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https://github.com/Starfish-develop/Starfish

Tools for Flexible Spectroscopic Inference
https://github.com/Starfish-develop/Starfish

astronomy astrophysics inference mcmc python spectra starfish

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Tools for Flexible Spectroscopic Inference

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README 

        
# Starfish

[![Documentation Status](https://readthedocs.org/projects/starfish/badge/?version=latest)](https://starfish.readthedocs.io/en/latest/?badge=latest)

[![Build Status](https://github.com/iancze/Starfish/workflows/CI/badge.svg?branch=master)](https://github.com/iancze/Starfish/actions)

[![Coverage Status](https://codecov.io/gh/iancze/Starfish/graph/badge.svg)](https://codecov.io/gh/iancze/Starfish/)

[![PyPI](https://img.shields.io/pypi/v/astrostarfish.svg)](https://pypi.org/project/astrostarfish/)

[![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.2221005.svg)](https://doi.org/10.5281/zenodo.2221005)



*Starfish* is a set of tools used for spectroscopic inference. We designed the package to robustly determine stellar parameters using high resolution spectral models.



**Warning!**



There have been major, breaking updates since version `0.2.0`, please see [this page](https://starfish.readthedocs.io/en/latest/conversion.html) regarding these changes if you are used to the old version!



### Citations



If you use this code or derivative components of this code in your research, please cite our [paper](https://ui.adsabs.harvard.edu/abs/2015ApJ...812..128C/abstract) as well as the [code](https://doi.org/10.5281/zenodo.2221006). See [`CITATION.bib`](CITATION.bib) for a BibTeX formatted reference of this work.



### Papers

* [Czekala et al. 2015](https://ui.adsabs.harvard.edu/#abs/2015ApJ...812..128C/abstract)

* [Gully-Santiago et al. 2017](https://ui.adsabs.harvard.edu/#abs/2017ApJ...836..200G/abstract)

* [Greene et al. 2018](https://ui.adsabs.harvard.edu/abs/2018ApJ...862...85G/abstract)

* [Zhang et al. 2021b](https://ui.adsabs.harvard.edu/abs/2020arXiv201112294Z/abstract)

* [Zhang et al. 2021c](https://ui.adsabs.harvard.edu/abs/2021arXiv210505256Z/abstract)



*If you have used Starfish in your work, please let us know and we can add you to this list!*



Please bear in mind that this package is under heavy development and features may evolve rapidly. If something doesn't work, please fill an [issue](https://github.com/iancze/Starfish/issues) on this repository. If you would like to contribute to this project (either with bugfixes, documentation, or new features) please feel free to fork the repository and submit a pull request!



# Installation Instructions



## Prerequisites



*Starfish* has several dependencies, however most of them should be satisfied by an up-to-date scientific python installation. We highly recommend using the [Anaconda Scientific Python Distribution](https://store.continuum.io/cshop/anaconda/) and updating to 

Python 3.6 or greater. This code makes no attempt to work on the Python 2.x series, and I doubt it will if you try. This package is tested across Linux, Mac OS X, and Windows. 



To make sure you are running the correct version of python, start a python interpreter via the system shell and you should see something similar



    $ python

    Python 3.6.1 |Anaconda custom (64-bit)| (default, May 11 2017, 13:25:24) [MSC v.1900 64 bit (AMD64)] on win32

    Type "help", "copyright", "credits" or "license" for more information.

    >>> 



If your shell says Python 2.x, try using the `python3` command instead of `python`.



## Installation



For the most current stable release of *Starfish*, use the releases from PyPI



    $ pip install astrostarfish



If you want to be on the most up-to-date version (or a development version), install from source via



    $ pip install git+https://github.com/iancze/Starfish.git#egg=astrostarfish



To test that you've properly installed *Starfish*, try doing the following inside of a Python interpreter session



```python

>>> import Starfish

>>> Starfish.__version__

'0.3.0'

```



If you see any errors, then something went wrong--please file an [issue](https://github.com/iancze/Starfish/issues).



Now that you've successfully installed the code, please see the [documentation](https://starfish.readthedocs.io/en/latest/) on how to begin using *Starfish* to solve your spectroscopic inference problem.



# Contributing

If you are interested in contributing to *Starfish*, first off, thank you! We appreciate your time and effort into

making our project better. To get set up in a development environment, it is highly recommended to develop in a

virtual environment. We use `pipenv` (pending a better PEP 517/518 compliant tool) to manage our environments, to get started clone the repository (and we recommend forking us first)



    $ git clone https://github.com//Starfish.git starfish

    $ cd starfish



and then create the virtual environment and install all the packages and developer dependencies from the `Pipfile` with



    $ pipenv install -d



and to enter the virtual environment, simply issue



    $ pipenv shell



whenever you're in the `starfish` folder.



We also enforce the `black` [code style](https://github.com/python/black). This tools allows automatically formatting everything for you, which is much easier than caring about it yourself! We have a [pre-commit](https://pre-commit.com/) hook that will *blacken* your code before you commit so you can avoid failing the CI tests because you forgot to format. To use this, just install the hook with 



    $ pipenv run pre-commit install



From then on, any commits will format your code before succeeding!



Take a look through the [issues](https://github.com/iancze/Starfish/issues) if you are looking for a place to start improving *Starfish*!



**Tests**



We use `pytest` for testing; within the virtual environment



    $ pytest



Note that we use the `black` code style and our CI testing will check that everything is formatted correctly. To check your code



    $ pytest --black



although if you follow the instructions for using *pre-commit* you should have no issues.



## Contributors



See [`CONTRIBUTORS.md`](CONTRIBUTORS.md) for a full list of contributors.