automatic model characterisation and doc generator

clinssen · May 14, 2024 · 877ef4f · 877ef4f
1 parent 0e2a980
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diff --git a/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[aeif_cond_exp_neuron_nestml].png
diff --git a/...els_library/nestml_current_pulse_response_[hh_cond_exp_traub_neuron_nestml].png b/...els_library/nestml_current_pulse_response_[hh_cond_exp_traub_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[hh_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[hh_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[iaf_chxk_2008_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[iaf_chxk_2008_neuron_nestml].png
diff --git a/...models_library/nestml_current_pulse_response_[iaf_cond_alpha_neuron_nestml].png b/...models_library/nestml_current_pulse_response_[iaf_cond_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[iaf_cond_beta_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[iaf_cond_beta_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[iaf_cond_exp_neuron_nestml].png
diff --git a/...s_library/nestml_current_pulse_response_[iaf_cond_exp_sfa_rr_neuron_nestml].png b/...s_library/nestml_current_pulse_response_[iaf_cond_exp_sfa_rr_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[iaf_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[iaf_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[iaf_psc_delta_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[iaf_psc_delta_neuron_nestml].png
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diff --git a/doc/models_library/nestml_current_pulse_response_[izhikevich_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[izhikevich_neuron_nestml].png
diff --git a/doc/models_library/nestml_current_pulse_response_[mat2_psc_exp_neuron_nestml].png b/doc/models_library/nestml_current_pulse_response_[mat2_psc_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[aeif_cond_exp_neuron_nestml]_small.png
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diff --git a/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[hh_psc_alpha_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_chxk_2008_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_cond_alpha_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_cond_beta_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_cond_exp_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[iaf_psc_alpha_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[iaf_psc_delta_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_psc_delta_neuron_nestml].png
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diff --git a/doc/models_library/nestml_fI_curve_[iaf_psc_exp_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[iaf_psc_exp_neuron_nestml].png
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diff --git a/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[izhikevich_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml].png b/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml]_small.png b/doc/models_library/nestml_fI_curve_[mat2_psc_exp_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve.png b/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[aeif_cond_alpha]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response.png b/doc/models_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response.png
diff --git a/...els_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response_small.png b/...els_library/nestml_models_library_[aeif_cond_alpha]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve.png b/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[aeif_cond_exp]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[aeif_cond_exp]_synaptic_response.png b/doc/models_library/nestml_models_library_[aeif_cond_exp]_synaptic_response.png
diff --git a/...odels_library/nestml_models_library_[aeif_cond_exp]_synaptic_response_small.png b/...odels_library/nestml_models_library_[aeif_cond_exp]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_f-I_curve.png b/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_f-I_curve.png
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diff --git a/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_synaptic_response.png b/doc/models_library/nestml_models_library_[hh_cond_exp_traub]_synaptic_response.png
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diff --git a/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve.png b/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[hh_psc_alpha]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response.png b/doc/models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response.png
diff --git a/...models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response_small.png b/...models_library/nestml_models_library_[hh_psc_alpha]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[iaf_cond_alpha]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response.png
diff --git a/...dels_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response_small.png b/...dels_library/nestml_models_library_[iaf_cond_alpha]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_beta]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_cond_beta]_f-I_curve.png
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diff --git a/doc/models_library/nestml_models_library_[iaf_cond_beta]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_cond_beta]_synaptic_response.png
diff --git a/...odels_library/nestml_models_library_[iaf_cond_beta]_synaptic_response_small.png b/...odels_library/nestml_models_library_[iaf_cond_beta]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[iaf_cond_exp]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_cond_exp]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_cond_exp]_synaptic_response.png
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diff --git a/doc/models_library/nestml_models_library_[iaf_psc_alpha]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_psc_alpha]_f-I_curve.png
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diff --git a/doc/models_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response.png
diff --git a/...odels_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response_small.png b/...odels_library/nestml_models_library_[iaf_psc_alpha]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_psc_delta]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_psc_delta]_f-I_curve.png
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diff --git a/doc/models_library/nestml_models_library_[iaf_psc_delta]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_psc_delta]_synaptic_response.png
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diff --git a/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve.png b/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[iaf_psc_exp]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response.png b/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response.png
diff --git a/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response_small.png b/doc/models_library/nestml_models_library_[iaf_psc_exp]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve.png b/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve.png
diff --git a/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve_small.png b/doc/models_library/nestml_models_library_[izhikevich]_f-I_curve_small.png
diff --git a/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response.png b/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response.png
diff --git a/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response_small.png b/doc/models_library/nestml_models_library_[izhikevich]_synaptic_response_small.png
diff --git a/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml].png b/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[aeif_cond_exp_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[hh_cond_exp_traub_neuron_nestml].png b/doc/models_library/nestml_psp_[hh_cond_exp_traub_neuron_nestml].png
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diff --git a/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[hh_psc_alpha_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[iaf_chxk_2008_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[iaf_cond_alpha_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_cond_alpha_neuron_nestml].png
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diff --git a/doc/models_library/nestml_psp_[iaf_cond_beta_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_cond_beta_neuron_nestml].png
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diff --git a/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[iaf_cond_exp_sfa_rr_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[iaf_psc_alpha_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[iaf_psc_delta_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml].png b/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[iaf_psc_exp_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[izhikevich_neuron_nestml].png b/doc/models_library/nestml_psp_[izhikevich_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[izhikevich_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[izhikevich_neuron_nestml]_small.png
diff --git a/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml].png b/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml].png
diff --git a/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml]_small.png b/doc/models_library/nestml_psp_[mat2_psc_exp_neuron_nestml]_small.png
diff --git a/extras/nestml_model_doc_generator.py b/extras/nestml_model_doc_generator.py
@@ -41,12 +41,14 @@ class NESTMLModelDocGenerator:
 
