Merge pull request #469 from CEED/jed/doc-examples

Jed/doc examples

doc: split examples into separate files in the source tree

* Copy examples/**.rst into the source directory so they can be picked
up by Sphinx.
* Some minor corrections/clarifications to docs that

doc: split examples into separate files in the source tree

* Copy examples/**.rst into the source directory so they can be picked
up by Sphinx.
* Some minor corrections/clarifications to docs that I noticed while
splitting them apart (shame on me for bundling in this commit).

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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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Merge branch 'jrwrigh/ns-dmplex' into jed/ns-dmplex [PR #430]

* jrwrigh/ns-dmplex:
fix(navierstokes): Remove Units redefinition
fix(nsplex): Add nsplex macro, ifdefs to functions
test(navierst

Merge branch 'jrwrigh/ns-dmplex' into jed/ns-dmplex [PR #430]

* jrwrigh/ns-dmplex:
fix(navierstokes): Remove Units redefinition
fix(nsplex): Add nsplex macro, ifdefs to functions
test(navierstokes): Remove stdout output for testing
test(nsplex): Remove stdout output during test
nsplex: Update nsplex /tests/output file
navierstokes: Rename User struct to UserNS
nsplex: Update stdoutParsing.py for new nsplex outputs
nsplex: Print dm_plex_box_faces value
nsplex: Print FEM space degree
nsplex: Move python parsing function to stdoutParsing.py
nsplex: Calculate computation time
nsplex advection2d: choose only the smooth initial condition
nsplex advection2d: make solution time-dependent
nsplex: Calculate exact solution at final time
nsplex: Implement ICs_PetscMultiplicity function
nsplex: Add non_zero_time flag to problemData
nsplex: Create SetupContext struct, add to ICs* qfuncs
nsplex: Move User_ and Units_ to common.h
Update .gitignore with misc editor dirs

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Update .gitignore with misc editor dirs

*.dylib and *.json added to .gitignore

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

Python Interface

Python - update gitignore

Python - inital python ceed interface

Merge pull request #360 from CEED/jed/config-flags

Jed/config flags and string processing

Makefile: add flags to config.mk and add NVCC_CXX

CUDA usually does not support the latest gcc, but an older version C++
compiler is only needed internally by nvcc. NVCC_CXX allows the user
to spec

Makefile: add flags to config.mk and add NVCC_CXX

CUDA usually does not support the latest gcc, but an older version C++
compiler is only needed internally by nvcc. NVCC_CXX allows the user
to specify a compatible C++ compiler for CUDA while still using a
modern release for *.cpp sources.

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Merge pull request #261 from CEED/valeria/update-gitignore

Update top level .gitignore

Update top level .gitignore

Add Basis argument to TensorContractCreate

Squashed 'tests/junit-xml/' content from commit 9bb2675

git-subtree-dir: tests/junit-xml
git-subtree-split: 9bb2675bf0058742da04285dcdcf8781eee03db0

Merge branch 'mfem-bp-update' [PR #101]

* mfem-bp-update:
Move dims variables inside of loop
Put if/else inside of loop in .okl files
Add build dir to gitignore
Revert to using offsets in .o

Merge branch 'mfem-bp-update' [PR #101]

* mfem-bp-update:
Move dims variables inside of loop
Put if/else inside of loop in .okl files
Add build dir to gitignore
Revert to using offsets in .okl files
[OCCA] Qfunction data dim is set from basis
[OCCA] Initialized restriction kernels to occaUndefined
[OCCA] Attempting to 'turn on' CEED_EVAL_GRAD for output
Update MFEM bp1.okl, add bp3.okl

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Add build dir to gitignore

Doxygen cleanup

Merge branch 'jed/codecov' [PR #112]

* jed/codecov:
Add codecov.io

Add codecov.io

Merge branch 'master' into evector_support

Merge branch 'template-backend' [PR #63]

* template-backend:
Add template backend, requested in issue #38
Split Ref into multiple files, update style

Split Ref into multiple files, update style