nstat-toolbox 0.4.1__tar.gz

nstat_toolbox-0.4.1/PKG-INFO

@@ -0,0 +1,278 @@
+Metadata-Version: 2.4
+Name: nstat-toolbox
+Version: 0.4.1
+Summary: Python port of the nSTAT toolbox
+Author: Cajigas Lab
+Requires-Python: >=3.10
+Description-Content-Type: text/markdown
+Requires-Dist: numpy>=1.24
+Requires-Dist: scipy>=1.10
+Requires-Dist: matplotlib>=3.7
+Requires-Dist: sympy>=1.13
+Requires-Dist: PyYAML>=6.0
+Requires-Dist: nbformat>=5.10
+Requires-Dist: nbclient>=0.10
+Provides-Extra: dev
+Requires-Dist: pytest>=8.0; extra == "dev"
+Requires-Dist: scikit-image>=0.22; extra == "dev"
+Requires-Dist: sphinx>=8.0; extra == "dev"
+Requires-Dist: sphinx-rtd-theme>=3.0; extra == "dev"
+Requires-Dist: myst-parser>=4.0; extra == "dev"
+Requires-Dist: packaging>=23.0; extra == "dev"
+Provides-Extra: spikeinterface
+Provides-Extra: neo
+Requires-Dist: neo>=0.13; extra == "neo"
+Requires-Dist: quantities>=0.15; extra == "neo"
+Provides-Extra: nwb
+Requires-Dist: pynwb>=2.8; extra == "nwb"
+Provides-Extra: pynapple
+Requires-Dist: pynapple>=0.7; extra == "pynapple"
+Provides-Extra: metrics
+Requires-Dist: pyspike>=0.8; extra == "metrics"
+Provides-Extra: nemos
+Requires-Dist: nemos>=0.2; extra == "nemos"
+Provides-Extra: dynamax
+Requires-Dist: dynamax>=0.1; extra == "dynamax"
+Provides-Extra: test-parity
+Requires-Dist: nemos>=0.2; extra == "test-parity"
+Requires-Dist: pykalman>=0.11; extra == "test-parity"
+Requires-Dist: statsmodels>=0.15; extra == "test-parity"
+Requires-Dist: nitime>=0.12; extra == "test-parity"
+Provides-Extra: clusterless
+Requires-Dist: replay_trajectory_classification>=1.4; extra == "clusterless"
+Provides-Extra: deep-learning
+Provides-Extra: all-extras
+Requires-Dist: neo>=0.13; extra == "all-extras"
+Requires-Dist: quantities>=0.15; extra == "all-extras"
+Requires-Dist: pynwb>=2.8; extra == "all-extras"
+Requires-Dist: pynapple>=0.7; extra == "all-extras"
+Requires-Dist: pyspike>=0.8; extra == "all-extras"
+Requires-Dist: nemos>=0.2; extra == "all-extras"
+Requires-Dist: pykalman>=0.11; extra == "all-extras"
+Requires-Dist: statsmodels>=0.15; extra == "all-extras"
+Requires-Dist: nitime>=0.12; extra == "all-extras"
+
+# nSTAT-python
+
+**Neural Spike Train Analysis Toolbox for Python**
+
+[![test-and-build](https://github.com/cajigaslab/nSTAT-python/actions/workflows/ci.yml/badge.svg)](https://github.com/cajigaslab/nSTAT-python/actions/workflows/ci.yml)
+
+> 📖 **New here?** Start with the
+> [**5-minute intro**](https://cajigaslab.github.io/nSTAT-python/intro.html) —
+> a friendly tour of the toolbox with runnable snippets, the
+> `nstat.extras` opt-in bridges, and the paper-example gallery.
+
+`nSTAT-python` is a Python port of the [nSTAT](https://github.com/cajigaslab/nSTAT)
+open-source neural spike train analysis toolbox. It implements a range of models and
+algorithms for neural spike train data analysis, with a focus on point-process
+generalized linear models (GLMs), model fitting, model-order analysis, and adaptive
+decoding. In addition to point-process algorithms, nSTAT also provides tools for
+Gaussian signals — from correlation analysis to the Kalman filter — applicable to
+continuous neural signals such as LFP, EEG, and ECoG.
