* update examples once more

* remove comments

* cleanup: remove codegen for now

* IntegartionTests: add grhd_tov_spherical1d ref test

* IntegrationTests: remove reltol from grhd_bondi_accretion test

* spherical1d: fix missing shift from maxspeed computation

* cleanup

* make spherical1d formulation work when r=0 is included by removing potential nans in source terms by enforcing symmetry

* make impose_symmetry! dispatch on project

* add tov example that runs with spherical1d formulation

* wip: change maxspeed implementation for tov star initial data

* cons2prim: use non-zero values for rho, eps thresholds

* fix: set atm density in bondi_accretion initial data

* implement tov initial data for spherical1d formulation

* add formulation parameter

* implement rhs for FVElement and rescaled_spherical1d

* implement equations for FVElement and rescaled_spherical1d

* mesh: implement differentiate for FVElement

* add grhd example par files

* update notebooks

* fix missing lapse factor in source terms

* fix typos

* fixup initialdata setup

* derivative computation needs jacobi

* rename cons2prim routines

* add atmosphering to cons2prim

* implement rhs! for rescaled_spherical1d formulation

* specialize timespeed computation based on equations

* add specialized equations for the rescaled GRHD version

* implement initialdata setup for tov case

* spherical accretion:make sure K, Gamma agree with loaded data

* expose spectral differentiation

* wrap SphericalAccretion solver into module; recompute bondi_accretion.h5 with less radial points

* refactor TOV solver to use OrdinaryDiffEq

* initialdata: cleanup dir

* add bondi accretion as ref test

* fix up loading of id file

* fv_rhs: implement fv_update_step! with source term

* add ROOTDIR const global so that parfiles can specify paths relative to project root

* update SphericalAccretion.jl

* update sympy nb

* cleanup initialdata setup

* equations: fix up Tmunu computation

* Revert "fix source term in dg and fv rhs computation"

This reverts commit 161cc034.

* Replace Interpolations.jl with BasicInterpolators.jl

* equation: add missing flux terms to sources; use outflow bdry condition on inner radius

* comments in cons2prim

* implement momentum constraint for debugging

* test SphericalAccretion

- copy Bugner's C version of the solver
- compare my results with Bugner's -- good agreement
- compare against literature results (Papadopoulos 1998,1999) --
  discrepancy in sign of vr, ur, otherwise good agreement

* SphericalAccretion: fix wrong definition of uc^r and Vc

* tweak impl more

* fix source term in dg and fv rhs computation

* fix equations and implement fv method

* equations: combine flux and source computation

* math: update spherical_accretion notebook

* SRHD: export module

* re-implemented GRHD eqs with a non-zero shift

* initialdata: add grhd_source.codegen.jl that was generated with TensorComponents.jl

* deps: need Interpolations.jl for initial data setup

* update math/spherical_accretion.py

* update setup

* start initialdata setup for bondi problem

* rework rhs.jl

* update deps and parameters

* update type defs

* initialdata: add HDF5 dep; write h5 output for SphericalAccretion.jl

* rename cons2prim.jl

* remove unused files

@with_signature: only need one LineNumberNode per @accepts, @returns unpacking block (!100)

* @with_signature: only need one LineNumberNode per @accepts, @returns unpacking block

* @with_signature: Insert 'LineNumberNodes' when unpacking vectors

* remove Base.getproperty overloads for meshes

* fixup Base.length definition for Mesh

* fix unit tests

* add the mesh arg (second_arg) as an ordinary argument into with_signature fn signature; also remove unused state_indices interface method

* remove mesh kw from with_signature function signature

* temporarily disable @timeit around broadcast_computation, because it introduces allocs

* inline fn call in broadcast_computation to avoid allocs

* use views and maximum(abs, ...) to avoid allocs

* make min_grid_spacing dimension agnostic for FVElement

* inline mesh helpers

* more let arguments, just in case closure bug hits again ...

