Merge branch '10-include-semantic-versioning' into 'master'

ref:copasi/dune-copasi Closes [#10]

See merge request [!14]

  [#10]: gitlab.dune-project.org/NoneNone/issues/10
  [!14]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/14


Closes #10

Merge branch 'remove_non_ascii_chars' into 'master'

ref:copasi/dune-copasi

-   was causing compile error with clang on linux for me due to
    `'\xC2', '\xA0'` chars not being constexpr:
    -   `Dune::Logging::format_string<char, 'T', 'i', 'm', 'e', ' ', 'S', 't', 'e', 'p', ' ', '{', ':', '.', '2', 'e', '}', ' ', '+', ' ', '{', ':', '.', '2', 'e', '}', '\xC2', '\xA0', '-', '>', ' ', '{', ':', '.', '2', 'e', '}'>, 0>'`

See merge request [!15]

  [!15]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/15

Liam Keegan authored 5 years ago and Santiago Ospina De Los Ríos committed 5 years ago

- was causing compile error with clang due to '\xC2', '\xA0' chars:
  - Dune::Logging::format_string<char, 'T', 'i', 'm', 'e', ' ', 'S', 't', 'e', 'p', ' ', '{', ':', '.', '2', 'e', '}', ' ', '+', ' ', '{', ':', '.', '2', 'e', '}', '\xC2', '\xA0', '-', '>', ' ', '{', ':', '.', '2', 'e', '}'>, 0>'

Merge branch '17-travis-pipeline-fails-at-building-state' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

Fixes Travis pipeline

### 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]]
    -   [x] [![Build status][2]]

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

### Related issues

Closes [#17]

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

<!--
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Its changes are supposed to be merged into the master branch.

Briefly explain __how__ you achieved the proposal of the task.

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See merge request [!13]

  [Build Status]: https://gitlab.dune-project.org/copasi/dune-copasi/badges/17-travis-pipeline-fails-at-building-state/pipeline.svg
  [![Build Status]]: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
  [1]: https://travis-ci.org/SoilRos/dune-copasi.svg?branch=17-travis-pipeline-fails-at-building-state
  [![Build Status][1]]: https://travis-ci.org/SoilRos/dune-copasi/branches
  [2]: https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/17-travis-pipeline-fails-at-building-state?svg=true
  [![Build status][2]]: https://ci.appveyor.com/project/SoilRos/dune-copasi/history
  [#17]: gitlab.dune-project.org/NoneNone/issues/17
  [!13]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/13


Closes #17

Merge branch 'cmake_install_fix' into 'master'

See merge request [!11]

  [!11]: Nonecopasi/dune-copasi/merge_requests/11

[ci-skip]

[skip-ci]

[skip-ci]

[ci-skip]

Merge branch '2-include-more-options-to-initializate-stetes' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

Implements TIFF input data for the solver.

The section model.data is read if defined. It should contain a key assigned to
a path of a valid gayscale tiff of 16 bits. e.g.

    [model.data]
    tiff_data = data/tiff/flower-minisblack-16.tif

The key can be latter used in the initial condition of a compartment as a
function of the **grid** \$x\$ and \$y\$ coordinates. If arguments are out of
bound of the tiff image the function will return 0.

    [model.<compartment>.initial]
    u_0 = tiff_data(x,y)

The arguments of the function may be anything defined on muparser. This is
useful to shift and scale the data. Additionaly, data is interpreted between 0
and 1 depending on the photometric information (*zero_is_white* or
*zero_is_black*). In case data has another scale, its result may be scaled as
any other function in muparser. e.g.

    [model.<compartment>.initial]
    u_0 = 1.3+5.1*tiff_data(2*x, y+0.25)

### Is there something that needs to be double checked?

<!-- Is there something a reviewer should look out for _especially_? -->

No

### Can this MR be accepted?

-   [x] Implemented \...
    -   [x] Generic tiff reader
    -   [x] muParser function for tiff data
-   [x] Added/Updated tests:
    -   [x] Unit test for tiff reader
    -   [x] System test for initial condition
-   [ ] 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 [#2]

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

<!--
PLEASE READ THIS!