+
+One of nSTAT's key strengths is point-process generalized linear models for spike
+train signals that provide a formal statistical framework for processing signals
+recorded from ensembles of single neurons. It also has extensive support for model
+fitting, model-order analysis, and adaptive decoding.
+
+Although created with neural signal processing in mind, nSTAT can be used as a
+generic tool for analyzing any types of discrete and continuous signals, and thus
+has wide applicability.
+
+Like all open-source projects, nSTAT will benefit from your involvement,
+suggestions and contributions. This platform is intended as a repository for
+extensions to the toolbox based on your code contributions as well as for flagging
+and tracking open issues.
+
+The current release can be installed from PyPI: `pip install nstat-toolbox`
+
+Lab websites:
+- Neuroscience Statistics Research Laboratory: https://www.neurostat.mit.edu
+- RESToRe Lab: https://www.med.upenn.edu/cajigaslab/
+
+## How to install nSTAT
+
+```bash
+python -m pip install nstat-toolbox
+```
+
+From source:
+
+```bash
+git clone git@github.com:cajigaslab/nSTAT-python.git
+cd nSTAT-python
+python -m pip install -e .[dev]
+```
+
+Install the example dataset:
+
+```bash
+nstat-install --download-example-data always
+```
+
+Equivalent Python API:
+
+```python
+from nstat.data_manager import ensure_example_data
+data_dir = ensure_example_data(download=True)
+```
+
+Quickstart:
+
+```bash
+cd /path/to/nSTAT-python
+pip install -e .[dev]
+nstat-install --download-example-data always
+pytest -q && python tools/paper_examples/build_gallery.py
+```
+
+## Paper Examples (Self-Contained)
+
+Canonical source files:
+- `examples/paper/*.py`
+- `nstat/paper_examples_full.py`
+
+Single command to regenerate the paper-example gallery metadata:
+
+```bash
+python tools/paper_examples/build_gallery.py
+```
+
+This writes `docs/paper_examples.md`, `docs/figures/manifest.json`, and
+refreshes the canonical README paper-example table from
+`examples/paper/manifest.yml`.
+
+| Example | Thumbnail | What question it answers | Run command | Links |
+|---|---|---|---|---|
+| Example 01 | ![Example 01](docs/figures/example01/fig01_constant_mg_summary.png) | Do mEPSCs follow constant vs piecewise Poisson firing under Mg2+ washout? | `python examples/paper/example01_mepsc_poisson.py` | [Script](examples/paper/example01_mepsc_poisson.py) · [Figures](docs/figures/example01/) |
+| Example 02 | ![Example 02](docs/figures/example02/fig01_data_overview.png) | How do explicit whisker stimulus and spike history improve thalamic GLM fits? | `python examples/paper/example02_whisker_stimulus_thalamus.py` | [Script](examples/paper/example02_whisker_stimulus_thalamus.py) · [Figures](docs/figures/example02/) |
+| Example 03 | ![Example 03](docs/figures/example03/fig01_simulated_and_real_rasters.png) | How do PSTH and SSGLM capture within-trial and across-trial dynamics? | `python examples/paper/example03_psth_and_ssglm.py` | [Script](examples/paper/example03_psth_and_ssglm.py) · [Figures](docs/figures/example03/) |
+| Example 04 | ![Example 04](docs/figures/example04/fig01_example_cells_path_overlay.png) | Which receptive-field basis (Gaussian vs Zernike) better fits place cells? | `python examples/paper/example04_place_cells_continuous_stimulus.py` | [Script](examples/paper/example04_place_cells_continuous_stimulus.py) · [Figures](docs/figures/example04/) |
+| Example 05 | ![Example 05](docs/figures/example05/fig01_univariate_setup.png) | How well do adaptive/hybrid point-process filters decode stimulus and reach state? | `python examples/paper/example05_decoding_ppaf_pphf.py` | [Script](examples/paper/example05_decoding_ppaf_pphf.py) · [Figures](docs/figures/example05/) |
+
+Expanded paper-example index and figure gallery:
+- [docs/paper_examples.md](docs/paper_examples.md)
+
+Plot style policy:
+
+```python
+from nstat.plot_style import set_plot_style
+
+# Modern readability-focused plots (default)
+set_plot_style('modern')
+
+# Legacy visual style for strict reproduction
+set_plot_style('legacy')
+```
+
+Rendered help documentation (GitHub Pages):
+- https://cajigaslab.github.io/nSTAT-python/
+
+For mathematical and programmatic details of the toolbox, see:
+
+Cajigas I, Malik WQ, Brown EN. nSTAT: Open-source neural spike train analysis
+toolbox for Matlab. Journal of Neuroscience Methods 211: 245–264, Nov. 2012.
