Making code consistent with SPM25 (#501)

* updated CMC code (#474)

* switched from symbolic arrays to list of symbolic parameters. Needed to be able to set tunable flag for individual parameters of the array. Added untune! utility function to set tunable flag to false on list elements.

* added new approach to set tunable flag for the connection matrix also to the tutorial

* use generate_weight_param also in StimulusBlox and ObserverBlox connectors and set standard connection weight to non-tunable

* fixed and cleaned code

* minor changes

* update MTK compat

* added Project.toml to test

* fixed MTK compat once more

* added more packages to test environment needed in GraphDynamics tests

* remove test deps and unnecessary deps

* add Test to tect project

* remove Test dep from main Project

* add missing test deps

* add Statistics dep

* removed [extras] from Project.toml

* added [extras] again.

* fixed norm difference between MATLAB and Julia, MATLAB provides operator norms as default, thus use opnorm in Julia.

* fixed untune in tutorial

docs/src/tutorials/spectralDCM.jl

@@ -72,7 +72,7 @@ end
 
 # ## Run the simulation and plot the results
 
-# setup simulation of the model, time in milliseconds
+# setup simulation of the model, time in seconds
 tspan = (0.0, 512.0)
 prob = SDEProblem(simmodel, [], tspan)
 dt = 2   # 2 seconds (units are milliseconds) as measurement interval for fMRI
@@ -155,7 +155,7 @@ for (i, idx) in enumerate(CartesianIndices(A_prior))
 end
 # we avoid simplification of the model in order to exclude some parameters from fitting
 @named fitmodel = system_from_graph(g, simplify=false)
-# With the function `changetune` we can provide a dictionary of parameters whose tunable flag should be changed, for instance set to false to exclude them from the optimizatoin procedure.
+# With the function `changetune`` we can provide a dictionary of parameters whose tunable flag should be changed, for instance set to false to exclude them from the optimizatoin procedure.
 # For instance the the effective connections that are set to zero in the simulation:
 untune = Dict(A[3] => false, A[7] => false)
 fitmodel = changetune(fitmodel, untune)                 # 3 and 7 are not present in the simulation model

src/datafitting/spDCM_VL.jl

@@ -311,7 +311,7 @@ function integration_step(dfdx, f, v, solenoid=false)
         Q  = Q/opnorm(Q, 2)/8;
 
         f  = f  - Q*f;
-        dfdx = dfdx - Q*dfdx;
+        dfdx = dfdx - Q*dfdx;        
     end
 
     # (expm(dfdx*t) - I)*inv(dfdx)*f ~~~ could also be done with expv (expv(t, dFdθθ, dFdθθ \ dFdθ) - dFdθθ \ dFdθ) but doesn't work with Dual.
@@ -320,9 +320,9 @@ function integration_step(dfdx, f, v, solenoid=false)
     t = exp(v - spm_logdet(dfdx)/n)
 
     if t > exp(16)
-        dx = - dfdx \ f    # -inv(dfdx)*f
+        dx = - dfdx \ f   # -inv(dfdx)*f
     else
-        dx = (exp(t * dfdx) - I) * inv(dfdx)*f    # (expm(dfdx*t) - I)*inv(dfdx)*f
+        dx = (exp(t * dfdx) - I) * inv(dfdx)*f # (expm(dfdx*t) - I)*inv(dfdx)*f
     end
 
     return dx