Automatic model characterisation and doc generator (#920)

nest · Jun 5, 2024 · 4fb3c96 · 4fb3c96
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diff --git a/doc/models_library/aeif_cond_alpha_characterisation.rst b/doc/models_library/aeif_cond_alpha_characterisation.rst
diff --git a/doc/models_library/aeif_cond_alpha.rst → ...models_library/aeif_cond_alpha_neuron.rst b/doc/models_library/aeif_cond_alpha.rst → ...models_library/aeif_cond_alpha_neuron.rst
@@ -1,5 +1,5 @@
-aeif_cond_alpha
-###############
+aeif_cond_alpha_neuron
+######################
 
 
 aeif_cond_alpha - Conductance based exponential integrate-and-fire neuron model
@@ -50,22 +50,22 @@ Parameters
     :widths: auto
 
 
-    "C_m", "pF", "281.0pF", "membrane parametersMembrane Capacitance"    
+    "C_m", "pF", "281.0pF", "Membrane Capacitance"    
     "refr_T", "ms", "2ms", "Duration of refractory period"    
     "V_reset", "mV", "-60.0mV", "Reset Potential"    
     "g_L", "nS", "30.0nS", "Leak Conductance"    
     "E_L", "mV", "-70.6mV", "Leak reversal Potential (aka resting potential)"    
-    "a", "nS", "4nS", "spike adaptation parametersSubthreshold adaptation"    
+    "a", "nS", "4nS", "Subthreshold adaptation"    
     "b", "pA", "80.5pA", "Spike-triggered adaptation"    
     "Delta_T", "mV", "2.0mV", "Slope factor"    
     "tau_w", "ms", "144.0ms", "Adaptation time constant"    
     "V_th", "mV", "-50.4mV", "Threshold Potential"    
     "V_peak", "mV", "0mV", "Spike detection threshold"    
-    "E_exc", "mV", "0mV", "synaptic parametersExcitatory reversal Potential"    
+    "E_exc", "mV", "0mV", "Excitatory reversal Potential"    
     "tau_syn_exc", "ms", "0.2ms", "Synaptic Time Constant Excitatory Synapse"    
     "E_inh", "mV", "-85.0mV", "Inhibitory reversal Potential"    
     "tau_syn_inh", "ms", "2.0ms", "Synaptic Time Constant for Inhibitory Synapse"    
-    "I_e", "pA", "0pA", "constant external input current"
+    "I_e", "pA", "0pA", "Constant external input current"
 
 
 
@@ -101,14 +101,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `aeif_cond_alpha <https://github.com/nest/nestml/tree/master/models/neurons/aeif_cond_alpha_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `aeif_cond_alpha_neuron <https://github.com/nest/nestml/tree/master/models/neurons/aeif_cond_alpha_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: aeif_cond_alpha_characterisation.rst
+.. include:: aeif_cond_alpha_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:54.055963
+   Generated at 2024-05-22 14:51:14.532753
diff --git a/doc/models_library/aeif_cond_exp_characterisation.rst b/doc/models_library/aeif_cond_exp_characterisation.rst
diff --git a/doc/models_library/aeif_cond_exp.rst → doc/models_library/aeif_cond_exp_neuron.rst b/doc/models_library/aeif_cond_exp.rst → doc/models_library/aeif_cond_exp_neuron.rst
@@ -1,5 +1,5 @@
-aeif_cond_exp
-#############
+aeif_cond_exp_neuron
+####################
 
 
 aeif_cond_exp - Conductance based exponential integrate-and-fire neuron model
@@ -102,14 +102,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `aeif_cond_exp <https://github.com/nest/nestml/tree/master/models/neurons/aeif_cond_exp_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `aeif_cond_exp_neuron <https://github.com/nest/nestml/tree/master/models/neurons/aeif_cond_exp_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: aeif_cond_exp_characterisation.rst
+.. include:: aeif_cond_exp_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:54.284516
+   Generated at 2024-05-22 14:51:14.484055
diff --git a/doc/models_library/aeif_cond_exp_neuron_characterisation.rst b/doc/models_library/aeif_cond_exp_neuron_characterisation.rst
@@ -0,0 +1,18 @@
+Synaptic response
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml].png
+   :alt: aeif_cond_exp_neuron postsynaptic response
+
+Response to pulse current injection
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png
+   :alt: aeif_cond_exp_neuron current pulse response
+
+f-I curve
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml].png
+   :alt: aeif_cond_exp_neuron f-I curve
+
diff --git a/doc/models_library/hh_cond_exp_destexhe.rst → ...s_library/hh_cond_exp_destexhe_neuron.rst b/doc/models_library/hh_cond_exp_destexhe.rst → ...s_library/hh_cond_exp_destexhe_neuron.rst
@@ -1,5 +1,5 @@
-hh_cond_exp_destexhe
-####################
+hh_cond_exp_destexhe_neuron
+###########################
 
