Bugfixes 4th sep

VERSION

@@ -1 +1 @@
-v1.1.1
+v1.1.2

deerlab/dd_models.py

@@ -125,7 +125,7 @@ def _multirice3dfun(r,nu,sig):
     r = r.T
     s2 = sig**2
     I_scaled = spc.ive(n/2-1, nu*r/s2)
-    P = nu**(n/2-1)/s2*r**(n/2)*np.exp(-(r**2+nu**2)/(2*s2)+nu*r/s2)*I_scaled
+    P = nu**(1-n/2)/s2*r**(n/2)*np.exp(-(r**2+nu**2)/(2*s2)+nu*r/s2)*I_scaled
     P[P<0] = 0
 
     # Normalization

deerlab/solvers.py

@@ -426,6 +426,11 @@ def snlls(y, Amodel, par0=None, lb=None, ub=None, lbl=None, ubl=None, nnlsSolver
             * ``0`` : Work silently (default).
             * ``1`` : Display progress including the non-linear least-squares' solver termination report.
             * ``2`` : Display progress including the non-linear least-squares' solver iteration details.
+
+        .. caution::
+
+            The verbose output from the non-linear least-squares solver uses a different definition of the cost function than DeerLab.
+            DeerLab uses the sum of squares of the residuals divided by the number of data points, whereas the non-linear least-squares solver uses the sum of squares of the residuals divided by 2.
 
     Returns
     -------
@@ -594,7 +599,8 @@ def linear_problem(y,A,optimize_alpha,alpha):
 
 
         if optimize_alpha:
-            output = dl.selregparam((y-yfrozen)[mask], Ared[mask,:], linSolver, regparam, 
+            linsolver_result = lambda AtA, Aty: parseResult(linSolver(AtA, Aty))
+            output = dl.selregparam((y-yfrozen)[mask], Ared[mask,:], linsolver_result, regparam, 
                                         weights=weights[mask], regop=L, candidates=regparamrange, 
                                         noiselvl=noiselvl,searchrange=regparamrange,full_output=True)
             alpha = output[0]

docsrc/source/changelog.rst

@@ -24,6 +24,12 @@ Release Notes
 - |fix| : Something which was not working as expected or leading to errors has been fixed.
 - |api| : This will require changes in your scripts or code.
 
+Release ``v1.1.2`` - September 2023
+------------------------------------------
+- |fix| : Fixes an error in the normalisation of the rice models (:pr:`459`).
+- |fix| : Removes the broken three spin example (:pr:`427`).
+- |fix| : Fixes an error in the linear solver for linearly constrained not non-negative problems.
+
 Release ``v1.1.1`` - August 2023
 ------------------------------------------
 - |fix| : Fixes an error in the `FitResult.evaluate` function. (:pr:`454`)

docsrc/source/installation.rst

@@ -45,7 +45,7 @@ DeerLab installs the following packages:
 * `joblib <https://joblib.readthedocs.io/en/latest/>`_ - Library lightweight pipelining and parallelization.
 * `tqdm <https://github.com/tqdm/tqdm>`_ - A lightweight package for smart progress meters.
 * `dill <https://github.com/uqfoundation/dill>`_ - An extension of Python's pickle module for serializing and de-serializing python objects.
-* `quadprog <https://pypi.org/project/quadprog/>`_ - A quadratic programming solver
+* `quadprog <https://pypi.org/project/quadprog/>`_ - A quadratic programming solver (Only for Python versions < 3.11)
 
 Importing DeerLab
 ------------------
@@ -74,9 +74,6 @@ Any DeerLab version released after v0.10.0 can be installed via ``pip`` using th
 
 		python -m pip install deerlab==x.y.z
 
-DeerLab version prior to 0.10 are written in MATLAB and are still available from an `archived repository <https://github.com/JeschkeLab/DeerLab-Matlab>`_. 
-Download and installation instruction for the MATLAB environment are provided in the released documentation. MATLAB releases have been deprecated and no further support is provided.
-
 
 Installing from source
 *****************************
@@ -130,10 +127,18 @@ On a **Windows** computer, if you are trying to run a DeerLab function, you migh
 
     ImportError: DLL load failed: The specified module could not be found.
 
-This happens when the MKL libraries have not been properly linked in ``numpy``, ``scipy`` or ``cvxopt`` 
-installations (typically ``numpy``). This can happen due to firewall restrictions,
-user rights, or internet connection issues during the DeerLab installation. To solve this, the
-best solution is to manually install as follows. 
+This issue can occur when a specific python package is not installled properly. This typicaly happens when installing the MKL linked libaries but can 
+occur when installing packages normaly from PyPI. This can happen due to firewall restrictions,
+user rights, or internet connection issues during the DeerLab installation.
+
+If your where installing packages from PyPI (i.e. via pip) then please uninstall the package and reinstall it.
+
+.. code-block:: text
+
+    python -m pip uninstall <package_name>
+    python -m pip install <package_name>
+
+If you were trying to install the MKL linked libraries then please follow the instructions below.
 
 1) Go to https://www.lfd.uci.edu/~gohlke/pythonlibs/#numpy
 
@@ -167,7 +172,7 @@ During installation on certain systems (e.g. some computation clusters) using on
 the following error might be raised during the installation:
 
 .. code-block:: text
-
+    
     Error while finding module specification for 'setup.py'
     (ModuleNotFoundError: __path__ attribute not found on 'setup' while trying to find 'setup.py')