Add paper (#29)

TEB-model · Jun 9, 2020 · fb11cad · fb11cad
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diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md
@@ -1,5 +1,5 @@
 # How to contribute
 
-Thank you for considering contributing. In general, you can contribute by reporting an issue or by directly contributing to the source code. For the latter, fork our repository, clone the fork, make your changes, and create a pull request (PR) with a **clear description** of your changes -- if you are unfamiliar about forking/creating PR, please see [this guide](https://guides.github.com/activities/forking/) first. If/when your changes are merged, you will appear as one of our [Contributors](https://github.com/teb-model/teb/graphs/contributors). If you would like to know more about specific development guidelines and testing, please refer to our [README.md](README.md) file.
+Thank you for considering contributing. In general, you can contribute by reporting an issue or by directly contributing to the source code. For the latter, fork our repository, clone the fork, make your changes, and create a pull request (PR) with a **clear description** of your changes -- if you are unfamiliar about forking/creating PRs, please see [this guide](https://guides.github.com/activities/forking/) first. If/when your changes are merged, you will appear as one of our [Contributors](https://github.com/teb-model/teb/graphs/contributors). If you would like to know more about specific development guidelines and testing, please refer to our [README.md](README.md) file.
 
 If you would like to report a bug, please check if similar issue have already been reported at [https://github.com/teb-model/teb/issues](https://github.com/teb-model/teb/issues). If none exist please create a new issue, including as many details as possible about your system and issue encountered.
diff --git a/README.md b/README.md
@@ -5,7 +5,7 @@
 
 [![Build Status](https://travis-ci.com/teb-model/teb.svg?branch=master)](https://travis-ci.com/teb-model/teb)
 
-[Overview](#overview) | [Prerequisites](#prerequisites) | [Installation](#installation) | [Documentation](#documentation) | [Example application](#example-application) | [Testing](#testing) | [How to cite](#how-to-cite) | [Contributing](#contributing) | [Copyright and license](#copyright-and-license) | [References](#references)
+[Overview](#overview) | [Prerequisites](#prerequisites) | [Installation](#installation) | [Documentation](#documentation) | [Example application](#example-application) | [Testing](#testing) | [How to cite](#how-to-cite) | [Contributing](#contributing) | [Copyright and license](#copyright-and-license)
 </div>
 
 ## Overview
@@ -25,13 +25,14 @@ This enhanced software and platform for TEB (Town Energy Balance; [Masson, 2000]
 
 To build the Town Energy Balance (TEB) executable and library on Windows, Linux and macOS, clone this repository and run the following commands from your command prompt:
 
-```bash
-mkdir build && cd build
+```
+mkdir build
+cd build
 cmake -DCMAKE_BUILD_TYPE=Release ..
 cmake --build .
 ```
 
-By default, we set the real type to an 8 byte wide. This behaviour is controlled by the optional `USE_REAL8` flag (default ON).
+By default, we set the real type to an 8 byte wide. This behavior is controlled by the optional `USE_REAL8` flag (default ON).
 
 <details>
 <summary>Note for Windows Users</summary>
@@ -52,28 +53,28 @@ cmake --build .
 
 ## Documentation
 
-This section includes links to software and model documentation. If you are new to TEB and simply looking to easily get started, please refer to the [Example application](#example-application) instead.
+This section includes links to software and model documentation. If you are new to TEB and simply looking to easily get started, please refer to the [example application](#example-application) instead.
 
 ### Software
 
-See the [software documentation](docs/software-docs.md) for a general overview. For configuration options available at runtime please refer to [namelist options](docs/namelist-options.md).
+See [software documentation](docs/software-docs.md) for a general overview. For configuration options available at runtime please refer to [namelist options](docs/namelist-options.md).
 
 ### Scientific
-The complete scientific documentation is included with the [SURFEX scientific documentation](http://www.umr-cnrm.fr/surfex/IMG/pdf/surfex_scidoc_v8.1.pdf).
+The complete scientific documentation is included in the [SURFEX scientific documentation](http://www.umr-cnrm.fr/surfex/IMG/pdf/surfex_scidoc_v8.1.pdf).
 
 
 ### Code browser
-The API documentation and code browser is available at [https://teb-model.github.io/teb](https://teb-model.github.io/teb).
+The code browser is available at [https://teb-model.github.io/teb](https://teb-model.github.io/teb).
 
 
 ## Example application
 
-[`tutorial.ipynb`](examples/CAPITOUL/tutorial.ipynb) provides a simple tutorial detailing how TEB can be used to to estimate the buildings' energy demand for cooling using sample data and parameters from the CAPITOUL (Canopy and Aerosol Particles Interactions in TOulouse Urban Layer; Masson et al., 2008) campaign.
+To get started with TEB, see [`examples/CAPITOUL/README.md`](examples/CAPITOUL/README.md). The folder contains a simple tutorial in [Jupyter Notebook](https://jupyter.org/) to estimate the buildings' energy demand for cooling using TEB and data and parameters from the CAPITOUL (Canopy and Aerosol Particles Interactions in TOulouse Urban Layer; [Masson et al., 2008](https://doi.org/10.1007/s00703-008-0289-4)) campaign.
 
 
 ## Testing
 
-Tests are run using the CAPITOUL data provided in `examples/CAPITOUL`. Tests are found in `tests/tests.py` and an overview is given in [`tests/README.md`](tests/README.md). All tests are automatically run at every commit using Continous Integration. If you are looking to run your tests locally on Linux or macOS, first make sure you have installed all the [prerequisites](#prerequisites), then from the command prompt:
+Tests are run using the CAPITOUL data provided in `examples/CAPITOUL`. Tests are found in `tests/tests.py` and an overview is given in [`tests/README.md`](tests/README.md). All tests are automatically run at every commit using Continuos Integration. If you are looking to run your tests locally on Linux or macOS, first make sure you have installed all the [prerequisites](#prerequisites), then from the command prompt:
 
