Merge branch 'master' into feat/cppDynamicArray

mstimberg · web-flow · commit b3968aec9754 · 2025-09-08T10:47:15.000+02:00
diff --git a/.github/workflows/post_release_updates.yml b/.github/workflows/post_release_updates.yml
@@ -11,7 +11,7 @@ jobs:
         contents: write
         pull-requests: write
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: true  # Needed to push changes back to the repository
           fetch-depth: 0
diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -24,7 +24,7 @@ jobs:
       matrix:
         os: [ windows-latest, macOS-13, macOS-14 ]
     steps:
-      - uses:  actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses:  actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -44,17 +44,15 @@ jobs:
             f.write(f"dir={str(user_cache_path(appname='cibuildwheel', appauthor='pypa'))}")
         shell: python
       - name: Cache cibuildwheel tools
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         with:
           path: ${{ steps.cibuildwheel-cache.outputs.dir }}
           key: ${{ runner.os }}-cibuildwheel
       - name: Build wheels
-        uses: pypa/cibuildwheel@95d2f3a92fbf80abe066b09418bbf128a8923df2 # v3.0.1
+        uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # v3.1.4
         env:
           CIBW_PROJECT_REQUIRES_PYTHON: ">=${{ needs.get_python_versions.outputs.min-python }}"
           CIBW_ARCHS: auto64
-          # Do not build for PyPy
-          CIBW_SKIP: 'pp*'
           CIBW_TEST_COMMAND: python {project}/dev/continuous-integration/run_simple_test.py
           CIBW_TEST_REQUIRES: pytest
         with:
@@ -75,7 +73,7 @@ jobs:
         config: [{arch: auto64, image: ubuntu-24.04},
                  {arch: aarch64, image: ubuntu-24.04-arm}] 
     steps:
-      - uses:  actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses:  actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -100,12 +98,12 @@ jobs:
             f.write(f"dir={str(user_cache_path(appname='cibuildwheel', appauthor='pypa'))}")
         shell: python
       - name: Cache cibuildwheel tools
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         with:
           path: ${{ steps.cibuildwheel-cache.outputs.dir }}
           key: ${{ matrix.config.image }}-${{ matrix.config.arch }}-cibuildwheel
       - name: Build wheels
-        uses: pypa/cibuildwheel@95d2f3a92fbf80abe066b09418bbf128a8923df2 # v3.0.1
+        uses: pypa/cibuildwheel@c923d83ad9c1bc00211c5041d0c3f73294ff88f6 # v3.1.4
         env:
           CIBW_PROJECT_REQUIRES_PYTHON: ">=${{ needs.get_python_versions.outputs.min-python }}"
           CIBW_ARCHS_LINUX: ${{ matrix.config.arch }}
@@ -133,7 +131,7 @@ jobs:
       - build-linux
     steps:
       - name: load distribution 📦
-        uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e # v4.2.1
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           pattern: packages-*
           merge-multiple: true
@@ -155,7 +153,7 @@ jobs:
       - build-linux
     steps:
       - name: load distribution 📦
-        uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e # v4.2.1
+        uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
         with:
           pattern: packages-*
           merge-multiple: true
@@ -171,13 +169,13 @@ jobs:
     if: ${{ github.event_name == 'push' || (github.event.pull_request.author_association == 'COLLABORATOR' || github.event.pull_request.author_association == 'OWNER') }}
     steps:
     - name: Checkout repository
-      uses:  actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      uses:  actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
       with:
         persist-credentials: false
       # https://github.com/actions/checkout/
     - name: Docker meta
       id: meta
-      uses: docker/metadata-action@902fa8ec7d6ecbf8d84d538b9b233a880e428804 # v5.7.0
+      uses: docker/metadata-action@c1e51972afc2121e065aed6d45c65596fe445f3f # v5.8.0
       # https://github.com/docker/metadata-action
       with:
         images: |
@@ -203,20 +201,20 @@ jobs:
       # https://github.com/docker/setup-buildx-action
     - name: Login to DockerHub
       if: ${{ github.event_name == 'push' && github.repository == 'brian-team/brian2' && github.actor != 'dependabot[bot]'}}
-      uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3.4.0
+      uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
       # https://github.com/docker/login-action
       with:
         username: ${{ secrets.DOCKERHUB_USERNAME }}
         password: ${{ secrets.DOCKERHUB_TOKEN }}
     - name: Login to GitHub Container Registry
       if: ${{ github.event_name == 'push' && github.repository == 'brian-team/brian2' && github.actor != 'dependabot[bot]'}}
-      uses: docker/login-action@74a5d142397b4f367a81961eba4e8cd7edddf772 # v3.4.0
+      uses: docker/login-action@184bdaa0721073962dff0199f1fb9940f07167d1 # v3.5.0
       with:
         registry: ghcr.io
         username: ${{ github.repository_owner }}
         password: ${{ secrets.GITHUB_TOKEN }}
     - name: load Linux x86 distribution 📦
-      uses: actions/download-artifact@95815c38cf2ff2164869cbab79da8d1f422bc89e # v4.2.1
+      uses: actions/download-artifact@634f93cb2916e3fdff6788551b99b062d0335ce0 # v5.0.0
       with:
         pattern: packages-linux-*
         merge-multiple: true
diff --git a/.github/workflows/static_analysis.yml b/.github/workflows/static_analysis.yml
@@ -13,7 +13,7 @@ jobs:
       security-events: write
     steps:
       - name: Checkout repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - name: Install the latest version of uv
diff --git a/.github/workflows/test_latest.yml b/.github/workflows/test_latest.yml
@@ -38,7 +38,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -105,7 +105,7 @@ jobs:
 
