Merge pull request #796 from NeuralEnsemble/nest-dev

Run test suite with NEST 3.7-rc1

.github/workflows/full-test.yml

@@ -44,9 +44,9 @@ jobs:
       if: startsWith(matrix.os, 'ubuntu')
       run: |
         python -m pip install cython
-        wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.6.tar.gz -O nest-simulator-3.6.tar.gz
-        tar xzf nest-simulator-3.6.tar.gz
-        cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dwith-mpi=ON ./nest-simulator-3.6
+        wget https://github.com/nest/nest-simulator/archive/refs/tags/v3.7.tar.gz -O nest-simulator-3.7.tar.gz
+        tar xzf nest-simulator-3.7.tar.gz
+        cmake -DCMAKE_INSTALL_PREFIX=$HOME/.local -Dwith-mpi=ON ./nest-simulator-3.7
         make
         make install
     - name: Install PyNN itself

doc/installation.txt

@@ -96,7 +96,7 @@ Now test that NEURON works with PyNN:
 Installing NEST and PyNEST
 ==========================
 
-NEST 3.4-3.6 can be downloaded from `<http://www.nest-simulator.org/download/>`_.
+NEST 3.4-3.7 can be downloaded from `<http://www.nest-simulator.org/download/>`_.
 Earlier versions of NEST may not work with this version of PyNN.
 The full installation instructions are available at `<https://nest-simulator.readthedocs.io/en/v3.4/installation/index.html/>`_.
 

pyNN/nest/extensions/CMakeLists.txt

@@ -11,31 +11,23 @@ cmake_minimum_required( VERSION 2.8.12 )
 # For more informations on how to extend and use your module see:
 #           https://nest.github.io/nest-simulator/extension_modules
 
-# 1) Name your module here, i.e. add later with -Dexternal-modules=my:
-set( SHORT_NAME pynn )
-
-#    the complete module name is here:
+# 1)   the complete module name is here:
 set( MODULE_NAME pynn_extensions )
 
 # 2) Add all your sources here
 set( MODULE_SOURCES
-    pynn_extensions.h pynn_extensions.cpp
+    pynn_extensions.cpp
     simple_stochastic_synapse.h
     stochastic_stp_synapse.h
     stochastic_stp_synapse_impl.h
     )
 
-# 3) We require a header name like this:
-set( MODULE_HEADER ${MODULE_NAME}.h )
-# containing the class description of the class extending the SLIModule
-
 # 4) Specify your module version
 set( MODULE_VERSION_MAJOR 1 )
 set( MODULE_VERSION_MINOR 0 )
 set( MODULE_VERSION "${MODULE_VERSION_MAJOR}.${MODULE_VERSION_MINOR}" )
 
-# 5) Leave the rest as is. All files in `sli` will be installed to
-#    `share/nest/sli/`, so that NEST will find the during initialization.
+# 5) Leave the rest as is.
 
 # Leave the call to "project(...)" for after the compiler is determined.
 
@@ -118,20 +110,6 @@ if ( NEST_INCLUDES )
   endforeach ()
 endif ()
 
-# Get, if NEST is build as a (mostly) static application. If yes, also only build
-# static library.
-execute_process(
-    COMMAND ${NEST_CONFIG} --static-libraries
-    RESULT_VARIABLE RES_VAR
-    OUTPUT_VARIABLE NEST_STATIC_LIB
-    OUTPUT_STRIP_TRAILING_WHITESPACE
-)
-if ( NEST_STATIC_LIB )
-  set( BUILD_SHARED_LIBS OFF )
-else ()
-  set( BUILD_SHARED_LIBS ON )
-endif ()
-
 # Get all linked libraries.
 execute_process(
     COMMAND ${NEST_CONFIG} --libs
@@ -214,46 +192,28 @@ add_custom_target( dist
     )
 
