Release v0.12.1 (#59)

JeschkeLab · Nov 6, 2020 · aadf280 · aadf280
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -1,24 +1,46 @@
 
 -------------------------------
 
-Release Notes v0.12.0 - October 2020
+Release v0.12.1 - October 2020
 ---------------------------------
 
 #### Overall changes
 
-* The regularization operator matrices ``regoperator`` now include the edges of the distribution (#38). Now the smoothness penalty is imposed on the distribution edges avoiding the accumulation of distribution mass at the edges of ``r``. 
+* The calculation of the Jacobian for covariance-based uncertainty analysis has been simplified providing a significant boost in performance for all fit functions ([#55](https://github.com/JeschkeLab/DeerLab/pull/55)). 
 
-* The interface for defining dipolar pathways has been simplified (#41). For example, a signal with two dipolar pathways had to be defined as ``pathways = [[Lam0,np.nan], [lam1,T0]]``. Now the unmodulated pathway can just be defined by its amplitude and does not require the use of ``np.nan``, e.g. ``pathways = [Lam0, [lam1,T0]]``.
+* The Jacobian computation is more robust, now taking into consideration parameter boundaries ([#58](https://github.com/JeschkeLab/DeerLab/pull/58)). This solves errors such as the ones reported in [#50](https://github.com/JeschkeLab/DeerLab/issues/50).
+
+* Broken examples in the documentation have been corrected ([#57](https://github.com/JeschkeLab/DeerLab/pull/57)).
+
+* When requesting attributes or method of a UncertQuant object under disabled uncertainty analysis (``uqanalysis=False``) now it will prompt an explanatory error instead of just crashing ([#56](https://github.com/JeschkeLab/DeerLab/issues/56)). 
+
+#### Specific changes
+
+* ``fitsignal``: corected the behaviour of the scaling output (``fit.scale``). Now all fitted dipolar signals (``fit.V``) have the same scaling as the input signal ([#53](https://github.com/JeschkeLab/DeerLab/issues/53)). 
+
+* ``regparamrange``: relaxed the exception handling to catch errors occuring under certain conditions. The function seems to crash due to LAPACK or SVD non-convergence errors during the GSVD, now these are catched and the alpha-range is estimated using simple SVD as an approximation. This function might be deprecated in a future release ([#42](https://github.com/JeschkeLab/DeerLab/issues/42)).   
+
+-------------------------------
+
+
+Release v0.12.0 - October 2020
+---------------------------------
+
+#### Overall changes
+
+* The regularization operator matrices ``regoperator`` now include the edges of the distribution ([#38](https://github.com/JeschkeLab/DeerLab/pull/38)). Now the smoothness penalty is imposed on the distribution edges avoiding the accumulation of distribution mass at the edges of ``r``. 
+
+* The interface for defining dipolar pathways has been simplified ([#41](https://github.com/JeschkeLab/DeerLab/pull/41)). For example, a signal with two dipolar pathways had to be defined as ``pathways = [[Lam0,np.nan], [lam1,T0]]``. Now the unmodulated pathway can just be defined by its amplitude and does not require the use of ``np.nan``, e.g. ``pathways = [Lam0, [lam1,T0]]``.
 
 * The project version control has been switched from the Git-flow to the GitHub-flow design. The default branch has been switched from ``master`` to ``main``, which is now always production-ready. All new contributions are merged into ``main`` exclusively by pull requests.
 
-* The dependency on the ``lambda`` parameter has been removed from all phenomenological background models, and kept only for physical models (#43). Their interface with ``dipolarbackground`` and ``dipolarkernel`` have been updated accordingly. 
+* The dependency on the ``lambda`` parameter has been removed from all phenomenological background models, and kept only for physical models ([#43](https://github.com/JeschkeLab/DeerLab/pull/43)). Their interface with ``dipolarbackground`` and ``dipolarkernel`` have been updated accordingly. 
 
 #### New features: 
 
-* ``diststats``: New function to calculate different statistical quantities of the distance distribution and their corresponding uncertainties (#38).
+* ``diststats``: New function to calculate different statistical quantities of the distance distribution and their corresponding uncertainties ([#37](https://github.com/JeschkeLab/DeerLab/pull/37)).
 
-* ``bootan``: Introduced the option ``cores`` to parallelize the bootstrapping using multiple CPU. 
+* ``bootan``: Introduced the option ``cores`` to parallelize the bootstrapping using multiple CPUs ([#35](https://github.com/JeschkeLab/DeerLab/pull/35)). 
 
