pulling changes to docs on master

DESCRIPTION

@@ -1,6 +1,6 @@
 Name: ODE Test Problems
-Version: 0.0.1
-Date: May 10, 2023
+Version: 0.2.0
+Date: November 7, 2023
 depends: octave (>= 6.4.0)
 Author: Steven Roberts, Andrey A. Popov, Arash Sarshar, Adrian Sandu
 Maintainer: Steven Roberts

docs/conf.py

@@ -26,6 +26,7 @@
 primary_domain = 'mat'
 matlab_src_dir = '../toolbox'
 matlab_keep_package_prefix = False
+matlab_auto_link = 'basic'
 
 autodoc_default_options = {
     'member-order': 'bysource',

docs/generate_problem_rst.py

@@ -30,7 +30,7 @@
 .. automodule:: +otp.{problem.parent.name}.+presets
 ''')
 
-        for preset in problem.parent.glob('+presets/*.m'):
+        for preset in sorted(problem.parent.glob('+presets/*.m')):
             stream.write(f'''
 .. autoclass:: {preset.stem}
     :members:

docs/references.bib

@@ -55,17 +55,16 @@ @Article{PR74
 }
 
 
-@Article{Rob67,
+@Article{Rob66,
     title={The Solution of a Set of Reaction Rate Equations},
     author={Robertson, H.H.},
     journal={Walsh, J., Ed., Numerical Analysis, An introduction},
-    year={1967},
+    year={1966},
     pages= {178--182},
-    publisher = "Academic Press",
-    address   = "Cambridge, Massachusetts",
+    volume={178182},
+    publisher = {Academic Press}
 }
 
-
 @article{SLH70,
     author = {Seinfeld, J. H. and Lapidus, Leon and Hwang, Myungkyu},
     title = {Review of Numerical Integration Techniques for Stiff Ordinary Differential Equations},
@@ -105,5 +104,78 @@ @inproceedings{Lor96
   volume={1},
   number={1},
   year={1996},
-  organization={Reading}
+  organization={Reading},
+  doi={10.1017/CBO9780511617652.004}
 }
+
+@article{PS19,
+  title={A Bayesian approach to multivariate adaptive localization in ensemble-based data assimilation with time-dependent extensions},
+  author={Popov, Andrey A and Sandu, Adrian},
+  journal={Nonlinear Processes in Geophysics},
+  volume={26},
+  number={2},
+  pages={109--122},
+  year={2019},
+  publisher={Copernicus Publications G{\"o}ttingen, Germany},
+  doi={10.5194/npg-26-109-2019}
+}
+
+@article{FN74,
+    author = {Field, Richard J. and Noyes, Richard M.},
+    title = "{Oscillations in chemical systems. {IV}. {L}imit cycle behavior in a model of a real chemical reaction}",
+    journal = {The Journal of Chemical Physics},
+    volume = {60},
+    number = {5},
+    pages = {1877-1884},
+    year = {1974},
+    issn = {0021-9606},
+    doi = {10.1063/1.1681288}
+}
+
+@incollection{EH76,
+    title = {Comparing Numerical Methods for the Solution of Stiff Systems of {ODE}s Arising in Chemistry},
+    editor = {L. LAPIDUS and W.E. SCHIESSER},
+    booktitle = {Numerical Methods for Differential Systems},
+    publisher = {Academic Press},
+    pages = {45-66},
+    year = {1976},
+    isbn = {978-0-12-436640-4},
+    doi = {10.1016/B978-0-12-436640-4.50008-3},
+    author = {W.H. Enright and T.E. Hull}
+}
+
+@article{GW82,
+    author = {Björn A. Gottwald and Gerhard Wanner},
+    title ={Comparison of Numerical Methods for Stiff Differential Equations in Biology and Chemistry},
+    journal = {SIMULATION},
+    volume = {38},
+    number = {2},
+    pages = {61-66},
+    year = {1982},
+    doi = {10.1177/003754978203800206}
+}
+
+
+@article{Asc89,
+author = {Ascher, Uri},
+title = {On Symmetric Schemes and Differential-Algebraic Equations},
+journal = {SIAM Journal on Scientific and Statistical Computing},
+volume = {10},
+number = {5},
+pages = {937-949},
+year = {1989},
+doi = {10.1137/0910054}
+}
+
+@article{Pet86,
+ author = {L. R. Petzold},
+ journal = {SIAM Journal on Numerical Analysis},
+ number = {4},
+ pages = {837--852},
+ publisher = {Society for Industrial and Applied Mathematics},
+ title = {Order Results for Implicit Runge-Kutta Methods Applied to Differential/ Algebraic Systems},
+ volume = {23},
+ year = {1986},
+ url = {https://www.jstor.org/stable/2157625}
+}
+

docs/requirements.txt

@@ -1,9 +1,9 @@
 sphinx==6.2.1
 sphinx-autobuild==2021.3.14
-sphinx_rtd_theme==1.2.0
-sphinxcontrib-matlabdomain==0.18.0
+sphinx_rtd_theme==1.3.0
+sphinxcontrib-matlabdomain==0.20.2
 sphinxcontrib-napoleon==0.7
 sphinx-math-dollar==1.2.1
 sphinxcontrib-bibtex==2.5.0
-myst-parser==1.0.0
-pyyaml==6.0
+myst-parser==2.0.0
+pyyaml==6.0.1

docs/structure/index.rst

@@ -8,4 +8,6 @@ TODO
    :maxdepth: 1
    :glob:
 
