Restructured IFDIFF initialization

.gitattributes

@@ -0,0 +1,28 @@
+* text=auto
+
+*.fig binary
+*.mat binary
+*.mdl binary diff merge=mlAutoMerge
+*.mdlp binary
+*.mex* binary
+*.mlapp binary
+*.mldatx binary
+*.mlproj binary
+*.mlx binary
+*.p binary
+*.sfx binary
+*.sldd binary
+*.slreqx binary merge=mlAutoMerge
+*.slmx binary merge=mlAutoMerge
+*.sltx binary
+*.slxc binary
+*.slx binary merge=mlAutoMerge
+*.slxp binary
+
+## Other common binary file types
+*.docx binary
+*.exe binary
+*.jpg binary
+*.pdf binary
+*.png binary
+*.xlsx binary

Examples/ParameterEstimation_WhiteCabbage/plot_sensitivities_cabbage.m

@@ -1,5 +1,5 @@
 %% Solution ifdiff
-initPaths();
+
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/ParameterEstimation_WhiteCabbage/test_Cabbage.m

@@ -1,5 +1,5 @@
 %% Solution ifdiff
-initPaths();
+
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('whiteCabbageRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/canonicalExample/AnalyticalSensitivities/Gmatrices_VDE_df_exact.m

@@ -1,5 +1,5 @@
 %% Solution with ifdiff
-initPaths();
+
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/canonicalExample/AnalyticalSensitivities/analyticalSensitivities_test.m

@@ -1,5 +1,5 @@
 %% Solution ifdiff
-%initPaths();
+
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/canonicalExample/analyticalSolution.m

@@ -27,8 +27,8 @@
 ylabel('\sigma_2(t)')
 set(gca, 'FontSize', 24);
 set(gca, 'Box', 'off');
+
 %% Solution ifdiff
-initPaths();
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/canonicalExample/canonicalExampleRHS_extended_test.m

@@ -3,7 +3,6 @@
 initstates = [1 0];
 %p = 5.437;
 p = 0.5;
-%initPaths()
 %%
 
 options = odeset('AbsTol', 1e-14, 'RelTol', 1e-12);

Examples/canonicalExample/sensitivities_CanonicalExample.m

@@ -1,5 +1,5 @@
 %% Solution with ifdiff
-initPaths();
+
 integrator = @ode45;
 odeoptionsrhs_test = odeset( 'AbsTol', 1e-14,'RelTol', 1e-12);
 datahandle    = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptionsrhs_test);

Examples/predatorprey_filippov/testpprhs.m

@@ -54,13 +54,15 @@
 
 
 %% EULER Integration
-euler_fname = fullfile('.', 'Examples', 'predatorprey_filippov', sprintf('sol_euler_%.0e.mat', eulerStep));
+[owndir, ~] = fileparts(mfilename('fullpath'));
+euler_fname = fullfile(owndir, sprintf('sol_euler_%.0e.mat', eulerStep));
 if doEuler
-    fprintf('Integrating with integrator %s...\n', func2str(intEuler))
+    fprintf('Integrating with integrator %s (might take a while) ...\n', func2str(intEuler))
     figure(fignum);
     th = tic();
     sol_euler = intEuler(@(t,x) pprhs(t,x,p), tspan, x0_1, eulerStep);
     time_euler = toc(th); fprintf('Euler took %g s\n', time_euler);
+    fprintf('Saving result to %s for later reuse.\n', euler_fname);
     save(euler_fname, "sol_euler");
 elseif isfile(euler_fname)
     fprintf('Loading sol_euler from file %s\n', euler_fname);
@@ -150,8 +152,8 @@ function errorPlot(fignum, x1, y1, y2, intname1, intname2)
       if (i == nextout)
          X(:,k) = Xi; k = k + 1; 
          nextout = nextout + ceil(1 / sfac);
-         if ~mod(i/stepcount, 0.1), fprintf('.'); end
       end
+      if ~mod(floor(100*i/stepcount), 10), fprintf('.'); end
    end
    fprintf('\n')
    T = linspace(tspan(1), tspan(end), ceil(stepcount*sfac)+1);

Examples/statejump/bounceball.m

@@ -1,6 +1,4 @@
 % Solve the bouncing ball problem and plot the solutions and sensitivities
-initPaths();
-
 solver = @ode15s;
 options    = odeset('AbsTol', 1e-8, 'RelTol', 1e-6);
 

Examples/statejump/bounceballError.m

@@ -6,8 +6,6 @@
 % This is because having to set h_+ to a value slightly above zero is a burden imposed by IFDIFF, so it
 % should also factor into the error
 
-initPaths();
-
 % INITIAL DATA
 g     = 9.807;
 gamma = 0.9;

