doc: disable hoverxref until upgrade + sphinx-3.0 support is ready

doc: upgrade to sphinx-3.0

Pin breathe==4.14.2

Workaround https://github.com/michaeljones/breathe/issues/495

Reported-by: Jeremy L. Thompson <jeremy.thompson@colorado.edu>

doc: use hoverxref master

Merge pull request #502 from CEED/jed/python-autopep8

Python: apply autopep8 and add to CI

Small doc fixes (#499)

* A small shift in notation

* Docs: Clarify ex2-surface mathematical description

* Refactor \boldsymbol -> \bm

* Refactor \mathbf -> \bm

* Sphinx: clear html_stati

Small doc fixes (#499)

* A small shift in notation

* Docs: Clarify ex2-surface mathematical description

* Refactor \boldsymbol -> \bm

* Refactor \mathbf -> \bm

* Sphinx: clear html_static_path

This is needed to avoid the 'html_static_path entry '_static' does not exist' warning

https://github.com/readthedocs/readthedocs.org/issues/1776

* Fix some incosistencies

* Invert inner products (u,v) -> (v,u)

* Add SVG figure for coordinates on the sphere

* doc: use dirhtml on readthedocs

* Improve caption of sphere coords figure

* Add reference to figure in the bps on the cubed-sphere section

Co-authored-by: Jed Brown <jed@jedbrown.org>

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Python: apply autopep8 and add to CI

libCEED-0.6

Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>

User manual style: alphabetize refs

v0.6: Add release notes

Doc: exclude examples/README.rst

This is needed otherwise sphinx launches a warning about the examples/README.rst file not being included in any toctree

Convert examples/README.md -> examples/README.rst and include section on how to run examples in top-level README

Merge branch 'master' into valeria/jupyter-notebook-tutorials

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-au

Solid Mechanics Example (#474)

libCEED + PETSc Solid Mechanics example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: Valeria Barra <valeriabarra21@gmail.com>


* Solids - initial commit of elasticity example

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - add VLA macro

* Solids - fix test for mesh file output string

* Solids - update documentation

Co-authored-by: Jeremy L Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Arash Mehraban <arashm81@gmail.com>

* Solids - update README

* Solids - update ctx struct and casting for CUDA

* Tests - clean up test conditions for GPU backends

* GPU - fix falbacks identified

* CUDA - whitelist FDM Inverse

* make style

* doc: solids editing/correctness

* Solids - separate FE boilerplate into its own function

* Solids - clean up double includes

* doc: add more complete explanation of hyperelasticity and formulation

* Solids - Use ISGetSize for global number of face sets (had no effect on PETSc bug in MR 2615)

* edited docs for hyperFS

* Improve doc of solids example with some constitent notation and fonts

* HyperSS docs modified

* edited typo

* linearization added

* fixed a typo

* Improved doc

* doc: more writing on hyperelasticity and implementation tradeoffs

* Solids - fix typo

* Solids - compute and store C, Cinv, and S as symmetric

* Solids - use new Newton linearization, but its not converging

* Solids - update BC handling

* Solids - update README with new BC options

* removed old notation

* Solids - whitespace changes only in documentation

* doc: adjust differential notation and derive dP(dF)

* Solids - small documentation flow edits

* Solids - simplify setting BCs

* Solids - Symmetritize e in SS

* Solids - set more reasonable default number of steps for nonlinear

* Solids - fix documentation typo

* Solids - clean up computation of deltaS

* Solids - fix sample runs

* Solids - fix hyperSS jacobian

* Solids - fix hyperSS documentation

* Solids - clean up code for hyperSS

* Solids - add file and function docstrings

* doc: commutative diagram of linearization and stable stress expression

* Solids - update hyperSS documentation with linearization

* doc: further tips on stable computation

* Solids - fix typo with trace in hyperSS

* Solids - intro and hyperSS documentation updates

* Solids - update hyperFS for numerical stability with small E and nearly incompressible

* examples/solids: simpler C = I + 2E

* Solids - more compact/readable E computation

* Solids - minor style consistency change

* Solids - replace log1p with series approximation, log1p is not vectorized in libc

