Make create_gitlab_ci branch up-to-date before merging into master (#418)

* first working SDC version (M and Minv)

* Update playground.py

* cleaning up

* Added some hyphens in plots (#389)

* Removed seperate file for GPU Dahlquist implementation (#391)

Co-authored-by: Thomas <t.baumann@fz-juelich.de>

* Review (#388)

* Bug is fixed and added new code

* new code for the table

* Edits in markdown file

* some edits in test

* Bugs fix

* Codecov

* I cleaned up my code and separated classes to make it easier to work with. It is not ready yet; if Codecov fails, I will include more tests.

* forgot black

* flake8

* bug fix

* Edits codes according to the comments

* Edited codes according to the comments in the GitHub

* Defined new function in stability_simulation.py to check stability for
given points and excluded codecov function that generates a table.

* small edits for codecov

* removed no cover

* NCCL communicators (#392)

* Added wrapper for MPI communicator to use NCCL under the hood

* Small fix

* Moved NCCL communicator wrapper to helpers

---------

Co-authored-by: Thomas <t.baumann@fz-juelich.de>

* Version bump for new release

* proper readme and link

* Started playground for machine learning generated initial guesses for (#394)

SDC

* playing with FEniCS

* blackening

* Bug fix (#395)

* readme file changes

* fixed bugs for stability plots and some edits in README file

* some edits

* typo in citation

* Bump version

* Bug fix (#396)

* Clear documentation and some edits in the code

* forgot black

* some changes

* bump version

* Cosmetic changes (#398)

* Parallel SDC (Reloaded) project (#397)

TL: Added efficient diagonal preconditioners and associated project. Coauthored by @caklovicka

* Generic multi-component mesh  (#400)

* Generic multicomponent mesh

* new try

* Added a test for MultiComponentMesh

* Test that the type is conserved also after numpy operations

* Added documentation for how to use `MultiComponentMesh`

* Changed formatting of the documentation

* Update ci_pipeline.yml

* version freak show

* version freak show II

* version freak show III

* version freak show IV

* Update ci_pipeline.yml

* version freak show V

* 2D Brusselator problem (#401)

* Added 2D Brusselator problem from Hairer-Wanner II. Thanks @grosilho for
the suggestion!

* Added forgotten pytest marker

* Fix brain afk error

* Added work counter for right hand side evaluations

* Removed file for running Brusselator from project

* Retry at removing the file

* I need to go to git school

* Datatype `DAEMesh` for DAEs (#384)

* Added DAE mesh

* Updated all DAE problems and the SDC-DAE sweeper

* Updated playgrounds with new DAE datatype

* Adapted tests

* Minor changes

* Black.. :o

* Added DAEMesh only to semi-explicit DAEs + update for FI-SDC and ProblemDAE.py

* Black :D

* Removed unnecessary approx_solution hook + replaced by LogSolution hook

* Update WSCC9 problem class

* Removed unnecessary comments

* Removed test_misc.py

* Removed registering of newton_tol from child classes

* Update test_problems.py

* Rename error hook class for logging global error in differential variable(s)

* Added MultiComponentMesh - @brownbaerchen + @tlunet + @pancetta Thank ugit add pySDC/implementations/datatype_classes/MultiComponentMesh.py

* Updated stuff with new version of DAE data type

* (Hopefully) faster test for WSCC9

* Test for DAEMesh

* Renaming

* ..for DAEMesh.py

* Bug fix

* Another bug fix..

* Preparation for PDAE stuff (?)

* Changes + adapted first test for PDAE stuff

* Commented out test_WSCC9_SDC_detection() - too long runtime

* Minor changes for test_DAEMesh.py

* Extended test for DAEMesh - credits for @brownbaerchen

* Test for HookClass_DAE.py

* Update for DAEMesh + tests

* 

 - speed up test a bit (at least locally..)

