Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Documentation updates #115

Merged
merged 14 commits into from
Mar 25, 2021
Merged
Show file tree
Hide file tree
Changes from all commits
Commits
File filter

Filter by extension

Filter by extension

Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
10 changes: 4 additions & 6 deletions CHANGELOG.md
Original file line number Diff line number Diff line change
@@ -1,6 +1,4 @@

-------------------------------

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
Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
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
Expand Down
Loading