Added functionalities for the analysis of emission lines

README.rst

@@ -27,7 +27,7 @@
 .. image:: https://mybinder.org/badge_logo.svg
    :target: https://mybinder.org/v2/gh/tomasstolker/species/HEAD
 
-*species* is a toolkit for atmospheric characterization of directly imaged exoplanets. It provides a coherent framework for spectral and photometric analysis which builds on publicly-available data and models from various resources. There are tools available for both grid retrievals and free retrievals with Bayesian inference, color-magnitude and color-color diagrams, empirical spectral analysis, spectral and photometric calibration, and synthetic photometry. The package has been released on `PyPI <https://pypi.org/project/species/>`_ and is actively developed and maintained on Github.
+*species* is a toolkit for atmospheric characterization of directly imaged exoplanets. It provides a coherent framework for spectral and photometric analysis which builds on publicly-available data and models from various resources. There are tools available for both grid retrievals and free retrievals with Bayesian inference, color-magnitude and color-color diagrams, empirical spectral analysis, spectral and photometric calibration, analysis of emission lines, and synthetic photometry. The package has been released on `PyPI <https://pypi.org/project/species/>`_ and is actively developed and maintained on Github.
 
 Documentation
 -------------

docs/about.rst

@@ -6,7 +6,7 @@ About
 Questions & feedback
 --------------------
 
-*species* is developed by Tomas Stolker (stolker@strw.leidenuniv.nl). Feel free to send an email for questions, comments, or suggestions.
+*species* has been developed and is maintained by Tomas Stolker (stolker@strw.leidenuniv.nl). Feel free to send an email for questions, comments, or suggestions.
 
 Attribution
 -----------

docs/configuration.rst

@@ -28,7 +28,7 @@ The workflow with *species* can now be initiated with the :class:`~species.core.
    >>> import species
    >>> species.SpeciesInit()
 
-Alternatively, a configuration file with default values is automatically created when `species` is initiated and the configuration file is not present in the working folder.
+A configuration file with default values is automatically created when `species` is initiated and the file is not present in the working folder.
 
 .. tip::
    The same `data_folder` can be used in multiple configuration files. In this way, the data is only downloaded once and easily reused by a new instance of :class:`~species.core.setup.SpeciesInit`. Also the HDF5 database can be reused by simply including the same `database` in the configuration file.

docs/contributing.rst

@@ -3,4 +3,4 @@
 Contributing
 ============
 
-Contributions are very welcome, please consider `forking <https://help.github.com/en/articles/fork-a-repo>`_ the repository and creating a `pull request <https://github.com/tomasstolker/species/pulls>`_. Bug reports and feature requests can be provided by creating an `issue <https://github.com/tomasstolker/species/issues>`_ on the Github page.
+Contributions are very welcome so please consider `forking <https://help.github.com/en/articles/fork-a-repo>`_ the repository and creating a `pull request <https://github.com/tomasstolker/species/pulls>`_. Bug reports and feature requests can be provided by creating an `issue <https://github.com/tomasstolker/species/issues>`_ on the Github page.

docs/index.rst

@@ -3,11 +3,7 @@
 Documentation for *species*
 ===========================
 
-*species* is a toolkit for atmospheric characterization of directly imaged exoplanets. The package has been developed and is maintained by |stolker|.
-
-.. |stolker| raw:: html
-
-	<a href="https://home.strw.leidenuniv.nl/~stolker/" target="_blank">Tomas Stolker</a>
+*species* is a toolkit for atmospheric characterization of directly imaged exoplanets.
 
 .. toctree::
    :maxdepth: 2

docs/installation.rst

@@ -3,18 +3,18 @@
 Installation
 ============
 
-*species* is compatible with Python 3.6/3.7/3.8 and is available in the |pypi| and on |github|.
+*species* is compatible with Python 3.6/3.7/3.8 and is available in the `PyPI repository <https://pypi.org/project/species/>`_ and on `Github <https://github.com/tomasstolker/species>`_.
 