* Forgot to enable other tests again

* Removed if-else-statements for mesh type

* View for unknowns in implSysFlatten

* Fix for RK sweeper - changed nodes in BackwardEuler class (#403)

* Made aborting the step at growing residual optional (#405)

* `pySDC`-build-in `LagrangeApproximation` class in `SwitchEstimator` (#406)

* SE now uses LagrangeApproximation class + removed Lagrange class in SE

* Removed log message again (not corresponding to PR)

* version bump

* Added hook for logging to file (#410)

* Monodomain project (#407)

* addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems

* added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen)

* added exponential imex and mES, added parabolic_system in vec format

* added new stabilized integrators using multirate, splitting and exponential approaches

* before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods

* added first order exponential runge kutta as underlying collocation method. To be generalized to higher order

* generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly

* fixed a few things

* optimized a few things

* renamed project ExplicitStabilized to Monodomain

* removed deprecated problems

* fixed some renaming issues

* did refactoring of code and put in Monodomain_NEW

* removed old code and renamed new code

* added finite difference discretization

* added many things, cant remember

* old convergence_controller

* addded some classes from oldexplicit_stabilized branch. Mainly, the problems description, datatype classes, explicit stabilized classes. Tested for IMEX on simple problems

* added implicit,explicit,exponential integrator (in electrophysiology aka Rush-Larsen)

* added exponential imex and mES, added parabolic_system in vec format

* added new stabilized integrators using multirate, splitting and exponential approaches

* before adding exponential_runge_kutta as underlying method, instead of the traditional collocation methods

* added first order exponential runge kutta as underlying collocation method. To be generalized to higher order

* generalized exponential runge kutta to higher order. Added exponential multirate stabilized method using exponential RK but must tbe checked properly

* fixed a few things

* optimized a few things

* renamed project ExplicitStabilized to Monodomain

* removed deprecated problems

* fixed some renaming issues

* did refactoring of code and put in Monodomain_NEW

* removed old code and renamed new code

* added finite difference discretization

* added many things, cant remember

* added smooth TTP model for conv test, added DCT for 2D and 3D problems

* added plot stuff and run scripts

* fixed controller to original

* removed explicit stabilized files

* fixed other files

* removed obsolete splittings from ionic models

* removed old sbatch scripts

* removed mass transfer and sweeper

* fixed something

* removed my base transfer

* removed hook class pde

* removed FD files

* fixed some calls to FD stuff

* removed FEM FEniCSx files

* renamed FD_Vector to DCT_Vector

* added hook for output and visualization script

* removed plot scripts

* removed run scripts, except convergence

* removed convergence experiments script

* fixed TestODE

* added stability test in run_TestODE

* added stability test in run_TestODE

* added stability test in run_TestODE

* removed obsolete stuff in TestODE

* removed unneeded stuff from run_MonodomainODE

* cleaned a bit run_MonodomainODE

* removed utils/

* added few comments, cleaned a bit

* removed schedule from workflow

* restored tutorial step 7 A which I has modified time ago

* run black on monodomain project

* fixed a formatting thing

* reformatted everything with black

* Revert "revert formatted with black"

This reverts commit 82c82e9eb5396854c4892e1667b13975df3fb6bb.

* added environment file for monodomain project, started to add stuff in workflow

* added first test

* added package tqdm to monodomain environment

* added new TestODE using DCT_vectors instead of myfloat, moved phi_eval_lists from MonodomainODE to the sweeper

* deleted old TestODE and myfloat stuff

* renamed TestODEnew to TestODE

* cleaned a bit

* added stability, convergence and iterations tests. Changed a bit other scripts as needed

* reactivated other tests in workflow

* removed my tests temporarly

* added monodomain marker to project pyproject.toml

* changed files and function names for tests

* fixed convergence test

* made one test a bit shorter

* added test for SDC on HH and fixed missing feature in SDC imex sweeper for monodomain

