PyNEST-NG: A new Python interface for NEST directly connecting Python to C++ #3524

heplesser · 2025-07-10T20:29:28Z

A detailed description will follow. I create the PR now to allow references to it.

Review sections

…NCs, commented

…d map iteration from C++11 to C++17.

jessica-mitchell

Just a few minor fixes

doc/htmldoc/whats_new/v3.10/index.rst

Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>

…pynest-ng

suku248 · 2025-12-04T09:33:05Z

nestkernel/conn_parameter.h

@@ -27,14 +27,12 @@
 #include <limits>
 #include <vector>

+#include <boost/any.hpp>


With this NEST depends on boost.

babsey

Reviewing pyNEST folder (except examples subfolder) -> LGTM!

Please see several code suggestions inline.

babsey · 2025-12-04T08:29:34Z

pynest/nest/lib/hl_api_helper.py

@@ -362,7 +301,7 @@ def get_help_fname(obj):
        File name of the help text for obj
    """

-    docdir = sli_func("statusdict/prgdocdir ::")
+    docdir = nestkernel.ll_api_get_kernel_status()["docdir"]


Suggested change

docdir = nestkernel.ll_api_get_kernel_status()["docdir"]

docdir = nestkernel.llapi_get_kernel_status()["docdir"]

babsey · 2025-12-04T08:30:21Z

pynest/nest/lib/hl_api_info.py

@@ -80,7 +57,7 @@ def helpdesk():

    """

-    docdir = sli_func("statusdict/prgdocdir ::")
+    docdir = nestkernel.ll_api_get_kernel_status()["docdir"]


Suggested change

docdir = nestkernel.ll_api_get_kernel_status()["docdir"]

docdir = nestkernel.llapi_get_kernel_status()["docdir"]

babsey · 2025-12-04T08:42:38Z

pynest/nest/lib/hl_api_types.py

@@ -574,9 +569,10 @@ def __bool__(self):
        """Converts the NodeCollection to a bool. False if it is empty, True otherwise."""
        return len(self) > 0

-    def __array__(self, dtype=None):
+    def __array__(self, dtype=None, copy=None):


The copy argument of numpy.array is a boolean.

Suggested change

def __array__(self, dtype=None, copy=None):

def __array__(self, dtype=None, copy=False):

babsey · 2025-12-04T09:13:33Z

pynest/nest/lib/hl_api_types.py

@@ -942,21 +931,26 @@ def set(self, params=None, **kwargs):
            return

        if isinstance(params, (list, tuple)) and self.__len__() != len(params):
-            raise TypeError("status dict must be a dict, or a list of dicts of length {}".format(self.__len__()))
+            raise TypeError(f"status dict must be a dict, or a list of dicts of length {self.__len__()}")


Suggested change

raise TypeError(f"status dict must be a dict, or a list of dicts of length {self.__len__()}")

raise TypeError(f"Status dict must be a dict, or a list of dicts of length {self.__len__()}")

babsey · 2025-12-04T09:14:44Z

pynest/nest/lib/hl_api_types.py

-            raise TypeError("expected parameter datum")
+        if not isinstance(datum, nestkernel.ParameterObject):
+            raise TypeError(
+                "expected low-level parameter object; use the 'CreateParameter()' function to create a 'Parameter'."


Suggested change

"expected low-level parameter object; use the 'CreateParameter()' function to create a 'Parameter'."

"Expected low-level parameter object; use the 'CreateParameter()' function to create a 'Parameter'."

babsey · 2025-12-04T09:18:48Z

pynest/nest/ll_api.py

+            msg = f"`{self._name}` is a read only kernel attribute."
+            raise AttributeError(msg)


Suggested change

msg = f"`{self._name}` is a read only kernel attribute."

raise AttributeError(msg)

raise AttributeError(f"`{self._name}` is a read only kernel attribute.")

babsey · 2025-12-04T09:27:07Z

pynest/nest/lib/hl_api_info.py

@@ -80,7 +57,7 @@ def helpdesk():

    """

-    docdir = sli_func("statusdict/prgdocdir ::")
+    docdir = nestkernel.ll_api_get_kernel_status()["docdir"]
    help_fname = os.path.join(docdir, "html", "index.html")

    if not os.path.isfile(help_fname):


For better consistence, please include msg content into FileNotFoundError.

