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Documentation updates & Fix Sphinx warnings (#115)
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* documentation updates

* doc build: fix errors and warnings

* examples: fix error

* time2dist: fix Latex errors in docstring

* refactoring of docstrings in dd_models and bg_models (cherrypicked)

* dd_models: code refactor, corrected info structures, avoid sphinx warnings, improved autodocs

* docs: remove unused files in docs source

* suppress FutureWarning while compiling documentation

* docs: many edits to solve Sphinx warnings and errors

* docs: remove unused, outdated pages

* docs: further edits to solve Sphinx warnings

* bg_models: refactoring of the docstring, solved Sphinx warnings, improved autodoc

* ex_models: refactoring of the docstring, solved Sphinx warnings, improved autodoc

* docs: solve even further Sphinx warnings

Co-authored-by: Luis Fabregas <luis.fabregas@phys.chem.ethz.ch>
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stestoll and Luis Fabregas authored Mar 25, 2021
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10 changes: 4 additions & 6 deletions CHANGELOG.md
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-------------------------------

Release v0.13.0 - March 2021
---------------------------------

Expand All @@ -10,7 +8,7 @@ Release v0.13.0 - March 2021
- Added new experiment models for RIDME on systems with one to seven harmonic pathways (S=1/2 to S=7/2) to include all higher harmonics (overtones) ([#79](https://github.com/JeschkeLab/DeerLab/pull/79)).
- Bootstrapping is now embedded into ``fitmodel`` to automatically bootstrap all output quantities without the need to write additional script lines ([#55](https://github.com/JeschkeLab/DeerLab/issues/55)). In ``fitmodel`` a new option ``uq`` allows to switch between covariance or bootstrapping uncertainty quantification ([#88](https://github.com/JeschkeLab/DeerLab/pull/88)).
- The function ``fitmodel`` now returns ``Vmod`` and ``Vunmod``, the modulated and unmodulated contributionsto the fitted dipolar signal, respectively, along their uncertainties as additional outputs ([#78](https://github.com/JeschkeLab/DeerLab/pull/78)).
- Implemented initialization strategies in ``fitmultimodel`` for multi-model components ([#67](https://github.com/JeschkeLab/DeerLab/pull/67)). Three different new strategies ``'spread'``, ``'split'`` and ``'merge'`` will initialize the parameter values of the N-component fit based on the results of the N-1/N+1 component fit to improve quality of results and speed.
- Implemented several initialization strategies in ``fitmultimodel`` for multi-model components ([#67](https://github.com/JeschkeLab/DeerLab/pull/67)). Three different new strategies ``'spread'``, ``'split'`` and ``'merge'`` will initialize the parameter values of the N-component fit based on the results of the N-1/N+1 component fit to improve quality of results and speed.
- Added contribution guidelines to the documentation and automated list of DeerLab contributors.
- The function ``snlls`` now accepts additional custom penalties to include in the optimization ([#76](https://github.com/JeschkeLab/DeerLab/issues/76), [#108](https://github.com/JeschkeLab/DeerLab/pull/112)).

Expand All @@ -25,9 +23,10 @@ Release v0.13.0 - March 2021
- Adapted piece of code leading to a ``VisibleDeprecationWarning `` visible during execution of certain DeerLab functions.
- Improved interface of built-in plots in ``FitResult.plot()``. The method now returns a Matplotlib figure object (`matplotlib.figure.Figure`) instead of an axes object (``matplotlib.axes._subplots.AxesSubplot``) which can be modified more freely to adjust graphical elements ([#85](https://github.com/JeschkeLab/DeerLab/issues/85)). The method now takes an optional keyword ``FitResult.plot(show=True\False)`` to enable/disable rendering of the graphics upon calling the method ([#87](https://github.com/JeschkeLab/DeerLab/pull/87)).
- The fit objective values returned in ``FitResult.cost`` are now correct (previous versions had an erroneous 1/2 factor) ([#80](https://github.com/JeschkeLab/DeerLab/issues/80)). The value is now returned as a scalar value instead of a single-element list ([#81](https://github.com/JeschkeLab/DeerLab/issues/81)).
- Removed the re-normalization conventions ``K(t=0,r)=1`` and ``B(t=0)=1`` and associated options ``renormalize`` and ``renormpaths`` in the ``dipolarkernel`` and ``dipolarbackground`` functions ([#99](https://github.com/JeschkeLab/DeerLab/pull/99)) to avoid redundance issues between dipolar pathway amplitudes and signal scales ([#76](https://github.com/JeschkeLab/DeerLab/issues/76)).
- Removed the re-normalization conventions ``K(t=0,r)=1`` and ``B(t=0)=1`` and associated options ``renormalize`` and ``renormpaths`` in the ``dipolarkernel`` and ``dipolarbackground`` functions ([#99](https://github.com/JeschkeLab/DeerLab/pull/99)) to avoid identifiability issues between dipolar pathway amplitudes and signal scales during fitting ([#76](https://github.com/JeschkeLab/DeerLab/issues/76)).
- The fit convergence criteria ``tol`` (objective function tolerance) and ``maxiter`` (iteration limit) are now exposed as keyword argument in all fit functions ([#111](https://github.com/JeschkeLab/DeerLab/issues/111), [#112](https://github.com/JeschkeLab/DeerLab/pull/112)).
- Multiple improvements and corrections to the documentation ([#95](https://github.com/JeschkeLab/DeerLab/pull/95), [#96](https://github.com/JeschkeLab/DeerLab/pull/96), [#104](https://github.com/JeschkeLab/DeerLab/pull/104), [#106](https://github.com/JeschkeLab/DeerLab/pull/106), [#107](https://github.com/JeschkeLab/DeerLab/pull/107))
- Improvements and corrections to the documentation ([#95](https://github.com/JeschkeLab/DeerLab/pull/95), [#96](https://github.com/JeschkeLab/DeerLab/pull/96), [#104](https://github.com/JeschkeLab/DeerLab/pull/104), [#106](https://github.com/JeschkeLab/DeerLab/pull/106), [#107](https://github.com/JeschkeLab/DeerLab/pull/107))
- Corrections in the ``info`` dictionary of multiple ``dd_models``. The key ``Parameters`` of some models contained the wrong names.

#### Specific changes
- ``deerload``:
Expand Down Expand Up @@ -213,4 +212,3 @@ The following functions have been deprecated due to limited usability or due to

* ``correctphase``: now can handle 2D-datasets.

-------------------------------
2 changes: 1 addition & 1 deletion LICENSE
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MIT License

Copyright (c) 2019-2021 Luis Fabregas, Stefan Stoll, Gunnar Jeschke
Copyright (c) 2019-2021 Luis Fabregas, Stefan Stoll, Gunnar Jeschke, and other contributors

Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
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