Travis - error on Clang tidy issues

make: revise configure target

make configure now only caches non-default variables, identified by
whether they are simple (set with :=, as in config.mk) or originate
from the command line. Usage is

make: revise configure target

make configure now only caches non-default variables, identified by
whether they are simple (set with :=, as in config.mk) or originate
from the command line. Usage is similar to before, but should be less
fragile/simpler to edit, and support setting more things.

This includes saving OPT, superseding PR #422.

Reported-by: Veselin Dobrev <dobrev@llnl.gov>

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make: print-% target also mentions the flavor (simple vs recursive)

Simple variables are set with := and expanded eagerly. Recursive
variables are set with = and expanded in the context of the targ

make: print-% target also mentions the flavor (simple vs recursive)

Simple variables are set with := and expanded eagerly. Recursive
variables are set with = and expanded in the context of the target.

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make: use target-specific CPPFLAGS for -I and -D for all languages

Avoids redundancy and simplifies the job of setting CFLAGS, NVCCFLAGS, etc.

make: move -DUNDERSCORE to CPPFLAGS (it is semantically not a CFLAG)

make: support different MKL install schema

Merge pull request #446 from CEED/user-manual

Sphinx user manual published at libceed.readthedocs.io

doc: convert to Sphinx documentation at libceed.readthedocs.io

Some technical notes about the expanded docs/process:

* Doxygen is now restricted to API documentation. Sphinx docs are
incomplete

doc: convert to Sphinx documentation at libceed.readthedocs.io

Some technical notes about the expanded docs/process:

* Doxygen is now restricted to API documentation. Sphinx docs are
incomplete surrogates due to not hyperlinking code listings, though
we hope the Doxygen site can be removed eventually.

* PDF output uses XeTeX (unicode and OTF fonts) with TeX Gyre Pagella
and DejaVu Sans Mono. You may need to install these fonts in order
to build the PDF users manual.

* Obtaining the author list from Git has not worked on
ReadTheDocs (`git shortlog` is empty even though `git log` is not),
so we automatically generate it on developer machines with `make
doc`. If the author information is incorrect/mangled, edit .mailmap
to fix the mapping.

* Math semantics are based on the description here
https://github.com/sphinx-doc/sphinx/issues/3785

Sphinx chooses one of two setups for the maths.

* If there is a single equation, then we wrap the maths in
\begin{equation*} (or equation).

* If there are multiple equations (as determined by the presence of
an empty line), then we wrap the maths first in \begin{aligned}
and then in \begin{align*} (or align).

Co-authored-by: Jeremy L. Thompson <jeremy.thompson@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update READ

Merge branch 'jed/ns-dmplex' [PR #458]

* jed/ns-dmplex: (73 commits)
NS: remove density_current_primitive (still work in progress)
Remove a bunch of unused variables and update doc
Update README: remove density_current_primitive problem option for now
Use const in VLA declaration casts to suppress icc warning also in densitycurrent_primitive
Remove a bunch of unused or double-declared variables
Update README
NS: use const in VLA casts to suppress icc warning
NS: add command-line support for specifying DC center/axis
NS: return to insulated no-slip walls instead of full-Dirichlet
NS: remove dead code for scaling VTK output back to dimensional units
NS: add support for free slip wall boundary conditions
NS density_current: remove redundant initial/boundary condition and trailing whitespace
Some changes in documentation
Update top-level README
Update examples/README
Update examples/navier-stokes/README
Update .gitignore
Update documentation
Initialize *problem pointer as NULL
NS: move nsplex.c to navierstokes.c
...

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Enable MAGMA non-tensor basis (#424)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more

Enable MAGMA non-tensor basis (#424)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more framework for adding magma elem restrictions

* typo/old code error fixes for interface and header file, etc

* add the writedofs kernels

* fix nonconstants - template them for now

* fix bugs in non-tensor basis apply (interp and weight)

* update magma backend files from magma-dev to new branch

* add skeleton for elem restrictions

* start putting code and files for nontensor case

* more framework for adding magma elem restrictions

* typo/old code error fixes for interface and header file, etc

* add the writedofs kernels

* fix nonconstants - template them for now

* fix bugs in non-tensor basis apply (interp and weight)

* fix incorrect merge conflict resolution of header file

* fix bugs in lmode=notranspose elem restrictions
and in copying of indices to device

* test simpler kernels for lmode=transpose elem restrict

* swap element and component ordering in tensor basis actions

* update comments in restriction kernels to match swapped ordering

* fix if statement to work with CEED_VECTOR_NONE instead of NULL

* minor code cleanup

* skip t204-7 for magma after changing E-vector layout

* remove commented old calls for now

* use magma set/get vectors instead of cuda memcopies

* remove dead code

* make style changes

Co-authored-by: Stan Tomov <tomov@eecs.utk.edu>
Co-authored-by: abdelfattah83 <36712794+abdelfattah83@users.noreply.github.com>

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Merge pull request #414 from CEED/python/interface-v1

Python Interface

Python - update Makefile

Merge pull request #440 from CEED/jeremy/arm-travis

Travis - Update to Bionic, Add ARM64 and POWER8 arch

Travis - add Power8 arch

ns: add to tests (requires recent PETSc)

Merge pull request #427 from CEED/deps/update-to-c++11

[Deps] Updates to C++11

[Deps] Updates to C++11

Merge pull request #418 from CEED/jeremy/memcheck-serial

Serial Memcheck Backend

Memcheck - make serial memcheck backend

Merge pull request #405 from CEED/jeremy/astyle

Fix Style Indentation Errors

Tidy - use std=c99

Merge pull request #402 from CEED/jeremy/mkl-typo

Makefile - move --no-as-needed

Makefile - move --no-as-needed

Style - Fix indentation errors

Makefile - fix small MKL linking error (#401)

* Makefile - separate variable for MKLROOT linking