Fix third-factor plasticity buffering and add third factor plasticity tutorial #2222

Workflow file for this run

.github/workflows/nestml-build.yml at 99edfa7

	name: NESTML build

	on: [push, pull_request]

	concurrency:
	group: ${{ github.workflow }}-${{ github.ref }}
	cancel-in-progress: true

	jobs:

	link_checker:
	runs-on: ubuntu-latest
	steps:
	- uses: actions/checkout@v4

	- 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
	steps:
	# Checkout the repository contents
	- name: Checkout NESTML code
	uses: actions/checkout@v4

	# Setup Python version
	- name: Setup Python 3.8
	uses: actions/setup-python@v5
	with:
	python-version: 3.8

	# Install dependencies
	- name: Install apt dependencies
	run: \|
	sudo apt-get update
	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@v4

	# Setup Python version
	- name: Setup Python 3.8
	uses: actions/setup-python@v5
	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@v4
	with:
	distribution: 'zulu'
	java-version: '11.0.x'
	java-package: jre

	# Install Antlr4
	- name: Install Antlr4
	run: \|
	wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
	echo \#\!/bin/bash > 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

	# Install NESTML
	- 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

	- name: Generate Lexer and Parser using Antlr4
	run: \|
	cd pynestml/grammars
	./generate_lexer_parser

	# Run integration tests
	- name: Run integration tests
	run: \|
	rc=0
	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

	build_and_test_nest_desktop:
	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@v4

	# Setup Python version
	- name: Setup Python 3.8
	uses: actions/setup-python@v5
	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

	- 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
	- 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

	# Run integration tests
	- name: Run integration tests
	run: \|
	rc=0
	for fn in $GITHUB_WORKSPACE/tests/nest_desktop_tests/*.py; do
	pytest -s -o log_cli=true -o log_cli_level="DEBUG" ${fn} \|\| rc=1
	done;
	exit $rc
	build_and_test_nest:
	needs: [static_checks]
	runs-on: ubuntu-latest
	strategy:
	matrix:
	nest_branch: ["v2.20.2", "v3.0", "v3.8", "master"]
	fail-fast: false
	steps:
	# Checkout the repository contents
	- name: Checkout NESTML code
	uses: actions/checkout@v4

	# Setup Python version
	- name: Setup Python 3.8
	uses: actions/setup-python@v5
	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 Java
	- name: Install Java 11
	uses: actions/setup-java@v4
	with:
	distribution: 'zulu'
	java-version: '11.0.x'
	java-package: jre

	# Install Antlr4
	- name: Install Antlr4
	run: \|
	wget http://www.antlr.org/download/antlr-4.13.1-complete.jar
	echo \#\!/bin/bash > 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

	# 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

	- 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: \|
	# 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
	if: ${{ matrix.nest_branch == 'master' \|\| matrix.nest_branch == 'v2.20.2' }}
	env:
	LD_LIBRARY_PATH: ${{ env.NEST_INSTALL }}/lib/nest
	run: \|
	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 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:
	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
	echo "Now running Jupyter notebook: ${fn}"
	cd `dirname ${fn}`
	ipython3 ${fn}
	if [ $? -ne 0 ]; then
	echo "Error running Jupyter notebook: ${fn}"
	rc=1
	fi
	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@v4

	# Setup Python version
	- name: Setup Python 3.8
	uses: actions/setup-python@v5
	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

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Fix third-factor plasticity buffering and add third factor plasticity tutorial #2222

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Fix third-factor plasticity buffering and add third factor plasticity tutorial #2222

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