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

pnbabu · pnbabu · commit 7e1d4ac415c8 · 2023-06-27T14:16:33.000+02:00
diff --git a/.github/workflows/nestml-build.yml b/.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
diff --git a/pynestml/codegeneration/printers/nest_variable_printer.py b/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():
diff --git a/pynestml/codegeneration/printers/python_stepping_function_variable_printer.py b/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()) + "\"]]"
 
diff --git a/pynestml/codegeneration/printers/python_variable_printer.py b/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():
diff --git a/pynestml/codegeneration/python_code_generator_utils.py b/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'
diff --git a/pynestml/codegeneration/python_standalone_code_generator.py b/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):
diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronClass.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronClass.jinja2
@@ -576,7 +576,7 @@ 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;
diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronHeader.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/NeuronHeader.jinja2
@@ -231,7 +231,11 @@ 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.
@@ -248,12 +252,24 @@ public:
   void handle(nest::DataLoggingRequest &) override;//! allow recording with multimeter
 
 {%- 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 %}
   nest::port handles_test_event(nest::DataLoggingRequest&, nest::port) override;
+{%- endif %}
 
   // -------------------------------------------------------------------------
   //   Functions for getting/setting parameters and state values.
@@ -392,13 +408,25 @@ 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
   {
@@ -772,7 +800,11 @@ 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
@@ -783,7 +815,11 @@ 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 );
@@ -807,7 +843,11 @@ 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
@@ -821,7 +861,11 @@ 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
diff --git a/pynestml/codegeneration/resources_nest/point_neuron/common/SynapseHeader.h.jinja2 b/pynestml/codegeneration/resources_nest/point_neuron/common/SynapseHeader.h.jinja2
diff --git a/tests/python_standalone_tests/test_neuron_build_and_sim_analytic.py b/tests/python_standalone_tests/test_neuron_build_and_sim_analytic.py

Original file line number	Diff line number	Diff line change
`@@ -64,7 +64,8 @@ class PythonStandaloneCodeGenerator(NESTCodeGenerator):`
`64`	`64`	`"neuron": ["@NEURON_NAME@.py.jinja2"]`
`65`	`65`	`},`
`66`	`66`	`"module_templates": ["simulator.py.jinja2", "test_python_standalone_module.py.jinja2", "neuron.py.jinja2", "spike_generator.py.jinja2", "utils.py.jinja2"]`
`67`		`- }`
	`67`	`+ },`
	`68`	`+ "solver": "analytic"`
`68`	`69`	`}`
`69`	`70`
`70`	`71`	`def __init__(self, options: Optional[Mapping[str, Any]] = None):`
Original file line number	Diff line number	Diff line change
`@@ -576,7 +576,7 @@ void {{neuronName}}::handle(nest::DataLoggingRequest& e)`
`576`	`576`	`void {{neuronName}}::handle(nest::SpikeEvent &e)`
`577`	`577`	`{`
`578`	`578`	`assert(e.get_delay_steps() > 0);`
`579`		`- assert( e.get_rport() < static_cast< int >( B_.spike_inputs_.size() ) );`
	`579`	`+ assert( e.get_rport() < B_.spike_inputs_.size() );`
`580`	`580`
`581`	`581`	`double weight = e.get_weight();`
`582`	`582`	`size_t nestml_buffer_idx = 0;`