* stop using properties of mesh

* don't use absolute_maximum

* parameterize Project on equation

* remove rootfinders.jl and update unit tests

* remove my rootfinder types

* rework SphericalAccretion to use CairoMakie.jl and Roots.jl

* remove variablesarray.jl; rename _VariablesDict to Variables

* fix up readme badges

* update line coverage computation

* remove unused tests: test_variables.jl

* update coverage exclude patterns

* rename project dg1dTests to UnitTests

* remove BenchmarkTools from dg1dTests deps

remove BenchmarkTools

* rename new_broadcast_... to broadcast_...; also export broadcast_... methods

* eliminate legac=false option

* remove legacy option form @with_signature

fixup default options

* disable with_signature functions that used legacy version

* evict all occurences of broadcast_(volume|faces|bdry)_2!

* parameterize structs that contain an abstract Mesh

* update ref test data srhd_simple_wave_avmda

* fix up dispatch of register_variables; fix up smoothing on initial data

* mda: use inplace operations

* cons2prim: disable simd; disable atmosphering warning

* update blastwave1/2 av mda examples

* adjust tau when energy density exceeds lower bound

* don't recompute max speed for timestep

* determine initial viscosity using all dynamic variables as indicators

* add blastwave1 example

* add blastwave2 examples

* fixup blastwave2 test; don't smooth FVElement mesh initial data

* commit conservative_fixing experiments (not active)

* cons2prim: temporarily error in case speed is too large

* disable conservative_fixing again

* change fixedprms in setup

* fix domain assertion for blastwave1 test

* add initial data smoother based on Bernsteining

* do not recompute viscosity on initial data

* modify examples

* implement fd derivative again

* implement covariant regularization

* add prms to Project type

* add example parfiles

* update ref test data srhd_simple_wave_fv

the difference is quite pronounced

* use maximum of max_v instead of v for time step estimation

* update ref test data srhd_simple_wave_avmda

* compute cellmax_v properly; compute maxspeed in equation callback

* implement sod shock tube initial data

* insert line number nodes for better stack traces

* add ref test srhd_simple_wave_avmda

* undo some code deletion

* special case FV method on entropy production computation

* init EP for all setups

* add entropy tci computation that can work with precomputed entropy production

* add entropy viscosity computation that can work with precomputed entropy production

* compute entropy production in equation callback

* add ref test srhd_simple_wave_fv

reset ref data for srhd_simple_wave_fv

* update ref test

increase resolution ref test

increase tol for ref test and lower resolution

* add ref test srhd_simple_wave_fv

* implement FV version for SRHD eqs

* simplify timestep computation

* initial data setup functions need to take a mesh

* fixup speed computation burgers eq

* fix upload logic for diffoutput uploading

* update ref test data

* migrate all implementations to use new broadcasting interface

* evict broadcast_volume_2!

* remove cons2prim unit test

* add srhd_simple_wave.toml

* update ref test burger_sine_aventropy

* undo experiments in ev.jl

* undo changes to advection_sine ref test

* fix up entropy production computation

* fix entropy variables computation according to formulae from EFL and EHL papers

* WIP

* make AV regularization run

* disable conservative fixing as it causes wrong results in srhd_smooth test; update ref test data

* evict old broadcasting interface

* define entropy variables for polytrope

* compute fluxes after interpolating bdry data

* optimize mda computation

* fix ramping function for mda

* enable conservative_fixing every to make ref tests pass -- however, ref test restults don't look correct

update srhd_smooth ref test data

* move cons2prim in rhs down

* use only D as HRSC indicator

* fix simple wave initial data and disable conservative fixing as it
kills the simple wave propagation

* make bdry conditions work for shock tube test

* document print_idxs for @with_signature

* add mda_n_low, mda_n_high parameters that allow to control the truncation interval for the MDA heuristic

* fix logic in combining mda indicators from multiple vars

* enable TCIs for SRHD

* SRHD: allow to compute MDA AV from multiple vars and combine them with a max function

