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Implement models metadata as function attributes #143

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Apr 7, 2021
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Implement models metadata as function attributes #143

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c3ccb00
implement model metadata as function attributes
luisfabib Apr 7, 2021
70f7f5e
minor refactoring
luisfabib Apr 7, 2021
ae52159
update CHANGELOG
luisfabib Apr 7, 2021
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32 changes: 23 additions & 9 deletions CHANGELOG.md
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@@ -1,34 +1,38 @@

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

#### New features

- DeerLab now supports Python 3.9.
- The function ``fitsignal`` has been re-named to ``fitmodel`` for correctness and consistency with other functions ([#102](https://github.com/JeschkeLab/DeerLab/pull/102)).
- 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 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)).
- All fit functions now return the fit of the data along its uncertainty automatically as part of the ``FitResult`` object ([#130](https://github.com/JeschkeLab/DeerLab/issues/130), [#134](https://github.com/JeschkeLab/DeerLab/pull/134)).

#### Overall changes

- The performance of all fit functions has been considerably accelerated by removing call overheads in built-in DeerLab models ([#100](https://github.com/JeschkeLab/DeerLab/issues/100), [#101](https://github.com/JeschkeLab/DeerLab/pull/101)).
- All fit functions now return the fitted data and its uncertainty quantification as part of the ``FitResult`` object ([#130](https://github.com/JeschkeLab/DeerLab/issues/130), [#134](https://github.com/JeschkeLab/DeerLab/pull/134)).
- The performance of all fit functions has been considerably accelerated by removing call overheads in built-in DeerLab models ([#100](https://github.com/JeschkeLab/DeerLab/issues/100), [#101](https://github.com/JeschkeLab/DeerLab/pull/101), [#143](https://github.com/JeschkeLab/DeerLab/pull/143)).
- Improved robustness of the installer ([#65](https://github.com/JeschkeLab/DeerLab/pull/65)):
- The installer no longer assumes the alias ``pip`` to be setup on the system.
- The installation will now handle cases when system-wide privileges are not available ([#52](https://github.com/JeschkeLab/DeerLab/issues/52)).
- Improved robustness of the installation in Windows systems to avoid missing DLL errors ([#64](https://github.com/JeschkeLab/DeerLab/issues/64)).
- The installer will now get the latest Numpy/Scipy releases in Windows systems.
- Adapted piece of code leading to a ``VisibleDeprecationWarning `` visible during execution of certain DeerLab functions.
- The installer will now get the latest Numpy/Scipy releases in Windows systems available at the [Gohlke repository](https://www.lfd.uci.edu/~gohlke/pythonlibs/).
- 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 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)).
- 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.
- The keyword argument to request uncertainty quantification has been unified across all fitting functions. It is now ``uq``.
- 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), [#115](https://github.com/JeschkeLab/DeerLab/pull/115), [#122](https://github.com/JeschkeLab/DeerLab/pull/122))
- Corrections in the metadata of multiple ``dd_models``. The key ``Parameters`` of some models contained the wrong names.
- The metadata of the built-in models is now accessible and manipulable via function attributes (e.g. ``dd_gauss.parameters``) rather than trought a returned dictionary (e.g. ``dd_gauss()['Parameters']``) ([#143](https://github.com/JeschkeLab/DeerLab/pull/143)).
- The keyword argument to request uncertainty quantification has been unified across all fitting functions. It is now ``uq`` ([#120](https://github.com/JeschkeLab/DeerLab/pull/120)).
- The ``UncertQuant`` class has been renamed into ``UQResult`` ([#123](https://github.com/JeschkeLab/DeerLab/pull/123)).
- Uncertainty quantification is now tested numerically against an external package (``lmfit``) to ensue quality and accuracy ([#121](https://github.com/JeschkeLab/DeerLab/pull/121)).

