Merge pull request #893 from CEED/natalie/more-hip-launch-bounds

HIP: add atomics flag and more kernel launch bounds for performance improvements

Update required ROCm version to 4.2

Merge pull request #845 from CEED/jeremy/binder-url

readme - fix binder url

readme - fix binder url

Merge pull request #789 from CEED/will/julia-preferences

Julia interface updates (Preferences.jl)

[Julia] Update docs about preferences

Merge pull request #703 from CEED/jed/doc-myst-nb

doc: replace recommonmark with MyST

README: update badge and table style

doc: replace recommonmark with MyST and migrate ReST to MyST

This offers more familiar syntax for most writing, as well as natural
$\pi$ math (versus :math:`\pi`) and markdown syntax for all ReST
fe

doc: replace recommonmark with MyST and migrate ReST to MyST

This offers more familiar syntax for most writing, as well as natural
$\pi$ math (versus :math:`\pi`) and markdown syntax for all ReST
features.

The API doc stubs remain in ReST as recommended for autodoc.

https://myst-parser.readthedocs.io/en/latest/sphinx/use.html#use-sphinx-ext-autodoc-in-markdown-files

The change was largely implemented using
https://github.com/executablebooks/rst-to-myst/ with some manual
fix-ups. Tables (both ReST built-in tables and list-table) remain under
eval-rst until they can be manually updated.

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Merge pull request #487 from CEED/jed/python-packaging

Jed/python packaging

doc: update instructions for Python

Merge pull request #470 from CEED/jeremy/readme-doc-link

README - update link to API example

README - update link to API example

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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Update top-level README

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

Python Interface

Rename ceed examples and minor doc changes (#442)

* Rename ex-1 -> ex1-volume, ex2 -> ex2-surface and add ex2-surface.okl

* Update READMEs

* Update doc

README - update python install instructions

Python - update README

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

Serial Memcheck Backend

Memcheck - make serial memcheck backend

Merge pull request #353 from CEED/jeremy/xsmm-pkgconfig

Makefile - Detect MKLROOT for LIBXSMM linking

Makefile - Improve description for MKL