Merge remote-tracking branch 'upstream/master' into fix_multisynapse_…

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nest · Jun 20, 2024 · 101f4f0 · 101f4f0
2 parents f91df46 + 2c7c4a7
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diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -0,0 +1,12 @@
+version: 2
+updates:
+  - package-ecosystem: github-actions
+    directory: /
+    schedule:
+      interval: daily
+
+  - package-ecosystem: pip
+    directory: /
+    schedule:
+      interval: daily
+
diff --git a/.github/workflows/nestml-build.yml b/.github/workflows/nestml-build.yml
@@ -11,10 +11,10 @@ jobs:
   link_checker:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
 
       - name: Link Checker
-        uses: lycheeverse/lychee-action@v1.5.4
+        uses: lycheeverse/lychee-action@v1.10.0
         with:
           args: --verbose --no-progress **/*.md **/*.html **/*.rst
           fail: true
@@ -26,11 +26,11 @@ jobs:
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Setup Python version
       - name: Setup Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -57,11 +57,11 @@ jobs:
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Setup Python version
       - name: Setup Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -80,7 +80,7 @@ jobs:
 
       # Install Java
       - name: Install Java 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '11.0.x'
@@ -89,9 +89,9 @@ jobs:
       # Install Antlr4
       - name: Install Antlr4
         run: |
-          wget http://www.antlr.org/download/antlr-4.10-complete.jar
+          wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
           echo \#\!/bin/bash > antlr4
-          echo java -cp \"`pwd`/antlr-4.10-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
+          echo java -cp \"`pwd`/antlr-4.13.1-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
           echo >> antlr4
           chmod +x antlr4
           echo PATH=$PATH:`pwd` >> $GITHUB_ENV
@@ -123,16 +123,16 @@ jobs:
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        nest_branch: ["v2.20.2", "v3.0", "v3.6", "master"]
+        nest_branch: ["v2.20.2", "v3.0", "v3.7", "master"]
       fail-fast: false
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Setup Python version
       - name: Setup Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 
@@ -151,7 +151,7 @@ jobs:
 
       # Install Java
       - name: Install Java 11
-        uses: actions/setup-java@v2
+        uses: actions/setup-java@v4
         with:
           distribution: 'zulu'
           java-version: '11.0.x'
@@ -160,9 +160,9 @@ jobs:
       # Install Antlr4
       - name: Install Antlr4
         run: |
-          wget http://www.antlr.org/download/antlr-4.10-complete.jar
+          wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
           echo \#\!/bin/bash > antlr4
-          echo java -cp \"`pwd`/antlr-4.10-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
+          echo java -cp \"`pwd`/antlr-4.13.1-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
           echo >> antlr4
           chmod +x antlr4
           echo PATH=$PATH:`pwd` >> $GITHUB_ENV
@@ -227,7 +227,7 @@ jobs:
           done;
           exit $rc
 
-      # Run only the nest_integration_test for the NEST versions other than master and 2.20.2
+      # Run only the nest integration tests for NEST versions other than master and 2.20.2
       - name: Run integration tests
         if: ${{ !(matrix.nest_branch == 'master' || matrix.nest_branch == 'v2.20.2') }}
         env:
@@ -242,8 +242,13 @@ jobs:
           ipynb_fns=$(find $GITHUB_WORKSPACE/doc/tutorials -name '*.ipynb')
           rc=0
           for fn in $ipynb_fns; do
+              echo "Now running Jupyter notebook: ${fn}"
               cd `dirname ${fn}`
-              ipython3 ${fn} || rc=1
+              ipython3 ${fn}
+              if [ $? -ne 0 ]; then
+                  echo "Error running Jupyter notebook: ${fn}"
+                  rc=1
+              fi
           done;
           cd $GITHUB_WORKSPACE
           exit $rc
@@ -259,11 +264,11 @@ jobs:
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Setup Python version
       - name: Setup Python 3.8
-        uses: actions/setup-python@v4
+        uses: actions/setup-python@v5
         with:
           python-version: 3.8
 

diff --git a/doc/citing.rst b/doc/citing.rst
@@ -9,6 +9,8 @@ In general, please cite the software release that you are using. In case you wis
 Software releases
 -----------------
 
+Charl A.P. Linssen, Pooja N. Babu, Bernhard Rumpe and Abigail Morrison (2024). **NESTML 7.0.1.** Zenodo. `doi:10.5281/zenodo.10966350 <https://doi.org/10.5281/zenodo.10966350>`_.
+
 Charl A.P. Linssen, Pooja N. Babu, Jochen M. Eppler, Leander Ewert, Krzysztof Blaszczyk, Willem Wybo, Beck Strohmer, Bernhard Rumpe and Abigail Morrison (2023). **NESTML 7.0.0.** Zenodo. `doi:10.5281/zenodo.10125416 <https://doi.org/10.5281/zenodo.10125416>`_.
 
