Exosims

The ICD now has a complete list of universal parameters, organized by module:
https://cdn.rawgit.com/dsavransky/EXOSIMS/master/ICD/icd.pdf#subsection.4.3
The list is also available in the as-built documentation at:
https://cdn.rawgit.com/dsavransky/EXOSIMS/master/documentation/html/userparams.html

MissionSim:
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* [New method]: DRM2array, Creates an array corresponding to one element of the DRM dictionary.
* [New method]: filter_status, Finds the values of one DRM element, corresponding to a status value, for detection or characterization.
* [New attribute] verbose (boolean): Boolean used to create the vprint function, equivalent to the python print function with an extra verbose toggle parameter (True by default). The vprint function can be accessed by all modules from EXOSIMS.util.vprint.
* [Bugfix] The seed attribute is now effectively used to seed the random number generator of NumPy
* [Modified attributes] logfile and loglevel:moved from SurveySimulation to MissionSim

PlanetPopulation:
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* [New module] added SAG13 module, to be used together with SimulatedUniverse "SAG13Universe" module
* [Modified attributes] Rp and Mp are now in earthRad and earthMass units

OpticalSystem:
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* [New attributes]: dMag0 and WA0, Favorable planet delta magnitude and instrument working angle values used to calculate the minimum integration times for inclusion in target list.
* [Modified method]: calc_maxintTime renamed to calc_minintTime, to better describe what this method is effectively used for.
* [Modified attribute]: dMagLim, moved to Completeness
* [Modified attribute]: attenuation, replaced by optics, and moved to the scienceInstrument dict and the starlightSuppressionSystem dict.
* [New attributes]: scienceInstrument dict has a few new attributes: radDos (radiation dosage), PCeff (photon counting efficiency), lenslSamp (lenslet sampling)
* [New method]: calc_dMag_per_intTime, calculates the achievable dMag for given integration time and working angle
* [New method]: ddMag_dt, calculates the derivative of achievable dMag with respect to integration time

ZodiacalLight:
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* [Modfied method] change to fZ arguments: it now passes the Observatory and TargetList modules, to allow locally calling the spacecraft position (equatorial frame) and star position vectors (ecliptic frame), reducing the computing time

PostProcessing:
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* [Modified attribute]: FAmaxfluxratio renamed to FAdMag0 (default to 15) for standardization wrt other dMags (dMagLim, dMag0, dMagint)
* [Modified method] det_occur now correctly calls the BackgroundSource module

Completeness:
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* [New attribute]: dMagLim, previously in OpticalSystem
* [New attribute]: minComp, previously in TargetList

TargetList:
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* [New attribute]: staticStars, boolean used to force static target positions set at mission start time
* [Modified attribute]: moved minComp to Completeness
* [Modified method]: filter_target_list is no longer calling max_dmag_filter, because it was redundant (already calling the int_cutoff_filter with OS.dMag0 and the completeness_filter with Comp.dMagLim)
* [New method]: starprop, previously in Observatory, calculate the star position vector, also now has an optional argument to set the frame to ecliptic (instead of equatorial by default)
* [New method]: stellarTeff, calculate the effective stellar temperature based on B-V color.

Observatory:
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* [New attribute]: checkKeepoutEnd, boolean signifying if the keepout method must be called at the end of each observation.
* [New attributes]: koAngleMinMoon and koAngleMinEarth, both default to koAngleMin (value for the Sun)
* [Modified method]: starprop, moved to TargetList
* [Modified methods]: orbit and solarSystem_body_position, now have an optional argument to set the frame to ecliptic (instead of equatorial by default), cf. TargetList starprop

TimeKeeping:
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* [New attribute] waitTime (float) Default allocated duration to wait in units of day, when the Survey Simulation does not find any observable target.
* [New attribute] waitMultiple (float) Multiplier applied to the wait time in case of repeated empty lists of observable targets, which makes the wait time grow exponentially

Other:
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* Extensive updates to the ICD (https://cdn.rawgit.com/dsavransky/EXOSIMS/master/ICD/icd.pdf)
* Extensive updates to the documentation, including an improved Quick-Start guide (https://cdn.rawgit.com/dsavransky/EXOSIMS/master/documentation/html/quickstart.html) and installation notes (https://cdn.rawgit.com/dsavransky/EXOSIMS/master/documentation/html/install.html)
* A new run script (run/run_ipcluster_ensemble.py) is included to make parallel runs easier to setup and process. Tools for analyzing ensemble data are included in utils/read_ipcluster_ensemble.py).
* keplerSTM now automatically uses cython compiled code if present in the installation.

