nicolossus · nicolossus · Aug 25, 2023 · Jun 13, 2023 · Jun 28, 2023 · Jun 29, 2023
diff --git a/.github/workflows/build_dispatch.yml b/.github/workflows/build_dispatch.yml
@@ -1,5 +1,8 @@
 on: [push]
 
+permissions:
+  contents: read
+
 jobs:
   trigger_externals:
     if: ${{ github.repository_owner == 'nest' && github.ref_name == 'master' }}

diff --git a/.github/workflows/stale.yml b/.github/workflows/stale.yml
@@ -4,6 +4,9 @@ on:
   schedule:
   - cron: '31 8 * * *'
 
+permissions:
+  contents: read
+
 jobs:
   stale:
 

diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -17,9 +17,7 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>
 
-# Version range from minimum required (3.12 for macOS OpenMP)
-# up to newest version tested, see https://cliutils.gitlab.io/modern-cmake/chapters/basics.html
-cmake_minimum_required( VERSION 3.12...3.16 )
+cmake_minimum_required( VERSION 3.19 )
 
 # add cmake modules: for all `include(...)` first look here
 list( APPEND CMAKE_MODULE_PATH ${CMAKE_CURRENT_SOURCE_DIR}/cmake )

diff --git a/doc/htmldoc/conf.py b/doc/htmldoc/conf.py
@@ -169,6 +169,8 @@
 html_additional_pages = {"index": "index.html"}
 html_sidebars = {"**": ["logo-text.html", "globaltoc.html", "localtoc.html", "searchbox.html"]}
 
+html_favicon = "static/img/nest_favicon.ico"
+
 # -- Options for HTMLHelp output ------------------------------------------
 
 # Output file base name for HTML help builder.

diff --git a/doc/htmldoc/static/img/nest_favicon.ico b/doc/htmldoc/static/img/nest_favicon.ico
diff --git a/doc/htmldoc/templates/index.html b/doc/htmldoc/templates/index.html
@@ -6,6 +6,7 @@
 <html class="no-js"> <!--<![endif]-->
 
 <title>NEST documentation index </title>
+<link rel="icon" type="image/x-icon" href="_static/img/nest_favicon.ico">
 <meta charset="utf-8">
 <meta http-equiv="X-UA-Compatible" content="IE=edge,chrome=1">
 <meta name="viewport" content="width=device-width, initial-scale=1.0">

diff --git a/models/CMakeLists.txt b/models/CMakeLists.txt
@@ -17,7 +17,7 @@
 # You should have received a copy of the GNU General Public License
 # along with NEST.  If not, see <http://www.gnu.org/licenses/>.
 
-set( models_sources
+set(models_sources
     modelsmodule.h ${PROJECT_BINARY_DIR}/models/modelsmodule.cpp
     binary_neuron.h
     cm_compartmentcurrents.h cm_compartmentcurrents.cpp
@@ -28,15 +28,15 @@ set( models_sources
     ${MODELS_SOURCES_GENERATED}
 )
 
-add_library( models STATIC ${models_sources} )
-set_target_properties( models
+add_library(models STATIC ${models_sources})
+set_target_properties(models
     PROPERTIES
-    VERSION ${NEST_VERSION}
-    SOVERSION 3
+    POSITION_INDEPENDENT_CODE ON
 )
-target_link_libraries( models nestutil sli_lib nestkernel )
 
-target_include_directories( models PRIVATE
+target_link_libraries(models nestutil sli_lib nestkernel)
+
+target_include_directories(models PRIVATE
     ${PROJECT_SOURCE_DIR}/thirdparty
     ${PROJECT_SOURCE_DIR}/libnestutil
     ${PROJECT_BINARY_DIR}/libnestutil
@@ -46,12 +46,6 @@ target_include_directories( models PRIVATE
     ${PROJECT_SOURCE_DIR}/nestkernel
 )
 