 Charl A.P. Linssen, Pooja N. Babu, Levin Schmidt, Tom Tetzlaff, Maryada, Mohamed Ayssar Benelhedi, Jochen M. Eppler, Bernhard Rumpe and Abigail Morrison (2023). **NESTML 6.0.0.** Zenodo. `doi:10.5281/zenodo.8380365 <https://doi.org/10.5281/zenodo.8380365>`_.

diff --git a/doc/extending.rst b/doc/extending.rst
@@ -36,7 +36,7 @@ The default directory can be changed by specifying code generator options that o
 
 .. code-block:: bash
 
-   nestml --input_path models/neurons/iaf_psc_exp.nestml --codegen_opts /home/nest/work/codegen_options.json
+   nestml --input_path models/neurons/iaf_psc_exp_neuron.nestml --codegen_opts /home/nest/work/codegen_options.json
 
 An example ``codegen_options.json`` file for NEST could look as follows:
 

diff --git a/doc/fig/integration_order.pdf b/doc/fig/integration_order.pdf
diff --git a/doc/fig/integration_order.png b/doc/fig/integration_order.png
diff --git a/doc/fig/integration_order_example.png b/doc/fig/integration_order_example.png
diff --git a/doc/installation.rst b/doc/installation.rst
@@ -83,13 +83,15 @@ After installation, correct operation can be tested by:
 Anaconda installation
 ---------------------
 
-In preparation, `create a conda environment with NEST <https://nest-simulator.readthedocs.io/en/stable/installation/index.html>`_, and install some additional dependencies:
+In preparation, `create a conda environment with NEST <https://nest-simulator.readthedocs.io/en/stable/installation/index.html>`_, and install some additional dependencies.
+
+Please make sure to have the latest conda version installed and to create a new environment with the command below, i.e. installing all packages together at the start versus installing one by one.
 
 .. code-block:: bash
 
    conda create --name wnestml
    conda activate wnestml
-   conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython boost boost-cpp libboost
+   conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython boost boost-cpp libboost cmake make
    pip install nestml
 
 Test the path to ``c++``:

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"    
-    "t_ref", "ms", "0.0ms", "Refractory period"    
+    "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"
 
 
 
@@ -78,7 +78,9 @@ State variables
 
 
     "V_m", "mV", "E_L", "Membrane potential"    
-    "w", "pA", "0pA", "Spike-adaptation current"
+    "w", "pA", "0pA", "Spike-adaptation current"    
+    "refr_t", "ms", "0ms", "Refractory period timer"    
+    "is_refractory", "boolean", "false", ""
 
 
 
@@ -99,14 +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.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 2023-08-22 14:29:44.564178
+   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
@@ -52,7 +52,7 @@ Parameters
 
 
     "C_m", "pF", "281.0pF", "membrane parametersMembrane Capacitance"    
-    "t_ref", "ms", "0.0ms", "Refractory period"    
+    "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)"    
@@ -79,7 +79,9 @@ State variables
 
 
     "V_m", "mV", "E_L", "Membrane potential"    
-    "w", "pA", "0pA", "Spike-adaptation current"
+    "w", "pA", "0pA", "Spike-adaptation current"    
+    "refr_t", "ms", "0ms", "Refractory period timer"    
+    "is_refractory", "boolean", "false", ""
 
 
 
@@ -100,14 +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.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 2023-08-22 14:29:44.513192
+   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
@@ -66,6 +66,7 @@ Parameters
     "beta_h_init", "1 / ms", "(4.0 / (1.0 + exp((40.0mV - V_m) / 5.0mV))) / ms", ""    
     "alpha_p_init", "1 / ms", "0.0001 / (ms * mV) * (V_m + 30.0mV) / (1.0 - exp(-(V_m + 30.0mV) / 9.0mV))", ""    
     "beta_p_init", "1 / ms", "-0.0001 / (ms * mV) * (V_m + 30.0mV) / (1.0 - exp((V_m + 30.0mV) / 9.0mV))", ""    
+    "refr_T", "ms", "2ms", "Duration of refractory period"    
     "I_e", "pA", "0pA", "constant external input current"
 
 
@@ -78,10 +79,12 @@ State variables
     :widths: auto
 
 
-    "r", "integer", "0", "counts number of tick during the refractory period"    
     "g_noise_exc", "uS", "g_noise_exc0", ""    
     "g_noise_inh", "uS", "g_noise_inh0", ""    
     "V_m", "mV", "E_L", "Membrane potential"    
+    "V_m_old", "mV", "E_L", "Membrane potential at the previous timestep"    
+    "refr_t", "ms", "0ms", "Refractory period timer"    
+    "is_refractory", "boolean", "false", ""    
     "Act_m", "real", "alpha_m_init / (alpha_m_init + beta_m_init)", ""    
     "Act_h", "real", "alpha_h_init / (alpha_h_init + beta_h_init)", ""    
     "Inact_n", "real", "alpha_n_init / (alpha_n_init + beta_n_init)", ""    
@@ -115,14 +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.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 2023-08-22 14:29:44.766222
+   Generated at 2024-05-22 14:51:14.490875