Examples/statejump/bounceballZeno.m

@@ -1,6 +1,4 @@
 % Solve the bouncing ball problem with Zeno's phenomenon treatment and plot the solutions and sensitivities
-initPaths();
-
 solver = @ode15s;
 options    = odeset('AbsTol', 1e-8, 'RelTol', 1e-6);
 

Examples/statejump/jumpSensitivities.m

@@ -3,7 +3,6 @@
 % 2. IFDIFF with standard tolerances and FD step, plus relative error
 % 3. IFDIFF with strict tolerances and shorter FD step, plus relative error
 
-initPaths();
 [t0, tEnd, p, x0] = jumpSensitivityInitdata();
 
 % CONFIGURATION

Examples/statejump/sinCosMain.m

@@ -1,5 +1,3 @@
-initPaths();
-
 solver = @ode45;
 options = odeset('AbsTol', 1e-8, 'RelTol', 1e-6);
 

README.md

@@ -19,12 +19,13 @@ The file [Readme_Example.m](./Readme_Example.m) contains a self-explaining Matla
 
 
 # First Run Prerequisites
+
 Before using IFDIFF, it is mandatory to run the `make_mtreeplus` script once.  
 After starting Matlab, change to the IFDIFF directory and type `make_mtreeplus`.  
 This scripts generates a modified copy of Matlab's own parser class `mtree`, on which IFDIFF heavily relies.
 
-It is also advisable to initialize the paths needed for IFDIFF by invoking 
-`initPaths();` once on every new matlab session.
+It is advisable to initialize the paths needed for IFDIFF by invoking 
+`initIFDIFF();` once on every new matlab session.
 
 </br>
 
@@ -43,7 +44,7 @@ Preprocessing generates the `datahandle`, the central structure for switching de
 We set ODE solver and its options as usual. If not set, default values are used.
 
    ```matlab
-      initPaths();  % Initialise the paths for ifdiff
+      initIFDIFF();  % Initialise the paths for ifdiff -- needed only once per Matlab session
       integrator = @ode45; 
       odeoptions = odeset('AbsTol', 1e-14, 'RelTol', 1e-12);
       datahandle = prepareDatahandleForIntegration('canonicalExampleRHS', 'integrator', func2str(integrator), 'options', odeoptions);

Readme_Example.m

@@ -8,7 +8,7 @@
 % The ODE solver and the ODE options can be set by the user with name-value pairs. 
 % If unspecified, defaults are used.
 
-initPaths();            % Initialise the paths for ifdiff
+initIFDIFF();           % Initialise the paths for ifdiff
 integrator = @ode45;    % Choose integrator and options
 odeoptions = odeset('AbsTol', 1e-8, 'RelTol', 1e-6);
 

clearPaths.m

@@ -7,16 +7,14 @@ function clearPaths()
 %   OUTPUT
 %   [none]
 %
-%   See also INITPATHS whose changes are undone by CLEARPATHS.
+%   See also initIFDIFF whose paths additions are undone by CLEARPATHS.
 
 
-% Get absolute path to directory in which this file resides.
-[filePath, ~, ~] = fileparts(mfilename('fullpath'));
+% receive the required paths
+ifdiffpaths = generateIFDIFFpaths();
+
+% remove them from the search path
+rmpath(ifdiffpaths);
+
 
-rmpath(filePath);
-rmpath(genpath(fullfile(filePath, 'Tools')));
-rmpath(genpath(fullfile(filePath, 'Examples')));
-rmpath(genpath(fullfile(filePath, 'PreprocessedFunctions')));
-rmpath(fullfile(filePath, 'ComputeSensitivities'));
-rmpath(genpath(fullfile(filePath, 'GenerateFixedBranchingFunctions')));
 end