* SRHD: make srhd_smooth test run with AV (though not perfect)

* SRHD: add ldg_nflux

* update ref test srhd_smooth

* add more srhd parfiles

* split conservative fixing from cons2prim; fixup cons2prim so that symmetric shock tubes are actually symmetric

* update 0th order smoother

* compute viscosity for initial data

* use mix of conserved and primitives for flux computation

* cleanup equations

* cleanup cons2prim

* implement av entropy for 1d eq -- wip

* utilize kastaun cons2prim in llf

* remove cons2prim_insane and friends

* fix type instability in cons2prim caused by infamous closure bug

fixup cons2prim

* add Kastaun's cons2prim with conservative fixing

* rename variables

* remove comment

* convert llf to use new broadcasting interface

* convert cons2prim to new broadcasting

* convert entropy_variables, but it is todo

* remove unused

* convert flux to new broadcast interface

* convert speed to new broadcast interface

* clean up module file

* update euler_isentropic_flow ref test to use interpolate_aligned_ts

* reorganize testconfig.toml

* update advection_sine_glgl ref test to use interpolate_aligned_ts

* update advection2d_bump_threshold ref test to use aligned_ts

* remove unused toml files

* fix testparfiles to not list global options

* update heateq_sine ref test to use aligned_ts

* update burgers2d_gaussian_entropyav ref test to use aligned_ts

* update burgers2d_gaussian ref test to use aligned_ts

* update srhd_smooth ref test to use aligned_ts

* update euler_isentropic_flow ref test to use aligned_ts

* update advection2d_sine ref test to use aligned_ts

* update fv_euler_isentropic_flow ref test to use aligned_ts

update output.h5

* fixup success check

* add interpolate.h5 output for heateq_gaussian ref test

* use aligned_ts for heateq_gaussian ref test

* update ref test advection_sine to include interpolate.h5 output

* upgrade IntegrationTests to also compare interpolate.h5 outputs (if available)

* remove whitespaces

* use mktempdir instead of custom mockdir gymnastics

* trigger a TimeAlignedCB also when t+dt == next_t

* InterpolationCallback can only interpolate fields that are registered as dynamic, static or rhs

* add check for registered variable in get_variable

* add a few @inline decorations

* add isregistered method to cache and variablesdict types

* throw proper error message when unregistered variable is requested

* add test for InterpolationCallback

* fixup callback interface docs

* enable interpolation options of Output parameter section

* add parameters for interpolation output

* fixup InterpolatioCallback

* Invocation of CallbackSet should report the call status

I think initially the return value of all callbacks was meant
to indicate whether that callback was actually called.
I think what we need now is that callbacks return their status,
e.g. whether they failed or not.

* remove superfluous Base.show overloads

* add InterpolationCallback

use refactored meshinterpolator

* introduce AbstractSaveCallback

* update tests

* evict old plot functionality

evict remainders

* update dg1dTests manifest

* refactor MeshInterpolator to accept arrays for interpolation

* use ranges to construct the cells' extends, because they ensure that the endpoints are preserved

* add sod_shock_tube examples

* add examples mono and navier-stokes regularization of euler_isentropic_flow problem

* remove dead code

* update ref test burgers_sine_aventropy

* undo deletion

* remove dead code

* beautify log details when unequal number of output times is encountered

* refactor printing of failed test details

* im in a rush

* fix ref test log info

* remove unused var

* revert callbacks

* add invalid assertion in glgl integration method

* remove bernsteining from AV regularization

* add 0th order smoother

* remove lower threshold on entropy av

* wip -- tinker with applying Bernsteining to the LDG variables

* also forward project to rhs

* remove unnecessary computations from callback

* put lower threshold on entropy AV

* inline bernsteining workhorse

* use inplace ops for entropy TCI

* add ref test fv_euler_isentropic_flow

* fixup hrsc initialization for EulerEq

* fix args for Project constructor

* update deps; put compat bound on PrettyTables.jl

* add ref test euler_isentropic_flow_regulate-ns -- disabled for now

* add dispatch for av regularization in rhs!; wip implementation of new regularizations