-install( TARGETS models
-    LIBRARY DESTINATION ${CMAKE_INSTALL_LIBDIR}/nest
-    ARCHIVE DESTINATION ${CMAKE_INSTALL_LIBDIR}/nest
-    RUNTIME DESTINATION ${CMAKE_INSTALL_BINDIR}
-)
-
-FILTER_HEADERS( "${models_sources}" install_headers )
-install( FILES ${install_headers}
-    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/nest )
+FILTER_HEADERS("${models_sources}" install_headers)
+install(FILES ${install_headers}
+    DESTINATION ${CMAKE_INSTALL_INCLUDEDIR}/nest)
diff --git a/models/hh_psc_alpha.h b/models/hh_psc_alpha.h
@@ -92,6 +92,7 @@ The following parameters can be set in the status dictionary.
 V_m       mV      Membrane potential
 E_L       mV      Leak reversal potential
 C_m       pF      Capacity of the membrane
+t_ref     ms      Duration of refractory period
 g_L       nS      Leak conductance
 tau_ex    ms      Rise time of the excitatory synaptic alpha function
 tau_in    ms      Rise time of the inhibitory synaptic alpha function

diff --git a/models/hh_psc_alpha_clopath.h b/models/hh_psc_alpha_clopath.h
@@ -103,6 +103,7 @@ u_bar_bar   mV      Low-pass filtered u_bar_minus
 -------------------------------------------------------------------------------
 E_L         mV      Leak reversal potential
 C_m         pF      Capacity of the membrane
+t_ref       ms      Duration of refractory period
 g_L         nS      Leak conductance
 tau_ex      ms      Rise time of the excitatory synaptic alpha function
 tau_in      ms      Rise time of the inhibitory synaptic alpha function

diff --git a/models/hh_psc_alpha_gap.h b/models/hh_psc_alpha_gap.h
@@ -101,6 +101,7 @@ V_m          mV      Membrane potential
 E_L          mV      Leak reversal potential
 g_L          nS      Leak conductance
 C_m          pF      Capacity of the membrane
+t_ref        ms      Duration of refractory period
 tau_syn_ex   ms      Rise time of the excitatory synaptic alpha function
 tau_syn_in   ms      Rise time of the inhibitory synaptic alpha function
 E_Na         mV      Sodium reversal potential

diff --git a/models/iaf_tsodyks.cpp b/models/iaf_tsodyks.cpp
@@ -24,12 +24,14 @@
 
 // Includes from libnestutil:
 #include "dict_util.h"
+#include "iaf_propagator.h"
 #include "numerics.h"
-#include "propagator_stability.h"
 
 // Includes from nestkernel:
 #include "exceptions.h"
+#include "iaf_propagator.h"
 #include "kernel_manager.h"
+#include "numerics.h"
 #include "ring_buffer_impl.h"
 #include "universal_data_logger_impl.h"
 
@@ -289,8 +291,8 @@ nest::iaf_tsodyks::pre_run_hook()
   V_.P22_ = std::exp( -h / P_.Tau_ );
 
   // these are determined according to a numeric stability criterion
-  V_.P21ex_ = propagator_32( P_.tau_ex_, P_.Tau_, P_.C_, h );
-  V_.P21in_ = propagator_32( P_.tau_in_, P_.Tau_, P_.C_, h );
+  V_.P21ex_ = IAFPropagatorExp( P_.tau_ex_, P_.Tau_, P_.C_ ).evaluate( h );
+  V_.P21in_ = IAFPropagatorExp( P_.tau_in_, P_.Tau_, P_.C_ ).evaluate( h );
 
   V_.P20_ = P_.Tau_ / P_.C_ * ( 1.0 - V_.P22_ );
 
@@ -321,12 +323,8 @@ nest::iaf_tsodyks::pre_run_hook()
 void
 nest::iaf_tsodyks::update( const Time& origin, const long from, const long to )
 {
-  assert( to >= 0 and ( delay ) from < kernel().connection_manager.get_min_delay() );
-  assert( from < to );
-
   const double h = Time::get_resolution().get_ms();
 
-
   // evolve from timestep 'from' to timestep 'to' with steps of h each
   for ( long lag = from; lag < to; ++lag )
   {
@@ -349,11 +347,12 @@ nest::iaf_tsodyks::update( const Time& origin, const long from, const long to )
     S_.i_syn_ex_ += ( 1. - V_.P11ex_ ) * S_.i_1_;
 