 
 hh_cond_exp_destexhe - Hodgin Huxley based model, Traub, Destexhe and Mainen modified
@@ -118,14 +118,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `hh_cond_exp_destexhe <https://github.com/nest/nestml/tree/master/models/neurons/hh_cond_exp_destexhe_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `hh_cond_exp_destexhe_neuron <https://github.com/nest/nestml/tree/master/models/neurons/hh_cond_exp_destexhe_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: hh_cond_exp_destexhe_characterisation.rst
+.. include:: hh_cond_exp_destexhe_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:53.935360
+   Generated at 2024-05-22 14:51:14.490875
diff --git a/doc/models_library/hh_cond_exp_traub_characterisation.rst b/doc/models_library/hh_cond_exp_traub_characterisation.rst
diff --git a/doc/models_library/hh_cond_exp_traub.rst → ...dels_library/hh_cond_exp_traub_neuron.rst b/doc/models_library/hh_cond_exp_traub.rst → ...dels_library/hh_cond_exp_traub_neuron.rst
@@ -1,5 +1,5 @@
-hh_cond_exp_traub
-#################
+hh_cond_exp_traub_neuron
+########################
 
 
 hh_cond_exp_traub - Hodgkin-Huxley model for Brette et al (2007) review
@@ -122,14 +122,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `hh_cond_exp_traub <https://github.com/nest/nestml/tree/master/models/neurons/hh_cond_exp_traub_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `hh_cond_exp_traub_neuron <https://github.com/nest/nestml/tree/master/models/neurons/hh_cond_exp_traub_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: hh_cond_exp_traub_characterisation.rst
+.. include:: hh_cond_exp_traub_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:53.801490
+   Generated at 2024-05-22 14:51:14.653714
diff --git a/doc/models_library/hh_cond_exp_traub_neuron_characterisation.rst b/doc/models_library/hh_cond_exp_traub_neuron_characterisation.rst
@@ -0,0 +1,18 @@
+Synaptic response
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_cond_exp_traub_neuron_nestml].png
+   :alt: hh_cond_exp_traub_neuron postsynaptic response
+
+Response to pulse current injection
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_cond_exp_traub_neuron_nestml].png
+   :alt: hh_cond_exp_traub_neuron current pulse response
+
+f-I curve
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_cond_exp_traub_neuron_nestml].png
+   :alt: hh_cond_exp_traub_neuron f-I curve
+
diff --git a/doc/models_library/hh_moto_5ht.rst → doc/models_library/hh_moto_5ht_neuron.rst b/doc/models_library/hh_moto_5ht.rst → doc/models_library/hh_moto_5ht_neuron.rst
@@ -1,5 +1,5 @@
-hh_moto_5ht
-###########
+hh_moto_5ht_neuron
+##################
 
 
 hh_moto_5ht_nestml - a motor neuron model in HH formalism with 5HT modulation
@@ -126,14 +126,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `hh_moto_5ht <https://github.com/nest/nestml/tree/master/models/neurons/hh_moto_5ht_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `hh_moto_5ht_neuron <https://github.com/nest/nestml/tree/master/models/neurons/hh_moto_5ht_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: hh_moto_5ht_characterisation.rst
+.. include:: hh_moto_5ht_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:53.883052
+   Generated at 2024-05-22 14:51:14.627082
diff --git a/doc/models_library/hh_psc_alpha_characterisation.rst b/doc/models_library/hh_psc_alpha_characterisation.rst
diff --git a/doc/models_library/hh_psc_alpha.rst → doc/models_library/hh_psc_alpha_neuron.rst b/doc/models_library/hh_psc_alpha.rst → doc/models_library/hh_psc_alpha_neuron.rst
@@ -1,5 +1,5 @@
-hh_psc_alpha
-############
+hh_psc_alpha_neuron
+###################
 