General
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- Quick Start Guide updated, and link added to the EXOSIMS readme
- Updated terminal display during simulation
- Updated scripts: 3 sample scripts (sampleScript_coron, sampleScript_occulter, sampleScript_parallel_ensemble), 3 WFIRST templates (KnownRV, KeplerLike, EarthTwins), and a set of 5 test scripts.
- Added analysis_tools to utils (documentation in progress)

Survey Simulation
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- run_sim and run_ensemble now callable directly from MissionSimulation
- fixed a bug with linearJScheduler (Walker Dula)

Time Keeping
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- Observing Blocks (OBs) were added and new methods were created, to be compatible with a dynamic scheduler currently under development.
- Between 2 OBs, the mission current time is advancing to allow for non-planet-finding science (unless missionPortion = 1, meaning 100% of the time is devoted to planet-finding operations).
- Several observations can occur during 1 OB. Its duration is set by the variable OBduration.
- By default, OBduration is set to infinity and a new OB is created after each observation.
- The last OB end time is capped to the mission end time

Observatory
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- New boolean variable checkKeepoutEnd (True by default) can be set to False to make the end-keepout check optional
- telescopeKeepout was moved from OpticalSystem to Observatory, and replaced by koAngleMin and koAngleMax (for occulter), default to 45° and 90° respectively.

Optical System
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- The read noise contribution is now a variance term instead of a sigma value. The default value is 1e-6 e-/frame/pixel
- The following variables have been removed: focal, pitch. New input parameters are FoV and pixelNumber, such that pixelScale = 2×FoV/pixelNumber (arcsec), default to pixelScale = 2×10/1000 = 0.02 arcsec per pixel.
- core_platescale was added to the starlightSuppressionSystem parameters. It contains the specific platescale that was used to provide the coronagraph performance parameters, e.g., HLC tables all assume 0.3 lam/D/pix platescale. The rejection performance is then rescaled during the integration time calculation, based on the real pixelScale and lambda/D.
- Integration time negative values, infinite, and NAN, are all set to zero to avoid bugs
- The estimated integration time (calc_maxintTime) called in TargetList, now uses a working angle = (IWA+OWA)/2 whenever OWA is not infinite (or 2×IWA if OWA is infinite)
- The prototype scheduler can be optimized by allowing for Tint to vary. Added variables WAint and dMagint, the working angle and delta magnitude used for integration time calculation called in SurveySimulation. Default to WAint = IWA (detection mode) and dMagint = dMagLim.
- Added a paragraph to the ICD (section OpticalSystem) explaining how to use the detection IWA vs. global IWA
- New method: calc_contrast_per_intTime. This method is not currently called in the MissionSimulation. It is meant to be used as a tool to find instrument achievable contrast for one integration time per star, at one or more working angles.

Completeness
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- The completeness update was moved to the TargetList module
- The dynamic completeness stores is now stored in a *.dcomp file based on PlanetPhysicalModel, PlanetPopulation, OpticalSystem, StarCatalog, and TargetList modules
- Call-To-Action: Make sure to delete all previously generated *.acomp and *.dcomp files, and create new ones with future simulations.

We just released a new version of EXOSIMS in order to apply a few bug fixes and new functionalities we've been working on since the v1.0 release, such as:
* Added run_sim() and reset_sim() to MissionSim
* Added linear cost function scheduler
* Added new binary file L2_halo_orbit_six_month_v3.p for WFIRSTObservatoryL2 module
* Added parameter WALim to OpticalSystem: limiting working angle for integration time calculation, defaults to IWA
* Updated JPL ephemerides file
* Fixed Observatory.keepout bug that could cause an error due to array size mismatch
* Fixed BrownCompleteness Updates array
* FORECASTER update: user needs to download only the fitting_parameters.h5 file from
the FORECASTER GitHub repository
* Removed a few Runtime errors and warnings (such as divide-by-zero, invalid value encountered in arcsin)
* Updated ICD and Python documentation

This first release contains the following:
- all EXOSIMS prototype modules fully operational;
- specific implementations of most of the modules (BackgroundSources, Completeness, Observatory, OpticalSystem, PlanetPhysicalModel, PlanetPopulation, SimulatedUniverse, StarCatalog, SurveyEnsemble, TargetList, ZodiacalLight);
- a few examples of simulation specification JSON-formatted files;
- a detailed Interface Control Documentation (ICD);
- the as-built python documentation (currently under development).