You can find it at line 64. Sorry for this comment, it was out of reach.

pnbabu

The changes in the models directory look good to me overall. I have a few minor comments.

pnbabu · 2025-12-04T08:32:54Z

models/amat2_psc_exp.h

@@ -261,12 +261,12 @@ class amat2_psc_exp : public ArchivingNode

    Parameters_(); //!< Sets default parameter values

-    void get( DictionaryDatum& ) const; //!< Store current values in dictionary
+    void get( Dictionary& ) const; //!< Store current values in dictionary


Should we use Dictionary instead of dictionary in the comments here? I saw this in other models, but not here.

pnbabu · 2025-12-04T08:33:34Z

models/astrocyte_lr_1994.h

-    void get( DictionaryDatum& ) const;             //!< Store current values in dictionary
-    void set( const DictionaryDatum&, Node* node ); //!< Set values from dicitonary
+    void get( Dictionary& ) const;             //!< Store current values in Dictionary
+    void set( const Dictionary&, Node* node ); //!< Set values from dicitonary


Suggested change

void set( const Dictionary&, Node* node ); //!< Set values from dicitonary

void set( const Dictionary&, Node* node ); //!< Set values from Dictionary

pnbabu · 2025-12-04T08:55:18Z

models/cm_compartmentcurrents.cpp

@@ -34,8 +34,7 @@ nest::Na::Na( double v_comp )
  // some default initialization
  init_statevars( v_comp );
 }
-
-nest::Na::Na( double v_comp, const DictionaryDatum& channel_params )
+nest::Na::Na( double v_comp, const Dictionary& channel_params )


Suggested change

nest::Na::Na( double v_comp, const Dictionary& channel_params )

nest::Na::Na( double v_comp, const Dictionary& channel_params )

pnbabu · 2025-12-04T09:34:16Z

models/correlation_detector.h

@@ -326,15 +352,15 @@ correlation_detector::handles_test_event( SpikeEvent&, size_t receptor_type )
 }

 inline void
-correlation_detector::get_status( DictionaryDatum& d ) const
+nest::correlation_detector::get_status( Dictionary& d ) const


Why does this need the nest namespace here when it's already in the namespace?

pnbabu · 2025-12-04T09:34:30Z

models/correlation_detector.h

 {
  device_.get_status( d );
  P_.get( d );
  S_.get( d );
 }

 inline void
-correlation_detector::set_status( const DictionaryDatum& d )
+nest::correlation_detector::set_status( const Dictionary& d )


Same as above.

pnbabu · 2025-12-04T10:12:57Z

models/eprop_synapse_bsshslm_2020.h

+    // We must pass here if called by SetDefaults. In that case, the user will get and error
+    // message because the parameters for the synapse-specific optimizer have not been accessed.


Suggested change

// We must pass here if called by SetDefaults. In that case, the user will get and error

// message because the parameters for the synapse-specific optimizer have not been accessed.

// We must pass here if called by SetDefaults. In that case, the user will get an error

// message because the parameters for the synapse-specific optimizer have not been accessed.

pnbabu · 2025-12-04T10:39:52Z

models/iaf_cond_alpha_mc.cpp

- * Compartment name list
- * ---------------------------------------------------------------- */
-
-/* Harold Gutch reported some static destruction problems on OSX 10.4.


Should we keep this comment?

pnbabu · 2025-12-04T10:59:49Z

models/multimeter.cpp

+  std::vector< std::string > ad;
  for ( size_t j = 0; j < record_from_.size(); ++j )
  {
-    ad.push_back( LiteralDatum( record_from_[ j ] ) );
+    ad.push_back( record_from_[ j ] );
  }


Why do we copy this to a new vector?

pnbabu · 2025-12-04T11:02:56Z

models/music_cont_out_proxy.cpp

+  ///  std::vector< std::string > record_from;
+  ///
+  ///  for ( size_t j = 0; j < record_from_.size(); ++j )
+  ///  {
+  ///    record_from.push_back( record_from_[ j ] );
+  ///  }
+


Remove comment.

pnbabu · 2025-12-04T11:42:28Z

models/weight_recorder.cpp

 {
-  if ( d->known( names::senders ) )
+  auto get_or_create_nc = [ &d ]( NodeCollectionPTR& nc, const std::string& key )


Shouldn't this be called just get_nc instead of get_or_create_nc, as an empty NC sis already created in the constructor?

…ons to create.

Remove last instances of sli mentions from docs

jessica-mitchell

Looks good, I will finalize the What's new page during the release process

heplesser added 30 commits January 23, 2025 08:43

Adapt test to pytest-ng

4366e84

Fix support for tripartite

b4ea7a5

Fix test

7ab981c

Can now pass int values for double params

0200ae0

Fix openmp-check

e644660

Correctly handle missing senders/targets specs in weight recorder

b70dc9d

weight_recorder::Parameters_ elements must be initialized with empty …

3e159e9

…NCs, commented

Correctly read out pool size from param dict

65f66f9

Properly handle grid anchors

8c96b19

Removed test that is no longer sensible

998a209

Adapted test to new Create() behavior

b235bea

Fix connect_arrays

831522a

Fix test

be2451b

Fix further test

a08d38f

Adjust test to new syntax

74fb20f

Proper array comparison

6e464f3

Test for correct exception in test

f9675f6

Adjusted test

bfffd05

Skip test that does not longer work due to changes to Create() behavior

1aa2832

Fix test

4193016

Fix parameter names

c94f1f3

Fix test

e753fd1

Reverting parameter.h to 949f4...

