Merge branch 'master' into performance

Author: Hananel-Hazan

.github/workflows/black.yml

@@ -6,6 +6,6 @@ jobs:
   lint:
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v2
-      - uses: actions/setup-python@v2
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
       - uses: psf/black@stable

.github/workflows/python-app.yml

@@ -15,21 +15,14 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python 3.13
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
-<<<<<<< HEAD
-        python-version: 3.10
-    - name: Install Poetry
-      env:
-        POETRY_VERSION: 2.0.0
-=======
         python-version: 3.13
     - name: Install Poetry
       env:
         POETRY_VERSION: 2.1.2
->>>>>>> origin
       run: |
         curl -sSL https://install.python-poetry.org | python - -y &&\
             poetry config virtualenvs.create false

.github/workflows/pythonpackage.yml

@@ -9,34 +9,25 @@ jobs:
     strategy:
       max-parallel: 4
       matrix:
-<<<<<<< HEAD
-        python-version: ["3.10", "3.11", "3.12"]
-=======
-        python-version: ["3.10", "3.11", "3.12", "3.13"]
->>>>>>> origin
+        python-version: ["3.11", "3.12", "3.13"]
 
     steps:
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
     - name: Set up Python ${{ matrix.python-version }}
-      uses: actions/setup-python@v4
+      uses: actions/setup-python@v5
       with:
         python-version: ${{ matrix.python-version }}
     - name: Install Poetry
       env:
-<<<<<<< HEAD
-        POETRY_VERSION: 2.0.0
-=======
         POETRY_VERSION: 2.1.2
->>>>>>> origin
       run: |
-        curl -sSL https://install.python-poetry.org | python - -y &&\
-            poetry config virtualenvs.create false
+        curl -sSL https://install.python-poetry.org | python - -y
     - name: Install dependencies
       run: |
         poetry install
     - name: Format with black
       run: |
-        black .
+        poetry run black .
     - name: Test with pytest
       run: |
-        pytest
+        poetry run pytest

.pytest_cache/CACHEDIR.TAG

@@ -0,0 +1,51 @@
+# Changelog
+
+All notable changes to BindsNET are documented here. The format is based on
+[Keep a Changelog](https://keepachangelog.com/). For releases prior to the entries below,
+see the [GitHub releases / tags](https://github.com/BindsNET/bindsnet/releases).
+
+## [Unreleased]
+
+### Added
+- Reproducibility/transparency docs: `DATA.md` (dataset & stimulus declaration),
+  `REPRODUCING.md` (model→script→command→seed map), and a
+  `docs/source/models_spec.rst` neural-model specification page.
+- `CITATION.cff` with the paper citation and the Zenodo software DOI.
+- `CHANGELOG.md`.
+- `examples/breakout/README.md` documenting the `trained_shallow_ANN.pt` provenance.
+
+### Changed
+- README Python requirement aligned to `>=3.11,<3.14`; added a reproducible-install note.
+- `pyproject.toml` version bumped to 0.3.4 to match the released tag.
+
+## [0.3.4] - 2026-06-15
+
+Archived on Zenodo — concept DOI [10.5281/zenodo.20695115](https://doi.org/10.5281/zenodo.20695115),
+version DOI [10.5281/zenodo.20695116](https://doi.org/10.5281/zenodo.20695116).
+
+### Added
+- Sparse-tensor support for additional learning rules (plus a batch dimension and docs
+  for `sparse=True`).
+- Validation tests for the reward-modulated learning rules `MSTDP` and `MSTDPET`.
+- Regression test for a preallocated `Monitor` short-run bug (PR #761).
+- Read the Docs configuration for documentation builds.
+
+### Changed
+- `assign_labels` / evaluation: handle abstention for inactive samples, mark
+  never-firing neurons with `-1`, and accuracy/performance improvements.
+- CI: dropped Python 3.10 (project requires `>=3.11`); upgraded GitHub Actions; test on
+  Python 3.11/3.12/3.13.
+- Routine dependency updates via Poetry.
+
+### Fixed
+- `bernoulli_loader` now honors the `max_prob` kwarg (PR #743).
+- Bug with preallocated buffers and `torch.cat`.
+- `torch.save` compatibility for PyTorch 2.6.0.
+- Python 3.13 support / tests.
+- `eth_mnist` example.
+
+## [0.3.3] - 2024-10-18
+
+Baseline for this changelog. See the
+[releases page](https://github.com/BindsNET/bindsnet/releases) for the history of
+0.1.x–0.3.3.

.pytest_cache/README.md

@@ -0,0 +1,59 @@
+cff-version: 1.2.0
+message: "If you use BindsNET, please cite the article below."
+title: "BindsNET: A Machine Learning-Oriented Spiking Neural Networks Library in Python"
+type: software
+version: 0.3.4
+license: AGPL-3.0-only
+doi: 10.5281/zenodo.20695115
+repository-code: "https://github.com/BindsNET/bindsnet"
+url: "https://bindsnet-docs.readthedocs.io/"
+keywords:
+  - spiking
+  - neural
+  - networks
+  - pytorch
+authors:
+  - family-names: Hazan
+    given-names: Hananel
+  - family-names: Saunders
+    given-names: Daniel J.
+  - family-names: Khan
+    given-names: Hassaan
+  - family-names: Patel
+    given-names: Devdhar
+  - family-names: Sanghavi
+    given-names: Darpan T.
+  - family-names: Siegelmann
+    given-names: Hava T.
+  - family-names: Kozma
+    given-names: Robert
+identifiers:
+  - type: doi
+    value: 10.5281/zenodo.20695115
+    description: Concept DOI (resolves to the latest archived release)
+  - type: doi
+    value: 10.5281/zenodo.20695116
+    description: Archived software release v0.3.4
+preferred-citation:
+  type: article
+  title: "BindsNET: A Machine Learning-Oriented Spiking Neural Networks Library in Python"
+  doi: 10.3389/fninf.2018.00089
+  url: "https://www.frontiersin.org/article/10.3389/fninf.2018.00089"
+  journal: "Frontiers in Neuroinformatics"
+  volume: 12
+  year: 2018
+  authors:
+    - family-names: Hazan
+      given-names: Hananel
+    - family-names: Saunders
+      given-names: Daniel J.
+    - family-names: Khan
+      given-names: Hassaan
+    - family-names: Patel
+      given-names: Devdhar
+    - family-names: Sanghavi
+      given-names: Darpan T.
+    - family-names: Siegelmann
+      given-names: Hava T.
+    - family-names: Kozma
+      given-names: Robert