Version 3 - main thread

[rpoleski]

What is decided to be done for Version 3:

• [x] derivatives of magnification and complicated structure of PointLens - architecture changes are made by @jenniferyee in Version3_1 branch; #107 #108
• [x] lists used for multi-source models - @jenniferyee implements in Version3_1 branch; #117 ; Radek will review it; tests to be added
• [x] saving plots from examples (07, 08, and 16 are the only ones missing)
• [x] search for all "deprecated" are remove it - @rapoliveira
• [x] rename Caustics -> CausticsBinary and CausticsWithShear -> CausticsBinaryWithShear (and files) so that they're consistent with CausticsPointWithShear

Added later (only high-level ones):

• [x] shifting alpha by 180 deg to match Skowron+11 conventions - too be done only when we make significant changes to binary lens models, so that it's very unlikely that somebody will be able to run on V3 the code written for V2
• [x] making long-running tests shorter
• [x] increasing number of characters per line (to 120)
• [x] remove astropy.quantities from ModelParameters; also remove ModelParameters.pi_E

Also check MM_v3.md file for less changes that were not accepted yet.

Not decided yet and important:

• astrometric microlensing - probably too complicated for V3, hence, will got to V4,
• more advanced fitting fluxes of fluxes, e.g., keeping source colors similar or the same for data from different telescopes (at least 2 bands for at least 2 telescopes).

[rpoleski]

I reviewed this thread and made a list of necessary changes before merge:

• [x] ModelParameter - end of shear_G and rho_2 - PR by @rapoliveira
• [x] KeyError vs AttributeError in ModelParameters
• [x] __repr__ for multisource models in ModelParameters (no tests currently; _split_parameter_name() is useful for that)
• [x] placeholder and failing unit tests
• [x] Jun 3 comment by @jenniferyee (both tests mentioned there pass)
• [x] merge master to Version3_1 (done on Oct 11)

And changes that are not required:

• [ ] check "binary source" and "2 source" in docstrings etc.
• [ ] gammas for multiple source (Aug 16 comment)
• [ ] test example 16 once more
• [x] solve an issue suggested by Jen: https://github.com/rpoleski/MulensModel/issues/142
• [ ] why t_eff is not in ModelParameters._primary_source_params_head ?
• [x] example 8 - alpha shift by 180 - done by Raphael
• [ ] What is the purpose of Model._N_source_attr?
• [x] test that 1L3S + xallarap fails
• [x] JCY in unit tests
• [ ] simplify _check_for_parameters_incompatible_with_xallarap()
• [ ] check changes and look for comments to be removed: 1) magnificationcurve.py:156, 2) test_BinaryLens.py - first 100 lines - SOLVED, 3) test_FitData.py lines 980-983, 4) test_PointLens.py:139, 5) test_PointLensWithShear.py lines 54-86
• [ ] flake8 in examples/
• [ ] anything else from MM_v3.md that is not yet done

Some final tasks before merging:

• [x] document changes
• [ ] check tests coverage (73% in master)
• [ ] version number
• [ ] sphinx
• [x] flake8
• [x] README.md

[rpoleski]

List of major changes from the user perspective:

• Changing convention of alpha angle, i.e., shifting by 180 deg. This makes MM compatible with convention of Skowron et al. 2011.
• Allowing more than 2 sources.
• Removing astropy units from microlensing parameters.

List of technical changes:

• PointLensFiniteSource replaced by B0B1Utils. Introduction of EllipUtils.
• BinaryLens class removed.
• Binary classes introduced: BinaryLensPointSourceWM95Magnification, BinaryLensPointSourceVBBLMagnification, BinaryLensPointSourceMagnification, BinaryLensQuadrupoleMagnification, BinaryLensHexadecapoleMagnification, BinaryLensVBBLMagnification, BinaryLensAdaptiveContouringMagnification, BinaryLensPointSourceWithShearWM95Magnification, and BinaryLensPointSourceWithShearVBBLMagnification.
• Caustics replaced by CausticsBinary.
• CausticsWithShear replaced by CausticsBinaryWithShear.
• Parameters of Event.get_ref_fluxes() removed.
• The parameter fit_blending of Event methods get_chi2(), get_chi2_for_dataset(), get_chi2_per_point(), and get_chi2_gradient() removed. Use fix_blend_flux instead.
• Parameter type removed from FitData.get_residuals().
• Methods of class FitData removed: get_d_A_d_u_for_PSPL_model(), get_d_A_d_u_for_FSPL_model(), and get_d_A_d_u_for_point_lens_model().
• Properties FitData.magnification_curve and magnification_curves removed.
• Class FSPL_Derivatives removed. Most its methods are replaced by PointLens class.
• Methods MagnificationCurve.get_d_A_d_params() and get_d_A_d_rho() added.
• Property MagnificationCurve.methods_indices added.
• Parameter flux_ratio_constraint of Model.plot_magnification() removed.
• Parameters of data_ref, flux_ratio_constraint, fit_blending, f_source, and f_blend of Model.plot_lc() removed.
• Parameter show_data of Model.plot_trajectory() removed.
• Model.get_magnification(): parameter flux_ratio_constraint remove and parameter separate default value changed to None (which defaults to True if source_flux_ratio is provided and to False otherwise).
• Model.magnification() replaced by Model.get_magnification().
• Model.get_magnification_curve() and get_magnification_curves() added.
• Function which_parameters() from modelparameters.py removed as not useful and very complicated.
• Property ModelParameters.pi_E removed. Properties pi_E_E and pi_E_N are still there.
• Astropy units removed (i.e., now everything is a float) from ModelParameters properties: t_star, t_eff, t_E, alpha, ds_dt, dalpha_dt, t_star_1, t_star_2, gamma_parallel, gamma_perp, and gamma. Also removed from function get_alpha().
• In ModelParameters, the properties that are not defined raise AttributeError (previously rho was returning None, and some other ones raised KeyError).
• Warnings for unexpected values of angles (e.g., 1000 deg) in ModelParameters are not raised anymore.
• Changes in default values for t_0_par and t_0_kep. If the t_0_par is not defined, then it defaults to t_0_kep, t_0, t_0_1 in that order. If the t_0_kep is not defined, then it defaults to t_0_par, t_0, t_0_1 in that order.
• MulensData arguments coords, ra, and dec removed. Also property coords was removed.
• Parameters model and plot_residuals removed from MulensData.plot().
• Function get_pspl_magnification() from pointlens.py was removed. Use classes listed in next point instead.
• Added classes PointSourcePointLensMagnification, FiniteSourceUniformGould94Magnification, FiniteSourceLDYoo04Magnification, FiniteSourceUniformWittMao94Magnification, FiniteSourceLDWittMao94Magnification, FiniteSourceUniformLee09Magnification, and FiniteSourceLDLee09Magnification.
• PointLensWithShear replaced by PointSourcePointLensWithShearMagnification.
• Added new arguments of Trajectory: x and y. They can be provided instead of the times argument.

[jenniferyee]

Created 00_MMv3_changes.md in documents folder. Takes the notes from @rpoleski and organizes them by class and importance in a semi-formatted document.