Maint/updated jinja templates fix

.github/workflows/ebrains-push.yml

@@ -0,0 +1,25 @@
+name: Mirror to EBRAINS
+
+on:
+  push:
+    branches: [ master ]
+
+jobs:
+  sync_to_ebrains:
+    runs-on: ubuntu-latest
+    if: ${{ github.repository_owner == 'nest' }}
+    steps:
+      - name: sycnmaster
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "nest/nestml"
+          source_branch: "master"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_NESTML_GITLAB }}@gitlab.ebrains.eu/nest/nestml.git"
+          destination_branch: "main"
+      - name: synctags
+        uses: wei/git-sync@v3
+        with:
+          source_repo: "nest/nestml"
+          source_branch: "refs/tags/*"
+          destination_repo: "https://ghpusher:${{ secrets.EBRAINS_NESTML_GITLAB }}@gitlab.ebrains.eu/nest/nestml.git"
+          destination_branch: "refs/tags/*"

.github/workflows/nestml-build.yml

@@ -0,0 +1,138 @@
+name: NESTML compatibility check with older NEST versions
+
+on: [push, pull_request]
+
+jobs:
+  build_and_test:
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nest_branch: ["v2.20.2", "v3.3", "master"]
+      fail-fast: false
+    steps:
+      # Checkout the repository contents
+      - name: Checkout NESTML code
+        uses: actions/checkout@v2
+
+      # Setup Python version
+      - name: Setup Python 3.9
+        uses: actions/setup-python@v2
+        with:
+          python-version: 3.9
+
+      # Install dependencies
+      - name: Install apt dependencies
+        run: |
+          sudo apt-get update
+          sudo apt-get install libltdl7-dev libgsl0-dev libncurses5-dev libreadline6-dev pkg-config
+          sudo apt-get install python3-all-dev python3-matplotlib python3-numpy python3-scipy ipython3
+
+      # Install Python dependencies
+      - name: Python dependencies
+        run: |
+          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy
+          python -m pip install -r requirements.txt
+
+      # Static code analysis
+      - name: Static code style analysis
+        run: |
+          python3 extras/codeanalysis/check_copyright_headers.py && python3 -m pycodestyle $GITHUB_WORKSPACE -v --ignore=E241,E501,E714,E713,E714,E252,W503 --exclude=$GITHUB_WORKSPACE/doc,$GITHUB_WORKSPACE/.git,$GITHUB_WORKSPACE/NESTML.egg-info,$GITHUB_WORKSPACE/pynestml/generated,$GITHUB_WORKSPACE/extras,$GITHUB_WORKSPACE/build,$GITHUB_WORKSPACE/.github
+
+      # Install Java
+      - name: Install Java 11
+        uses: actions/setup-java@v1
+        with:
+          java-version: '11.0.x'
+          java-package: jre
+
+      # Install Antlr4
+      - name: Install Antlr4
+        run: |
+          wget http://www.antlr.org/download/antlr-4.10-complete.jar
+          echo \#\!/bin/bash > antlr4
+          echo java -cp \"`pwd`/antlr-4.10-complete.jar:$CLASSPATH\" org.antlr.v4.Tool \"\$@\" >> antlr4
+          echo >> antlr4
+          chmod +x antlr4
+          echo PATH=$PATH:`pwd` >> $GITHUB_ENV
+
+      # Install NEST simulator
+      - name: NEST simulator
+        run: |
+          python -m pip install cython
+          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
+          cd $GITHUB_WORKSPACE/..
+          NEST_SIMULATOR=$(pwd)/nest-simulator
+          NEST_INSTALL=$(pwd)/nest_install
+          echo "NEST_SIMULATOR = $NEST_SIMULATOR"
+          echo "NEST_INSTALL = $NEST_INSTALL"
+
+          git clone --depth=1 https://github.com/nest/nest-simulator --branch ${{ matrix.nest_branch }}
+          mkdir nest_install
+          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
+          cd nest_install
+          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
+          make && make install
+          cd ..
+
+      # Install NESTML (repeated)
+      - name: Install NESTML
+        run: |
+          cd $GITHUB_WORKSPACE
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          python setup.py install
+
+      - name: Generate Lexer and Parser using Antlr4
+        run: |
+          cd $GITHUB_WORKSPACE
+          find pynestml/generated -not -name __init__.py -a -not -name generated -delete
+          cd pynestml/grammars
+          ./generate_lexer_parser
+
+      # Unit tests
+      - name: Run unit tests
+        run: |
+          pytest -s -o norecursedirs='*' -o log_cli=true -o log_cli_level="DEBUG" tests || :
+          git ls-remote git://github.com/nest/nest-simulator.git | grep refs/heads/master | cut -f 1 > latest_nest_master_commit_hash.txt
+          echo "Latest NEST master commit hash:"
+          cat latest_nest_master_commit_hash.txt
+
+      # Integration tests: prepare (make module containing all NESTML models)
+      - name: Setup integration tests
+        run: |
+          cd $GITHUB_WORKSPACE
+          # exclude third factor plasticity models; these will only compile successfully if code generation is as a neuron+synapse pair
+          export ALL_MODEL_FILENAMES=`find models/neurons -name "*.nestml" | paste -sd " "`
+          echo $ALL_MODEL_FILENAMES
+          echo "NEST_INSTALL = ${{ env.NEST_INSTALL }}"
+          echo "NEST_VERSION = ${{ matrix.nest_branch }}"
+          sed -i 's|%NEST_PATH%|${{ env.NEST_INSTALL }}|' tests/nest_tests/resources/nest_codegen_opts.json
+          sed -i 's|%NEST_VERSION%|${{ matrix.nest_branch }}|' tests/nest_tests/resources/nest_codegen_opts.json
+          nestml --input_path $ALL_MODEL_FILENAMES --target_path target --suffix _nestml --logging_level INFO --module_name nestml_allmodels_module --codegen_opts tests/nest_tests/resources/nest_codegen_opts.json
+
+      # Integration tests
+      - name: Run integration tests
+        env:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          cd $GITHUB_WORKSPACE
+          rc=0
+          for fn in $GITHUB_WORKSPACE/tests/nest_tests/*.py; do
+              pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
+          done;
+          exit $rc
+
+      # Run IPython/Jupyter notebooks
+      - name: Run Jupyter notebooks
+        if: ${{ matrix.nest_branch == 'master' }}
+        run: |
+          cd $GITHUB_WORKSPACE
+          ipynb_fns=$(find $GITHUB_WORKSPACE/doc/tutorials -name '*.ipynb')
+          rc=0
+          for fn in $ipynb_fns; do
+              cd `dirname ${fn}`
+              ipython3 ${fn} || rc=1
+          done;
+          cd $GITHUB_WORKSPACE
+          exit $rc