     // get read access to the correct input-buffer slot
-    const index input_buffer_slot = kernel().event_delivery_manager.get_modulo( lag );
+    const size_t input_buffer_slot = kernel().event_delivery_manager.get_modulo( lag );
     auto& input = B_.input_buffer_.get_values_all_channels( input_buffer_slot );
 
     // the spikes arriving at T+1 have an immediate effect on the state of the
     // neuron
+
     V_.weighted_spikes_ex_ = input[ Buffers_::SYN_EX ];
     V_.weighted_spikes_in_ = input[ Buffers_::SYN_IN ];
 
@@ -412,7 +411,6 @@ nest::iaf_tsodyks::update( const Time& origin, const long from, const long to )
       S_.x_ -= delta_y_tsp;
       S_.y_ += delta_y_tsp;
 
-
       // send spike with datafield
       SpikeEvent se;
       se.set_offset( delta_y_tsp );
@@ -436,7 +434,7 @@ nest::iaf_tsodyks::handle( SpikeEvent& e )
 {
   assert( e.get_delay_steps() > 0 );
 
-  const index input_buffer_slot = kernel().event_delivery_manager.get_modulo(
+  const size_t input_buffer_slot = kernel().event_delivery_manager.get_modulo(
     e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ) );
 
   // Multiply with datafield from SpikeEvent
@@ -463,7 +461,7 @@ nest::iaf_tsodyks::handle( CurrentEvent& e )
   const double c = e.get_current();
   const double w = e.get_weight();
 
-  const index input_buffer_slot = kernel().event_delivery_manager.get_modulo(
+  const size_t input_buffer_slot = kernel().event_delivery_manager.get_modulo(
     e.get_rel_delivery_steps( kernel().simulation_manager.get_slice_origin() ) );
 
   if ( 0 == e.get_rport() )

diff --git a/models/iaf_tsodyks.h b/models/iaf_tsodyks.h
@@ -191,15 +191,15 @@ class iaf_tsodyks : public ArchivingNode
   using Node::handle;
   using Node::handles_test_event;
 
-  port send_test_event( Node&, rport, synindex, bool ) override;
+  size_t send_test_event( Node&, size_t, synindex, bool ) override;
 
   void handle( SpikeEvent& ) override;
   void handle( CurrentEvent& ) override;
   void handle( DataLoggingRequest& ) override;
 
-  port handles_test_event( SpikeEvent&, rport ) override;
-  port handles_test_event( CurrentEvent&, rport ) override;
-  port handles_test_event( DataLoggingRequest&, rport ) override;
+  size_t handles_test_event( SpikeEvent&, size_t ) override;
+  size_t handles_test_event( CurrentEvent&, size_t ) override;
+  size_t handles_test_event( DataLoggingRequest&, size_t ) override;
 
   void get_status( DictionaryDatum& ) const override;
   void set_status( const DictionaryDatum& ) override;
@@ -409,16 +409,16 @@ class iaf_tsodyks : public ArchivingNode
 };
 
 
-inline port
-nest::iaf_tsodyks::send_test_event( Node& target, rport receptor_type, synindex, bool )
+inline size_t
+nest::iaf_tsodyks::send_test_event( Node& target, size_t receptor_type, synindex, bool )
 {
   SpikeEvent e;
   e.set_sender( *this );
   return target.handles_test_event( e, receptor_type );
 }
 
-inline port
-iaf_tsodyks::handles_test_event( SpikeEvent&, rport receptor_type )
+inline size_t
+iaf_tsodyks::handles_test_event( SpikeEvent&, size_t receptor_type )
 {
   if ( receptor_type != 0 )
   {
@@ -427,8 +427,8 @@ iaf_tsodyks::handles_test_event( SpikeEvent&, rport receptor_type )
   return 0;
 }
 
-inline port
-iaf_tsodyks::handles_test_event( CurrentEvent&, rport receptor_type )
+inline size_t
+iaf_tsodyks::handles_test_event( CurrentEvent&, size_t receptor_type )
 {
   if ( receptor_type == 0 )
   {
@@ -444,8 +444,8 @@ iaf_tsodyks::handles_test_event( CurrentEvent&, rport receptor_type )
   }
 }
 