     steps:
       - name: Checkout Repository
-        uses:  actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses:  actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -151,7 +151,7 @@ jobs:
           echo "Cython cache dir: $CACHE_DIR"
           echo "cachedir=$CACHE_DIR" >> "$GITHUB_OUTPUT"
       - name: restore Cython cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         if: ${{ ! matrix.standalone }}
         with:
           key: cython-extensions-latest-${{ matrix.os }}-${{ matrix.python-version }}-32bit-${{ matrix.float_dtype_32 }}
diff --git a/.github/workflows/testsuite.yml b/.github/workflows/testsuite.yml
@@ -20,7 +20,7 @@ jobs:
     name: Run linters with pre-commit
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+      - uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           persist-credentials: false
       - uses: actions/setup-python@a26af69be951a213d495a4c3e4e4022e16d87065 # v5.6.0
@@ -65,7 +65,7 @@ jobs:
         shell: bash -l {0}
     steps:
       - name: Checkout Repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
+        uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
         with:
           fetch-depth: 0
           persist-credentials: false
@@ -108,7 +108,7 @@ jobs:
           PYTHON_BINARY: ${{ steps.python.outputs.python-path }}
 
       - name: restore Cython cache
-        uses: actions/cache@5a3ec84eff668545956fd18022155c47e93e2684 # v4.2.3
+        uses: actions/cache@0400d5f644dc74513175e3cd8d07132dd4860809 # v4.2.4
         if: ${{ ! matrix.standalone }}
         with:
           key: cython-extensions-${{ matrix.os.image }}-${{ matrix.python-version }}-32bit-${{ matrix.float_dtype_32 }}
@@ -152,12 +152,12 @@ jobs:
       run:
         shell: bash -l {0}
     steps:
-      - name: Checkout Repository
-        uses: actions/checkout@11bd71901bbe5b1630ceea73d27597364c9af683 # v4.2.2
-        with:
-          fetch-depth: 0
-          persist-credentials: false
-          submodules: true
+    - name: Checkout Repository
+      uses: actions/checkout@08c6903cd8c0fde910a37f88322edcfb5dd907a8 # v5.0.0
+      with:
+        fetch-depth: 0
+        persist-credentials: false
+        submodules: true
 
