CI: Test Matlab interface on GHA (#1451)

Compiles and runs a subset of Matlab examples on GHA. Should prevent regularly breaking the Matlab interface... 

Reports missed expectations, but does not fail. Currently, '/model_steadystate/sensifwdbyhandpreeq' reports wrong sx0, sx, sy and sllh, independently of these changes.

Closes #1449 

* CI: Test Matlab interface on GHA

* Fix model_neuron test config; regenerate expected results; m-file for recompilation, tests to GHA

* Update doc

.github/workflows/test_matlab.yml

@@ -0,0 +1,21 @@
+name: Matlab
+on: [push, pull_request, workflow_dispatch]
+
+jobs:
+  matlab:
+    name: Matlab
+
+    runs-on: ubuntu-20.04
+
+    steps:
+    - uses: actions/checkout@master
+    - run: git fetch --prune --unshallow
+
+    - run: echo "AMICI_DIR=$(pwd)" >> $GITHUB_ENV
+
+    - name: Install MATLAB
+      uses: matlab-actions/setup-matlab@v0
+    - name: Run script
+      uses: matlab-actions/run-command@v0
+      with:
+        command: cd matlab; installAMICI; addpath tests; testModels

documentation/CI.md

@@ -1,6 +1,7 @@
 # Continuous integration (CI) and tests
 
-AMICI uses a continuous integration pipeline running on https://travis-ci.org/.
+AMICI uses a continuous integration pipeline running via
+https://github.com/features/actions.
 This includes the following steps:
 
 - Checking existence and format of documentation
@@ -67,7 +68,7 @@ This code is to be updated whenever `amici::Model` changes.
 
 ### Regenerating C++ code of the test models
 
-Regeneration of the model code must done whenever `amici::Model` or
+Regeneration of the model code has to be done whenever `amici::Model` or
 the Matlab model import routines change.
 
 This is done with
@@ -89,7 +90,7 @@ replace `tests/cpputest/expectedResults.h5` by
 Before replacing the test results, confirm that only expected datasets have
 changed, e.g. using 
 
-    h5diff -v -r 1e-8 tests/cpputest/expectedResults.h5 tests/cpputest/writeResults.h5.bak | less
+    h5diff -v --relative 1e-8 tests/cpputest/expectedResults.h5 tests/cpputest/writeResults.h5.bak | less
 
 
 ## Adding/Updating tests

matlab/@amimodel/amimodel.m

@@ -241,6 +241,8 @@ function updateWrapPath(this,wrap_path)
 
         generateC(this)
 
+        generateRebuildM(this)
+
         compileC(this)
 
         generateM(this,amimodelo2)

matlab/@amimodel/generateRebuildM.m

@@ -0,0 +1,26 @@
+function generateRebuildM(this)
+% generateRebuildM generates a Matlab script for recompilation of this
+% model
+%
+% Return values:
+%  void
+
+
+filename = fullfile(this.wrap_path,'models',this.modelname,['rebuild_',this.modelname,'.m']);
+% would require struct to string conversion, skipping for now
+amimodelo2 = '[]';
+
+fid = fopen(filename, 'w');
+
+fprintf(fid, ['function ' ['rebuild_', this.modelname] '()\n']);
+fprintf(fid, ['modelName = ''' this.modelname ''';\n']);
+fprintf(fid, 'amimodel.compileAndLinkModel(modelName, '''', [], [], [], []);\n');
+fprintf(fid, ['amimodel.generateMatlabWrapper(' num2str(this.nx) ', ' num2str(this.ny) ...
+    ', ' num2str(this.np) ', ' num2str(this.nk) ', ' num2str(this.nz) ', ' num2str(this.o2flag) ', ' ...
+    amimodelo2 ', [''simulate_'' modelName ''.m''], ''' ...
+    this.modelname ''', ''' this.param ''', ' num2str(this.forward) ', ' num2str(this.adjoint) ');\n']);
+fprintf(fid, 'end\n');
+
+fclose(fid);
+end
+

matlab/amiwrap.m

@@ -169,8 +169,10 @@ function amiwrap( varargin )
     % generate the matlab wrapper
     disp('Generating M code ...')
     if(o2flag)
+        model.generateRebuildM()
         model.generateM(modelo2);
     else
+        model.generateRebuildM()
         model.generateM([]);
     end
 

matlab/tests/testModels.m

@@ -4,38 +4,59 @@ function testModels()
     % disable specific warnings for these tests, some tests are supposed
     % to produce warnings
     warningreset = warning;
-    warning('off','AMICI:mex:simulation')
-    warning('off','AMICI:mex:CVODES:CVode:TOO_MUCH_WORK')
+    warning('off','AMICI:simulation')
+    warning('off','AMICI:CVODES:CVode:TOO_MUCH_WORK')
 