#### Specific changes
- ``deerload``:
Expand All @@ -42,17 +46,27 @@ Release v0.13.0 - March 2021
- Removed the keyword argument ``uqanalysis=True/False``. The uncertainty quantification can now be disabled via the new keyword ``uq=None`` ([#98](https://github.com/JeschkeLab/DeerLab/pull/98)).
- Corrected the behaviour of built-in start values when manually specifying boundaries ([#73](https://github.com/JeschkeLab/DeerLab/pull/73)). If the built-in start values are outside of the user-specified boundaries the program will now automatically set the start values in the middle of the boundaries to avoid errors ([#72](https://github.com/JeschkeLab/DeerLab/issues/72)).
- Implemented the constraint ``Lam0+sum(lam)<=1`` to ensure the structural-identifiability of ``Lam0`` and ``V0`` during SNLLS optimization of experiment models with more than one modulated dipolar pathway (i.e. does not affect ``ex_4pdeer``) ([#76](https://github.com/JeschkeLab/DeerLab/issues/76),[#108](https://github.com/JeschkeLab/DeerLab/pull/108)).
- Removed the optional keyword argument ``regtype`` ([#137](https://github.com/JeschkeLab/DeerLab/pull/137)).
- ``fitregmodel``:
- Corrected the behaviour of the uncertainty quantification when disabling the non-negativity constraint ([#121](https://github.com/JeschkeLab/DeerLab/pull/121)).
- ``fitparamodel``:
- Made ``par0`` a positional argument instead of an optional keyword ([#70](https://github.com/JeschkeLab/DeerLab/issues/70)). to avoid errors when not defined ([#69](https://github.com/JeschkeLab/DeerLab/issues/69)).
- Keyword argument ``rescale`` has been renamed to ``fitscale`` ([#128])https://github.com/JeschkeLab/DeerLab/issues/128)).
- Keyword argument ``rescale`` has been renamed to ``fitscale`` ([#128](https://github.com/JeschkeLab/DeerLab/issues/128),[#129](https://github.com/JeschkeLab/DeerLab/pull/129)).
- ``snlls``:
- Corrected bug that was leading to the smoothness penalty being accounted for twice in the least-squares residual during optimization ([#103](https://github.com/JeschkeLab/DeerLab/issues/103)).
- Now returns the uncertainty quantification of linear and nonlinear parts as separate objects ``nonlinUncert`` and ``linUncert`` ([#108](https://github.com/JeschkeLab/DeerLab/pull/108)).
- Improved the covariance-based uncertainty analysis by including correlations between linear and non-linear parameters ([#108](https://github.com/JeschkeLab/DeerLab/pull/108)).
- Improved the behavior of signal scale determination ([#108](https://github.com/JeschkeLab/DeerLab/pull/108)).
- Enabled prescaling of the data to avoid scaling issues during uncertainty quantification ([#132](https://github.com/JeschkeLab/DeerLab/issue/132), [#133](https://github.com/JeschkeLab/DeerLab/pull/133)).
- Corrected the behaviour of the uncertainty quantification when disabling the regularization penalty ([#121](https://github.com/JeschkeLab/DeerLab/pull/121)).
- ``diststats``:
- Now compatible with non-uniformly defined distance distributions ([#92](https://github.com/JeschkeLab/DeerLab/issues/92), [#94](https://github.com/JeschkeLab/DeerLab/pull/94)).
- Added internal validation step to avoid non-sensical results when confounding the syntax ([#91](https://github.com/JeschkeLab/DeerLab/pull/91)).
- ``dipolarkernel``:
- Now allows defining pathways without unmodulated components.
- All optional keyword arguments can only be passed as named and not positional arguments ([#138](https://github.com/JeschkeLab/DeerLab/pull/138)).
- The keyword ``pathways`` now only takes lists of pathways and not modulation depth parameters. A new separate keyword ``mod`` takes the modulation depth parameter for the simplified 4-pulse DEER kernel ([#118](https://github.com/JeschkeLab/DeerLab/issues/118), [#138](https://github.com/JeschkeLab/DeerLab/pull/138)).
- Renmaed the background argument keyword ``B`` into ``bg`` ([#138](https://github.com/JeschkeLab/DeerLab/pull/138)).
- ``regparamrange``:
- Implemented new CSD algorithm to avoid LAPACK library crashes encountered when using multiple DeerLab functions calling ``regparamrange`` internally ([#68](https://github.com/JeschkeLab/DeerLab/pull/68)).
- ``correctphase``:
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