* reformatted with correct black options

* fixed a lint error

* another lint error

* adding tests with plot

* modified convergence test

* added test iterations in parallel

* removed plot from tests

* added plots without writing to file

* added write to file

* simplified plot

* new plot

* fixed plot in iterations parallel

* added back all tests and plots

* cleaned a bit

* added README

* fixed readme

* modified comments in controllers

* try to compute phi every step

* removed my controllers, check u changed before comuting phis

* enabled postprocessing in pipeline

* added comments to data_type classes, removed unnecessary methods

* added comments to hooks

* added comments to the problem classes

* added comments to the run scripts

* added comments to sweepers and transfer classes

* fixed the readme

* decommented if in pipeline

* removed recv_mprobe option

* changed back some stuff outiside of monodomain project

* same

* again

* fixed Thomas hints

* removed old unneeded move coverage folders

* fixed previously missed Thomas comments

* begin change datatype

* changed run_Monodomain

* added prints

* fixed prints

* mod print

* mod print

* mod print

* mod print

* rading init val

* rading init val

* removed prints

* removed prints

* checking longer time

* checking longer time

* fixed call phi eval

* trying 2D

* trying 2D

* new_data type passing tests

* removed coverage folders

* optmized phi eval lists

* before changing phi type

* changed eval phi lists

* polished a bit

* before switch indeces

* reformatted phi computaiton to its traspose

* before changing Q

* optimized integral of exp terms

* changed interfate to c++ code

* moved definition of dtype u f

* tests passed after code refactoring

* Generic MPI FFT class (#408)

* Added generic MPIFFT problem class

* Fixes

* Generalized to `xp` in preparation for GPUs

* Fixes

* Ported Allen-Cahn to generic MPI FFT implementation

* Ported Gray-Scott to generic MPI FFT (#412)

* Ported Gray-Scott to generic MPI FFT class

* `np` -> `xp`

* Reverted poor changes

* Update README.md (#413)

Added the ExaOcean grant identified and the "Supported by the European Union - NextGenerationEU." clause that they would like us to display.

* TIME-X Test Hackathon @ TUD: Test for `SwitchEstimator` (#404)

* Added piecewise linear interpolation to SwitchEstimator

* Started with test for SwitchEstimator [WIP]

* Test to proof sum_restarts when event occuring at boundary

* Started with test to check adapt_interpolation_info [WIP]

* Added test for SE.adapt_interpolation_info()

* Update linear interpolation + logging + changing tolerances

* Test for linear interpolation + update of other test

* Correction for finite difference + adaption tolerance

* Added test for DAE case for SE

* Choice of FD seems to be important for performance of SE

* Removed attributes from dummy probs (since the parent classes have it)

* Test for dummy problems + using functions from battery_model.py

* Moved standard params for test to function

* Updated hardcoded solutions for battery models

* Updated hardcoded solutions for DiscontinuousTestODE

* Updated docu in SE for FDs

* Lagrange Interpolation works better with baclward FD and alpha=0.9

* Added test for state function + global error

* Updated LogEvent hooks

* Updated hardcoded solutions again

* Adapted test_problems.py

* Minor changes

* Updated tests

* Speed-up test for buck converter

* Black..

* Use msg about convergence info in Newton in SE

* Moved dummy problem to file

* Speed up loop using mask

* Removed loop

* SDC-DAE sweeper for semi-explicit DAEs (#414)

* Added SI-SDC-DAE sweeper

* Starte with test for SemiImplicitDAE

* Test for SI-SDC sweeper

* Clean-up

* Removed parameter from function

* Removed test + changed range of loop in SI-sweeper

---------

Co-authored-by: Robert Speck <pancetta@users.noreply.github.com>
Co-authored-by: Thomas Baumann <39156931+brownbaerchen@users.noreply.github.com>
Co-authored-by: Thomas <t.baumann@fz-juelich.de>
Co-authored-by: Ikrom Akramov <96234984+ikrom96git@users.noreply.github.com>
Co-authored-by: Thibaut Lunet <thibaut.lunet@tuhh.de>
Co-authored-by: Lisa Wimmer <68507897+lisawim@users.noreply.github.com>
Co-authored-by: Giacomo Rosilho de Souza <jackrosilho@gmail.com>
Co-authored-by: Daniel Ruprecht <danielru@users.noreply.github.com>