+    % second-order currently not supported via rebuild_*.m (GitHub Actions)
+    %  only via wrapTestModels
     ignoredTests = {'/model_jakstat_adjoint/sensiadjointemptysensind', ...
-                    '/model_jakstat_adjoint/sensiforwardemptysensind'};
+                    '/model_jakstat_adjoint/sensiforwardemptysensind', ...
+                    '/model_jakstat_adjoint/sensi2adjoint', ...
+                    '/model_jakstat_adjoint/sensi2forward', ...
+                    '/model_jakstat_adjoint/sensi2forwardlogparam', ...
+                    '/model_neuron/sensi2forward'};
 
+    model_dir = [fileparts(mfilename('fullpath')) '/../../models/'];
     cd(fileparts(mfilename('fullpath')))
     addpath(genpath('../../tests/cpputest'));
     addpath(genpath('../examples'));
     % wrapTestModels()
-    cd(fileparts(mfilename('fullpath')))
 
+    cd(fileparts(mfilename('fullpath')))
     hdf5file = fullfile(fileparts(mfilename('fullpath')), ...
         '../../tests/cpputest', 'expectedResults.h5');
-
+    
     info = h5info(hdf5file);
     for imodel = 1:length(info.Groups)
-        if(~isempty(regexp(info.Groups(imodel).Name(2:end),'^model_neuron')))
+        modelname = info.Groups(imodel).Name(2:end);
+
+        if(~isempty(regexp(modelname,'^model_neuron')))
             model_atol = 1e-9;
             model_rtol = 1e-4;
         else
             model_atol = 1e-10;
             model_rtol = 1e-5;
         end
         for itest = 1:length(info.Groups(imodel).Groups)
-            if(ismember(info.Groups(imodel).Groups(itest).Name, ignoredTests))
+            testname = info.Groups(imodel).Groups(itest).Name;
+            if(ismember(testname, ignoredTests))
                 continue
             end
+
+            display(testname);
 
             [results,options,data,t,theta,kappa] = readDataFromHDF5(info.Groups(imodel).Groups(itest),hdf5file);
-            sol = getResults(info.Groups(imodel).Name(2:end),options,data,t,theta,kappa);
+
+            % rebuild model
+            old_path = addpath([model_dir modelname]);
+            old_pwd = cd([model_dir modelname]);
+            rebuild = str2func(['rebuild_' modelname]);
+            rebuild();
+            cd(old_pwd);
+
+            sol = getResults(modelname,options,data,t,theta,kappa);
             compareResults(sol,results);
+            path(old_path);
         end
     end
 

models/model_calvetti/model_calvetti.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_calvetti_h
 #define _amici_model_calvetti_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -67,7 +67,7 @@ class Model_model_calvetti : public amici::Model_DAE {
 
     virtual amici::Model* clone() const override { return new Model_model_calvetti(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype cj, const realtype *dx, const realtype *w, const realtype *dwdx) override {
         JSparse_model_calvetti(JSparse, t, x, p, k, h, cj, dx, w, dwdx);

models/model_calvetti/rebuild_model_calvetti.m

@@ -0,0 +1,5 @@
+function rebuild_model_calvetti()
+modelName = 'model_calvetti';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(6, 6, 0, 6, 0, 0, [], ['simulate_' modelName '.m'], 'model_calvetti', 'lin', 1, 1);
+end

models/model_dirac/model_dirac.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_dirac_h
 #define _amici_model_dirac_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -67,7 +67,7 @@ class Model_model_dirac : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_dirac(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_dirac(JSparse, t, x, p, k, h, w, dwdx);

models/model_dirac/rebuild_model_dirac.m

@@ -0,0 +1,5 @@
+function rebuild_model_dirac()
+modelName = 'model_dirac';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(2, 1, 4, 0, 0, 0, [], ['simulate_' modelName '.m'], 'model_dirac', 'log10', 1, 1);
+end

models/model_events/model_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_events_h
 #define _amici_model_events_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -81,7 +81,7 @@ class Model_model_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_events(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_events(JSparse, t, x, p, k, h, w, dwdx);

models/model_events/rebuild_model_events.m

@@ -0,0 +1,5 @@
+function rebuild_model_events()
+modelName = 'model_events';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(3, 1, 4, 4, 2, 0, [], ['simulate_' modelName '.m'], 'model_events', 'log10', 1, 1);
+end

models/model_jakstat_adjoint/model_jakstat_adjoint.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_h
 #define _amici_model_jakstat_adjoint_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_jakstat_adjoint : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_jakstat_adjoint(JSparse, t, x, p, k, h, w, dwdx);

models/model_jakstat_adjoint/rebuild_model_jakstat_adjoint.m

@@ -0,0 +1,5 @@
+function rebuild_model_jakstat_adjoint()
+modelName = 'model_jakstat_adjoint';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(9, 3, 17, 2, 0, 0, [], ['simulate_' modelName '.m'], 'model_jakstat_adjoint', 'log10', 1, 1);
+end

