Installation instructions

I recommend installing stctm in a clean conda environment, as with any new package.

Example command-line commands could look like this:

conda create -n mystctm_env python=3.10.4
conda activate mystctm_env

You can clone stctm directly from GitHub and place it in your installation at the path of your choice:

git clone https://github.com/cpiaulet/stctm.git
cd stctm
pip install -e .

Dependencies

The dependencies of stctm are: NumPy, scipy, emcee, corner, astropy, h5py, matplotlib, pandas, pysynphot, and tqdm (for progress bar with MCMC retrievals).

Stellar model package installation

You may also need the additional dependency pymsg (my personal favorite). To install pymsg, you can find instructions at MSG documentation, and then download the grid(s) of your choice from MSG grids.

Required inputs: the stellar models grid

The code needs as input a grid of stellar models as a function of wavelength, with a regular spacing in log g and effective temperature. I included in the repository an auxiliary file that allows you to create such a model grid (create_fixedR_grid_pymsg_template.py) using pymsg.

To make the first setup and testing of the installation easier, I provide on Zenodo the stellar models grid I generated for TRAPPIST-1. This grid is used in all the examples listed below, and contains a grid of models generated with the MSG package. You can download it from the latest Zenodo link: https://doi.org/10.5281/zenodo.15334399 (TRAPPIST_1_pymsg.h5).

To run all the tests and examples in this documentation, please copy this file to the folder example/R10000_model_grids. If you want to reproduce without any edits to the code all the tests and examples mentioned below, you will need to save this file with a relative path of ../../R10000_model_grids/TRAPPIST_1_pymsg.h5 relative to where the example run files for stctm and exotune are located.

To generate your own grid of interpolated models using MSG for any star of your choosing, following the instructions under Create your own grid of stellar models using MSG.

Testing your installation

I created a dummy spectrum (with only 1 point) so you can run a few-second test of the code on your laptop for both serial and parallel runs.

Copy the contents of the example/ directory wherever in your installation you want to run the code.
Make sure you have a suitable stellar models grid at the path recommended above.
Confirm that your environment paths are set up properly. Specifically, you need to have the CRDS_SERVER_URL, CRDS_PATH, and PYSYN_CDBS environment variables defined. You can do this via the command-line (see example below for CRDS_PATH):
```
export CRDS_PATH=/home/yourusername/crds_cache
```
or in the code of the analysis file itself:
```
import os
os.environ['CRDS_PATH'] = "/home/yourusername/crds_cache"
```
Navigate to your copy of stellar_contamination_analysis/template_analysis/ and run the following test in the command line:
```
stctm_TLS test_ini_stctm.toml
```

This should display print statements as the code is running, and create a directory with output files for this “mock” fit under stellar_contamination_results/.

To test instead that the parallel version of the code works (with my custom wrapper around multiprocessing Pool), you can simply run:

stctm_TLS test_ini_stctm.toml -parallel=True -ncpu=2 -res_suffix=singlebin_testcode_parallel

… and that’s it! You can read more in the following pages on how to customize what you do with stctm.