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

…elper
nest · Jul 3, 2023 · f3fb36e · f3fb36e
2 parents 6d85b49 + ff24afe
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diff --git a/.github/workflows/nestml-build.yml b/.github/workflows/nestml-build.yml
@@ -1,33 +1,84 @@
 name: NESTML build
+
 on: [push, pull_request]
 
 jobs:
-  nest-3-latest:
+
+  link_checker:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v3
+
+      - name: Link Checker
+        uses: lycheeverse/[email protected]
+        with:
+          args: --verbose --no-progress **/*.md **/*.html **/*.rst
+          fail: true
+        env:
+          GITHUB_TOKEN: ${{secrets.GITHUB_TOKEN}}
+
+  static_checks:
     runs-on: ubuntu-latest
-    strategy:
-      fail-fast: false
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       # Setup Python version
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          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
+
+      # Install Python dependencies
+      - name: Python dependencies
+        run: |
+          python -m pip install --upgrade pycodestyle
+          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
+
+  build_and_test_py_standalone:
+    needs: [static_checks]
+    runs-on: ubuntu-latest
+    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 libgsl0-dev libncurses5-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
+
       # Install Java
       - name: Install Java 11
-        uses: actions/setup-java@v1
+        uses: actions/setup-java@v2
         with:
+          distribution: 'zulu'
           java-version: '11.0.x'
           java-package: jre
 
@@ -41,130 +92,45 @@ jobs:
           chmod +x antlr4
           echo PATH=$PATH:`pwd` >> $GITHUB_ENV
 
-      # Install Python dependencies
-      - name: Python dependencies
-        run: |
-          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle
-          python -m pip install -r requirements.txt
-          python -m pip install scipy
-          # python -m pip uninstall --yes odetoolbox
-          # python -m pip install git+https://github.com/nest/ode-toolbox
-
+      # Install NESTML
       - name: Install NESTML
         run: |
-          echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.8/site-packages
+          #echo PYTHONPATH=`pwd` >> $GITHUB_ENV
+          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
           python setup.py install
 
       - 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
 
-      # 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
-
-      # 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
-
-      # Install NEST simulator
-      #- name: NEST simulator cache
-      #  id: nest_simulator_cache
-      #  uses: actions/cache@v2
-      #  env:
-      #    cache-name: nest-simulator-cache
-      #  with:
-      #    path: |
-      #      /home/runner/work/nestml/nest-simulator
-      #      /home/runner/work/nestml/nest_install
-      #    key: nest-simulator-${{ hashFiles('latest_nest_master_commit_hash.txt') }}
-
-      # Install NEST simulator
-      - name: NEST simulator
-        #if: steps.nest_simulator_cache.outputs.cache-hit != 'true'
-        run: |
-          #echo "Latest NEST master commit hash:"
-          #cat latest_nest_master_commit_hash.txt
-          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 = $NEST_INSTALL"
-
-          git clone --depth=1 https://github.com/nest/nest-simulator
-          mkdir nest_install
-          echo "NEST_INSTALL=$NEST_INSTALL" >> $GITHUB_ENV
-          cd nest_install
-          cmake -DCMAKE_INSTALL_PREFIX=$NEST_INSTALL $NEST_SIMULATOR
-          make && make install
-
-      # Install NESTML (repeated)
-      - name: Install NESTML
-        run: |
-          export PYTHONPATH=${{ env.PYTHONPATH }}:${{ env.NEST_INSTALL }}/lib/python3.9/site-packages
-          echo "PYTHONPATH=$PYTHONPATH" >> $GITHUB_ENV
-          python setup.py install
-
-      # Run IPython/Jupyter notebooks
-      - name: Run Jupyter notebooks
-        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
-
-      # 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 = ${{ env.NEST_INSTALL }}"
-          sed -i 's|%NEST_PATH%|${{ env.NEST_INSTALL }}|' 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
+      # Run integration tests
       - name: Run integration tests
         run: |
-          cd $GITHUB_WORKSPACE
           rc=0
-          for fn in $GITHUB_WORKSPACE/tests/nest_tests/*.py; do
+          for fn in $GITHUB_WORKSPACE/tests/python_standalone_tests/*.py; do
               pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} || rc=1
           done;
           exit $rc
 
