Exosims

Re-release of 2.1.3 to synchronize with PyPI.

Bugfix release correcting extraneous `calc_dMag_per_intTime` method from Nemati_2019 optical system

Minor bugfix release correcting bad interpolation errors in Nemati_2019 optical system. All interpolants which could potentially produce (non-phyiscal) negative values with cubic splines have been changed to linear fits instead.

Note: v2.1.1 was only released on pypi and not github. It is identical to 2.1.0. Starting with this version, all releases should be automatically synchronized between github and pypi.

New features:
* New module SubtypeCompleteness which calculates the probability that a detected planet belongs to a given sub-population.
* New option to specify common inclination for whole target systems (i.e., define an ecliptic) with individual planet inclinations distributed about it. The exozodiacal cloud is assumed to be aligned with the system inclination for all individual planet calculations.
* Option to set number of exozodi for each individual target system
* New optical system: Nemati2019, implementing the calculations in the famous spreadsheet
* New method for computing stellar spectra based on Pickles atlas (spectral data is now packaged with EXOSIMS). More atlases coming in subsequent releases.

Critical Bug Fixes:
* Full compatibility with astropy 4.0+ and numpy 1.16+ Fix. Everything works in Python 2.7.8+ and 3.6/3.7/3.8.

Notes:
* Starting with this release, EXOSIMS will be available on PyPI
* Python 2 support will be dropped within the next two releases.

Acknowledgements:
This release includes significant contributions from Corey Spohn, Dean Keithly, Gabriel Soto, and Walker Dula. Thanks also to Rhonda Morgan, Mike Turmon, and Ewan Douglas.

This release explicitly breaks backwards compatibility with v1.4, and is *incompatible* with astropy v4.0 (requirements and setup both specify `astropy<4.0`). A subsequent minor release will add astropy 4.0 compatibility. This release is largely similar to the recent SDET Final Report release, but does contain algorithmic differences (although is fully compatible in terms of all interfaces).

Many thanks to Dean Keithly, Gabriel Soto, Walker Dula, Mike Turmon, and Rhonda Morgan for their numerous contributions.

Major Changes
-----------------
EXOSIMS is now python 3 compatible and pip installable! EXOSIMS will be added to the python package index upon the next release (as soon as astropy 4.0 compatibility is fixed). We will maintain python 2 compatibility for the next few releases, but will drop python 2.7 support when required modules (astropy, scipy, etc.) become incompatible with their last-released python 2 supporting versions. There will be a final, stable python 2.7-compatible release prior to end of support.

Compiled documentation is now being hosted on readthedocs.io and is not packaged with the source code (only documentation sources are packaged).

Prototypes
-------------
All prototypes have been updated with bug fixes and algorithmic updates. In particular, the OpticalSystem and TargetList prototype now supports many more inputs, including tracking of close companions for target stars. The SurveySimulation prototype has had multiple additional sections or `run_sim` abstracted into their own methods to allow for easier overloading.

PlanetPopulation
------------------
Bug fixes throughout the existing planet populations. Multiple new planet populations have been added including:
* AlbedoByRadius - allows for albedo to be drawn as a function of planet radii
* DulzPlavchan - Modification of the SAG13 extrapolation incorporating dynamical stability constraints, based on work by Shannon Dulz and Peter Plavchan (in prep).

StarCatalog
--------------
EXOCAT has been updated and allow for combination of the existing data with updated WDS entries for close companions.

SurveySimulation
---------------------
Added multiple SDET-specific schedulers. All SLSQP-based schedulers, which were previously separate classes, have been combined into a single module.

TargetList
-------------
New GaiaCatTargetList allows for Gaia-based catalogs.

util
-------
New plotting and analysis utilities, including keepout map plotting and yield histogram plotting.

SDETfinal
The code in this release was used for all of the EXOSIMS simulations in the final report of the Exoplanet Exploration Office's Standards Definitions and Evaluation Team. It is intended to produce a snapshot of EXOSIMS as used in all of the SDET analyses to ensure future reproducibility of results.

A description of the team and their task is available at https://exoplanets.nasa.gov/system/internal_resources/details/original/562_ExSDET_Charter.pdf

The final report and associated results are available at https://exoplanets.nasa.gov/exep/studies/sdet/

This release contains a rollup of pending updates to be included in the upcoming v2.0, along with unique features used specifically in the final report analyses (as such, this release is distinct from the 2.0 release and is not guaranteed to produce the same exact results).

Additional plotting and execution utilities developed at JPL and used in the generation of the final report results are available at https://github.com/turmon/Exosims-Sandbox

This release includes major contributions from Walker Dula, Mike Turmon, and Rhonda Morgan.

Rollup of the last few months of bugfixes (in particular targeted at improved reproducibility when setting the random seed, and ensuring proper use of scaleOrbits) as well as new, non-ICD changing features (mostly new input parameters).

Specific updates:
- Fixing scaleOrbits support in BrownCompleteness.
- Adding support for albedo calculated from planet radius in GarrettCompleteness and removing unused pgrand method.
- Removing random seed generation from MissionSim (offloaded to SurveySimulation) and adding alias from MissionSim.seed to SurveySimulation.seed.
- Adding pixelScale as an input parameter in the instrument dictionary in the OpticalSystem prototype.
- Adding support for albedo calcualted from planet radius in PlanetPopulation prototype (pfromRp boolean).
- Adding Min input to SimulatedUniverse prototype and KeplerLike and SAG13 implementations (allows for setting all initial mean anomalies to given value).
- Adding error checking to SimulatedUniverse and TargetList prototypes to ensure KnownRV family of modules is properly used.
- Update to algorithm used in set_planet_phase in SimulatedUniverse prototype.
- Adding scaleWAdMag input (boolean) to SurveySimulation to toggle overwriting WAint and dMagint based on stellar properties.
- Moving order of random seed generation in SurveySimulation to ensure DRM repeatability.
- Adding dt_max input (float) to SurveySimulation to allow for variable time windows when selecting which targets are 'currently' scheduled for revisit.
- Adding new methods scheduleRevisit and revisitFilter to SurveySimulation to make overloading revisit logic easier.
- Cleanup of reset_sim method in SurveySimulation to ensure reproduceability.
- Adding sane handling of equal xmin, xmax in InverseTransformSampler.
- Removing use of np.flip in waypoint utility
- Adding AlbedoByRadius and JupiterTwin planet populations.
- Adding Walker Dula's det_only, char_only and tiered schedulers.
- Adding builddocs.bat, porting builddocs.sh to Windows systems.

Release Fix April 9, 2018: A bug was fixed in this release that prevented simulations from running properly after reset.