 
-if ( BUILD_SHARED_LIBS )
-  # When building shared libraries, also create a module for loading at runtime
-  # with the `Install` command.
-  add_library( ${MODULE_NAME}_module MODULE ${MODULE_SOURCES} )
-  set_target_properties( ${MODULE_NAME}_module
-      PROPERTIES
-      COMPILE_FLAGS "${NEST_CXXFLAGS} -DLTX_MODULE"
-      LINK_FLAGS "${NEST_LIBS}"
-      PREFIX ""
-      OUTPUT_NAME ${MODULE_NAME} )
-  install( TARGETS ${MODULE_NAME}_module
-      DESTINATION ${CMAKE_INSTALL_LIBDIR}
-      )
-endif ()
-
-# Build dynamic/static library for standard linking from NEST.
-add_library( ${MODULE_NAME}_lib ${MODULE_SOURCES} )
-if ( BUILD_SHARED_LIBS )
-  # Dynamic libraries are initiated by a `global` variable of the `SLIModule`,
-  # which is included, when the flag `LINKED_MODULE` is set.
-  target_compile_definitions( ${MODULE_NAME}_lib PRIVATE -DLINKED_MODULE )
-endif ()
-set_target_properties( ${MODULE_NAME}_lib
+# Create a module for loading at runtime
+# with the `Install` command.
+add_library( ${MODULE_NAME}_module MODULE ${MODULE_SOURCES} )
+target_link_libraries(${MODULE_NAME}_module ${USER_LINK_LIBRARIES})
+set_target_properties( ${MODULE_NAME}_module
     PROPERTIES
-    COMPILE_FLAGS "${NEST_CXXFLAGS}"
+    COMPILE_FLAGS "${NEST_CXXFLAGS} -DLTX_MODULE"
     LINK_FLAGS "${NEST_LIBS}"
+    PREFIX ""
     OUTPUT_NAME ${MODULE_NAME} )
+install( TARGETS ${MODULE_NAME}_module
+    DESTINATION ${CMAKE_INSTALL_LIBDIR}
+    )
 
 # Install library, header and sli init files.
-install( TARGETS ${MODULE_NAME}_lib DESTINATION ${CMAKE_INSTALL_LIBDIR} )
-install( FILES ${MODULE_HEADER} DESTINATION ${CMAKE_INSTALL_INCLUDEDIR} )
-install( DIRECTORY sli DESTINATION ${CMAKE_INSTALL_DATADIR} )
 
 message( "" )
 message( "-------------------------------------------------------" )
 message( "${MODULE_NAME} Configuration Summary" )
 message( "-------------------------------------------------------" )
 message( "" )
 message( "C++ compiler         : ${CMAKE_CXX_COMPILER}" )
-message( "Build static libs    : ${NEST_STATIC_LIB}" )
 message( "C++ compiler flags   : ${CMAKE_CXX_FLAGS}" )
 message( "NEST compiler flags  : ${NEST_CXXFLAGS}" )
 message( "NEST include dirs    : ${NEST_INCLUDES}" )

pyNN/nest/extensions/pynn_extensions.cpp

@@ -5,32 +5,12 @@
 
 */
 
-#include "pynn_extensions.h"
-
 // include headers with your own stuff
 #include "simple_stochastic_synapse.h"
 #include "stochastic_stp_synapse.h"
 #include "stochastic_stp_synapse_impl.h"
 
-// Includes from nestkernel:
-#include "connection_manager_impl.h"
-#include "connector_model_impl.h"
-#include "dynamicloader.h"
-#include "exceptions.h"
-#include "genericmodel.h"
-#include "kernel_manager.h"
-#include "model.h"
-#include "model_manager_impl.h"
-#include "nest.h"
-#include "nest_impl.h"
-#include "nestmodule.h"
-#include "target_identifier.h"
-
-// Includes from sli:
-#include "booldatum.h"
-#include "integerdatum.h"
-#include "sliexceptions.h"
-#include "tokenarray.h"
+#include "nest_extension_interface.h"
 