 
 hh_psc_alpha - Hodgkin-Huxley neuron model
@@ -110,14 +110,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `hh_psc_alpha <https://github.com/nest/nestml/tree/master/models/neurons/hh_psc_alpha_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `hh_psc_alpha_neuron <https://github.com/nest/nestml/tree/master/models/neurons/hh_psc_alpha_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: hh_psc_alpha_characterisation.rst
+.. include:: hh_psc_alpha_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:53.850147
+   Generated at 2024-05-22 14:51:14.446835
diff --git a/doc/models_library/hh_psc_alpha_neuron_characterisation.rst b/doc/models_library/hh_psc_alpha_neuron_characterisation.rst
@@ -0,0 +1,18 @@
+Synaptic response
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml].png
+   :alt: hh_psc_alpha_neuron postsynaptic response
+
+Response to pulse current injection
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[hh_psc_alpha_neuron_nestml].png
+   :alt: hh_psc_alpha_neuron current pulse response
+
+f-I curve
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml].png
+   :alt: hh_psc_alpha_neuron f-I curve
+
diff --git a/doc/models_library/hill_tononi.rst → doc/models_library/hill_tononi_neuron.rst b/doc/models_library/hill_tononi.rst → doc/models_library/hill_tononi_neuron.rst
@@ -1,5 +1,5 @@
-hill_tononi
-###########
+hill_tononi_neuron
+##################
 
 
 hill_tononi - Neuron model after Hill & Tononi (2005)
@@ -142,14 +142,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `hill_tononi <https://github.com/nest/nestml/tree/master/models/neurons/hill_tononi_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `hill_tononi_neuron <https://github.com/nest/nestml/tree/master/models/neurons/hill_tononi_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: hill_tononi_characterisation.rst
+.. include:: hill_tononi_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:54.143368
+   Generated at 2024-05-22 14:51:14.539823
diff --git a/doc/models_library/iaf_chxk_2008.rst → doc/models_library/iaf_chxk_2008_neuron.rst b/doc/models_library/iaf_chxk_2008.rst → doc/models_library/iaf_chxk_2008_neuron.rst
@@ -1,5 +1,5 @@
-iaf_chxk_2008
-#############
+iaf_chxk_2008_neuron
+####################
 
 
 iaf_chxk_2008 - Conductance based leaky integrate-and-fire neuron model used in Casti et al. 2008
@@ -92,14 +92,11 @@ Equations
 Source code
 +++++++++++
 
-The model source code can be found in the NESTML models repository here: `iaf_chxk_2008 <https://github.com/nest/nestml/tree/master/models/neurons/iaf_chxk_2008_neuron.nestml>`_.
+The model source code can be found in the NESTML models repository here: `iaf_chxk_2008_neuron <https://github.com/nest/nestml/tree/master/models/neurons/iaf_chxk_2008_neuron.nestml>`_.
 
-Characterisation
-++++++++++++++++
-
-.. include:: iaf_chxk_2008_characterisation.rst
+.. include:: iaf_chxk_2008_neuron_characterisation.rst
 
 
 .. footer::
 
-   Generated at 2023-11-16 11:40:53.989187
+   Generated at 2024-05-22 14:51:14.647974
diff --git a/doc/models_library/iaf_chxk_2008_neuron_characterisation.rst b/doc/models_library/iaf_chxk_2008_neuron_characterisation.rst
@@ -0,0 +1,18 @@
+Synaptic response
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml].png
+   :alt: iaf_chxk_2008_neuron postsynaptic response
+
+Response to pulse current injection
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_current_pulse_response_[iaf_chxk_2008_neuron_nestml].png
+   :alt: iaf_chxk_2008_neuron current pulse response
+
+f-I curve
++++++++++++++++++
+
+.. figure:: https://raw.githubusercontent.com/clinssen/nestml/model_doc_gen/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml].png
+   :alt: iaf_chxk_2008_neuron f-I curve
+
diff --git a/doc/models_library/iaf_cond_alpha_characterisation.rst b/doc/models_library/iaf_cond_alpha_characterisation.rst