       - name: Setup Conda and Python
         uses: conda-incubator/setup-miniconda@835234971496cad1653abb28a638a281cf32541f # v3.2.0
diff --git a/CONTRIBUTORS b/CONTRIBUTORS
@@ -53,3 +53,4 @@ Samuele De Cristofaro (@Samuele-DeCristofaro)
 Sagar Shahari (@maverick4code)
 Palash Chitnavis (@PalashChitnavis)
 Mrigesh Thakur (@Legend101Zz)
+Liam Keegan (@lkeegan)
diff --git a/README.md b/README.md
@@ -30,6 +30,7 @@ If you use Brian for your published research, we kindly ask you to cite our arti
 [![Contributor Covenant](https://img.shields.io/badge/Contributor%20Covenant-v1.4%20adopted-ff69b4.svg)](CODE_OF_CONDUCT.md)
 [![Discourse topics](https://img.shields.io/discourse/topics?server=https%3A%2F%2Fbrian.discourse.group)](https://brian.discourse.group)
 [![Discourse chat](https://img.shields.io/badge/discourse-chat-4EC820?logo=discourse&link=https%3A%2F%2Fbrian.discourse.group%2Fchat)](https://brian.discourse.group/chat)
+[![Neuromorphic Computing](https://img.shields.io/badge/Collaboration_Network-Open_Neuromorphic-blue)](https://open-neuromorphic.org/neuromorphic-computing/)
 [![code style: black](https://img.shields.io/badge/code%20style-black-000000.svg)](https://github.com/psf/black)
 
 ## Quickstart
diff --git a/brian2/codegen/runtime/cython_rt/templates/synapses.pyx b/brian2/codegen/runtime/cython_rt/templates/synapses.pyx
@@ -1,22 +1,55 @@
-{# USES_VARIABLES { _queue } #}
+{# USES_VARIABLES { _queue_capsule } #}
 {% extends 'common_group.pyx' %}
 
+{% block template_support_code %}
+from cpython.pycapsule cimport PyCapsule_GetPointer
+from libcpp.vector cimport vector
+from cython.operator cimport dereference
+# We declare minimal C++ interface here - only methods we actually want to use
+# This avoids importing the full SpikeQueue wrapper and its dependencies
+cdef extern from "cspikequeue.cpp":
+    cdef cppclass CSpikeQueue:
+        vector[int32_t]* peek();
+        void advance();
+{% endblock %}
+
 {% block maincode %}
-    cdef _numpy.ndarray[int32_t, ndim=1, mode='c'] _spiking_synapses = _queue.peek()
+     # Extract the raw C++ object pointer from the Python capsule.
+    cdef object capsule = _queue_capsule
+    cdef CSpikeQueue* cpp_queue = <CSpikeQueue*>PyCapsule_GetPointer(capsule, "CSpikeQueue")
+
+    # Now we call the C++ peek method directly to get the current spike vector.
+    # This returns a pointer to std::vector<int32_t> containing synapse IDs
+    # that are ready for processing in the current time step.
+    cdef vector[int32_t]* spike_vector = cpp_queue.peek()
+    cdef size_t num_spikes = dereference(spike_vector).size()
+
+    # Early exit for empty queue - avoid all processing overhead
+    if num_spikes == 0:
+        cpp_queue.advance()
+        return
+
+    # Access the underlying raw data pointer of the vector
+    cdef int32_t* spike_data = &dereference(spike_vector)[0]
 
     # scalar code
     _vectorisation_idx = 1
     {{ scalar_code | autoindent }}
 
-    cdef size_t _spiking_synapse_idx
 
-    for _spiking_synapse_idx in range(len(_spiking_synapses)):
-        # vector code
-        _idx = _spiking_synapses[_spiking_synapse_idx]
+    cdef size_t i = 0
+    cdef int32_t synapse_id
+    while i < num_spikes:
+        synapse_id = spike_data[i]
+
+        _idx = synapse_id
         _vectorisation_idx = _idx
+
         {{ vector_code | autoindent }}
 
-    # Advance the spike queue
-    _queue.advance()
+        i += 1
+
+    # Move the queue forward to the next time step
+    cpp_queue.advance()
 
 {% endblock %}
diff --git a/brian2/codegen/runtime/cython_rt/templates/synapses_push_spikes.pyx b/brian2/codegen/runtime/cython_rt/templates/synapses_push_spikes.pyx
@@ -1,9 +1,30 @@
+{# USES_VARIABLES { _queue_capsule } #}
 {% extends 'common_group.pyx' %}
 