 #### Specific changes
 
@@ -29,7 +51,7 @@ Release Notes v0.12.0 - October 2020
     - Fixed bug when propagating uncertainty to scalar functions.
 
 * ``deerload``: 
-    - Fixed UTF-8 error when loading certain spectrometer files in MacOS (#30)
+    - Fixed UTF-8 error when loading certain spectrometer files in MacOS ([#30](https://github.com/JeschkeLab/DeerLab/pull/30))
 
 * ``fitsignal``:
     - The fitted scale of the signal is now properly calculated when fitting fully parametric signals. 
@@ -44,37 +66,37 @@ Release Notes v0.12.0 - October 2020
 -------------------------------
 
 
-Release Notes v0.11.0 - September 2020
+Release v0.11.0 - September 2020
 ---------------------------------
 
 #### Overall changes
 
-* All Gauss models (``dd_gauss``,etc.) now use the standard deviation ``sigma`` instead of the FWHM as the width parameter for consistency with other method such as Rice distributions. (#19)
+* All Gauss models (``dd_gauss``,etc.) now use the standard deviation ``sigma`` instead of the FWHM as the width parameter for consistency with other method such as Rice distributions ([#19](https://github.com/JeschkeLab/DeerLab/pull/19)).
 
 * All hard-wired random seeds have been removed. 
 
-* A new method ``plot()`` has been added to the ``FitResult`` class returned by all fit functions. This will create a basic plot of the fit results. (#7)
+* A new method ``plot()`` has been added to the ``FitResult`` class returned by all fit functions. This will create a basic plot of the fit results ([#7](https://github.com/JeschkeLab/DeerLab/pull/7)).
 
 #### Specific changes
 * ``snlls``: 
-    - Renamed option ``penalty`` as ``reg`` and improved its interface (#13).
-    - The regularization parameter of the optimal solution is returned now (#20).
+    - Renamed option ``penalty`` as ``reg`` and improved its interface ([#13](https://github.com/JeschkeLab/DeerLab/pull/13)).
+    - The regularization parameter of the optimal solution is returned now ([#20](https://github.com/JeschkeLab/DeerLab/pull/20)).
 
 * ``whitegaussnoise``: Added a ``seed`` option to select static noise realizations.
 
 * ``correctzerotime``: 
-    - Fixed bug when zero-time is at start/end of array (#24).
+    - Fixed bug when zero-time is at start/end of array ([#24](https://github.com/JeschkeLab/DeerLab/pull/24)).
     - Function no longer rescales the experimental data passed on to the function. 
 
 * ``fitsignal``:  
-    - The regularization parameter of the optimal solution is returned now (#20).
+    - The regularization parameter of the optimal solution is returned now ([#20](https://github.com/JeschkeLab/DeerLab/pull/20)).
     - Bug fixed when fitting dipolar evolution functions (no background and no experiment models) with a parametric distance distribution. 
 
-* ``fitmultimodel``: Start points are now spread over constrained parameter space grid instead of being randomble initiated (#22).
+* ``fitmultimodel``: Start points are now spread over constrained parameter space grid instead of being randomble initiated ([#22](https://github.com/JeschkeLab/DeerLab/pull/22)).
 
 * ``deerload``: 
-    - Now returns the time axis in microseconds instead of nanoseconds (#21).
-    - The bug appearing when loading certain BES3T files has been fixed (#14).
+    - Now returns the time axis in microseconds instead of nanoseconds ([#21](https://github.com/JeschkeLab/DeerLab/pull/21)).
+    - The bug appearing when loading certain BES3T files has been fixed ([#14](https://github.com/JeschkeLab/DeerLab/pull/14)).
 
 * ``fitregmodel``: Now returns the fitted dipolar signal in the ``FitResult`` output
 
@@ -83,10 +105,10 @@ Release Notes v0.11.0 - September 2020
 
 -------------------------------
 
-Release Notes v0.10.0 - August 2020
+Release v0.10.0 - August 2020
 -----------------------------
 
-As of this version, DeerLab is written in Python in contrast to older versions based on MATLAB.
+As of this version, DeerLab is based on Python in contrast to older versions based on MATLAB found [here](https://github.com/JeschkeLab/DeerLab-Matlab).
 
 #### Deprecated functions
 The following functions have been deprecated due to limited usability or due to functionality overlap with other DeerLab functions: ``aptkernel``, ``backgroundstart``, ``fitbackground``, ``paramodel``, and ``time2freq``. 

diff --git a/VERSION b/VERSION
@@ -1 +1 @@
-v0.13.0-dev
+v0.12.1