.gitignore

@@ -2,6 +2,7 @@
 target/
 .idea/
 .mypy_cache/
+.eggs/
 build/
 buildNest/
 venv/
@@ -26,3 +27,14 @@ venv
 *.gdf
 *~
 *.iml
+/generated/
+/NESTML.egg-info/
+.pydevproject
+linkingModel.py
+
+
+/generated_aeif_cond_alpha/
+/generated_goal/
+/generated_snapshot/
+/generated_RingBufferStar/
+/generated_cout/

.readthedocs.yml

@@ -1,7 +1,13 @@
-type: sphinx
-configuration: doc/sphinx-apidoc/conf.py
+version: 2
+
+build:
+    os: ubuntu-20.04
+    tools:
+        python: "3.9"
+
+sphinx:
+    configuration: doc/sphinx-apidoc/conf.py
+
 python:
-    version: 3
-    requirements_file: requirements.txt
-formats:
-    - none
+    install:
+    - requirements: doc/requirements.txt

doc/citing.rst

@@ -9,6 +9,12 @@ In general, please cite the software release that you are using. In case you wis
 Software releases
 -----------------
 
+Charl A.P. Linssen, Pooja N. Babu, Jingxuan He,  Jochen Martin Eppler, Bernhard Rumpe and Abigail Morrison (2022). **NESTML 5.1.0.** Zenodo. `doi:10.5281/zenodo.7071624 <https://doi.org/10.5281/zenodo.7071624>`_.
+
+Charl A.P. Linssen, Pooja N. Babu, Ayssar Benelhedi, Robin De Schepper, Tanguy Fardet, Jochen Martin Eppler, Bernhard Rumpe and Abigail Morrison (2022). **NESTML 5.0.0.** Zenodo. `doi:10.5281/zenodo.5784175 <https://doi.org/10.5281/zenodo.5784175>`_.
+
+Pooja Nagendra Babu, Charl Linssen, Jochen Martin Eppler, Tobias Schulte to Brinke, Abolfazl Ziaeemehr, Tanguy Fardet, Younes Bouhadjar, Renato Duarte, Bernhard Rumpe and Abigail Morrison (2021). **NESTML 4.0.** Zenodo. `doi:10.5281/zenodo.4740083 <https://doi.org/10.5281/zenodo.4740083>`_.
+
 Charl Linssen, Bernhard Rumpe, Sebastian Berns, Tanguy Fardet, Konstantin Perun, Tobias Schulte to Brinke, Dennis Terhorst, Jochen M. Eppler and Abigail Morrison (2020). **NESTML 3.1.** Zenodo. `doi:10.5281/zenodo.3697733 <http://doi.org/10.5281/zenodo.3697733>`_.
 
 Konstantin Perun, Philip Traeder, Jochen Martin Eppler, Dimitri Plotnikov, Tammo Ippen, Tanguy Fardet, Guido Trensch, Sanin Aleksey, Inga Blundell and Jakob Jordan (2018) **NESTML 3.0.** Zenodo. `doi:10.5281/zenodo.1412608 <http://doi.org/10.5281/zenodo.1412608>`_.