nespinoza / exoctk Goto Github PK

ExoCTK is an open-source, modular data analysis package focused primarily on atmospheric characterization of exoplanets. The subpackages included are:

• Contamination and Visibility Calculator
• Integrations and Groups Calculator
• Transit Light-Curve Fitter
• Limb Darkening Calculator
• Phase Constraint Calculator
• Atmospheric Forward Modeling

For more information on each package visit our documentation at readthedocs.

Most packages are also available through interactive tools at our web portal.

The following are instructions on how to install the exoctk package for both users and contributors. The exoctk repository provides a conda environment containing all of the dependencies needed to install and execute the exoctk software.

You must first have a working installation of anaconda or miniconda for Python 3. If you do not yet have this on your system, you can visit the following links for download and installation instructions:

• Anaconda
• Miniconda

To obtain the exoctk package with the necessary environment files, clone the repository directly from GitHub:

git clone https://github.com/ExoCTK/exoctk.git
cd exoctk

You can install the ExoCTK conda environment via the env/environment-<PYTHON_VERSION>.yml files (relative to the parent directory of where the repository was installed). Note that there are separate environment files for each version of python that exoctk supports. First, one should ensure that their version of conda is up to date:

conda update conda

Next, one should activate the base environment:

conda activate base

Next, one can create the exoctk conda environment via the appropriate environment-<PYTHON_VERSION>.yml file. One can find these files under the env directory and should run the following command in that directory:

conda env create -f environment-<PYTHON_VERSION>.yml

where <PYTHON_VERSION> is the version of python you are using (e.g. environment-3.8.yml)

Lastly, one can activate the newly-created environment with:

conda activate exoctk-<PYTHON_VERSION>

where again, <PYTHON_VERSION> is the version of python you are using (e.g. exoctk-3.8)

In order to install the exoctk package within the newly-created conda environment, run the exoctk setup script:

pip install -e .

The exoctk data package will be available through the MAST portal soon! Until then...

The suggested way to obtain the data is to execute the exoctk.utils.download_exoctk_data() function. This function will download a series of compressed files from Box, extract the files, and organize them into a exoctk_data/ directory. Note that this can only be done once the exoctk package has been fully installed (see instructions above).

Lastly, export an environment variable for EXOCTK_DATA.

• For Mac OS/Linux, add the line

export EXOCTK_DATA='/path/to/your/unzipped/directory/exoctk_data/'

to your .bashrc or .bash_profile.

• For Windows, add an environment variable using System Utility.

Users may also download individual components of the exoctk data package directly through the Box website. Please note that materials must ultimately be placed within a exoctk_data/ directory, and the EXOCTK_DATA environment variable be set in order for the exoctk package to work properly.

If you find that the exoctk conda is missing a required dependency, please feel free to submit a GitHub Issue detailing the problem.

If you use ExoCTK for work/research presented in a publication (whether directly, or as a dependency to another package), we recommend and encourage the following acknowledgment:

This research made use of the open source Python package exoctk, the Exoplanet Characterization Toolkit (Bourque et al, 2021).

where (Bourque et al, 2021) is a citation of the Zenodo record, e.g.:

@software{matthew_bourque_2021_4556063,
  author       = {Matthew Bourque and
                  Néstor Espinoza and
                  Joseph Filippazzo and
                  Mees Fix and
                  Teagan King and
                  Catherine Martlin and
                  Jennifer Medina and
                  Natasha Batalha and
                  Michael Fox and
                  Jules Fowler and
                  Jonathan Fraine and
                  Matthew Hill and
                  Nikole Lewis and
                  Kevin Stevenson and
                  Jeff Valenti and
                  Hannah Wakeford},
  title        = {The Exoplanet Characterization Toolkit (ExoCTK)},
  month        = feb,
  year         = 2021,
  publisher    = {Zenodo},
  version      = {1.0.0},
  doi          = {10.5281/zenodo.4556063},
  url          = {https://doi.org/10.5281/zenodo.4556063}
}

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