+- DOI: [10.1016/j.jneumeth.2012.08.009](https://doi.org/10.1016/j.jneumeth.2012.08.009)
+- PubMed: [22981419](https://pubmed.ncbi.nlm.nih.gov/22981419/)
+
+## Paper-Aligned Toolbox Map
+
+To keep terminology and workflows consistent with the 2012 toolbox paper,
+the documentation includes a dedicated mapping page:
+[docs/PaperOverview.md](docs/PaperOverview.md).
+
+This page ties the Python toolbox to the paper's workflow categories:
+
+- Class hierarchy and object model (`SignalObj`, `Covariate`, `Trial`,
+  `Analysis`, `FitResult`, `DecodingAlgorithms`)
+- Fitting and assessment workflow (GLM fitting, diagnostics, summaries)
+- Simulation workflow (conditional intensity and thinning examples)
+- Decoding workflow (univariate/bivariate and history-aware decoding)
+- Example-to-paper section mapping via `nSTATPaperExamples`
+
+If you use nSTAT in your work, please remember to cite the above paper in any publications.
+nSTAT is protected by the GPL v2 Open Source License.
+
+The code repository for the Python port of nSTAT is hosted on GitHub at
+https://github.com/cajigaslab/nSTAT-python.
+The paper-example dataset is distributed separately from the Git repository:
+- Figshare dataset DOI: https://doi.org/10.6084/m9.figshare.4834640.v3
+- Paper DOI: https://doi.org/10.1016/j.jneumeth.2012.08.009
+
+## Code audit (2026-03-11)
+
+The Python port was verified against the MATLAB reference through a comprehensive
+5-phase audit covering all 16 classes and 484 methods. **466 methods found in
+Python, 6 nominal (MATLAB-infrastructure) gaps.** Full class-level and behavioral
+parity verified.
+
+**Python bugs fixed during the port:**
+
+- `SignalObj.std()` used `ddof=0`; MATLAB uses `ddof=1` (N-1 normalization)
+- `CovariateCollection.isCovPresent()` off-by-one in boundary check
+- `SpikeTrainCollection.psthGLM()` was a stub; now wired to the full GLM path
+- `SpikeTrainCollection.getNSTnames()` / `getUniqueNSTnames()` ignored the
+  `selectorArray` filter parameter
+- `nspikeTrain.getNST()` missing resample check on retrieval
+
+**MATLAB bugs discovered (13 total, filed as GitHub issues):**
+
+- `FitResult.m` — KS test used `sampleRate` as bin width instead of
+  `1/sampleRate`, invalidating goodness-of-fit for any sampleRate != 1
+- `CIF.m` — `symvar()` reordered variables alphabetically, causing silent
+  argument mismatch for non-alphabetical variable names
+- `SignalObj.m` — `findPeaks('minima')` returned maxima; `findGlobalPeak('minima')`
+  crashed; handle aliasing mutated input signals in arithmetic
+- `DecodingAlgorithms.m` — `isa(condNum,'nan')` always false; `ExplambdaDeltaCubed`
+  used `.^2` instead of `.^3`
+- `Analysis.m` — Granger causality mask zeroed all columns instead of column `i`
+
+See [parity/report.md](parity/report.md) for the full audit.