 Installation from PyPI
 ----------------------
 
-*species* can be installed with the |pip|:
+The Python package can be installed with the `pip package manager <https://packaging.python.org/tutorials/installing-packages/>`_:
 
 .. code-block:: console
 
     $ pip install species
 
-And to update to the most recent version:
+Or, to update to the most recent version:
 
 .. code-block:: console
 
@@ -39,7 +39,7 @@ And running the setup script to install the package and its dependencies:
     $ python setup.py install
 
 .. important::
-   If an error occurs when running ``setup.py`` then possibly ``pip`` needs to be updated the latest version:
+   If an error occurs when running ``setup.py`` then possibly ``pip`` needs to be updated to the latest version:
 
    .. code-block:: console
 
@@ -62,21 +62,9 @@ Do you want to make changes to the code? Please fork the `species` repository on
 Testing `species`
 -----------------
 
-The installation can be tested by starting Python in interactive mode and printing the `species` version:
+The installation can now be tested, for example by starting Python in interactive mode and printing the version number of the installed package:
 
 .. code-block:: python
 
     >>> import species
     >>> species.__version__
-
-.. |pypi| raw:: html
-
-   <a href="https://pypi.org/project/species/" target="_blank">PyPI repository</a>
-
-.. |github| raw:: html
-
-   <a href="https://github.com/tomasstolker/species" target="_blank">Github</a>
-
-.. |pip| raw:: html
-
-   <a href="https://packaging.python.org/tutorials/installing-packages/" target="_blank">pip package manager</a>

docs/overview.rst

@@ -6,12 +6,12 @@ Overview
 Introduction
 ------------
 
-*species* provides a coherent framework for spectral and photometric analysis of directly imaged planets and brown dwarfs. This page contains a short overview of the various data that are supported and some of the tools and features that have been implemented.
+*species* provides a coherent framework for spectral and photometric analysis of directly imaged planets and brown dwarfs. This page contains a short overview of the various data that are supported and some of the tools and features that are provided.
 
 Supported data
 --------------
 
-The *species* toolkit benefits from publicly available data resources such as photometric and spectral libraries, atmospheric model spectra, evolutionary tracks, and photometry of directly imaged planets and brown dwarfs. The relevant data are automatically downloaded and added to the HDF5 database, which acts as the central data storage for a workflow. All data are stored in a fixed format such that the analysis and plotting tools can easily access and manipulate the data.
+The toolkit benefits from publicly available data resources such as photometric and spectral libraries, atmospheric model spectra, evolutionary tracks, and photometry of directly imaged, low-mass objects. The relevant data are automatically downloaded and added to the HDF5 database, which acts as the central data storage for a workflow. All data are stored in a fixed format such that the analysis and plotting tools can easily access and process the data.
 
 The following data and models are currently supported:
 
@@ -55,7 +55,7 @@ The following data and models are currently supported:
 - Extinction cross sections computed with `PyMieScatt <https://pymiescatt.readthedocs.io>`_
 - Optical constants compiled by `Mollière et al. (2019) <https://ui.adsabs.harvard.edu/abs/2019A%26A...627A..67M/abstract>`_
 
-Please give credit to the relevant authors when using any of the external data in a publication. More information is available on the respective websites. Support for other datasets can be requested by creating an `issue <https://github.com/tomasstolker/species/issues>`_ on the Github page.
+Please give credit to the relevant references when using any of the external data in a publication. More information is available on the respective websites. Support for other datasets can be requested by creating an `issue <https://github.com/tomasstolker/species/issues>`_ on the Github page.
 
 Analysis tools
 --------------
@@ -72,3 +72,4 @@ After adding the relevant data to the database, the user can take advantage of t
 - Computing synthetic fluxes from isochrones and model spectra (see :class:`~species.read.read_isochrone.ReadIsochrone`)
 - Flux calibration of photometric and spectroscopic data (see :class:`~species.read.read_calibration.ReadCalibration`, :class:`~species.analysis.fit_model.FitModel`, and :class:`~species.analysis.fit_spectrum.FitSpectrum`).
 - Empirical comparison of spectra to infer the spectral type (see :class:`~species.analysis.empirical.CompareSpectra`).
+- Analyzing emission lines from accreting planets (see :class:`~species.analysis.emission_line.EmissionLine`).

docs/species.analysis.rst

@@ -4,6 +4,14 @@ species.analysis package
 Submodules
 ----------
 
+species.analysis.emission\_line module
+--------------------------------------
+
+.. automodule:: species.analysis.emission_line
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
 species.analysis.empirical module
 ---------------------------------
 

docs/tutorials.rst

@@ -20,6 +20,7 @@ This page contains a list of tutorials which highlight some of the functionaliti
    tutorials/spectral_library.ipynb
    tutorials/fitting_model_spectra.ipynb
    tutorials/flux_calibration.ipynb
+   tutorials/emission_line.ipynb
 
 .. important::
    A flux calibrated spectrum of Vega is used for the conversion between a flux density and magnitude. The magnitude of Vega is set to 0.03 for all filters. If needed, the magnitude of Vega can be changed with the ``vega_mag`` attribute of a ``SyntheticPhotometry`` object: