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

.github/workflows/nestml-build.yml

@@ -47,6 +47,73 @@ jobs:
  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@v2
+ with:
+ distribution: 'zulu'
+ java-version: '11.0.x'
+ java-package: jre
+
+ # Install Antlr4
+ - name: Install Antlr4
+ run: |
+ wget http://www.antlr.org/download/antlr-4.10-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` >> $GITHUB_ENV
+
+ # Install NESTML
+ - name: Install NESTML
+ run: |
+ export PYTHONPATH=${{ 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:
  needs: [static_checks]
  runs-on: ubuntu-latest

pynestml/codegeneration/printers/nest_variable_printer.py

@@ -47,7 +47,6 @@ def __init__(self, expression_printer: ExpressionPrinter, with_origin: bool = Tr
  super().__init__(expression_printer)
  self.with_origin = with_origin
  self.with_vector_parameter = with_vector_parameter
- self._state_symbols = []
 
  def print_variable(self, variable: ASTVariable) -> str:
  """
@@ -159,8 +158,6 @@ def _print_buffer_value(self, variable: ASTVariable) -> str:
  return variable_symbol.get_symbol_name() + '_grid_sum_'
 
  def _print(self, variable: ASTVariable, symbol, with_origin: bool = True) -> str:
- assert all([type(s) == str for s in self._state_symbols])
-
  variable_name = CppVariablePrinter._print_cpp_name(variable.get_complete_name())
 
  if symbol.is_local():

pynestml/codegeneration/printers/python_stepping_function_variable_printer.py

@@ -45,7 +45,7 @@ def print_variable(self, node: ASTVariable) -> str:
  symbol = node.get_scope().resolve_to_symbol(node.get_complete_name(), SymbolKind.VARIABLE)
 
  if symbol.is_state() and not symbol.is_inline_expression:
- if node.get_complete_name() in self._state_symbols:
+ if "_is_numeric" in dir(node) and node._is_numeric:
  # ode_state[] here is---and must be---the state vector supplied by the integrator, not the state vector in the node, node.S_.ode_state[].
  return "ode_state[node.S_.ode_state_variable_name_to_index[\"" + CppVariablePrinter._print_cpp_name(node.get_complete_name()) + "\"]]"
 

pynestml/codegeneration/printers/python_variable_printer.py

@@ -45,7 +45,6 @@ def __init__(self, expression_printer: ExpressionPrinter, with_origin: bool = Tr
  super().__init__(expression_printer)
  self.with_origin = with_origin
  self.with_vector_parameter = with_vector_parameter
- self._state_symbols = []
 
  @classmethod
  def _print_python_name(cls, variable_name: str) -> str:
@@ -146,8 +145,6 @@ def _print_vector_parameter_name_reference(self, variable: ASTVariable) -> str:
  return self._expression_printer.print(vector_parameter)
 
  def _print(self, variable, symbol, with_origin: bool = True) -> str:
- assert all([type(s) == str for s in self._state_symbols])
-
  variable_name = PythonVariablePrinter._print_python_name(variable.get_complete_name())
 
  if symbol.is_local():

pynestml/codegeneration/python_code_generator_utils.py

@@ -19,21 +19,22 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST. If not, see <http://www.gnu.org/licenses/>.
 
+from pynestml.meta_model.ast_variable import ASTVariable
 from pynestml.symbols.variable_symbol import VariableSymbol
 from pynestml.symbols.variable_symbol import BlockType
 
 
 class PythonCodeGeneratorUtils:
 
  @classmethod
- def print_symbol_origin(cls, variable_symbol: VariableSymbol) -> str:
+ def print_symbol_origin(cls, variable_symbol: VariableSymbol, variable: ASTVariable) -> str:
  """
  Returns a prefix corresponding to the origin of the variable symbol.
  :param variable_symbol: a single variable symbol.
  :return: the corresponding prefix
  """
  if variable_symbol.block_type in [BlockType.STATE, BlockType.EQUATION]:
- if numerical_state_symbols and variable_symbol.get_symbol_name() in numerical_state_symbols:
+ if "_is_numeric" in dir(variable) and variable._is_numeric:
  return 'self.S_.ode_state[self.S_.ode_state_variable_name_to_index["%s"]]'
 
  return 'self.S_.%s'

pynestml/codegeneration/python_standalone_code_generator.py

@@ -64,7 +64,8 @@ class PythonStandaloneCodeGenerator(NESTCodeGenerator):
  "neuron": ["@NEURON_NAME@.py.jinja2"]
  },
  "module_templates": ["simulator.py.jinja2", "test_python_standalone_module.py.jinja2", "neuron.py.jinja2", "spike_generator.py.jinja2", "utils.py.jinja2"]
- }
+ },
+ "solver": "analytic"
  }
 
  def __init__(self, options: Optional[Mapping[str, Any]] = None):

pynestml/codegeneration/resources_nest/point_neuron/common/NeuronClass.jinja2

@@ -786,7 +786,7 @@ void {{neuronName}}::handle(nest::DataLoggingRequest& e)
 void {{neuronName}}::handle(nest::SpikeEvent &e)
 {
  assert(e.get_delay_steps() > 0);
- assert( e.get_rport() < static_cast< int >( B_.spike_inputs_.size() ) );
+ assert( e.get_rport() < B_.spike_inputs_.size() );
 
  double weight = e.get_weight();
  size_t nestml_buffer_idx = 0;

pynestml/codegeneration/resources_nest/point_neuron/common/NeuronHeader.jinja2

@@ -241,7 +241,11 @@ public:
  /**
  * Used to validate that we can send {{ output_event.OutputEvent() }} to desired target:port.
  **/
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ size_t send_test_event(nest::Node& target, size_t receptor_type, nest::synindex, bool) override;
+{%- else %}
  nest::port send_test_event(nest::Node& target, nest::rport receptor_type, nest::synindex, bool) override;
+{%- endif %}
 
  // -------------------------------------------------------------------------
  // Functions handling incoming events.
@@ -261,6 +265,7 @@ public:
 
  void handle(nest::DataLoggingRequest &) override;//! allow recording with multimeter
 
+<<<<<<< HEAD
 {%- if use_gap_junctions %}
  void handle( nest::GapJunctionEvent& ) override;
  nest::port handles_test_event( nest::GapJunctionEvent&, nest::rport ) override;
@@ -270,7 +275,27 @@ public:
 
 {%- endif %}
 
+=======
+{%- if has_spike_input %}
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ size_t handles_test_event(nest::SpikeEvent&, size_t) override;
+{%- else %}
+ nest::port handles_test_event(nest::SpikeEvent&, nest::port) override;
+{%- endif %}
+{%- endif %}
+{%- if has_continuous_input %}
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ size_t handles_test_event(nest::CurrentEvent&, size_t) override;
+{%- else %}
+ nest::port handles_test_event(nest::CurrentEvent&, nest::port) override;
+{%- endif %}
+{%- endif %}
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ size_t handles_test_event(nest::DataLoggingRequest&, size_t) override;
+{%- else %}
+>>>>>>> upstream/master
  nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
+{%- endif %}
 
  // -------------------------------------------------------------------------
  // Functions for getting/setting parameters and state values.
@@ -409,13 +434,25 @@ private:
  * @note Excluded lower and upper bounds are defined as MIN_, MAX_.
  * Excluding port 0 avoids accidental connections.
  **/
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ static const size_t MIN_SPIKE_RECEPTOR = 1;
+{%- else %}
  static const nest::port MIN_SPIKE_RECEPTOR = 1;
+{%- endif %}
 {%- set ns = namespace(count=1) %}
+{%- else %}
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ static const size_t MIN_SPIKE_RECEPTOR = 0;
 {%- else %}
  static const nest::port MIN_SPIKE_RECEPTOR = 0;
+{%- endif %}
 {%- set ns = namespace(count=0) %}
 {%- endif %}
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+ static const size_t PORT_NOT_AVAILABLE = -1;
+{%- else %}
  static const nest::port PORT_NOT_AVAILABLE = -1;
+{%- endif %}
 
  enum SynapseTypes
  {
@@ -817,7 +854,11 @@ private:
 
 }; /* neuron {{neuronName}} */
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+inline size_t {{neuronName}}::send_test_event(nest::Node& target, size_t receptor_type, nest::synindex, bool)
+{%- else %}
 inline nest::port {{neuronName}}::send_test_event(nest::Node& target, nest::rport receptor_type, nest::synindex, bool)
+{%- endif %}
 {
  // You should usually not change the code in this function.
  // It confirms that the target of connection @c c accepts @c {{ output_event.OutputEvent() }} on
@@ -828,7 +869,11 @@ inline nest::port {{neuronName}}::send_test_event(nest::Node& target, nest::rpor
 }
 {%- if has_spike_input %}
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+inline size_t {{neuronName}}::handles_test_event(nest::SpikeEvent&, size_t receptor_type)
+{%- else %}
 inline nest::port {{neuronName}}::handles_test_event(nest::SpikeEvent&, nest::port receptor_type)
+{%- endif %}
 {
 {%- if (neuron.get_multiple_receptors())|length > 1 or neuron.is_multisynapse_spikes() %}
  assert( B_.spike_inputs_.size() == NUM_SPIKE_RECEPTORS );
@@ -852,7 +897,11 @@ inline nest::port {{neuronName}}::handles_test_event(nest::SpikeEvent&, nest::po
 {%- endif %}
 {%- if has_continuous_input %}
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+inline size_t {{neuronName}}::handles_test_event(nest::CurrentEvent&, size_t receptor_type)
+{%- else %}
 inline nest::port {{neuronName}}::handles_test_event(nest::CurrentEvent&, nest::port receptor_type)
+{%- endif %}
 {
  // You should usually not change the code in this function.
  // It confirms to the connection management system that we are able
@@ -866,7 +915,11 @@ inline nest::port {{neuronName}}::handles_test_event(nest::CurrentEvent&, nest::
 }
 {%- endif %}
 
+{%- if not (nest_version.startswith("v2") or nest_version.startswith("v3.0") or nest_version.startswith("v3.1") or nest_version.startswith("v3.2") or nest_version.startswith("v3.3") or nest_version.startswith("v3.4")) %}
+inline size_t {{neuronName}}::handles_test_event(nest::DataLoggingRequest& dlr, size_t receptor_type)
+{%- else %}
 inline nest::port {{neuronName}}::handles_test_event(nest::DataLoggingRequest& dlr, nest::port receptor_type)
+{%- endif %}
 {
  // You should usually not change the code in this function.
  // It confirms to the connection management system that we are able