     def __init__(self):
         self.model_doc_rst = ""
+        self.base_dir = os.path.join("doc", "models_library")
+        os.mkdir(self.base_dir)
 
     def generate_all_models(self):
         codegen_opts = {}
 
         generate_nest_target(input_path=["models/neurons"],
-                             target_path="/tmp/nestml-autodoc",
+                             target_path=os.path.join(self.base_dir, "nestml-autodoc-target"),
                              logging_level="DEBUG",
                              module_name="nestml_autodoc_module",
                              suffix="_nestml",
@@ -141,15 +143,15 @@ def _test_model_current_pulse(self, model_name, I_min=-100E-12, I_max=500E-12, N
 
         ax[-1].set_xlabel("Time [ms]")
 
-        plt.savefig("/tmp/nestml_current_pulse_response_[" + model_name + "].png")
+        plt.savefig(os.path.join(self.base_dir, "nestml_current_pulse_response_[" + model_name + "].png"))
         plt.close(fig)
 
 
     def _test_model_fI_curve(self, model_name, model_opts=None, model_initial_state=None):
         r"""Make f-I curve"""
         t_stop = 1000.  # [ms]
 
-        I_stim_vec = np.linspace(10E-12, 1E-9, 20)  # [A] XXX: should be 100 points
+        I_stim_vec = np.linspace(10E-12, 1E-9, 100)  # [A]
         rate = float("nan") * np.ones_like(I_stim_vec)
         for i, I_stim in enumerate(I_stim_vec):
             nest.ResetKernel()
@@ -195,7 +197,7 @@ def _test_model_fI_curve(self, model_name, model_opts=None, model_initial_state=
             ax[0].set_xlabel(r"$I_\text{stim}$ [pA]")
             plt.tight_layout()
 
-            plt.savefig("/tmp/nestml_fI_curve_[" + model_name + "]" + fname_snip + ".png")
+            plt.savefig(os.path.join(self.base_dir, "nestml_fI_curve_[" + model_name + "]" + fname_snip + ".png"))
             plt.close(fig)
 
     def _test_model_psp(self, model_name, max_weight: float = 10., model_opts=None,
@@ -245,7 +247,7 @@ def _test_model_psp(self, model_name, max_weight: float = 10., model_opts=None,
             ax[0].set_ylabel("$V_m$ [mV]")
             plt.tight_layout()
 
-            plt.savefig("/tmp/nestml_psp_[" + model_name + "]" + fname_snip + ".png")
+            plt.savefig(os.path.join(self.base_dir, "nestml_psp_[" + model_name + "]" + fname_snip + ".png"))
             plt.close(fig)
 
     def generate_synapse_models_documentation(self, models):