suppress warning and stdout messages in Jupyter notebooks (#1161)

Author: clinssen

doc/tutorials/active_dendrite/nestml_active_dendrite_tutorial.ipynb

@@ -923,15 +923,14 @@ def ode_toolbox_analysis(self, neuron: ASTModel, kernel_buffers: Mapping[ASTKern
 
         return analytic_solver, numeric_solver
 
-    def update_symbol_table(self, neuron) -> None:
+    def update_symbol_table(self, model) -> None:
         """
         Update symbol table and scope.
         """
-        SymbolTable.delete_model_scope(neuron.get_name())
+        SymbolTable.delete_model_scope(model.get_name())
         symbol_table_visitor = ASTSymbolTableVisitor()
-        neuron.accept(symbol_table_visitor)
-        CoCosManager.check_cocos(neuron, after_ast_rewrite=True)
-        SymbolTable.add_model_scope(neuron.get_name(), neuron.get_scope())
+        model.accept(symbol_table_visitor)
+        SymbolTable.add_model_scope(model.get_name(), model.get_scope())
 
     def get_spike_update_expressions(self, neuron: ASTModel, kernel_buffers, solver_dicts, delta_factors) -> Tuple[Dict[str, ASTAssignment], Dict[str, ASTAssignment]]:
         r"""

doc/tutorials/inhomogeneous_poisson/inhomogeneous_poisson.ipynb

@@ -24,13 +24,14 @@
 import re
 import tempfile
 import uuid
-from pynestml.meta_model.ast_node import ASTNode
 
+from pynestml.meta_model.ast_node import ASTNode
 from pynestml.meta_model.ast_variable import ASTVariable
 from pynestml.symbols.symbol import SymbolKind
 from pynestml.symbols.variable_symbol import BlockType
 from pynestml.symbols.variable_symbol import VariableSymbol
 from pynestml.visitors.ast_visitor import ASTVisitor
+from pynestml.utils.logger import Logger
 
 
 class NESTCodeGeneratorUtils:
@@ -82,6 +83,9 @@ def generate_code_for(cls,
         """
         from pynestml.frontend.pynestml_frontend import generate_nest_target
 
+        # convert string to level to check correct formatting
+        Logger.string_to_level(logging_level)
+
         # generate temporary install directory
         install_path = tempfile.mkdtemp(prefix="nestml_target_")
 
@@ -130,6 +134,9 @@ def generate_code_for(cls,
         if codegen_opts:
             _codegen_opts.update(codegen_opts)
 
+        if logging_level.upper() != "DEBUG":
+            _codegen_opts["redirect_build_output"] = True    # hide stdout and stderr if not in DEBUG log level
+
         if not module_name:
             # generate unique ID
             uniq_id = str(uuid.uuid4().hex)

doc/tutorials/izhikevich/nestml_izhikevich_tutorial.ipynb

@@ -97,13 +97,12 @@ def get_end_column(self):
         """
         return self.end_column
 
-    def equals(self, source_position):
+    def equals(self, source_position) -> bool:
         """
         Checks if the handed over position is equal to this.
         :param source_position: a source position.
         :type source_position: ASTSourceLocation
         :return: True if equal, otherwise False.
-        :rtype: bool
         """
         if not isinstance(source_position, ASTSourceLocation):
             return False
@@ -112,6 +111,12 @@ def equals(self, source_position):
                 and self.get_end_line() == source_position.get_end_line()
                 and self.get_end_column() == source_position.get_end_column())
 
+    def __eq__(self, other) -> bool:
+        return self.equals(other)
+
+    def __hash__(self) -> int:
+        return hash((self.get_start_line(), self.get_start_column(), self.get_end_line(), self.get_end_column()))
+
     def before(self, source_position):
         """
         Checks if the handed over position is smaller than this.

doc/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.ipynb

@@ -112,7 +112,7 @@ def set_log(cls, log, counter):
         cls.curr_message = counter
 
     @classmethod
-    def log_message(cls, node: ASTNode = None, code: MessageCode = None, message: str = None, error_position: ASTSourceLocation = None, log_level: LoggingLevel = None):
+    def log_message(cls, node: ASTNode = None, code: MessageCode = None, message: str = None, error_position: ASTSourceLocation = None, log_level: LoggingLevel = None, allow_duplicates: bool = False):
         """
         Logs the handed over message on the handed over node. If the current logging is appropriate, the message is also printed.
 
@@ -121,6 +121,7 @@ def log_message(cls, node: ASTNode = None, code: MessageCode = None, message: st
         :param error_position: the position on which the error occurred.
         :param message: a message.
         :param log_level: the corresponding log level.
+        :param allow_duplicates: whether to ignore or suppress duplicate messages.
         """
         if cls.log_frozen:
             return
@@ -137,16 +138,19 @@ def log_message(cls, node: ASTNode = None, code: MessageCode = None, message: st
         from pynestml.meta_model.ast_model import ASTModel
 
         if isinstance(node, ASTModel):
-            cls.log[cls.curr_message] = (
-                node.get_artifact_name(), node, log_level, code, error_position, message)
+            new_log_entry = (node.get_artifact_name(), node, log_level, code, error_position, message)
         else:
             if cls.current_node is not None:
                 artifact_name = cls.current_node.get_artifact_name()
             else:
                 artifact_name = ""
 
-            cls.log[cls.curr_message] = (artifact_name, cls.current_node,
-                                         log_level, code, error_position, message)
+            new_log_entry = (artifact_name, cls.current_node, log_level, code, error_position, message)
+
+        if not allow_duplicates and new_log_entry in cls.log.values():
+            return
+
+        cls.log[cls.curr_message] = new_log_entry
 
         cls.curr_message += 1
         if cls.no_print:

doc/tutorials/sequence_learning/sequence_learning.ipynb

@@ -155,7 +155,7 @@ def test_valid_numerator_of_unit_one(self):
 
     def test_invalid_names_of_neurons_unique(self):
         model = self._parse_and_validate_model(os.path.join(os.path.realpath(os.path.join(os.path.dirname(__file__), 'invalid')), 'CoCoMultipleNeuronsWithEqualName.nestml'))
-        assert len(Logger.get_all_messages_of_level_and_or_node(model, LoggingLevel.ERROR)) == 3
+        assert len(Logger.get_all_messages_of_level_and_or_node(model, LoggingLevel.ERROR)) == 2
 
     def test_valid_names_of_neurons_unique(self):
         self._parse_and_validate_model(os.path.join(os.path.realpath(os.path.join(os.path.dirname(__file__), 'valid')),  'CoCoMultipleNeuronsWithEqualName.nestml'))