exoctk

The Exoplanet Characterization Tool Kit

https://github.com/exoctk/exoctk

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The Exoplanet Characterization Tool Kit

README.rst

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Introduction
------------
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 `_.

Installation
------------

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.


Download Anaconda or Miniconda
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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 `_


Obtain the ``exoctk`` Package
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

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


Environment Installation
~~~~~~~~~~~~~~~~~~~~~~~~
You can install the ExoCTK ``conda`` environment via the ``env/environment-.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-.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-.yml


where ```` is the version of python you are using (e.g. ``environment-3.11.yml``)

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

::

  conda activate exoctk-

where again, ```` is the version of python you are using (e.g. ``exoctk-3.11``)


Package Installation
~~~~~~~~~~~~~~~~~~~~

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

::

  pip install -e .


Obtain the ``exoctk`` Data
~~~~~~~~~~~~~~~~~~~~~~~~~~

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.


Missing Dependencies?
~~~~~~~~~~~~~~~~~~~~~
If you find that the `exoctk` `conda` is missing a required dependency, please feel free to `submit a GitHub Issue `_ detailing the problem.


Citation
--------

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
                      Nstor 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}
    }

Want to stay up-to-date with our releases and updates?
------------------------------------------------------

Subscribe to our newsletter by sending an email with a blank body and subject to ``exoctk-news-subscribe-request@maillist.stsci.edu`` from the email you want to enroll. You should then receive a confirmation email with instructions on how to confirm your subscription, please be sure to do so within 48 hours.

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