docs/index.md

@@ -122,7 +122,7 @@ Without any warning or error, the __naive approach with tight tolerances leads t
 With the switching point detection in IFDIFF, after a single call to a preparation routine, 
 integration is just as simple as before:
 ```matlab
-   initPaths();                                              % initialise the paths for ifdiff (only once)
+   initIFDIFF();                                             % initialise IFDIFF (only once)
    tspan = [0 20]; x0 = [1;0]; p = 5.437;                    % set time horizon, initial value, parameter
    integrator = @ode45;                                      % choose integrator
    odeoptions = odeset('AbsTol', 1e-5, 'RelTol', 1e-3);      % set integrator options, here: low accuracy

generateIFDIFFpaths.m

@@ -0,0 +1,35 @@
+function [pathStr, pathList] = generateIFDIFFpaths()
+% [pathStr, pathList] = generateIFDIFFpaths()
+%
+% Generates a character array with all paths for IFDIFF.
+% The character array can be passed to addpath or rmpath
+%
+% INPUT:    none
+%
+% OUTPUT:   pathStr --> character array with paths needed/used by IFDIFF
+%          pathList --> cell array of sub-paths
+%           
+%
+% Andreas Sommer, Jul2025
+% code@andreas-sommer.eu
+%
+
+
+% get directory this file resides in
+[selfdir, ~] = fileparts(mfilename('fullpath'));
+
+% list all IFDIFF pars
+pathList = { selfdir  ... % main directory of IFDIFF
+           , genpath(fullfile(selfdir, 'Tools'))                           ...
+           , genpath(fullfile(selfdir, 'Examples'))                        ...
+           , genpath(fullfile(selfdir, 'PreprocessedFunctions'))           ...
+           ,         fullfile(selfdir, 'ComputeSensitivities')             ... % no subdirs
+           , genpath(fullfile(selfdir, 'GenerateFixedBranchingFunctions')) ...
+           };
+
+% combine them into a single path specification
+pathStr = strjoin(pathList, pathsep());
+
+% finito
+end
+

initIFDIFF.m

@@ -0,0 +1,23 @@
+function initIFDIFF()
+% initIFDIFF()
+%
+% Initializes IFDIFF, setting up paths.
+%
+% INPUT:    none
+%
+% OUTPUT:   none
+%
+%
+% Andreas Sommer, Jul2025
+% code@andreas-sommer.eu
+%
+
+
+% receive the required paths
+ifdiffpaths = generateIFDIFFpaths();
+
+% add them to the search path at the beginning (search them first)
+addpath(ifdiffpaths, '-begin'); 
+
+
+end % of function

speedtracker/commands/RunBenchmarksCommand.m

@@ -136,7 +136,7 @@
             end
 
             % Main: run the benchmarks and return the results
-            initPaths();
+            initIFDIFF();
             try
                 speedtrackerRunner = speedtrackerRunner.run(snapshots, benchmarks);
             catch error

test/TestHelperFunctions.m

@@ -5,11 +5,11 @@ function setPath(testCase)
             originalPath = path;
             testCase.addTeardown(@path, originalPath);
 
-            if ~exist('initPaths', 'file')
+            if ~exist('initIFDIFF', 'file')
                 % We are probably in the test directory, so check parent directory
                 cd('..');
             end
-            initPaths();
+            initIFDIFF();
 
             % Get absolute path to directory in which this file resides.
             [filePath, ~, ~] = fileparts(mfilename('fullpath'));

test/TestIgnore.m

@@ -5,11 +5,11 @@ function setPath(testCase)
             originalPath = path;
             testCase.addTeardown(@path, originalPath);
 
-            if ~exist('initPaths', 'file')
+            if ~exist('initIFDIFF', 'file')
                 % We are probably in the test directory, so check parent directory
                 cd('..');
             end
-            initPaths();
+            initIFDIFF();
 
             % Get absolute path to directory in which this file resides.
             [filePath, ~, ~] = fileparts(mfilename('fullpath'));

test/TestPreprocessing.m

@@ -5,11 +5,11 @@ function setPath(testCase)
             originalPath = path;
             testCase.addTeardown(@path, originalPath);
 
-            if ~exist('initPaths', 'file')
+            if ~exist('initIFDIFF', 'file')
                 % We are probably in the test directory, so check parent directory
                 cd('..');
             end
-            initPaths();
+            initIFDIFF();
 
             % Get absolute path to directory in which this file resides.
             [filePath, ~, ~] = fileparts(mfilename('fullpath'));

test/TestSensitivities.m

@@ -3,7 +3,7 @@
     methods(TestClassSetup)
         function setup(~)
             cd("..");
-            initPaths();
+            initIFDIFF();
         end
     end
 

test/TestSolverCompatibility.m

@@ -15,7 +15,7 @@
 
         subway_tspan = [0 65];
         subway_x0 = [0; 0; 0];
-        % subway_p initialized later because we need to initPaths() before
+        % subway_p initialized later because we need to initIFDIFF() before
         subway_rhsFunction = 'newYorkCitySubwayModelRhs';
         subway_odeoptions = odeset( 'AbsTol', 1e-20, 'RelTol', 1e-10);
         subway_xEnd = [2112.07361577; 0.00124794; 4124.77885608];
@@ -41,15 +41,15 @@ function setPath(testCase)
             originalPath = path;
             testCase.addTeardown(@path, originalPath);
 
-            if ~exist('initPaths', 'file')
+            if ~exist('initIFDIFF', 'file')
                 % We are probably in the test directory, so check parent directory
                 cd('..');
             end
-            initPaths();
+            initIFDIFF();
 
-            % Get absolute path to directory in which initPaths resides.
+            % Get absolute path to directory in which initIFDIFF resides.
             % This should be the IFDIFF project root directory.
-            [filePath, ~, ~] = fileparts(which('initPaths'));
+            [filePath, ~, ~] = fileparts(which('initIFDIFF'));
             addpath(fullfile(filePath, 'Examples', 'subway'));
         end
         function setParameters(testCase)