+
+## MATLAB Toolbox
+
+The original MATLAB nSTAT toolbox lives in a separate repository:
+
+- https://github.com/cajigaslab/nSTAT
+
+That repository is MATLAB-focused and retains:
+
+- Original MATLAB class/source files
+- MATLAB helpfiles and help index (`helpfiles/helptoc.xml`)
+- MATLAB example workflows, including `.mlx` examples
+
+## Related Python projects
+
+> 📚 **Visual summary** with per-bridge cards, install matrix, and code snippets:
+> [`extras_summary.html`](https://cajigaslab.github.io/nSTAT-python/extras_summary.html).
+> **What's New** (per-iteration change summaries):
+> [`whats_new.html`](https://cajigaslab.github.io/nSTAT-python/whats_new.html).
+
+nstat ships **opt-in bridges** (`nstat.extras.*`) to libraries in the
+modern Python systems-neuroscience stack.  Install each via its
+optional-dep group:
+
+| Library | Use case | Bridge module | Install |
+|---|---|---|---|
+| [Neo](https://github.com/NeuralEnsemble/python-neo) | I/O for Spike2 / NEX / Blackrock / Plexon / TDT / NWB | `nstat.extras.interop.neo` | `pip install nstat-toolbox[neo]` |
+| [pynapple](https://github.com/pynapple-org/pynapple) | Time-series + epoch math, NWB-native | `nstat.extras.interop.pynapple` | `pip install nstat-toolbox[pynapple]` |
+| [pynwb](https://github.com/NeurodataWithoutBorders/pynwb) | BRAIN-Initiative NWB:N standard reader | `nstat.extras.interop.nwb` | `pip install nstat-toolbox[nwb]` |
+| [NeMoS](https://github.com/flatironinstitute/nemos) | JAX Poisson-GLM (cross-validation reference) | `nstat.extras.validation.nemos_bridge` | `pip install nstat-toolbox[nemos]` |
+| [pykalman](https://github.com/pykalman/pykalman) | Pure-NumPy Kalman (cross-validation reference) | `nstat.extras.validation.pykalman_bridge` | `pip install nstat-toolbox[test-parity]` |
+| [statsmodels](https://www.statsmodels.org) | Poisson GLM (IRLS — tightest cross-validation oracle, ~1e-9 agreement) | `nstat.extras.validation.statsmodels_bridge` | `pip install nstat-toolbox[test-parity]` |
+| [PySpike](https://github.com/mariomulansky/PySpike) | ISI / SPIKE-distance spike-train metrics | `nstat.extras.metrics.spike_distances` | `pip install nstat-toolbox[metrics]` |
+| [Dynamax](https://github.com/probml/dynamax) | EM-trained linear-Gaussian state-space models (foundation for unported MATLAB `KF_EM` / `PP_EM` / `mPPCO_EM`) | `nstat.extras.em.dynamax_bridge` | `pip install nstat-toolbox[dynamax]` (pulls JAX ~200 MB) |
+
+For ecosystem peers nstat does **not** wrap (spike sorting, calcium
+imaging, deep-learning decoders), see
+[`parity/integration_opportunities.md`](parity/integration_opportunities.md)
+for the rationale and recommended alternatives:
+
+- **[SpikeInterface](https://github.com/SpikeInterface/spikeinterface)** — spike sorting (nstat assumes pre-sorted data).
+- **[Elephant](https://github.com/NeuralEnsemble/elephant)** — overlapping spike-train statistics; Neo-typed.
+- **[ssqueezepy](https://github.com/OverLordGoldDragon/ssqueezepy)** — wavelet synchrosqueezing; planned `nstat.extras.spectral`.
+
+Install every bridge at once: `pip install nstat-toolbox[all-extras]`
+(does **not** include `[dynamax]` due to JAX install size — install
+that group separately if you need EM-trained state-space models).

