Merge remote-tracking branch 'upstream/master' into HEAD

.github/workflows/nestml-build.yml

@@ -118,12 +118,12 @@ jobs:
           done;
           exit $rc
 
-  build_and_test:
+  build_and_test_nest:
     needs: [static_checks]
     runs-on: ubuntu-latest
     strategy:
       matrix:
-        nest_branch: ["v2.20.2", "v3.0", "v3.5", "master"]
+        nest_branch: ["v2.20.2", "v3.0", "v3.6", "master"]
       fail-fast: false
     steps:
       # Checkout the repository contents
@@ -247,3 +247,72 @@ jobs:
           done;
           cd $GITHUB_WORKSPACE
           exit $rc
+
+
+  build_and_test_nest_compartmental:
+    needs: [static_checks]
+    runs-on: ubuntu-latest
+    strategy:
+      matrix:
+        nest_branch: ["master"]
+      fail-fast: false
+    steps:
+      # Checkout the repository contents
+      - name: Checkout NESTML code
+        uses: actions/checkout@v3
+
+      # Setup Python version
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v4
+        with:
+          python-version: 3.8
+
+      # 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 pandas
+          python -m pip install -r requirements.txt
+
+      # Install NEST simulator
+      - name: NEST simulator
+        run: |
+          python -m pip install cython
+          echo "GITHUB_WORKSPACE = $GITHUB_WORKSPACE"
+          NEST_SIMULATOR=$(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 $NEST_SIMULATOR
+          make && make install
+          cd ..
+
+      # Install NESTML (repeated)
+      - name: Install NESTML
+        run: |
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
+          python setup.py install
+
+      # Integration tests
+      - name: Run integration tests
+        env:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          rc=0
+          for fn in $GITHUB_WORKSPACE/tests/nest_compartmental_tests/*.py; do
+              pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
+          done;
+          exit $rc

.gitignore

@@ -1,10 +1,19 @@
 .settings/
 target/
 .idea/
+.vscode
 .mypy_cache/
+.pytest_cache/
 build/
 buildNest/
 venv/
+spinnaker-install/
+spinnaker-target/
+report/
+reports/
+nestml-*/
+*.egg-info
+stash/
 
 
 __*
@@ -16,7 +25,7 @@ PyNESTML.egg-info/
 *.pyc
 
 !__init__.py
-
+!*.jinja2
 *.jar
 venv
 

doc/citing.rst

@@ -9,6 +9,10 @@ In general, please cite the software release that you are using. In case you wis
 Software releases
 -----------------
 
+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>`_.
+
 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>`_.

doc/installation.rst

@@ -16,7 +16,31 @@ NESTML can then be installed into your local user directory via:
 
 .. code-block:: bash
 
-   pip install --pre nestml
+   pip install nestml
+
+
+Installing the latest release from PPA (Linux)
+----------------------------------------------
+
+NESTML can be installed via the ``apt`` package manager. This requires superuser (sudo) access. First, add the NEST PPA:
+
+.. code-block:: bash
+
+   sudo add-apt-repository ppa:nest-simulator/nest
+
+Then update the index and install the necessary packages:
+
+.. code-block:: bash
+
+   sudo apt update
+   sudo apt install nest python3-nestml
+   python3 -m pip install --upgrade odetoolbox pygsl antlr4-python3-runtime==4.10
+
+Before running NEST or NESTML, make sure the correct environment variables are set by running the following command:
+
+.. code-block:: bash
+
+   source /usr/bin/nest_vars.sh
 
 
 Installing the latest development version from GitHub
@@ -65,7 +89,7 @@ In preparation, `create a conda environment with NEST <https://nest-simulator.re
 
    conda create --name wnestml
    conda activate wnestml
-   conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython
+   conda install -c conda-forge nest-simulator ipython cxx-compiler pyqt wxpython boost boost-cpp libboost
    pip install nestml
 
 Test the path to ``c++``:

doc/nestml_language/nestml_language_concepts.rst

@@ -488,6 +488,9 @@ The following functions are predefined in NESTML and can be used out of the box:
    * - ``max``
      - x, y
      - Returns the maximum of x and y. Both parameters should be of the same type. The return type is equal to the type of the parameters.
+   * - ``abs``
+     - x
+     - Returns the absolute value of x. The return type is equal to the type of x.
    * - ``clip``
      - x, y, z
      - Returns x if it is in [y, z], y if x < y and z if x > z. All parameter types should be the same and equal to the return type.

doc/requirements.txt

@@ -9,13 +9,13 @@ nbsphinx==0.9.1
 typing_extensions==4.5.0
 sphinx_rtd_theme==1.2.0
 nbclient==0.7.4
-
+sphinx-design
 
 # the following list is a direct copy from requirements.txt in the root directory (requirements for NESTML itself rather than for doc building)
 numpy >= 1.8.2
 scipy
 sympy >= 1.1.1,!= 1.11, != 1.11.1
-antlr4-python3-runtime == 4.10
+antlr4-python3-runtime == 4.12
 setuptools
 Jinja2 >= 2.10
 typing;python_version<"3.5"