-  nest-2:
+  build_and_test:
+    needs: [static_checks]
     runs-on: ubuntu-latest
     strategy:
+      matrix:
+        nest_branch: ["v2.20.2", "v3.0", "v3.1", "v3.2", "v3.3", "v3.4", "master"]
       fail-fast: false
-    env:
-      NEST_VERSION_MAJOR: 2
     steps:
       # Checkout the repository contents
       - name: Checkout NESTML code
-        uses: actions/checkout@v2
+        uses: actions/checkout@v3
 
       # Setup Python version
-      - name: Setup Python 3.9
-        uses: actions/setup-python@v2
+      - name: Setup Python 3.8
+        uses: actions/setup-python@v4
         with:
-          python-version: 3.9
+          python-version: 3.8
 
       # Install dependencies
       - name: Install apt dependencies
@@ -176,64 +142,104 @@ jobs:
       # Install Python dependencies
       - name: Python dependencies
         run: |
-          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle
+          python -m pip install --upgrade pip pytest jupyterlab matplotlib pycodestyle scipy pandas
           python -m pip install -r requirements.txt
-          python -m pip install scipy
-          # python -m pip uninstall --yes odetoolbox
-          # python -m pip install git+https://github.com/nest/ode-toolbox
 
-      - name: Install NESTML
+      # Install Java
+      - name: Install Java 11
+        uses: actions/setup-java@v2
+        with:
+          distribution: 'zulu'
+          java-version: '11.0.x'
+          java-package: jre
+
+      # Install Antlr4
+      - name: Install Antlr4
         run: |
-          echo PYTHONPATH=`pwd` >> $GITHUB_ENV
-          python setup.py install
+          wget http://www.antlr.org/download/antlr-4.10-complete.jar
+          echo \#\!/bin/bash > antlr4
+          echo java -cp \"`pwd`/antlr-4.10-complete.jar:$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"
-          echo "NEST_VERSION_MAJOR = $NEST_VERSION_MAJOR"
 
-          git clone --depth=1 https://github.com/nest/nest-simulator --branch v2.20.2
-          cd nest-simulator
-          git status
-          cd ..
+          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/python3.9/site-packages
+          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
 
+      - name: Generate Lexer and Parser using Antlr4
+        run: |
+          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
+
       # 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 = ${{ env.NEST_INSTALL }}"
-          sed -i 's|%NEST_PATH%|${{ env.NEST_INSTALL }}|' tests/nest_tests/resources/nest2_allmodels_codegen_opts.json
-          cat tests/nest_tests/resources/nest2_allmodels_codegen_opts.json
-          nestml --input_path $ALL_MODEL_FILENAMES --target_path target --target_platform NEST2 --suffix _nestml --logging_level INFO --module_name nestml_allmodels_module --codegen_opts tests/nest_tests/resources/nest2_allmodels_codegen_opts.json
+          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
+        if: ${{ matrix.nest_branch == 'master' || matrix.nest_branch == 'v2.20.2' }}
         env:
           LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
         run: |
-          cd $GITHUB_WORKSPACE
           rc=0
-          pytest -s -o log_cli=true -o log_cli_level="DEBUG" tests/nest_tests/nest2_compat_test.py || rc=1
+          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 only the nest_integration_test for the 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:
+          LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
+        run: |
+          pytest -s -o log_cli=true -o log_cli_level="DEBUG" tests/nest_tests/nest_integration_test.py
+
+      # Run IPython/Jupyter notebooks
+      - name: Run Jupyter notebooks
+        if: ${{ matrix.nest_branch == 'master' }}
+        run: |
+          ipynb_fns=$(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
diff --git a/.readthedocs.yml b/.readthedocs.yml
@@ -1,12 +1,13 @@
 version: 2
 
 build:
-    image: latest
+    os: ubuntu-20.04
+    tools:
+        python: "3.9"
 
 sphinx:
     configuration: doc/sphinx-apidoc/conf.py
 
 python:
-    version: 3.8
     install:
     - requirements: doc/requirements.txt
diff --git a/README.md b/README.md
@@ -1,4 +1,4 @@
-[![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/) [![Build Status](https://travis-ci.org/nest/nestml.svg?branch=master)](https://travis-ci.org/nest/nestml)
+[![astropy](http://img.shields.io/badge/powered%20by-AstroPy-orange.svg?style=flat)](http://www.astropy.org/) [![NESTML build](https://github.com/nest/nestml/actions/workflows/nestml-build.yml/badge.svg)](https://github.com/nest/nestml/actions/)
 
 # NESTML: The NEST Modelling Language
 

diff --git a/doc/citing.rst b/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, 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>`_.