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Update README with latest information and links to doc #161

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@@ -1,13 +1,16 @@
<!-- PROJECT SHIELDS -->
[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.10562516.svg)](https://doi.org/10.5281/zenodo.10562516)
[![DOI][zenodo-shield]][zenodo-url]
[![GPL v3 License][license-shield]][license-url]
[![Unit tests][github-actions-unit-tests-shield]][github-actions-unit-tests-url]
[![CodeQL][github-actions-codeql-shield]][github-actions-codeql-url]
[![Documentation Status][readthedocs-shield]][readthedocs-url]
[![Issues][issues-shield]][issues-url]
[![Contributors][contributors-shield]][contributors-url]
[![GitHub Commit Activity][commit-activity-shield]][commit-activity-url]
[![Forks][forks-shield]][forks-url]
[![Stargazers][stars-shield]][stars-url]
[![Issues][issues-shield]][issues-url]
[![LabSid YouTube Channel][youtube-shield]][youtube-url]
<!-- [![GPL v3 License][license-shield]][license-url] -->


<!-- PROJECT LOGO -->
<br />
Expand All @@ -31,42 +34,14 @@
</p>



<!-- TABLE OF CONTENTS -->
<details open="open">
<summary><h2 style="display: inline-block">Table of Contents</h2></summary>
<ol>
<li>
<a href="#about-the-project">About The Project</a>
<ul>
<li><a href="#main-features">Main features</a></li>
</ul>
</li>
<li>
<a href="#getting-started">Getting Started</a>
<ul>
<li><a href="#prerequisites">Prerequisites</a></li>
<li><a href="#installation">Installation</a></li>
</ul>
</li>
<li><a href="#usage">Usage</a></li>
<li><a href="#roadmap">Roadmap</a></li>
<li><a href="#contributing">Contributing</a></li>
<li><a href="#license">License</a></li>
<li><a href="#contact">Contact</a></li>
<li><a href="#acknowledgements">Acknowledgements</a></li>
</ol>
</details>


<!-- ABOUT THE PROJECT -->
## About The Project

The Rainfall rUnoff Balance Enhanced Model (RUBEM) is a hydrological model for transforming precipitation into surface and subsurface runoff. The model is based on equations that represent the physical processes of the hydrological cycle, with spatial distribution defined by pixel, in distinct vegetated and non-vegetated covers, and has the flexibility to study a wide range of applications, including impacts of changes in climate and land use, has flexible spatial resolution, the inputs are raster-type matrix files obtained from remote sensing data and operates with a reduced number of parameters arranged in a configuration file that facilitates its modification throughout the area.
The Rainfall rUnoff Balance Enhanced Model (RUBEM) [^MELLOetal2022a][^MELLOetal2022b] is a hydrological model for transforming precipitation into surface and subsurface runoff. The model is based on equations that represent the physical processes of the hydrological cycle, with spatial distribution defined by pixel, in distinct vegetated and non-vegetated covers, and has the flexibility to study a wide range of applications, including impacts of changes in climate and land use, has flexible spatial resolution, the inputs are raster-type matrix files obtained from remote sensing data and operates with a reduced number of parameters arranged in a configuration file that facilitates its modification throughout the area.

### Main features

The model was developed based on classical concepts of hydrological processes and equations based mainly on SPHY (TERINK et al., 2015), WEAP (YATES et al., 2005), and WetSpass-M (ABDOLLAHI et al. , 2017). The main features of the developed model are:
The model was developed based on classical concepts of hydrological processes and equations based mainly on SPHY [^TERINKetal2015], WEAP [^YATESetal2005], and WetSpass-M [^ABDOLLAHIetal2017]. The main features of the developed model are:

- Distributed monthly step model;
- Hydrological process based on soil water balance in each pixel, and flow total calculated after composition of the resulting accumulated flow, according to Direction drainage network flow established by the digital elevation model (DEM);
Expand All @@ -83,35 +58,25 @@ To get a local copy up and running follow these simple steps.