* Solids - refactor common components between hyperFSF and hyperFSdF

* examples/solids: use PETSc dependency flags for incremental rebuild

* examples/solids: extend range of log1p_series via shift/scale

* Solids - add bc_clamp_max option to specify maximum displacement for clamped boundary

* make style

* Solids - update with sample run informantion and spellchecking

* Doc - typo fixes

* Solids - homogonize presentation of command line options

* examples/solids: fix -Wmisleading-indentation

* examples/fluids: PETSc 3.13 compatibility

* examples/solids: use log1p for numerical stability in hyperSS

* doc: copy editing in examples/solids

* Solids - update documentation on running the code

* Solids - convert README to rst and include in documentation

* Solids - clean dependency file

* Solids - use log1p approximation in hyperSS as well

* Solids - update README to explain mms

* Solids - switch range on hyperSS log1p series approximation

* Solids - update README to clarify mandatory options

* Solids - add link to sample meshes

* Solids - simplify listing of mesh options

* Travis - use newer PETSc

* Solids - update sample run to list [.exo file] instead of name of sample mesh

* Solids - update make clean to remove src/*.d

* examples/solids: makefile cleanup

* make style

* doc examples/solids: clean up and explain nondimensionalization

* examples/solids: document algebraic solver

* examples/solids: use CG for Chebyshev eig estimation

* doc: fix references to examples/fluids

* Solids - remove mesh folder

* Solids - drop expicit ExodusII requirement, PETSc supports many types of meshes

* doc: mention PETSc --download-exodusii for Exodus

* doc: fix latexpdf

* Fix \longrightarrow rendering in PDF

* Solids - fix toctree link to README for pdflatex

* Examples and BPs Docs: Homogenize math with dS and dV and other tiny esthetics

* Solids - fix unshifted series for hyperSS log1p

* Improve doc of bpssphere: Add differential for consistency with all other examples and explain domain for clarity

* Solids - include sample mesh image

* Move mesh figure after note and slightly rename inclusion marker

Co-authored-by: Arash Mehraban <arashm81@gmail.com>
Co-authored-by: Jed Brown <jed@jedbrown.org>
Co-authored-by: valeriabarra <valeriabarra21@gmail.com>

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User manual and jupyter-notebook: a bit of rewording

User manual: Introductory sentences for each API class

Convert README.md -> README.rst and include README parts in gettingstarted.rst

doc: update instructions for Python

User manual: Small wording changes

User manual: Add Gallery of QFunctions and small consistency improvements

User manual: style

Add VLA support for CUDA backends (#481)

* CUDA - add VLA support for CUDA backends

* Navier-Stokes - guard #include math.h for CUDA

* Navier-Stokes - fix struct definitions for code generatio

Add VLA support for CUDA backends (#481)

* CUDA - add VLA support for CUDA backends

* Navier-Stokes - guard #include math.h for CUDA

* Navier-Stokes - fix struct definitions for code generation

* Navier-Stokes - fix file location of mass QFunction

* Navier-Stokes - minor style consistency

* Navier-Stokes - more context sturct fixing

* Navier-Stokes - cast context to stop CUDA errors

* Navier-Stokes - change helper functions to inline to silence CUDA errors

* CUDA - clean up CEED_Q_VLA definition for cuda/gen

* Navier-Stokes - populate TODOs for undocumenced functions

* Doc - document libCEED macros

* CUDA - use -default-device for NVRTC

* Tests - add t507 to test VLA support

* CUDA - fix my bug in dim, Q1d for cuda/gen

* Tests - update tap/junit to reflect current CUDA capabilities

* make style

* CUDA - check output bases for dim, Q1d as well (this fixes multigrid example support)

* CUDA - fix readSliceQuads, not all arguments were defined

* Navier-Stokes - document all functions in Navier-Stokes QFunction files

* make style

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doc: note about double and single dot contraction added to FEMtheory

doc: switch from mathjax to katex

NS: stabilization added to doc

Thanks-to: Valeria Barra <valeriabarra21@gmail.com>