creating a docs setup

# Welcome to MkDocs

# pyThermoGIS

For full documentation visit [mkdocs.org](https://www.mkdocs.org).

**pyThermoGIS** is a Python package that provides API access to the [ThermoGIS](https://www.thermogis.nl/en) doublet simulations and economic calculations. 

## Commands

This package allows a user to simulate geothermal doublets providing the following parameters: 

* `mkdocs new [dir-name]` - Create a new project.

* `mkdocs serve` - Start the live-reloading docs server.

* `mkdocs build` - Build the documentation site.

* `mkdocs -h` - Print help message and exit.

- Top depth

- Thickness (mean & standard deviation)

- Porosity

- Permeability (mean & standard deviation)

- Temperature (Optional: if not provided, a temperature gradient will be used)

## Project layout

    mkdocs.yml    # The configuration file.

    docs/

        index.md  # The documentation homepage.

        ...       # Other markdown pages, images and other files.

The code will simulate a Geothermal doublet, utilizing ThermoGIS with DoubletCalc1D as the engine to produce values of:

- power [Mega Watt Hour]

- heat pump power [Mega Watt Hour]

- capex (Capital expenditure) [Million €]

- opex (Operational expenditure) [€/kW]

- utc (Unit Technical Cost [€cent/kWH])

- npv (Net-present-value)

- hprod (Discounted Heat Produced)

- cop 

- cophp

- pressure 

- flow rate [m³/hr]

- well depth [m]

For details on how these parameters are calculated we refer users to the [Thermogis calculation webpage](https://www.thermogis.nl/en/calculation-model)

The simulations are conducted in Java, and this package uses [JPype](https://jpype.readthedocs.io/en/latest/userguide.html) to create a Python-Java binding.

It uses [xarray](https://docs.xarray.dev/en/stable/index.html) to handle input and output parameters, a User should inform themselves and learn the usage of the Xarray package.

This module can be combined with the [pygridsio](https://pypi.org/project/pygridsio/) package to read and process 2D raster data.

## What can this package *not* do?

This package provides a narrow access point to the doublet simulations and UTC economic calculations from ThermoGIS, it does not implement the following ThermoGIS processes/methodologies:

- Stacking of Aquifers

- Calculation of Potential maps

- Calculation of Resources

- Calculation of Overview maps

- HTO-ATES simulations

- Property Modelling

- Temperature Modelling

- Reading, and writing of grid files (Checkout [pygridsio](https://pypi.org/project/pygridsio/))

# Installation

PyThermoGIS has been designed to be used in one of two ways; either as a python package you import into your own python projects, or as a standalone package where you can access the calculations via a CLI.

Either way, you need to Install a Java 17 VM and store the ThermoGIS Jar:

## 1. Install Java 17 and Download the ThermoGIS JAR

This package requires a Java 17 VM (we recommend using [Amazon Corretto 17](https://docs.aws.amazon.com/corretto/latest/corretto-17-ug/downloads-list.html)) and a ThermoGIS Jar file (Version >=1.7).

*(You can find the JAR in this repository's resources folder or request it via the [ThermoGIS website](https://www.thermogis.nl/).)*

### 🧱 Required Environment Variables

- `JAVA_HOME`: Path to the Java 17 installation

  *(e.g., on Windows: `C:\Program Files\Amazon Corretto\jdk17.0.0_0`)*

- `THERMOGIS_JAR`: Path to the ThermoGIS `.jar` file; __including__ the name of the jar file

  *(e.g. `/path/to/the/thermogis-1.7.0-shaded.jar`)*

---

## 2a) import pyThermoGIS into your own python projects

This repository is currently hosted privately on [ci.tno.nl](https://ci.tno.nl) and will become publicly available in the future. 

Until then you will need to use Gitlab API keys to use this module:

### 🔐 Step-by-step Installation

##### a. Create a Personal Access Token (PAT)

1. Log in to GitLab.

2. Navigate to **Preferences > Access Tokens**.

3. Create a token with the following scopes:

   - `read_api`

   - `read_package_registry`

4. Copy and store the token securely (you won’t be able to see it again).

#### b. Install pyThermoGIS using pip

```

pip install pythermogis --index-url https://__token__:<your_personal_token>@ci.tno.nl/gitlab/api/v4/projects/18271/packages/pypi/simple

```

> 💡 If you already use another index, consider using `--extra-index-url` instead.

---

### 2b) Installation for further development or Standalone usage

Clone and install from source with Pixi:

```bash

git clone https://gitlab.com/your-repo/pythermogis.git

cd pythermogis

pixi install

```

(Make sure you have followed the step installing a Java17 VM and saving the ThermoGIS Jar)

---

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nav:

  - Home: index.md

  - Installation: install/install.md

  - Theory: theory/modelling_geothermal_doublets.md

  - Usage:

      - Basic Usage: usage/basic_usage.md

      - Examples: usage/advanced_examples.md

  - API Reference:

      - doublet: reference/doublet.md

      - utc_properties: reference/utc_properties.md