well-Balanced Second-Order Finite Element Approximation of the
+  Shallow Water Equations with Friction
+  <https://doi.org/10.1137/17M1156162>`_ (2018) J.L. Guermond, M.Q. de
+  Luna, B. Popov, C.E. Kees, and M.W. Farthing *SIAM Journal on
+  Scientific Computing* 40(6), A3873-A3901.
+* `Dual-Scale Galerkin Methods for Darcy Flow
+  <https://doi.org/10.1016/j.jcp.2017.10.047>`_ (2018) G. Wang, G. Scovazzi, L. Nouveau,
+  C.E. Kees, Simone Rossi, O. Colomes, and A. Main (2018) *Journal of
+  Computational Physics* 354, 111-134.
+* `Implementation details of the level set two-phase Navier-Stokes
+  equations in Proteus
+  <https://www.clemson.edu/science/departments/math-stat/documents/technical-reports/TR2017_10_ab.nb.aw.ck.pdf>`_ (2017) A. Bentley, N. Bootland, A. Wathen, C. Kees,
+  *Technical-Report-TR2017-10-ab.nb.aw.ck*.
+* `Evaluation of Galerkin and Petrov-Galerkin Model Reduction for
+  Finite Element Approximations of the Shallow Water Equations
+  <https://doi.org/10.1016/j.cma.2017.01.027>`_ (2017) A. Lozovsky, M. W. Farthing,
+  and C.E. Kees, *Computational Methods in Applied Mechanics and
+  Engineering* 318, 537-571.
+* `POD-Based Model Reduction for Stabilized Finite Element
+  Approximations of Shallow Water Flows
+  <https://doi.org/10.1016/j.cam.2016.01.029>`_ (2016) A. Lozovskiy,
+  M.W. Farthing, C.E. Kees, E. Gildin *Journal of Computational and
+  Applied Mathematics*, 302, 50-70.
+* `An Immersed Structure Approach for Fluid-Vegetation Interaction
+  <https://doi.org/10.1016/j.advwatres.2015.02.014>`_ (2015)
+  S.A. Mattis, C.N. Dawson, C.E. Kees, M.W. Farthing, *Advances in
+  Water Resources*, 80,1-16.
+* `Finite Element Methods for Variable Density Flow And Solute
+  Transport <https://doi.org/10.1007/s10596-012-9330-2>`_ (2013)
+  T.J. Povich, C.N. Dawson, M.W. Farthing, C.E. Kees *Computational
+  Geosciences* 17(3), 529-549.
+* `Numerical simulation of water resources problems: Models, methods,
+  and trends
+  <https://doi.org/10.1016/j.advwatres.2012.05.008>`_ (2013)
+  Cass T. Miller, Clint N. Dawson, Matthew W. Farthing, Thomas Y. Hou,
+  Jingfang Huang, Christopher E. Kees, C.T. Kelley, and Hans Petter
+  Langtangen *Advances in Water Resources*, 51, 405-437,
+* `Numerical modeling of drag for flow through vegetated domains and
+  porous structures
+  <http://dx.doi.org/10.1016/j.advwatres.2012.01.002>`_ (2012)
+  S.A. Mattis, C. N. Dawson, C. E. Kees, and M. W. Farthing, *Advances
+  in Water Resources*, 39, pp44-59
+* `Parallel Computational Methods and Simulation for Coastal and
+  Hydraulic Applications Using the Proteus Toolkit
+  <http://www.dlr.de/sc/en/Portaldata/15/Resources/dokumente/pyhpc2011/submissions/pyhpc2011_submission_11.pdf>`_
+  (2011) C. E. Kees and M. W. Farthing (2011) *Supercomputing11:
+  Proceedings of the PyHPC11 Workshop*
+* `A Conservative Level Set Method for Variable-Order Approximations
+  and Unstructured Meshes
+  <http://dx.doi.org/10.1016/j.jcp.2011.02.030>`_ (2011) C.E. Kees,
+  I. Akkerman, Y. Bazilevs, and M. W. Farthing *Journal of
+  Computational Physics* 230(12), pp4536–4558
+* `Locally Conservative, Stabilized Finite Element Methods For
+  Variably Saturated Flow
+  <http://dx.doi.org/10.1016/j.cma.2008.06.005>`_ (2008) Kees, C.E.,
+  M. W. Farthing, and C. N. Dawson, *Computer Methods in Applied
+  Mechanics and Engineering*, 197, pp4610-4625
+* `Locally Conservative, Stabilized Finite Element Methods for a Class
+  of Variable Coefficient Navier-Stokes Equations
+  <http://chl.erdc.usace.army.mil/ERDC-CHL-TR-09-12>`_ (2009)
+  C. E. Kees, M. W. Farthing, and M. T. Fong, *ERDC/CHL TR-09-12*
+* `Evaluating Finite Element Methods for the Level Set Equation
+  <http://chl.erdc.usace.army.mil/ERDC-CHL-TR-09-11>`_ (2009)
+  M. W. Farthing and C. E. Kees, *ERDC/CHL TR-09-11*
+* `A Review of Methods for Moving Boundary Problems
+  <http://chl.erdc.usace.army.mil/ERDC-CHL-TR-09-10>`_ (2009)
+  C. E. Kees, M. W. Farthing, T. C. Lackey, and R. C. Berger,
+  *ERDC/CHL TR-09-10*
+* `Implementation of Discontinuous Galerkin Methods for the Level Set
+  Equation on Unstructured Meshes
+  <http://chl.erdc.usace.army.mil/library/publications/chetn/pdf/chetn-xiii-2.pdf>`_
+  (2008) M. W. Farthing and C. E. Kees, *ERDC/CHL CHETN-XIII-2*
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`modindex`
+* :ref:`search`
+
+Source Code Documentation
+=========================
+
+.. toctree::
+   :maxdepth: 1
+   :caption: General
+   :name: sec-general
+
+   API docs <apicapi>
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Tools
+   :name: sec-tools
+
+   tools/boundary_conditions
+   tools/spatial_tools
+   tools/two_phase_flow
+   tools/wave_tools
+
+.. toctree::
+   :maxdepth: 1
+   :caption: Models
+   :name: sec-models
+
+   models/body_dynamics
+   models/free_surface
+   models/mesh_adaptivity
+   models/mesh_motion
+   models/navier_stokes
+   models/SWFlows