Update documentation for config

README.md

@@ -3,8 +3,8 @@
 [![Documentation Status](https://readthedocs.org/projects/fwl-proteus/badge/?version=latest)](https://fwl-proteus.readthedocs.io/en/latest/?badge=latest)
 [![License](https://img.shields.io/badge/License-Apache_2.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
-![PROTEUS banner](https://raw.githubusercontent.com/FormingWorlds/PROTEUS/main/docs/images/PROTEUS_white.png#gh-light-mode-only)
-![PROTEUS banner](https://raw.githubusercontent.com/FormingWorlds/PROTEUS/main/docs/images/PROTEUS_black.png#gh-dark-mode-only)
+![PROTEUS banner](https://raw.githubusercontent.com/FormingWorlds/PROTEUS/main/docs/assets/PROTEUS_white.png#gh-light-mode-only)
+![PROTEUS banner](https://raw.githubusercontent.com/FormingWorlds/PROTEUS/main/docs/assets/PROTEUS_black.png#gh-dark-mode-only)
 
 # PROTEUS Framework for Planetary Evolution
 
@@ -42,13 +42,11 @@ Hamish Innes            | hamish.innes[at]fu-berlin.de |
 
 | Object                | Description                                               |
 | -                     | -                                                         |
-| `start_proteus.py`    | Main PROTEUS Python script                                |
 | `README.md`           | Overview file                                             |
 | `pyproject.toml`	    | Project configuration file                                |
 | `CODE_OF_CONDUCT.md`	| Project code of conduct                                   |
 | `LICENSE.txt`         | Project license                                           |
 | `src/proteus`         | Source code for PROTEUS                                   |
-| `SPIDER/`             | Submodule SPIDER                                          |
 | `output/`             | Output folder with subfolders for each model run          |
 | `input/`              | Input folder (e.g. stellar spectra, example configs)      |
 | `docs/`			    | Documentation source files                                |

docs/config.md

@@ -0,0 +1,140 @@
+# Configuration file
+
+PROTEUS uses [TOML](https://toml.io/en/) to structure its configuration files.
+
+All of the parameters required to run the model are
+listed below with short explanations of their purpose and the values
+they accept. Configuration files can contain blank lines. Comments are
+indicated with a `#` symbol. Whitespace indentation is purely stylistic.
+
+Not all of these parameters will be used, depending on the
+configuration, but they must all be provided.
+
+## Adding a new parameter
+
+So, you are developing a new model and want to add some parameters?
+Follow these steps:
+
+1. Decide on a good parameter name (*e.g.* `my_star_var`), and under which section to place it (*e.g.* `star`).
+   Add the new variable to the [config submodule](https://github.com/FormingWorlds/PROTEUS/tree/main/src/proteus/config/_star.py).
+2. Add the type for your variable, *e.g.* [float][], [int][], [str][].
+   You can also add complex types, please check the [code](https://github.com/FormingWorlds/PROTEUS/tree/main/src/proteus/config) for inspiration.
+3. Add a [validator](https://www.attrs.org/en/stable/api.html#module-attrs.validators)!
+   If your variable has a maximum value (*e.g.* 10), you can add a validator to make sure
+   that any values above 10 are rejected: `my_star_var: float = field(validator=attrs.validators.le(10))`
+4. Add a description for your new variable under `Attributes` in the docstring.
+   The documentation uses the description to generate this documentation.
+5. Update the example [input configs](https://github.com/FormingWorlds/PROTEUS/tree/main/input).
+   Proteus checks tests all input configs in this directory are valid.
+6. Use your parameter in your code, *i.e.*: `config.star.my_star_var`
+
+```python title="src/proteus/config/_star.py"
+class Star:
+    """Stellar parameters.
+
+    Attributes
+    ----------
+    my_star_var: float
+        Star variable, must be 10 or lower!
+    """
+    my_star_var: float = field(validator=attrs.validators.le(10))
+```
+
+Proteus uses [attrs](https://www.attrs.org) for its
+parameter handling. Please see the [examples](https://www.attrs.org/en/stable/examples.html)
+for more information how to work with attrs.
+
+### Examples
+
+Have a look at the [input configs](https://github.com/FormingWorlds/PROTEUS/tree/main/input)
+for ideas of how to set up your config in practice.
+
+## Root parameters
+
+::: proteus.config._config
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## General parameters
+
+::: proteus.config._params
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Star
+
+::: proteus.config._star
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Star system and planetary orbit
+
+::: proteus.config._orbit
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Planetary structure
+
+::: proteus.config._struct
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Atmosphere climate
+
+::: proteus.config._atmos_clim
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Atmospheric escape
+
+::: proteus.config._escape
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Magma ocean / mantle
+
+::: proteus.config._interior
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Outgassing
+
+::: proteus.config._outgas
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source
+
+## Delivery
+
+::: proteus.config._delivery
+    options:
+      heading_level: 3
+      show_root_heading: False
+      show_root_toc_entry: False
+      members_order: source