Installation

1 Gen TSO Installation

You can install Gen TSO from PyPI with the following command (compatible with Python3.9+):

pip install gen_tso

Now you are ready to launch the Gen TSO application. You can do that with this prompt command:

tso
Note

If this is your first time or see any warning, you may need to look at the Pandeia installation section below

Note

If you find Numpy compilation issues when instaling gen_tso, it’s better to install into a freshly new virtual environment, since the new Numpy2 is incompatible with many older installed packages.


2 Pandeia Engine

To use pandeia you need to download some files as per their documentation.

2.1 Reference data

If you don’t have it yet, download the latest pandeia reference data, unzip it, and place it in the folder pointed by $pandeia_refdata. Here’s the current latest version: https://stsci.app.box.com/v/pandeia-refdata-v4p0-jwst

If this is your first time using pandeia, you likely need to setup a $pandeia_refdata environment variable (e.g., in your ~/.bashrc, ~/.bash_profile, or whichever bash file your machine uses).

Then you will need to start a new prompt terminal or source your bash file, e.g.:

source ~/.bashrc

You should end up with something like this:

echo $pandeia_refdata
/home/USERNAME/data/pandeia_data-4.0-jwst

2.2 Atlases data

Pandeia also needs some stellar and throughput files to simulate exoplanet spectra. Use one of the options below to stay up to date:

Use this prompt command to automatically check and upload the required atlases

tso --update_db

If this is your first time using pandeia, you likely need to setup a synphot $PYSYN_CDBS environment variable (e.g., in your ~/.bashrc file) pointing to the trds directory (see below).

Then, download these reference files (e.g., with the wget command below) and place them inside the folder pointed by $PYSYN_CDBS (make sure to keep the trds/... folder structure of the downloaded files):

wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_kurucz-1993-atlas_multi_v2_synphot4.tar
wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_pheonix-models_multi_v3_synphot5.tar
wget https://archive.stsci.edu/hlsps/reference-atlases/hlsp_reference-atlases_hst_multi_everything_multi_v15_sed.tar

Lastly, download the Vega reference spectrum and place the file in your $PYSYN_CDBS trds/calspec/ folder.

wget https://ssb.stsci.edu/trds/calspec/alpha_lyr_stis_010.fits

If everything went right, then you should see something similar to this:

# (remember to source your bash file or start a new prompt terminal)
echo $PYSYN_CDBS
/home/USERNAME/data/pysynphot/trds

ls $PYSYN_CDBS
calspec  comp  grid  mtab


3 NASA Exoplanet Archive (optional)

Gen TSO is updated regularly to ensure that the exoplanet database remains mostly up to date. But if you want to update the planet data up to the current date, you can run this prompt command:

tso --update_exo


Live status check

While you are running the Gen TSO application, click on this gear icon at the top right of the screen:

This will pop up a more detailed panel indicating whether any database needs to be updated (and if needed, it will give you the instructions to do so):

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