This is an example of how to list things you need to use the software and how to install them.

* From Miniconda base envionment create a new conda envionment
- From Miniconda base envionment create a new conda envionment

```sh
conda create --name rubem python=3.7
conda env create -n rubem --file env-prod.yml
```
* Activate the new environment

Windows

```powershell
conda activate rubem
```

Linux, macOS

```sh
source activate rubem
```

- Activate the new environment

- Windows

```powershell
conda activate rubem
```

* Install GDAL conda package

```sh
conda install -c conda-forge gdal
```

* Install PCRaster conda package

```sh
conda install -c conda-forge pcraster
```
- Linux, macOS

```sh
source activate rubem
```

### Installation

Expand All @@ -122,16 +87,19 @@ This is an example of how to list things you need to use the software and how to
<!-- USAGE EXAMPLES -->
## Usage

* Typical usage example
```sh
python rubem.py --configfile config.ini
```
* Help usage example
```sh
python rubem.py -h
```
- Typical usage example

```sh
python rubem --configfile config.ini
```

- Help usage example

_For more examples, please refer to the [Documentation](https://rubem.readthedocs.io/en/latest)_.
```sh
python rubem -h
```

_For more examples, please refer to the [user guide](https://rubem.readthedocs.io/en/latest/userguide.html) and [tutorials](https://rubem.readthedocs.io/en/latest/tutorials.html)._

<!-- ROADMAP -->
## Roadmap
Expand All @@ -147,30 +115,35 @@ Contributions are what make the open source community such an amazing place to b
<!-- LICENSE -->
## License

Distributed under the GPLv3 License. See [`LICENSE.md`](https://github.com/LabSid-USP/RUBEM/blob/main/LICENSE.md) for more information.
Distributed under the GPLv3 License. See [`LICENSE.md`](https://github.com/LabSid-USP/RUBEM/blob/main/LICENSE) for more information.

<!-- CONTACT -->
## Contact

In any of our communication channels please abide by the [RUBEM Code of Conduct](https://github.com/LabSid-USP/RUBEM). In summary, being friendly and patient, considerate, respectful, and careful in your choice of words.
> [!TIP]
> In any of our communication channels please abide by the [Code of Conduct](https://github.com/LabSid-USP/.github/blob/main/CODE_OF_CONDUCT.md#code-of-conduct). In summary, being friendly and patient, considerate, respectful, and careful in your choice of words.

- Contact us at: [[email protected]](mailto:[email protected])

- FAQ: [https://rubem.readthedocs.io/en/latest/faq.html](https://rubem.readthedocs.io/en/latest/faq.html)
- Support Form: [https://forms.gle/JmxWKoXh4C29V2rD8](https://forms.gle/JmxWKoXh4C29V2rD8)

- Project Link: [https://github.com/LabSid-USP/RUBEM](https://github.com/LabSid-USP/RUBEMHydrological)


<!-- ACKNOWLEDGEMENTS -->
## Acknowledgements

* [Laboratório de Sistemas de Suporte a Decisões Aplicados à Engenharia Ambiental e de Recursos Hídricos](http://labsid.eng.br/Contato.aspx)
* [Departamento de Engenharia Hidráulica e Ambiental da Escola Politécnica da Universidade de São Paulo](http://www.pha.poli.usp.br/)
* [Fundo Patrimonial Amigos da Poli](https://www.amigosdapoli.com.br/)
- [Laboratório de Sistemas de Suporte a Decisões Aplicados à Engenharia Ambiental e de Recursos Hídricos](https://labsid.poli.usp.br/)
- [Departamento de Engenharia Hidráulica e Ambiental da Escola Politécnica da Universidade de São Paulo](http://www.pha.poli.usp.br/)
- [Fundo Patrimonial Amigos da Poli](https://www.amigosdapoli.com.br/)