-   *
+   problem
+   rhs
+   parameters

docs/structure/parameters.rst

@@ -0,0 +1,6 @@
+Parameters
+================================================================================
+
+.. automodule:: +otp
+.. autoclass:: Parameters
+    :members:

toolbox/+otp/+ascherlineardae/+presets/Canonical.m

@@ -1,23 +1,21 @@
 classdef Canonical < otp.ascherlineardae.AscherLinearDAEProblem
-    %CANONICAL The problem formulation of the linear DAE from the literature
-    %
-    % See
-    %    Ascher, Uri. "On symmetric schemes and differential-algebraic equations."
-    %    SIAM journal on scientific and statistical computing 10.5 (1989): 937-949.
-
+    % The problem defined by Uri Ascher in :cite:p:`Asc89` (sec. 2) which uses time span $t ∈ [0, 1]$ and intial 
+    % condition $[y_0, z_0]^T = [1, β]^T$.
+
     methods
-        function obj = Canonical(beta)
-            tspan = [0.0; 1];
-
-            if nargin < 1
-                beta = 0.5;
-            end
-
-            params = otp.ascherlineardae.AscherLinearDAEParameters;
-            params.Beta = beta;
-
-            y0 = [1; beta];
+        function obj = Canonical(varargin)
+            % Create the Canonical Ascher Linear DAE problem object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. The accepted names are
+            %
+            %    - ``Beta`` – Value of $β$.
 
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 1, varargin{:});
+            y0 = [1; params.Beta];
+            tspan = [0.0; 1.0];
             obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);
         end
     end

toolbox/+otp/+ascherlineardae/+presets/Petzold.m

@@ -0,0 +1,15 @@
+classdef Petzold < otp.ascherlineardae.AscherLinearDAEProblem
+    % The Petzold DAE example :cite:p:`Pet86` as a special case of the Ascher linear DAE problem. This preset uses time
+    % span $t ∈ [0, 1]$ and $β = 0 $ with the initial condition $[y_0, z_0]^T = [1, 0]^T$.
+
+    methods
+        function obj = Petzold()
+            % Create the Petzold Ascher Linear DAE problem object.
+
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 0);
+            y0 = [1; params.Beta];
+            tspan = [0.0; 1.0];
+            obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);
+        end
+    end
+end

toolbox/+otp/+ascherlineardae/+presets/Stiff.m

@@ -0,0 +1,15 @@
+classdef Stiff < otp.ascherlineardae.AscherLinearDAEProblem
+    % The Stiff example from :cite:p:`Asc89`. A variant of the Ascher linear DAE problem which uses time span 
+    % $t ∈ [0, 1]$ and $β = 100$ with the initial condition $[y_0, z_0]^T = [1, 100]^T$.
+
+    methods
+        function obj = Stiff()
+            % Create the stiff Ascher Linear DAE problem object.
+
+            params = otp.ascherlineardae.AscherLinearDAEParameters('Beta', 100);
+            y0 = [1; params.Beta];
+            tspan = [0.0; 1.0];
+            obj = obj@otp.ascherlineardae.AscherLinearDAEProblem(tspan, y0, params);
+        end
+    end
+end

toolbox/+otp/+ascherlineardae/AscherLinearDAEParameters.m

@@ -1,7 +1,21 @@
-classdef AscherLinearDAEParameters
-    %ASCHERLINEARDAEPARAMETERS 
+classdef AscherLinearDAEParameters < otp.Parameters
+    % Parameters for Ascher Linear DAE problem 
     properties
-        %Beta is an arbitrary scalar parameter
-        Beta %MATLAB ONLY: (1,1) {mustBeNumeric} = 0.5
+        % A scalar parameter $β$ in the linear model. It affects the stifness of the problem.
+        Beta %MATLAB ONLY: (1,1) {mustBeNumeric} = 1
+    end
+
+    methods
+        function obj = AscherLinearDAEParameters(varargin)
+            % Create a Ascher Linear DAE parameters object.
+            %
+            % Parameters
+            % ----------
+            % varargin
+            %    A variable number of name-value pairs. A name can be any property of this class, and the subsequent
+            %    value initializes that property.
+
+            obj = obj@otp.Parameters(varargin{:});
+        end
     end
 end