models/model_jakstat_adjoint_o2/model_jakstat_adjoint_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_jakstat_adjoint_o2_h
 #define _amici_model_jakstat_adjoint_o2_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_jakstat_adjoint_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_jakstat_adjoint_o2(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_jakstat_adjoint_o2(JSparse, t, x, p, k, h, w, dwdx);

models/model_nested_events/model_nested_events.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_nested_events_h
 #define _amici_model_nested_events_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -70,7 +70,7 @@ class Model_model_nested_events : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_nested_events(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_nested_events(JSparse, t, x, p, k, h, w, dwdx);

models/model_nested_events/rebuild_model_nested_events.m

@@ -0,0 +1,5 @@
+function rebuild_model_nested_events()
+modelName = 'model_nested_events';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(1, 1, 5, 0, 0, 0, [], ['simulate_' modelName '.m'], 'model_nested_events', 'log10', 1, 1);
+end

models/model_neuron/model_neuron.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_h
 #define _amici_model_neuron_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -84,7 +84,7 @@ class Model_model_neuron : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_neuron(JSparse, t, x, p, k, h, w, dwdx);

models/model_neuron/rebuild_model_neuron.m

@@ -0,0 +1,5 @@
+function rebuild_model_neuron()
+modelName = 'model_neuron';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(2, 1, 4, 2, 1, 0, [], ['simulate_' modelName '.m'], 'model_neuron', 'log10', 1, 1);
+end

models/model_neuron_o2/model_neuron_o2.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_neuron_o2_h
 #define _amici_model_neuron_o2_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -86,7 +86,7 @@ class Model_model_neuron_o2 : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_neuron_o2(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_neuron_o2(JSparse, t, x, p, k, h, w, dwdx);

models/model_robertson/model_robertson.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_robertson_h
 #define _amici_model_robertson_h
-/* Generated by amiwrap (R2017b) 0a85246ec55554a1db269634c806f27f071f487f */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -68,7 +68,7 @@ class Model_model_robertson : public amici::Model_DAE {
 
     virtual amici::Model* clone() const override { return new Model_model_robertson(*this); };
 
-    const  std::string getAmiciCommit() const override { return "0a85246ec55554a1db269634c806f27f071f487f"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype cj, const realtype *dx, const realtype *w, const realtype *dwdx) override {
         JSparse_model_robertson(JSparse, t, x, p, k, h, cj, dx, w, dwdx);

models/model_robertson/rebuild_model_robertson.m

@@ -0,0 +1,5 @@
+function rebuild_model_robertson()
+modelName = 'model_robertson';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(3, 3, 3, 1, 0, 0, [], ['simulate_' modelName '.m'], 'model_robertson', 'log10', 1, 1);
+end

models/model_steadystate/model_steadystate.h

@@ -1,6 +1,6 @@
 #ifndef _amici_model_steadystate_h
 #define _amici_model_steadystate_h
-/* Generated by amiwrap (R2017b) 3ea04a1664d926c46fab5cd80a389f2b0460c053 */
+/* Generated by amiwrap (R2017b) 236df9fa88b9059f699cbe6d987f5d5e5709dcfb */
 #include <cmath>
 #include <memory>
 #include "amici/defines.h"
@@ -67,7 +67,7 @@ class Model_model_steadystate : public amici::Model_ODE {
 
     virtual amici::Model* clone() const override { return new Model_model_steadystate(*this); };
 
-    const  std::string getAmiciCommit() const override { return "3ea04a1664d926c46fab5cd80a389f2b0460c053"; };
+    const  std::string getAmiciCommit() const override { return "236df9fa88b9059f699cbe6d987f5d5e5709dcfb"; };
 
     virtual void fJSparse(SUNMatrixContent_Sparse JSparse, const realtype t, const realtype *x, const realtype *p, const realtype *k, const realtype *h, const realtype *w, const realtype *dwdx) override {
         JSparse_model_steadystate(JSparse, t, x, p, k, h, w, dwdx);

models/model_steadystate/rebuild_model_steadystate.m

@@ -0,0 +1,5 @@
+function rebuild_model_steadystate()
+modelName = 'model_steadystate';
+amimodel.compileAndLinkModel(modelName, '', [], [], [], []);
+amimodel.generateMatlabWrapper(3, 3, 5, 4, 0, 0, [], ['simulate_' modelName '.m'], 'model_steadystate', 'log10', 1, 1);
+end

tests/generateTestConfig/example_neuron.py

@@ -21,7 +21,7 @@ def __init__(self):
         self.modelOptions['pscale'] = 2
 
         self.solverOptions['atol'] = 1e-16
-        self.solverOptions['maxsteps'] = 1e45
+        self.solverOptions['maxsteps'] = 1e5
         self.solverOptions['nmaxevent'] = 22
         self.solverOptions['rtol'] = 1e-12
         self.solverOptions['sens_ind'] = []