- 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

[skip-ci]

[skip-ci]

Always call `write_states` but only write on configured writers. That means that some or all  writers are allowed to be not configured at write call 

- replace All and None with constexpr functions

When applying clang-format in another commit, the inclusion order of the local operator changed and showed a lack of include files in it

The idea here is to set a flag for each stage of the model setup and a policy that sets the required stages for a certain configuration. For example, the `write` policy requires the model to configure the stages of grid function space, coefficient vector and writer.
Scape writer configuration if "writer" section is not present in config

In case the ini file does not contain the "writer" section then, the whole writer setup is skipped and no error will be shown.

Liam Keegan authored 4 years ago and Santiago Ospina De Los Ríos committed 4 years ago

This class helps to the usage of enums as bit flags. In particular it makes
automatic convertions that allow bitwise operations directly on the enum. Moreover,
it allows to use these enums on constant expressions as well.

add bit_flags.hh to cmake install

Merge branch 'fix_gcc_10_compilation' into 'master'

ref:copasi/dune-copasi\>

-   non-const lambdas defined in a header have external linkage
    -   so if two compilation units include them get 'multiple definition'
        errors (at least with gcc 10)
    -   put lambdas defined in a header file inside anonymous namespace to
        resolve this
    -   resolves [#24]

Closes [#24]

See merge request [!23]

  [#24]: gitlab.dune-project.org/NoneNone/issues/24
  [!23]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/23


Closes #24

[skip-ci]

  - make lambdas defined in a header file static
  - resolves 'multiple definition' errors seen with gcc 10

[skip-ci]

Merge branch '21-release-v0-2' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

Bump version to 0.2.0

### Can this MR be accepted?

-   [x] Implemented
-   [x] Pipelines passing <!-- please check for new warnings -->
     <!-- change all occurences of <branch> for your branch name -->

    -   [x] [![Build Status]]
    -   [x] [![Build Status][1]]
    -   [ ] [![Build status][2]]

-   [x] Delete branch option set <!-- unless there's a good reason -->

### Related issues

Closes [#21]

<!-- For automatic closing, do not forget the commas between issue numbers-->

<!--
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Briefly explain __how__ you achieved the proposal of the task.

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See merge request [!20]

  [Build Status]: https://gitlab.dune-project.org/copasi/dune-copasi/badges/<branch>/pipeline.svg
  [![Build Status]]: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
  [1]: https://travis-ci.org/SoilRos/dune-copasi.svg?branch=<branch>
  [![Build Status][1]]: https://travis-ci.org/SoilRos/dune-copasi/branches
  [2]: https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/<branch>?svg=true
  [![Build status][2]]: https://ci.appveyor.com/project/SoilRos/dune-copasi/history
  [#21]: gitlab.dune-project.org/NoneNone/issues/21
  [!20]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/20


Closes #21

Merge branch 'ci_fixes' into 'master'

ref:copasi/dune-copasi

-   add libs to CMake install files
-   fix path to executable for ldd/otool in travis CI
-   remove debugging output from appveyor CI

See merge request [!19]

  [!19]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/19

- add libs to CMake install files
- fix path to executable for ldd/otool in travis CI
- remove debugging output from appveyor CI

Merge branch 'hotfix/fix-setup-image' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

Fix the pipeline where the GitLab CI job setup was failing. The order of the
dune modules was wrong. Additionally, it adds new forms of triggering the
rebuilt of the base image other than using the master branch.

Closes \#

<!-- For automatic closing, do not forget the commas between issue numbers-->

<!--
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A Merge Request should be associated to a certain task or issue.
Its changes are supposed to be merged into the master branch.

Briefly explain __how__ you achieved the proposal of the task.

IMPORTANT: Make sure to set the merge request WIP if you are not finished yet.
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See merge request [!18]

  [!18]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/18