- lkeegan/libsbml-static -> spatial-model-editor/sme_deps_common
  - /opt/libs -> /opt/smelibs
  - C:/libs -> C:/smelibs

* Aditionally, the branch `latest` will also be pushed with a `latest` tag.

Resolve "Support 3D simulations"

Closes #31

See merge request !27

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Resolve "Add simple adaptive timestepping"

Closes #29, #30, #12, #28, and #26

See merge request !25

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Before, the md comparison version was not obtaining the grid functions from the latest state and led to much higher errors and a different result with respect to sd executable

- Full verbosity of one step method
- Fix code format on executables

- There was an error on the coefficients of the evolution of the gaussian equation.
- Reduced simulated time and diffusion to make bell fit almost always in the domain.

  - now uses `in` as initial state instead of `out`
  - previous behaviour was ok until commit aa186676 which changes `out` in between calls

  - closes #30

  - this is thrown if the iterative solver doesn't converge
  - e.g. "SolverAbort: breakdown in BiCGSTAB - omega -0 <= EPSILON 1e-80 after 1835.5 iterations"

  - was doing a step from `out` -> `out`
  - this resulted in null ptr deref after a failed integration step
  - instead do a step from `prev_out` -> `out`, where `prev_out` is a temporary which stores the previous `out` value
  - closes #29

fix dt > max_step error message

  - minor change to existing code:
    - include <dune/copasi/common/filesystem.hh> instead of <filesystem>
    - use namespace `fs` instead of `std::filesystem`
    - where by default `fs` is just an alias for `std::filesystem`
  - if -DUSE_FALLBACK_FILESYSTEM=ON in CMake configuration
    - `fs` instead uses implementation from https://github.com/gulrak/filesystem
    - no longer links or depends on std::filesystem
    - needed for macOS < 10.15 which doesn't have std::filesystem support

  - mingw gcc on msys will not implicitly convert std::filesystem::path to std::string
  - `cannot convert 'path' (type 'const std::filesystem::__cxx11::path') to type 'const string&' {aka 'const std::__cxx11::basic_string<char>&'}`
  - https://stackoverflow.com/a/57377681/6465472

  - remove coefficient_mapper.hh
  - add stepper.hh
  - sort lists alphabetically

  - https://github.com/vector-of-bool/CMakeCM/blob/master/modules/FindFilesystem.cmake
  - previous CMake failed with clang if linking with libstdc++

The approach used before was never successful because binding time of the coefficient mapper was to slow compared to a fully coupled solution. This means that an OS approach would have to be reworked from the PDELab assembler directly. 
This commit removes that and adds support for the new model stepper:
* Remove coefficient mapper and its use on local operators
* Remove the operator map of objects within the model class
* Move read/write responsibility to model state
* Allow states to be independent of models. Thus, allowing several different states coexist for a given model.
* Multiple domain model now needs only one file path and each sub-domain file name is deduced from the state.
* Writer might write on different files on request
* Clean up logger output
* Update meaningful logging values on the ini file
* Improved errors when a config file is incorrect
* Default executable now use simple adaptive steppers
* Stepper now can use all PDELab RK methods

This time stepper is inspired on the boost odeit steppers signatures. To be able to use it, the current models need to be modified so that it exports operators and states can be exchanged easily.
The advantage of this approach is that time evolution can be fine tuned by users at will. Moreover, it allows to have several valid states on the same model and be separately advanced in time.

* Time is default initialized to NaN
* Added a bool cast to check faster if state is valid
* Add standard filesystem flags in CMake

* For this, the structure of the ini file. Now time stepping information has an independent section for the model
* The test for dune_copasi_md break with these changes
* dune_copasi_sd does not longer accept multiple compartment settings

Scape state write

See merge request !24

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