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.
-->

See merge request [!3]

  [Build Status]: https://gitlab.dune-project.org/copasi/dune-copasi/badges/2-include-more-options-to-initializate-stetes/pipeline.svg
  [![Build Status]]: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
  [1]: https://travis-ci.org/SoilRos/dune-copasi.svg?branch=2-include-more-options-to-initializate-stetes
  [![Build Status][1]]: https://travis-ci.org/SoilRos/dune-copasi
  [2]: https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/2-include-more-options-to-initializate-stetes?svg=true
  [![Build status][2]]: https://ci.appveyor.com/project/SoilRos/dune-copasi/history
  [#2]: gitlab.dune-project.org/NoneNone/issues/2
  [!3]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/3


Closes #2

[ci-skip]

[ci skip]

Merge branch '6-use-dune-grid-master-branch' into 'master'

ref:copasi/dune-copasi

Merge branch '5-add-analytic-jacobians' into 'master'

ref:copasi/dune-copasi

### What does this MR do?

It implements anaylitic jacobians for volume and skeleton integrals in the
local operator. Additionally it add installation rules for CMake.

### Is there something that needs to be double checked?

<!-- Is there something a reviewer should look out for _especially_? -->

No.

### Can this MR be accepted?

-   [x] Implemented
    -   [x] jacobian_volume
    -   [x] jacobian_skeleton
-   [x] Added tests:
    -   [x] Both numerical and analyitical jacobians are tested against a
        reference solution.
-   [ ] Pipelines passing <!-- please check for new warnings -->
     <!-- change all occurences of <branch> for your branch name -->

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

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

### Related issues

Closes [#5]

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

<!--
PLEASE READ THIS!

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.
-->

See merge request [!7]

  [Build Status]: https://gitlab.dune-project.org/copasi/dune-copasi/badges/5-add-analytic-jacobians/pipeline.svg
  [![Build Status]]: https://gitlab.dune-project.org/copasi/dune-copasi/pipelines
  [1]: https://travis-ci.org/SoilRos/dune-copasi.svg?branch=5-add-analytic-jacobians
  [![Build Status][1]]: https://travis-ci.org/SoilRos/dune-copasi
  [2]: https://ci.appveyor.com/api/projects/status/6605joy2w17qvca8/branch/5-add-analytic-jacobians?svg=true
  [![Build status][2]]: https://ci.appveyor.com/project/SoilRos/dune-copasi/branch/5-add-analytic-jacobians
  [#5]: gitlab.dune-project.org/NoneNone/issues/5
  [!7]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/7


Closes #5

[skip-ci]

Merge branch '3-add-ci-for-windows-and-macos' into 'master'

ref:copasi/dune-copasi Closes [#3]

See merge request [!9]

  [#3]: gitlab.dune-project.org/NoneNone/issues/3
  [!9]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/9


Closes #3

Merge branch '4-add-gitlab-description-templates-for-mr-and-issues' into 'master'

ref:copasi/dune-copasi Closes [#4]

See merge request [!6]

  [#4]: gitlab.dune-project.org/copasi/dune-copasi/issues/4
  [!6]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/6


Closes #4

[skip-ci]

Merge branch 'cmake_fix' into 'master'

ref:copasi/dune-copasi

-   fix "INTERACE" typo in Findmuparser cmake module
    -   for static muparser library, need to define "MUPARSER_STATIC" (on
        windows)
        -   changed Findmuparser to do so if DUNE_USE_ONLY_STATIC_LIBS is
            defined
        -   otherwise behaviour is unchanged
    -   on windows mkdir() only takes one argument

See merge request [!4]

  [!4]: gitlab.dune-project.org/copasi/dune-copasi/merge_requests/4

  - fix "INTERACE" typo in Findmuparser cmake module
  - for static muparser library, need to define "MUPARSER_STATIC" (on windows)
    - changed Finemuparser to do so if DUNE_USE_ONLY_STATIC_LIBS is defined
    - otherwise behaviour is unchanged
  - on windows mkdir() only takes one argument