* add a namedtuple for parameters to Project struct

* fix call to broadcast in callbacks.jl

* add av_regularization parameter

* dispatch TODO on Symbol

* IntegrationTests: print Inf norm if mismatch is found

* update refdata burgers_sine_avmda

* update refdata burgers_sine_avdb

* update refdata burgers_sine_aventropy

* update refdata burgers_sine_avtci

* fixup constructor call

* more examples

* update output times; fixup gitignore

* utilize Sandbox to parse expressions from parfiles

* fixup ScalarEq bump initial data

* add examples folder with parfiles that are not ref tested

* specialize timestep for AV scheme

* implement 1st order fd approx for derivative of regularization term

* enable callbacks

* add prms field to ScalarEq's project struct

also add av_derivative_scheme parameter to ScalarEq project
to be used subsequentely

* simplify dispatch of rhs!

* update some ref tests

- euler_isentropic_flow
- euler_sod_shock_tube_bernstein
needed because previously we employed a timestep that was too large,
because it only used the local cell width but not the smallest grid
spacing

* add ref test for FV euler sod shock tube

* update ScalarEq so that FV version can use non-periodic bdry conditions

* implement FV method for Euler equation

- also refactor timestep to work with DG and FV elements
- also refactored fv_update_step! methods to now accept buffers for bdry
  values

* remove more Riemann solver stuff

* remove non-existent export

* evict riemannsolver.jl and broadcast_[volume,faces,bdry]!

* evict Riemann solver related stuff from SRHD

* evict Riemann solver related stuff from EulerEq

* evict Riemann solver related stuff from ScalarEq

* convert all in EulerEq

remove unrelated file

* convert all in ScalarEq

* re-enable srhd_smooth test

update srhd_smooth reftest

* evict old broadcasting methods

Add a finite volume method for ScalarEq

See merge request !75

* add reftest fv_advection_sine

* migrate all of ScalarEq to use broadcast_*_2! methods

* add isperiodic method for meshes

* fix grid spacing computation for SpectralElement

* fixup parametric types to subtype Mesh1d/2d

* make TODO error more comprehensive

* fixup cfl usage; add abstractions for min grid spacing

* enable add mesh kwarg to Evolution setup in order to enable FV evolution

* add timestep! and rhs! for FVElement

* do away with the State(...) syntax

* add docs to dg_rhs methods

* add FV stepper

* limit dg_rhs.jl methods to Meshes with SpectralElement

* add mesh kwarg to Evolution so that we can use a spearate stepper based on mesh type

* add a scheme parameter to Mesh

* add FVElement type

Refactor CFL parameter usage

See merge request !74

* fix tests

* remove an unreachable check

can't be reached, because a error would be thrown earlier
when multiplying a number with nothing

* remove cfl field from Evolution struct

* move cfl parameter from Mesh to Evolution section

also update all reftest parfiles

* remove CFL field from Mesh

* apply CFL factor in evolve loop and not inside projects

call the right interpolator for HRSC/smoother.jl

See merge request !73

* call the right interpolator

Allow dispatch on second argument

See merge request !72

* enable mesh argument in broadcasting methods

* remove debug statement

* fix docs

* add unit test

* disable euler_sod_shock_tube_entropyav ref test

* fixup tests

* enable mesh as second arg for legacy mode

make main() accept numbers which correspond to testparfiles() list

See merge request !70

* make main() accept numbers which correspond to testparfiles() list

bump version

See merge request !69

* bump version

Cleanup

See merge request !68

* rm deps BenchmarkTools, GLob, InteractiveUitls, LaTeXStrings, REPL; update dg1dTests' dependencies

* remove Plots, PlotThemes, Interpolations