 // -- Interface to dynamic module loader ---------------------------------------
 
@@ -54,42 +34,25 @@
  * registration will take place in the file `static_modules.h`, which is
  * generated by cmake.
  */
-#if defined( LTX_MODULE ) | defined( LINKED_MODULE )
-pynn::PyNNExtensions pynn_extensions_LTX_mod;
-#endif
-// -- DynModule functions ------------------------------------------------------
-
-pynn::PyNNExtensions::PyNNExtensions()
-{
-#ifdef LINKED_MODULE
-  // register this module at the dynamic loader
-  // this is needed to allow for linking in this module at compile time
-  // all registered modules will be initialized by the main app's dynamic loader
-  nest::DynamicLoaderModule::registerLinkedModule( this );
-#endif
-}
 
-pynn::PyNNExtensions::~PyNNExtensions()
+namespace pynn
 {
+  class PyNNExtensions : public nest::NESTExtensionInterface
+  {
+  public:
+      PyNNExtensions() {}
+      ~PyNNExtensions() {}
+
+      void initialize() override;
+  };
 }
 
-const std::string
-pynn::PyNNExtensions::name( void ) const
-{
-  return std::string( "PyNN extensions for NEST" ); // Return name of the module
-}
-
-const std::string
-pynn::PyNNExtensions::commandstring( void ) const
-{
-  // Instruct the interpreter to load pynn_extensions-init.sli
-  return std::string( "(pynn_extensions-init) run" );
-}
+pynn::PyNNExtensions pynn_extensions_LTX_module;
 
 //-------------------------------------------------------------------------------------
 
 void
-pynn::PyNNExtensions::init( SLIInterpreter* i )
+pynn::PyNNExtensions::initialize()
 {
   /* Register a neuron or device model.
      Give node type as template argument and the name as second argument.

pyNN/nest/extensions/simple_stochastic_synapse.h

@@ -149,7 +149,7 @@ class simple_stochastic_synapse : public nest::Connection< targetidentifierT >
    * @param t Thread
    * @param cp Common properties to all synapses.
    */
-  void send( nest::Event& e, size_t t, const CommonPropertiesType& cp );
+  bool send( nest::Event& e, size_t t, const CommonPropertiesType& cp );
 
   // The following methods contain mostly fixed code to forward the
   // corresponding tasks to corresponding methods in the base class and the w_
@@ -182,13 +182,13 @@ template < typename targetidentifierT >
 constexpr nest::ConnectionModelProperties simple_stochastic_synapse< targetidentifierT >::properties;
 
 template < typename targetidentifierT >
-inline void
+inline bool
 simple_stochastic_synapse< targetidentifierT >::send( nest::Event& e,
   size_t t,
   const CommonPropertiesType& props )
 {
   if ( nest::get_vp_specific_rng( t )->drand() < (1 - p_) )  // drop spike
-    return;
+    return false;
 
   // Even time stamp, we send the spike using the normal sending mechanism
   // send the spike to the target
@@ -197,6 +197,7 @@ simple_stochastic_synapse< targetidentifierT >::send( nest::Event& e,
   e.set_receiver( *ConnectionBase::get_target( t ) );
   e.set_rport( ConnectionBase::get_rport() );
   e(); // this sends the event
+  return true;
 }
 
 template < typename targetidentifierT >

pyNN/nest/extensions/stochastic_stp_synapse.h

@@ -106,7 +106,7 @@ class stochastic_stp_synapse : public nest::Connection< targetidentifierT >
    * \param e The event to send
    * \param cp Common properties to all synapses (empty).
    */
-  void send( nest::Event& e, size_t t, const CommonPropertiesType& cp );
+  bool send( nest::Event& e, size_t t, const CommonPropertiesType& cp );
 
   class ConnTestDummyNode : public nest::ConnTestDummyNodeBase
   {
@@ -159,7 +159,7 @@ constexpr nest::ConnectionModelProperties stochastic_stp_synapse< targetidentifi
  * \param cp Common properties object, containing the stochastic_stp parameters.
  */
 template < typename targetidentifierT >
-inline void
+inline bool
 stochastic_stp_synapse< targetidentifierT >::send( nest::Event& e,
   size_t thr,
   const CommonPropertiesType& )
@@ -212,6 +212,7 @@ stochastic_stp_synapse< targetidentifierT >::send( nest::Event& e,
   }
 
   t_lastspike_ = t_spike;
+  return release;
 }
 
 } // namespace