documentation fixing headers and index

tardis-sn · Dec 3, 2024 · 38953cd · 38953cd
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diff --git a/docs/Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs.ipynb b/docs/Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Custom Star Model"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -12,7 +19,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Using MARCS to get .mod files\n",
+    "## Using MARCS to get .mod files\n",
     "\n",
     "STARDIS uses files from the [MARCS site](https://marcs.oreme.org/), which \"contains about 52,000 stellar atmospheric models of spectral types F, G and K\". Here we will only be discussing the aspects of MARCS needed for STARDIS. To get started, [go to the 'Search Marcs' tab of the MARCS site](https://marcs.oreme.org/data/)"
    ]
@@ -89,7 +96,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### One last thing: gzipped files\n",
+    "## gzipped files\n",
     "\n",
     "when you download a mod file from MARCS, it will be gzipped (shown by the file ending with '.mod.gz'). By default STARDIS will assume you have extracted the file, however you can add a line to the yaml file 'gzipped: True' as shown below and STARDIS will take care of this for you.\n",
     "\n",
@@ -104,6 +111,11 @@
     "\n",
     "```"
    ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": []
   }
  ],
  "metadata": {

diff --git a/docs/Custom_atomic_data/Custom_atomic_data.ipynb b/docs/Custom_atomic_data/Custom_atomic_data.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Custom Atomic Data"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -53,7 +60,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Using VALD linelists\n",
+    "## Using VALD linelists\n",
     "\n",
     "Possibly one of the most important reasons you would want to use a custom atomic data file would be to take advantage of a tailored VALD linelist. You can refer to [VALD's documentation](https://www.astro.uu.se/valdwiki) for information on these lists if you are unfamiliar. To create a detailed and accurate stellar spectrum, we highly recommend looking into using a VALD linelist bundled into your atomic data."
    ]

diff --git a/docs/index.rst b/docs/index.rst
@@ -10,14 +10,20 @@ This is the documentation for STARDIS.
    Quickstart <quickstart/quickstart>
    Downloading and Installation <installation>
    Physics of STARDIS <physics/physics_of_stardis>
+   Contributing <contributing>
+   Bibliography <bibliography>
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Example Notebooks
+
    Custom Atomic Data <Custom_atomic_data/Custom_atomic_data>
    Possible STARDIS Outputs <possible_stardis_outputs/possible_stardis_outputs>
    Custom Star Model <Custom_Star_Model_with_Marcs/Custom_Star_Model_with_Marcs>
    Using STARDIS in Parallel <using_stardis_in_parallel/stardis_in_parallel>
    Changing Parameters <Changing_Parameters/Changing_Parameters>
-   Example Notebooks <example_notebooks/rotation_broadening>
-   Contributing <contributing>
-   Bibliography <bibliography>
+   Rotation Broadening <rotation_broadening/rotation_broadening>
+
 
 Indices and tables
 ==================

diff --git a/docs/possible_stardis_outputs/possible_stardis_outputs.ipynb b/docs/possible_stardis_outputs/possible_stardis_outputs.ipynb
@@ -1,5 +1,12 @@
 {
  "cells": [
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "# Possible STARDIS Outputs"
+   ]
+  },
   {
    "cell_type": "markdown",
    "metadata": {},
@@ -25,13 +32,15 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "#### STARDIS simulations contain a variety of information, and depending on your needs you can have different parts of a simulation returned."
+    "## Selecting Result Options"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
+    "STARDIS simulations contain a variety of information, and depending on your needs you can have different parts of a simulation returned.\n",
+    "\n",
     "There are three parts of the simulation you can choose to return:\n",
     "- Stellar_Model\n",
     "- Stellar_Plasma\n",
@@ -40,13 +49,6 @@
     "Regardless of which are set to return, the simulation will always produce the stellar spectrum (such as the one displayed in the quickstart notebook)."
    ]
   },
-  {
-   "cell_type": "markdown",
-   "metadata": {},
-   "source": [
-    "## Selecting Result Options"
-   ]
-  },
   {
    "cell_type": "markdown",
    "metadata": {},

diff --git a/...ample_notebooks/rotation_broadening.ipynb → ...tion_broadening/rotation_broadening.ipynb b/...ample_notebooks/rotation_broadening.ipynb → ...tion_broadening/rotation_broadening.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "# STARDIS"
+    "# Rotation Broadening"
    ]
   },
   {

diff --git a/..._notebooks/rotation_broadening_config.yml → ...broadening/rotation_broadening_config.yml b/..._notebooks/rotation_broadening_config.yml → ...broadening/rotation_broadening_config.yml
diff --git a/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb b/docs/using_stardis_in_parallel/stardis_in_parallel.ipynb
@@ -4,7 +4,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "### Setting number of threads used in running a STARDIS simulation"
+    "# Using STARDIS in Parallel"
    ]
   },
   {