- fix missing imports
- duplciated has_signature def
- testparfiles() relative paths

following the discussion from
https://discourse.julialang.org/t/create-an-implicit-environment-with-package-directories/109207

* add update_test helper script

* add ref test balancedburgers_kink_avmda

* fix time step computation for AV method

* simplify inf clipping

* mda: use local instead of global speed to compute baseline av

* favor likely case in if in mda computation

* implement av dragging

* add av_drag parameter

* spice up IntergrationTests logging with colors

* fix 0th order AV smoother

* implement BalancedBurgers equation

* fix fv stepping to also add dt to source term

* cleanup

* rm old ERK evolutions

* fixup fv ref tests

* rename rk steppers to ode_step!

* for FV methods forward dt from evolution via cache

fixes mismatch in dt values that were used in the time stepper and the
rhs functions
the mismatch was caused by the time stepper always applying the CFL
(and output callbacks could further shorten the proposed time step)
eventually, this lead to wrong propagation speeds, which can be seen
by the test results of fv_advection_sine (we expect same profile as
initial data after two revolutions, but we actually saw 2.5)

only add dt for FV evolutions

* fixup kwarg forwarding in register_variables

* implement a minimal git dirty logging

* restructure variable registration

* implement rhs for av regularization

* update callbacks

* implement ldg and av regularization

* mesh: forward more methods to cache

* dispatch TODO error

* forward Cache methods to Mesh

* nospecialize setup and initialdata

* 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