 ``` bash
 python -m pip install -r requirements.txt
@@ -94,19 +95,18 @@ python tests/test.py --build_type=Debug --case=integration
 
 When using the TEB software, please cite both model, and software (with version) as follows:
 
-| Model        | Software | Version*                   |
-| ------------ | -------- | -------------------------- |
-| Masson, 2000 | XXXX     | [see Zenodo](https://XXXX) |
+| Physical model                                          | This software                                      | Version*       |
+| ------------------------------------------------------- | -------------------------------------------------- | -------------- |
+| [Masson, 2000](https://doi.org/10.1023/A:1002463829265) | [Meyer, 2020](https://doi.org/10.21105.joss.02008) | [see Zenodo]() |
 
 
 The corresponding reference list should be as follows:
 
 > Masson, V., 2000: A Physically-Based Scheme For The Urban Energy Budget In Atmospheric Models. Boundary-Layer Meteorology, 94, 357–397, https://doi.org/10.1023/A:1002463829265.
 
-> XXXX *In preparation*
+> Meyer, D., Schoetter, R., Masson, V., Grimmond, S., 2020: Enhanced software and platform for the Town Energy Balance (TEB) model. Journal of Open Source Software. https://doi.org/10.21105.joss.02008.
 
-
-*please make sure to cite the same version you are using with the correct DOI. For a list of all available versions see the list of versions on [Zenodo](XXXX).
+*please make sure to cite the same version you are using with the correct DOI. For a list of all available versions see the list of versions on [Zenodo]().
 
 
 ## Contributing
@@ -116,11 +116,4 @@ Please see the [CONTRIBUTING.md](CONTRIBUTING.md) file.
 
 ## Copyright and license
 
-General copyright name and year is clearly stated at the top of each source file. All software released under [CeCILL version 2.1](Licence_CeCILL_V2.1-en.txt).
-
-
-## References
-
-> Masson, V., 2000: A Physically-Based Scheme For The Urban Energy Budget In Atmospheric Models. Boundary-Layer Meteorology, 94, 357–397, https://doi.org/10.1023/A:1002463829265.
-
-> Masson, V., and Coauthors, 2008: The Canopy and Aerosol Particles Interactions in TOulouse Urban Layer (CAPITOUL) experiment. Meteorol Atmos Phys, 102, 135–157, https://doi.org/10.1007/s00703-008-0289-4.
+Copyright stated at the top of source files. Software released under [CeCILL version 2.1](Licence_CeCILL_V2.1-en.txt).
diff --git a/docs/tutorial.ipynb b/docs/tutorial.ipynb
diff --git a/examples/CAPITOUL/README.md b/examples/CAPITOUL/README.md
@@ -1,6 +1,6 @@
 # CAPITOUL case
 
-In this folder data are provided to run TEB (Masson, 2000) with sample input data from the CAPITOUL (Canopy and Aerosol Particles Interactions in TOulouse Urban Layer; Masson et al., 2008) campaign. Data are provided for demonstration purposes only and are not quality controlled (i.e. should not be used to conduct scientific experiments). Both data and tutorial are only meant to guide the user through setting up a simple experiment in TEB. If you are looking to conduct a scientific experiment, please download and process the data yourself (see the [software documentation page](../../docs/software-docs.md)) and amend the input namelist accordingly (see the [namelist options page](../../docs/namelist-options)). 
+In this folder data are provided to run TEB (Masson, 2000) with sample input data from the CAPITOUL (Canopy and Aerosol Particles Interactions in TOulouse Urban Layer; Masson et al., 2008) campaign. Data are provided for demonstration purposes only and are not quality controlled (i.e. should not be used to conduct scientific experiments). Both data and tutorial are only meant to guide the user through setting up a simple experiment in TEB. If you are looking to conduct a scientific experiment, please download and process the data yourself (see the [software documentation page](../../docs/software-docs.md)) and amend the input namelist accordingly (see the [namelist options page](../../docs/namelist-options.md)). 
 
 ## Install Python packages
 

diff --git a/examples/CAPITOUL/tutorial.ipynb b/examples/CAPITOUL/tutorial.ipynb
diff --git a/external/minimal-dx/CMakeLists.txt b/external/minimal-dx/CMakeLists.txt
@@ -5,7 +5,7 @@ include(ExternalProject)
 
 ExternalProject_Add(minimaldx-project
     GIT_REPOSITORY https://github.com/dmey/minimal-dx.git
-    GIT_TAG master
+    GIT_TAG 0.1.3
     CMAKE_ARGS
         -DCMAKE_BUILD_TYPE=${CMAKE_BUILD_TYPE}
         -DCMAKE_Fortran_COMPILER=${CMAKE_Fortran_COMPILER}