prepare documentation

docs/conf.py

@@ -23,7 +23,7 @@
     "sphinx_rtd_theme",
     "sphinx.ext.autodoc",
     "sphinx.ext.autosummary",
-    # "myst_parser",
+    "myst_parser",
 ]
 
 templates_path = ["_templates"]

wiki/FAQ.md → docs/faq.md

@@ -1,3 +1,5 @@
+# FAQ
+
 ## How do I create Parker wind profiles?
 
 Add the parameters of the planet/star system to the *$SUNBATHER_PROJECT_PATH/planets.txt* file. Make sure the SED you specify in _planets.txt_ is present in the _$CLOUDY_PATH/data/SED/_ folder in the right format. Then run the `construct_parker.py` module in your terminal (use `-help` to see the arguments). 
@@ -87,4 +89,4 @@ The `construct_parker.py` module always creates a profile up until 20 $R_p$ and
 
 The `convergeT_parker.py` module by default simulates the atmosphere with *Cloudy* up until 8 $R_p$ and this can be changed with the `-altmax` argument. 
 
-The `RT.FinFout()` function by default makes a transit spectrum based on the full *Cloudy* simulation (so up until 8 $R_p$), but you can give an upper boundary in cm with the `cut_at` argument. For example, if you want to include only material up until the planet's Roche radius when making the transit spectrum, it generally doesn't hurt to leave `construct_parker.py` and `convergeT_parker.py` at the default values, and just pass `cut_at=mysimulation.p.Rroche` to `RT.FinFout()` (assuming `mysimulation` is the `tools.Sim` object of your *Cloudy* simulation).
+The `RT.FinFout()` function by default makes a transit spectrum based on the full *Cloudy* simulation (so up until 8 $R_p$), but you can give an upper boundary in cm with the `cut_at` argument. For example, if you want to include only material up until the planet's Roche radius when making the transit spectrum, it generally doesn't hurt to leave `construct_parker.py` and `convergeT_parker.py` at the default values, and just pass `cut_at=mysimulation.p.Rroche` to `RT.FinFout()` (assuming `mysimulation` is the `tools.Sim` object of your *Cloudy* simulation).

wiki/Glossary.md → docs/glossary.md

@@ -1,3 +1,4 @@
+# Glossary
 This wiki page is a glossary that provides additional information on various modules/classes/functionalities included in _sunbather_. We also refer to "Hazy", which is the official documentation of _Cloudy_ and can be found in your _$CLOUDY_PATH/docs/_ folder. 
 
 

docs/index.md

@@ -0,0 +1,16 @@
+# sunbather documentation
+
+Welcome to the _sunbather_ docs! On the left side, you\'ll find the
+table of contents.
+
+![Sunbather logo](logo_text.png)
+
+```{toctree} Table of Contents
+:depth: 2
+installation
+glossary
+faq
+api
+Notebook: Fit Helium \<fit_helium.ipynb\>
+Notebook: Predict UV \<predict_UV.ipynb\>
+```

wiki/Installation.md → docs/installation.md

@@ -1,14 +1,3 @@
-# Installing _Cloudy_
-
-_sunbather_ has been developed and tested with _Cloudy v17.02_ and _v23.01_. Newer versions of _Cloudy_ are likely also compatible with _sunbather_, but this has not been thoroughly tested. Therefore, we currently recommend using _v23.01_. Complete _Cloudy_ download and installation instructions can be found [here](https://gitlab.nublado.org/cloudy/cloudy/-/wikis/home). In short, for most Unix systems, the steps are as follows:
-
-1. Go to the [v23 download page](https://data.nublado.org/cloudy_releases/c23/) and download the "c23.01.tar.gz" file (or go to the [v17 download page](https://data.nublado.org/cloudy_releases/c17/old/) and  download the "c17.02.tar.gz" file).
-2. Extract it in a location where you want to install _Cloudy_.
-3. `cd` into the _/c23.01/source/_ or _/c17.02/source/_ folder and compile the code by running `make`.
-4. Quickly test the _Cloudy_ installation: in the source folder, run `./cloudy.exe`, type "test" and hit return twice. It should print "Cloudy exited OK" at the end.
-
-If you have trouble installing _Cloudy_, we refer to the download instructions linked above, as well as the _Cloudy_ [help forum](https://cloudyastrophysics.groups.io/g/Main/topics).
-
 # Installing _sunbather_
 
 1. Clone _sunbather_ from Github. The code runs entirely in Python. It was developed using Python 3.9.0 and the following packages are prerequisites: `numpy (v1.24.3), pandas (v1.1.4), matplotlib (v3.7.1), scipy (v1.8.0), astropy (v5.3), p-winds (v1.3.4)`. _sunbather_ also succesfully ran with the newest versions (as of Sep. 18, 2023) of these packages. We have however not yet thoroughly tested all of its functionality with these newer versions, so we currently cannot guarantee that it works, but feel free to try! In any case, we recommend making a Python [virtual environment](https://realpython.com/python-virtual-environments-a-primer/) to run _sunbather_ in.
@@ -22,7 +11,19 @@ If you have trouble installing _Cloudy_, we refer to the download instructions l
 5. Copy the stellar spectra from _/sunbather/stellar_SEDs/_ to _$CLOUDY_PATH/data/SED/_ . These include the [MUSCLES](https://archive.stsci.edu/prepds/muscles/) spectra.
 6. Test your _sunbather_ installation: run _/sunbather/tests/test.py_, which should print "Success". If the test fails, feel free to open an issue or contact [email protected] with your error.
 
-# Getting started
+## Installing _Cloudy_
+
+_sunbather_ has been developed and tested with _Cloudy v17.02_ and _v23.01_. Newer versions of _Cloudy_ are likely also compatible with _sunbather_, but this has not been thoroughly tested. Therefore, we currently recommend using _v23.01_. Complete _Cloudy_ download and installation instructions can be found [here](https://gitlab.nublado.org/cloudy/cloudy/-/wikis/home). In short, for most Unix systems, the steps are as follows:
+
+1. Go to the [v23 download page](https://data.nublado.org/cloudy_releases/c23/) and download the "c23.01.tar.gz" file (or go to the [v17 download page](https://data.nublado.org/cloudy_releases/c17/old/) and  download the "c17.02.tar.gz" file).
+2. Extract it in a location where you want to install _Cloudy_.
+3. `cd` into the _/c23.01/source/_ or _/c17.02/source/_ folder and compile the code by running `make`.
+4. Quickly test the _Cloudy_ installation: in the source folder, run `./cloudy.exe`, type "test" and hit return twice. It should print "Cloudy exited OK" at the end.
+
+If you have trouble installing _Cloudy_, we refer to the download instructions linked above, as well as the _Cloudy_ [help forum](https://cloudyastrophysics.groups.io/g/Main/topics).
+
+
+## Getting started
 
 1. To get familiar with _sunbather_, we recommend you go through the Jupyter notebooks in the _/sunbather/examples/_ folder, where example use cases (such as creating atmospheric profiles, calculating transmission spectra and fitting observational data) are worked out and explained. 
-2. For more details on how to use the code, check out the Glossary and FAQ pages on this wiki. We specifically recommend you read the glossary sections "The _planets.txt_ file" and "Stellar SED handling". 
+2. For more details on how to use the code, check out the Glossary and FAQ pages on this wiki. We specifically recommend you read the glossary sections "The _planets.txt_ file" and "Stellar SED handling". 

docs/logo_text.png

@@ -0,0 +1 @@
+../logo/Logo + text.png