+{% block template_support_code %}
+from cpython.pycapsule cimport PyCapsule_GetPointer
+# We declare minimal C++ interface here - only methods we actually want to use
+# This avoids importing the full SpikeQueue wrapper and its dependencies
+cdef extern from "cspikequeue.cpp":
+    cdef cppclass CSpikeQueue:
+        void push(int32_t *, int)
+{% endblock %}
+
 {% block before_code %}
     _owner.initialise_queue()
 {% endblock %}
 
 {% block maincode %}
-    _owner.push_spikes()
+    {% set eventspace=get_array_name(eventspace_variable)%}
+    cdef int spike_count
+    # Get the spike count from the last entry in the spike buffer
+    spike_count = {{eventspace}}[_num{{eventspace}}-1]
+
+    # Recover the C++ spike queue object from the PyCapsule passed at runtime
+    cdef object capsule = _queue_capsule
+    cdef CSpikeQueue* cpp_queue = <CSpikeQueue*>PyCapsule_GetPointer(capsule, "CSpikeQueue")
+
+    if spike_count > 0:
+    # Optimized: avoid the push_spikes method call overhead
+      cpp_queue.push({{eventspace}},spike_count)
 {% endblock %}
diff --git a/brian2/core/variables.py b/brian2/core/variables.py
@@ -1594,8 +1594,16 @@ def __hash__(self):
     # Get access to some basic properties of the underlying array
     @property
     def shape(self):
+        if isinstance(self.variable, DynamicArrayVariable):
+            # For dynamic variables, we need to make sure that their size is up-to-date in standalone mode
+            # We can trigger the update by asking for the values, even though we don't need them here
+            self.variable.get_value()
         if self.ndim == 1:
-            if not self.variable.scalar:
+            if (
+                hasattr(self, "group")
+                and hasattr(self.group, "start")
+                and hasattr(self.group, "stop")
+            ):
                 # This is safer than using the variable size, since it also works for subgroups
                 # see GitHub issue #1555
                 size = self.group.stop - self.group.start
diff --git a/brian2/devices/cpp_standalone/device.py b/brian2/devices/cpp_standalone/device.py
@@ -1258,11 +1258,14 @@ def run(
             s = arg.split("=")
             if len(s) == 2:
                 for var in self.array_cache:
-                    if (
-                        hasattr(var.owner, "name")
-                        and var.owner.name + "." + var.name == s[0]
-                    ):
-                        self.array_cache[var] = None
+                    try:
+                        if (
+                            hasattr(var.owner, "name")
+                            and var.owner.name + "." + var.name == s[0]
+                        ):
+                            self.array_cache[var] = None
+                    except ReferenceError:
+                        pass  # Happens when ephemeral subgroups have been used to set a variable
         run_args = ["--results_dir", self.results_dir] + run_args
         # Invalidate the cached end time of the clock and network, to deal with stopped simulations
         for clock in self.clocks:
diff --git a/brian2/synapses/cythonspikequeue.pyx b/brian2/synapses/cythonspikequeue.pyx
@@ -5,10 +5,10 @@
 from libcpp.vector cimport vector
 from libcpp.pair cimport pair
 from libcpp.string cimport string
-
 import cython
 from cython.operator import dereference
 from cython.operator cimport dereference
+from cpython.pycapsule cimport PyCapsule_New
 
 cimport numpy as np
 import numpy as np
@@ -54,6 +54,15 @@ cdef class SpikeQueue:
     def _full_state(self):
         return self.thisptr._full_state()
 
+    def get_capsule(self):
+        """
+        Returns a PyCapsule object wrapping the underlying C++ CSpikeQueue pointer.
+
+        PyCapsules are used to safely pass raw C/C++ pointers between Python modules
+        or C extensions without exposing the actual implementation details to Python.
+        """
+        return PyCapsule_New(<void*>self.thisptr, "CSpikeQueue", NULL)
+
     cdef object __weakref__  # Allows weak references to the SpikeQueue
 
     def _restore_from_full_state(self, state):
diff --git a/brian2/synapses/synapses.py b/brian2/synapses/synapses.py
diff --git a/brian2/tests/test_monitor.py b/brian2/tests/test_monitor.py