-inline port
-iaf_tsodyks::handles_test_event( DataLoggingRequest& dlr, rport receptor_type )
+inline size_t
+iaf_tsodyks::handles_test_event( DataLoggingRequest& dlr, size_t receptor_type )
 {
   if ( receptor_type != 0 )
   {

diff --git a/models/modelsmodule.cpp b/models/modelsmodule.cpp
diff --git a/models/stdp_dopamine_synapse.h b/models/stdp_dopamine_synapse.h
@@ -97,7 +97,7 @@ Parameters
  b                   real          Dopaminergic baseline concentration
  Wmin                real          Minimal synaptic weight
  Wmax                real          Maximal synaptic weight
-==================== ============= ======================================================
+=================== ============== ======================================================
 
 The common properties can only be set by :py:func:`.SetDefaults` and apply
 to all instances of the synapse model.

diff --git a/modelsets/full b/modelsets/full
@@ -56,6 +56,7 @@ iaf_psc_exp_htum
 iaf_psc_exp_multisynapse
 iaf_psc_exp_ps
 iaf_psc_exp_ps_lossless
+iaf_tsodyks
 izhikevich
 jonke_synapse
 lin_rate

diff --git a/nestkernel/modelrange_manager.h b/nestkernel/modelrange_manager.h
@@ -99,7 +99,7 @@ nest::ModelRangeManager::get_status( DictionaryDatum& )
 inline bool
 nest::ModelRangeManager::is_in_range( size_t node_id ) const
 {
-  return ( node_id <= last_node_id_ and node_id >= first_node_id_ );
+  return ( node_id > 0 and node_id <= last_node_id_ and node_id >= first_node_id_ );
 }
 
 inline std::vector< modelrange >::const_iterator

diff --git a/pynest/nest/lib/hl_api_types.py b/pynest/nest/lib/hl_api_types.py
@@ -252,7 +252,7 @@ def __getitem__(self, key):
                     raise IndexError("Bool index array must be the same length as NodeCollection")
                 np_key = numpy.array(key, dtype=bool)
             # Checking that elements are not instances of bool too, because bool inherits from int
-            elif all(isinstance(x, int) and not isinstance(x, bool) for x in key):
+            elif all(isinstance(x, (int, numpy.integer)) and not isinstance(x, bool) for x in key):
                 np_key = numpy.array(key, dtype=numpy.uint64)
                 if len(numpy.unique(np_key)) != len(np_key):
                     raise ValueError("All node IDs in a NodeCollection have to be unique")

diff --git a/testsuite/pytests/sli2py_recording/test_spike_recorder.py b/testsuite/pytests/sli2py_recording/test_spike_recorder.py
@@ -0,0 +1,58 @@
+# -*- coding: utf-8 -*-
+#
+# test_spike_recorder.py
+#
+# This file is part of NEST.
+#
+# Copyright (C) 2004 The NEST Initiative
+#
+# NEST is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 2 of the License, or
+# (at your option) any later version.
+#
+# NEST is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with NEST.  If not, see <http://www.gnu.org/licenses/>.
+
+"""
+Test that ``spike_recorder`` behaves as expected.
+"""
+
+import nest
+import numpy.testing as nptest
+import pytest
+
+
+def simulator(resolution):
+    """
+    Simulate the system with provided time resolution and return spike times.
+    """
+
+    nest.ResetKernel()
+    nest.resolution = resolution
+
+    spike_times = [0.1, 5.0, 5.3, 5.33, 5.4, 5.9, 6.0]
+
+    sgen = nest.Create("spike_generator", params={"spike_times": spike_times, "precise_times": True})
+    srec = nest.Create("spike_recorder")
+
+    nest.Connect(sgen, srec)
+
+    nest.Simulate(8.0)
+
+    return srec.events["times"], spike_times
+
+
+@pytest.mark.parametrize("resolution", [1.0, 0.1, 0.02, 0.01, 0.001])
+def test_spike_recorder_different_resolutions(resolution):
+    """
+    Test that recorded spike times are independent of resolution.
+    """
+
+    actual_spikes, expected_spikes = simulator(resolution)
+    nptest.assert_almost_equal(actual_spikes, expected_spikes)