better parpool handling

fixed a bug in demo_clamp

Merge pull request #516 from sg-s/refactored-mexing

Refactored mexing

switched to new uislider-based puppeteer

removed some obsolete mechanisms

xfit.fit() now automatically saves models

added a gitattributes to suppress source in release

added GenericSynapse

fixed #488

they now compile

diff --git a/c++/synapses/nadim/A2ASynapse.hpp b/c++/synapses/nadim/A2ASynapse.hpp
index 93586f1..35449ef 100644
--- a/c++/synapses/nadim/A2ASynapse.hpp
+++ b/c++/synapses/nadim/A2ASynapse.hpp
@@ -7,6 +7,10 @@ class A2ASynapse: public synapse {

 public:

+    double Delta;
+    double Vth;
+    double k_;
+
     // specify parameters + initial conditions
     A2ASynapse(double g_, double s_)
     {
@@ -24,14 +28,14 @@ public:

     }

-    void integrate(double dt);
+    void integrate(void);

     void connect(compartment *pcomp1_, compartment *pcomp2_);
     int getFullState(double*, int);
     int getFullStateSize(void);
 };

-void A2ASynapse::integrate(double dt) {
+void A2ASynapse::integrate() {

     // figure out the voltage of the pre-synaptic neuron
     double V_pre = pre_syn->V;
@@ -40,11 +44,12 @@ void A2ASynapse::integrate(double dt) {
     double s_inf = 1.0/(1.0+exp((Vth - V_pre)/Delta));

     // integrate using exponential Euler
-    double tau_s = 100.0/(1.0+exp((Vth - V_pre)/k_);
+    double tau_s = 100.0/(1.0+exp((Vth - V_pre)/k_));

     s = s_inf + (s - s_inf)*exp(-dt/tau_s);

+    g = gmax*s;

 }

diff --git a/c++/synapses/nadim/NeuriteSyn.hpp b/c++/synapses/nadim/NeuriteSyn.hpp
index e570fcf..3fbd8c0 100644
--- a/c++/synapses/nadim/NeuriteSyn.hpp
+++ b/c++/synapses/nadim/NeuriteSyn.hpp
@@ -7,6 +7,10 @@ class NeuriteSyn: public synapse {

 public:

+    double Delta;
+    double Vth;
+    double k_;
+
     // specify parameters + initial conditions
     NeuriteSyn(double g_, double s_)
     {
@@ -24,15 +28,14 @@ public:

     }

-    void integrate(double dt);
+    void integrate(void);

     void connect(compartment *pcomp1_, compartment *pcomp2_);
     int getFullState(double*, int);
     int getFullStateSize(void);
 };

-void NeuriteSyn::integrate(double dt)
-{
+void NeuriteSyn::integrate(void) {

     // figure out the voltage of the pre-synaptic neuron
     double V_pre = pre_syn->V;
@@ -45,13 +48,12 @@ void NeuriteSyn::integrate(double dt)

     s = s_inf + (s - s_inf)*exp(-dt/tau_s);

-
+    g = gmax*s;

 }

-int NeuriteSyn::getFullState(double *syn_state, int idx)
-{
+int NeuriteSyn::getFullState(double *syn_state, int idx) {
     // give it the current synapse variable
     syn_state[idx] = s;
     idx++;
@@ -63,14 +65,12 @@ int NeuriteSyn::getFullState(double *syn_state, int idx)
 }

-int NeuriteSyn::getFullStateSize()
-{
+int NeuriteSyn::getFullStateSize() {
     return 2;
 }

-void NeuriteSyn::connect(compartment *pcomp1_, compartment *pcomp2_)
-{
+void NeuriteSyn::connect(compartment *pcomp1_, compartment *pcomp2_) {
     pre_syn = pcomp1_;
     post_syn = pcomp2_;

diff --git a/c++/synapses/nadim/Soma.hpp b/c++/synapses/nadim/Soma.hpp
index c4ff9ba..831f474 100644
--- a/c++/synapses/nadim/Soma.hpp
+++ b/c++/synapses/nadim/Soma.hpp
@@ -7,6 +7,10 @@ class Soma: public synapse {

 public:

+    double Delta;
+    double Vth;
+    double k_;
+
     // specify parameters + initial conditions
     Soma(double g_, double s_)
     {
@@ -24,15 +28,14 @@ public:

     }

-    void integrate(double dt);
+    void integrate(void);

     void connect(compartment *pcomp1_, compartment *pcomp2_);
     int getFullState(double*, int);
     int getFullStateSize(void);
 };

-void Soma::integrate(double dt)
-{
+void Soma::integrate(void) {

     // figure out the voltage of the pre-synaptic neuron
     double V_pre = pre_syn->V;
@@ -41,17 +44,16 @@ void Soma::integrate(double dt)
     double s_inf = 1.0/(1.0+exp((Vth - V_pre)/Delta));

     // integrate using exponential Euler
-    double tau_s = 100.0/(1.0+exp((Vth - V_pre)/k_);
+    double tau_s = 100.0/(1.0+exp((Vth - V_pre)/k_));

     s = s_inf + (s - s_inf)*exp(-dt/tau_s);

-
+    g = gmax*s;

 }

-int Soma::getFullState(double *syn_state, int idx)
-{
+int Soma::getFullState(double *syn_state, int idx) {
     // give it the current synapse variable
     syn_state[idx] = s;
     idx++;
@@ -63,14 +65,12 @@ int Soma::getFullState(double *syn_state, int idx)
 }

-int Soma::getFullStateSize()
-{
+int Soma::getFullStateSize() {
     return 2;
 }

-void Soma::connect(compartment *pcomp1_, compartment *pcomp2_)
-{
+void Soma::connect(compartment *pcomp1_, compartment *pcomp2_) {
     pre_syn = pcomp1_;
     post_syn = pcomp2_;

Merge branch 'master' of github.com:sg-s/xolotl