doc - update release notes

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

doc - add single precision release note

qf/op - make immutability conditions explicit

interface - promote field getters to public API

interface - refactor *GetFields to include number of fields

Allow CeedScalar to be single precision (#788)

One can modify `ceed.h` to include `ceed-f32.h` and then use single precision. This is tested for C in CI and has been tested by developers with Rust,

Allow CeedScalar to be single precision (#788)

One can modify `ceed.h` to include `ceed-f32.h` and then use single precision. This is tested for C in CI and has been tested by developers with Rust, Julia, and Python. This interface is evolving and should be considered experimental at this time (thus lack of automated build support).

* Introduce CeedScalarType enum

* WIP changes to allow different definitions of CeedScalar

* Introduce new header files for float and double

* Only use avx tensor contract and MAGMA non-tensor basis if CeedScalar is double

* WIP changes to allow CeedScalar to be float

* WIP start trying to adjust test tolerances for float or double

* fix typos in comments

* install ceed-f32/64 headers

* Fix missing casts for hipMAGMA element restrictions

* make CeedQFunctionContextGetContextSize available for Python bindings

* Changes to Python bindings to allow CeedScalar to be float

* WIP adjust Python tests for float or double

* make style

* remove QFunctionContextGetContextSize from backend header

* Use quotes instead of <> in include statement

* Remove unncessary includes

* Update tolerances for tests

* [Julia] allow CeedScalar to be Float32

* [Julia] Use Preferences instead of custom build configuration

# Conflicts:
# julia/LibCEED.jl/src/C.jl

* [Makefile] Change definition of CC_VENDOR so it works with cross-compilation

* [Julia] Use Preferences in CI

# Conflicts:
# .github/workflows/julia-test-with-style.yml

* [Julia] Update docs about preferences

* [Julia] Add test/Project.toml workaround for Preferences

* Add CeedGetScalarType to get the type of CeedScalar at runtime

* [Julia] Move functions from Ceed.jl to LibCEED.jl

* [Julia] Add support for getting library path and scalar type at runtime

* [Julia] Minor change to checking if CUDA is loaded

* [Julia] Check correct CeedScalar types in basis functions

* [Julia] Fix tests comparing with output file

* [Julia] Change devtests to use CeedScalar instead of Float64

* Update test 402 so context will be same size in double or float

* Update tolerances for ceed examples

* [Julia] CUDA fixes

* remove unused variable in t208

* SchurDecomposition: do not compute tau on final iteration

* Update tolerances for some basis tests (for single precision)

* Make style

* Python style fixes for basis test

* Add single precision output for t300 and t320 and adjust checks; skip t541 in single

* Add LCOV exclusions after moving to new line

* fix spacing

* Python: make CEED_EPSILON available as libceed.EPSILON

* Python: optional parameter to specify different output file for test comparison

* Python: update tests' use of EPSILON and change test_300 output file for single precision

* Python: add convenience function for getting dtype corresponding to CeedScalar

* rust - add single precision support

* [Julia] Fall back on Float64 if CeedGetScalarType is not available

* [Julia] style

* Adjust tolerance for t301

* xsmm - add single precision support

* avx - add single precision support

* Add initial single precision support for MAGMA non-tensor basis

* Skip t300 and t320 in single precision; revert Python t300 changes

* Revert output changes for t300 and t320 in junit

* [Julia] Changes to autogenerated bindings for mixed precision

* [Julia] style

* [Julia] Check scalar type when changing libceed library path

The check is also performed when the package is loaded. This prevents having to
restart the Julia session twice

* [Julia] Require JLLWrappers version 1.3

This is needed to use Preferences to change the library path

* Add documentation page for precision development

Co-authored-by: Will Pazner <will.e.p@gmail.com>

* Cleanup from merge: remove old README

* Return CEED_ALIGN to backend.h

* Make Fortran compiler (FC) optional; empty skips Fortran tests

Use in Python and Rust builds, which may not have a Fortran compiler
installed and thus would produce confusing output.

* Add single precision CI test for Noether

Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>

Co-authored-by: Will Pazner <will.e.p@gmail.com>
Co-authored-by: Jeremy L Thompson <jeremy@jeremylt.org>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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doc: add note on restrict qualified semantics for QFunctions

doc: provide altair-plot.css for ReadTheDocs

doc: skip CeedPragmaOptimizeOn/Off at Doxygen level

Sphinx does not understand the push/pop model, and this leads to
warnings. It's an idiosyncrasy that I don't think needs to be part of
the Sphinx

doc: skip CeedPragmaOptimizeOn/Off at Doxygen level

Sphinx does not understand the push/pop model, and this leads to
warnings. It's an idiosyncrasy that I don't think needs to be part of
the Sphinx site.

