PyNEST-NG: Fix CI and some tests

[nicolossus]

Tests still failing and description of bugs

Current testsuite summary:

  ----------------------------------------------------------------------
  NEST Testsuite Results
  ----------------------------------------------------------------------
  Phase                    Tests   Skipped  Failures    Errors      Time
  ----------------------------------------------------------------------
  07 pynesttests            2642         6        38         1     124.8
  08 cpptests                 29         0         0         0       0.0
  ----------------------------------------------------------------------
  Total                     2671         6        38         1     124.8
  ----------------------------------------------------------------------

test_parameter_operators.py

• Bug: Creating NEST Parameters as integers fails

nest.CreateParameter("constant", {"value": 2})

>>> NESTErrors.TypeMismatch: Expected datatype: Failed to cast
>>> 'value' from long to type double

• Flow:

// hl_api_types.py
def CreateParameter(parametertype, specs):
  return nestkernel.llapi_create_parameter({parametertype: specs})

// nestkernel_api.pyx
def llapi_create_parameter(object specs):
    cdef dictionary specs_dictionary = pydict_to_dictionary(specs)
    cdef ParameterPTR parameter
    parameter = create_parameter(specs_dictionary)
    obj = ParameterObject()
    obj._set_parameter(parameter)
    return nest.Parameter(obj)

// nest.cpp
ParameterPTR
create_parameter( const dictionary& param_dict )
{
  const auto n = param_dict.begin()->first;
  const auto pdict = param_dict.get< dictionary >( n );
  pdict.init_access_flags();
  auto parameter = create_parameter( n, pdict );
  pdict.all_entries_accessed( "create_parameter", "param" );
  return parameter;
}

ParameterPTR
create_parameter( const std::string& name, const dictionary& d )
{
  // The parameter factory will create the parameter
  return ParameterPTR( parameter_factory_().create( name, d ) );  // fails here
}

// ParameterFactory = GenericFactory< Parameter >;
ParameterFactory&
parameter_factory_( void )
{
  static ParameterFactory factory;
  return factory;
}


// generic_factory.h
template < class BaseT >
inline BaseT*
GenericFactory< BaseT >::create( const std::string& name, const dictionary& d ) const
{
  typename AssocMap::const_iterator i = associations_.find( name );
  std::cerr << "Factory name " << name << "\n";
  if ( i != associations_.end() )
  {
    return ( i->second )( d );
  }
  throw UndefinedName( name );
}

/*
Exception thrown by cast_value_() in dictionary.h

Note that we never enter any of the
 - create_parameter( const boost::any& value )
 - create_parameter( const double value )
 - create_parameter( const int value )
 - ...
*/

test_mip_corrdet.py

• Bug:
  • fails the if ( not t_sim.is_grid_time() ) check in nest.cpp

# One extra time step so that after conversion to deliver-events-first logic
# final spikes are delivered as in NEST 3 up to NEST 3.5.
nest.Simulate(100000.0 + nest.resolution)

>>> NESTErrors.BadParameter: The simulation time must be a multiple of
>>> the simulation resolution.

Further experimentation:

n = nest.Create("iaf_psc_alpha")
nest.Connect(n, n)
# nest.Simulate(10.0)  # OK
# nest.Simulate(100_000.0)  # OK
# nest.Simulate(10.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(10.1 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(100.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(100.1 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(1000.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(1000.1 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(10_000.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(10_000.1 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(20_000.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(20_000.1 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(30_000.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(30_000.1 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(30_000.5 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(32_767.0 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(32_767.1 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(32_767.5 + nest.resolution)  # OK but warning about not being multiple of min_delay
# nest.Simulate(32_768.0 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(32_769.0 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(33_000.0 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(40_000.0 + nest.resolution)  # NESTErrors.BadParameter
# nest.Simulate(60_000.0 + nest.resolution)  # NESTErrors.BadParameter
nest.Simulate(100_000.0 + nest.resolution)  # NESTErrors.BadParameter

test_multisynapse_models.py, test_issue_1140.py

• Bug: Not possible to set empty parameters.

test_sinusoidal_poisson_generator.py

• Behavior change: test_set_individual_spike_trains_on_creation() now raises error.
  • If intended, easy to fix test using pytest.raises context

In test_sp/

test_conn_builder.py, test_disconnect_multiple.py, (test_sp_autapses_multapses.py)

• Bug: Raises NESTErrors.UnaccessedDictionaryEntry: Unaccessed elements in syn_spec, in function Connect: post_synaptic_element pre_synaptic_element
  • I.e., all entries in syn_spec are either not accessed or access is not properly registered
• Same bug probably the reason test_sp_autapses_multapses.py fails

In test_spatial/

test_create_spatial.py, test_layer_get_set.py, test_mask_anchors_boundaries.py, test_spatial_distributions.py

• Bug: Seems to be several bugs in the spatial module. Needs closer inspection.