57d63a1

Fix parameter arithmetic on py level

eb3fd64

Fix test

6ad111f

Fix test

cfa559b

Fix bug in sp_manager param setting

f197f9a

Corrected handling of sp syn_specs

349a288

Work-around for syn_spec access checks in disconnect

9f75d45

Fixed test

bd4a6fa

akorgor self-requested a review December 3, 2025 18:44

akorgor approved these changes Dec 3, 2025

View reviewed changes

Remove explicit any_cast outside Dictionary where possible and update…

60bf6d7

…d map iteration from C++11 to C++17.

jessica-mitchell requested changes Dec 4, 2025

View reviewed changes

github-project-automation bot moved this from In progress to PRs pending approval in Kernel Dec 4, 2025

heplesser and others added 5 commits December 4, 2025 10:05

Fix rst syntax.

129dc53

Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>

Apply RST syntax fixes suggested by jessica-mitchell

6c05850

Co-authored-by: jessica-mitchell <mitchell20j@gmail.com>

Remove stray text

701b3f7

Merge branch 'pynest-ng' of github.com:heplesser/nest-simulator into …

bfffc94

…pynest-ng

Merge branch 'master' into pynest-ng

89ea67b

suku248 reviewed Dec 4, 2025

View reviewed changes

Adjust data type for easier interaction with Python

3884e20

babsey suggested changes Dec 4, 2025

View reviewed changes

heplesser added 2 commits December 4, 2025 10:57

Re-add early check for unaccessed dict entries

6af4960

Fix rounding in example

0104f12

pnbabu suggested changes Dec 4, 2025

View reviewed changes

heplesser added 9 commits December 4, 2025 16:17

Merge branch 'master' into pynest-ng

21257dd

Merge branch 'master' into pynest-ng

b854765

Allow passing param dict as second argument instead of number of neur…

d1de5d8

…ons to create.

Adapt examples to PyNEST-NG

5dfbac5

Trying to fix rst code blocks

72b808a

Further attempts at fixing rst

81d541e

Specify Python explicitly

2127a5c

Merge pull request #35 from jessica-mitchell/doc-changes

a01981b

Remove last instances of sli mentions from docs

Point to Pytest as test framework.

e089e47

jessica-mitchell approved these changes Dec 5, 2025

View reviewed changes

heplesser added 4 commits December 5, 2025 11:05

Added info about build_info dict and structured document a bit more

18d4a27

Merge branch 'master' into pynest-ng

dc8673d

Merge branch 'master' into pynest-ng

e9b612f

Adapt test to PyNEST-NG

1c84eb1

	docdir = nestkernel.ll_api_get_kernel_status()["docdir"]
	docdir = nestkernel.llapi_get_kernel_status()["docdir"]

	def __array__(self, dtype=None, copy=None):
	def __array__(self, dtype=None, copy=False):

	raise TypeError(f"status dict must be a dict, or a list of dicts of length {self.__len__()}")
	raise TypeError(f"Status dict must be a dict, or a list of dicts of length {self.__len__()}")

	"expected low-level parameter object; use the 'CreateParameter()' function to create a 'Parameter'."
	"Expected low-level parameter object; use the 'CreateParameter()' function to create a 'Parameter'."

		msg = f"`{self._name}` is a read only kernel attribute."
		raise AttributeError(msg)

	msg = f"`{self._name}` is a read only kernel attribute."
	raise AttributeError(msg)
	raise AttributeError(f"`{self._name}` is a read only kernel attribute.")

	void set( const Dictionary&, Node* node ); //!< Set values from dicitonary
	void set( const Dictionary&, Node* node ); //!< Set values from Dictionary

	nest::Na::Na( double v_comp, const Dictionary& channel_params )

	nest::Na::Na( double v_comp, const Dictionary& channel_params )

		// We must pass here if called by SetDefaults. In that case, the user will get and error
		// message because the parameters for the synapse-specific optimizer have not been accessed.

PyNEST-NG: A new Python interface for NEST directly connecting Python to C++ #3524

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PyNEST-NG: A new Python interface for NEST directly connecting Python to C++ #3524

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heplesser commented Jul 10, 2025 • edited by jessica-mitchell Loading Uh oh! There was an error while loading. Please reload this page.

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heplesser commented Jul 10, 2025 •

edited by jessica-mitchell

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