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bib: add DOI

doc: move from {math:numref} to {eq} (no visual change)

doc: replace ReST tables/list-table with MyST

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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Refactor Preconditioning Ingredients (#795)

* op - split preconditioning into separate file

* pc - move FDM to interface level

* pc - initial move of diagonal assembly to interface

* interf

Refactor Preconditioning Ingredients (#795)

* op - split preconditioning into separate file

* pc - move FDM to interface level

* pc - initial move of diagonal assembly to interface

* interface - only return error code or error

* doc - improve preconditioning helper function documentation

* pc - use qdata layout for interface diagonal assembly

* pc - update for consistency in naming, use of CeedChk, and static

* doc - spelling

* style - minor

* doc - add doc for CeedBuildMassLaplace

* doc - update release notes

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

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

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Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning u

Mooney-Rivlin model (#794)

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* WIP: Notes on using finite differencing for dS

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* remove extra print statement

* added coulped MR FSInitial-MRc qfunction

* MR coupled version doc update

* refactored MR to work with current version of main. Updated doc with dS for MR

* fixed documentation formatting

* update dS for MR in documentation

* cleaning up MR dS equations and wording

* minor changes in doc

* MR dS draft 1"

* MR coded, jacobian diverging

* added FSInitial-MR1.h

* fixed call option

* NH no longer needs mu_1 option

* processphysics and upated naming scheme

* added print strain at every increment cl option

* MR cleaned. started CSV file but not quite there

* examples/solids: write csv file

can be read using pandas:

In [2]: pd.read_csv('test.csv')
Out[2]:
increment energy
0 0.000000 0.000000
1 0.066667 0.002402
[...]

* examples/solids: add targets for CSV logging and Altair chart

The MR data is currently hacked because it isn't converging as I'd expect.

* fixed style

* solids/doc: added derivation of dS for MR

* added analytical dS in Jacobian evaluation

* fixed style

* updated doc and energy plot for MR

* MR almost done

* started removing integer division

* got rid of all integer divisions

* missed some 1/3

* fixed some typo

* rerunning plot files

* Mooney-Rivlin coupled model

* some minor changes

* Mooney-Rivlin coupled model

* some clean-up and update

* clean-up, rebased

* examples/solids: revise docs/derivation and fix Newton

The (fixed) Newton linearization yields an indefinite operator causing
Newton to fail (so output/MR-strain1.csv is broken). This can be handled
by switching to minres, but a better solution would be nice.

* format: added newlines and removed unused/commented code blocks

* doc: removed GP model dropdown.

* examples/solids: Mooney-Rivlin docs/notation

* examples/solids: Mooney-Rivlin notation and experimental configuration

* examples/solids: process -dm_plex_box_faces with PETSc main

* make style

* examples/solids: syntax fix and minor cleanup

* make style

* doc: fixing Holzapfel ref in Mooney-Rivlin

* added TESTARGS for Mooney-Rivlin

* fixed TESTARGS for MR

* tests/tap.sh: make test for solids examples with names

* WIP: adding test option. added -expect_final_strain_energy and RegressionTests_solids function but not sure how to actually pull the reference strain energy from the reference file

* examples/solids: add regression tests using expected strain energy

* examples/solids: error on MMS with model that does not provide manufactured solutions

* examples/solids: fix HIP via CEED_QFUNCTION_HELPER

* update in-line comments

* changed as Jeremy suggested

* examples/solids: make style

Co-authored-by: Rezgar Shakeri <Rezgar.Shakeri@colorado.edu>
Co-authored-by: Jed Brown <jed@jedbrown.org>

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Merge branch 'release'

Add JOSS paper citation (#790)

* Add JOSS paper link to README and update How-to-cite

* Add JOSS paper to User Manual and references

* Docs: bib format

Co-authored-by: Jed Brown <jed@jedbro

Add JOSS paper citation (#790)

* Add JOSS paper link to README and update How-to-cite

* Add JOSS paper to User Manual and references

* Docs: bib format

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

* Bib: Remove url field

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

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main: return to main development

post-release user manual citation update

libCEED 0.9.0

doc: handle CeedPragmaOptimizeOn/Off

fdm - add CeedPragmaOptimzeOff/On to disable complier optimizations that create floating point errors

clang - silence some pedantic warnings, fixes #742

doc - update release notes

doc - use docs.rs over self hosted documentation