<!-- MARKDOWN LINKS & IMAGES -->
[zenodo-shield]: https://zenodo.org/badge/DOI/10.5281/zenodo.10562516.svg
[zenodo-url]: https://doi.org/10.5281/zenodo.10562516
[readthedocs-shield]: https://readthedocs.org/projects/rubem/badge/?version=latest
[readthedocs-url]: https://rubem.readthedocs.io/en/latest/?badge=latest
[github-actions-unit-tests-shield]: https://github.com/LabSid-USP/RUBEM/actions/workflows/build-test-micromamba.yml/badge.svg
[github-actions-unit-tests-url]: https://github.com/LabSid-USP/RUBEM/actions/workflows/build-test-micromamba.yml
[github-actions-codeql-shield]: https://github.com/LabSid-USP/RUBEM/actions/workflows/codeql-analysis.yml/badge.svg
[github-actions-codeql-url]: https://github.com/LabSid-USP/RUBEM/actions/workflows/codeql-analysis.yml
[contributors-shield]: https://img.shields.io/github/contributors/LabSid-USP/RUBEM
[contributors-url]: https://github.com/LabSid-USP/RUBEM/graphs/contributors
[commit-activity-shield]: https://img.shields.io/github/commit-activity/m/LabSid-USP/RUBEM
Expand All @@ -182,6 +155,13 @@ In any of our communication channels please abide by the [RUBEM Code of Conduct]
[issues-shield]: https://img.shields.io/github/issues/LabSid-USP/RUBEM
[issues-url]: https://github.com/LabSid-USP/RUBEM/issues
[license-shield]: https://img.shields.io/github/license/LabSid-USP/RUBEM
[license-url]: https://github.com/LabSid-USP/RUBEM/blob/master/LICENSE.md
[license-url]: https://github.com/LabSid-USP/RUBEM/blob/master/LICENSE
[youtube-shield]: https://img.shields.io/youtube/channel/subscribers/UCZOGKRCW5mQOY9_w8L7lKJg
[youtube-url]: https://www.youtube.com/user/labsidengbr

<!-- MARKDOWN REFERENCES -->
[^ABDOLLAHIetal2017]: Abdollahi, K., Bashir, I., Harouna, M., Griensven, A., Huysmans, M., Batelaan, O., Verbeiren, B., A distributed monthly water balance model: formulation and application on Black Volta Basin, Environ Earth Sci, 76:198, 2017. https://doi.org/10.1007/s12665-017-6512-1
[^MELLOetal2022a]: Méllo Júnior, A.V.; Olivos, L.M.O.; Billerbeck, C.; Marcellini, S.S.; Vichete, W.D.; Pasetti, D.M.; da Silva, L.M.; Soares, G.A.d.S.; Tercini, J.R.B. Rainfall Runoff Balance Enhanced Model Applied to Tropical Hydrology. Water 2022, 14, 1958. https://doi.org/10.3390/w14121958
[^MELLOetal2022b]: Méllo Júnior, A.V.; Olivos, L.M.O.; Billerbeck, C.; Marcellini, S.S.; Vichete, W.D.; Pasetti, D.M.; da Silva, L.M.; Soares, G.A.d.S.; Tercini, J.R.B. Rainfall-Runoff Balance Enhanced Model Applied to Tropical Hydrology - Supplementary Document. Zenodo 2022. https://doi.org/10.5281/zenodo.6614981
[^TERINKetal2015]: Terink, W., Lutz, A. F., Simons, G. W. H., Immerzeel, W. W., & Droogers, P. SPHY v2.0: Spatial Processes in HYdrology. Geoscientific Model Development 2015, 8(7), 2009–2034. https://doi.org/10.5194/gmd-8-2009-2015
[^YATESetal2005]: Yates, D., Sieber, J., Purkey, D., & Huber-Lee, A. WEAP21—A Demand-, Priority-, and Preference-Driven Water Planning Model. Water International 2005, 30(4), 487–500. https://doi.org/10.1080/02508060508691893