nstat_toolbox-0.4.1/README.md

@@ -0,0 +1,224 @@
+# nSTAT-python
+
+**Neural Spike Train Analysis Toolbox for Python**
+
+[![test-and-build](https://github.com/cajigaslab/nSTAT-python/actions/workflows/ci.yml/badge.svg)](https://github.com/cajigaslab/nSTAT-python/actions/workflows/ci.yml)
+
+> 📖 **New here?** Start with the
+> [**5-minute intro**](https://cajigaslab.github.io/nSTAT-python/intro.html) —
+> a friendly tour of the toolbox with runnable snippets, the
+> `nstat.extras` opt-in bridges, and the paper-example gallery.
+
+`nSTAT-python` is a Python port of the [nSTAT](https://github.com/cajigaslab/nSTAT)
+open-source neural spike train analysis toolbox. It implements a range of models and
+algorithms for neural spike train data analysis, with a focus on point-process
+generalized linear models (GLMs), model fitting, model-order analysis, and adaptive
+decoding. In addition to point-process algorithms, nSTAT also provides tools for
+Gaussian signals — from correlation analysis to the Kalman filter — applicable to
+continuous neural signals such as LFP, EEG, and ECoG.
+
+One of nSTAT's key strengths is point-process generalized linear models for spike
+train signals that provide a formal statistical framework for processing signals
+recorded from ensembles of single neurons. It also has extensive support for model
+fitting, model-order analysis, and adaptive decoding.
+
+Although created with neural signal processing in mind, nSTAT can be used as a
+generic tool for analyzing any types of discrete and continuous signals, and thus
+has wide applicability.
+
+Like all open-source projects, nSTAT will benefit from your involvement,
+suggestions and contributions. This platform is intended as a repository for
+extensions to the toolbox based on your code contributions as well as for flagging
+and tracking open issues.
+
+The current release can be installed from PyPI: `pip install nstat-toolbox`
+
+Lab websites:
+- Neuroscience Statistics Research Laboratory: https://www.neurostat.mit.edu
+- RESToRe Lab: https://www.med.upenn.edu/cajigaslab/
+
+## How to install nSTAT
+
+```bash
+python -m pip install nstat-toolbox
+```
+
+From source:
+
+```bash
+git clone git@github.com:cajigaslab/nSTAT-python.git
+cd nSTAT-python
+python -m pip install -e .[dev]
+```
+
+Install the example dataset:
+
+```bash
+nstat-install --download-example-data always
+```
+
+Equivalent Python API:
+
+```python
+from nstat.data_manager import ensure_example_data
+data_dir = ensure_example_data(download=True)
+```
+
+Quickstart:
+
+```bash
+cd /path/to/nSTAT-python
+pip install -e .[dev]
+nstat-install --download-example-data always
+pytest -q && python tools/paper_examples/build_gallery.py
+```
+
+## Paper Examples (Self-Contained)
+
+Canonical source files:
+- `examples/paper/*.py`
+- `nstat/paper_examples_full.py`
+
+Single command to regenerate the paper-example gallery metadata:
+
+```bash
+python tools/paper_examples/build_gallery.py
+```
+
+This writes `docs/paper_examples.md`, `docs/figures/manifest.json`, and
+refreshes the canonical README paper-example table from
+`examples/paper/manifest.yml`.
+
+| Example | Thumbnail | What question it answers | Run command | Links |
+|---|---|---|---|---|
+| Example 01 | ![Example 01](docs/figures/example01/fig01_constant_mg_summary.png) | Do mEPSCs follow constant vs piecewise Poisson firing under Mg2+ washout? | `python examples/paper/example01_mepsc_poisson.py` | [Script](examples/paper/example01_mepsc_poisson.py) · [Figures](docs/figures/example01/) |
+| Example 02 | ![Example 02](docs/figures/example02/fig01_data_overview.png) | How do explicit whisker stimulus and spike history improve thalamic GLM fits? | `python examples/paper/example02_whisker_stimulus_thalamus.py` | [Script](examples/paper/example02_whisker_stimulus_thalamus.py) · [Figures](docs/figures/example02/) |
+| Example 03 | ![Example 03](docs/figures/example03/fig01_simulated_and_real_rasters.png) | How do PSTH and SSGLM capture within-trial and across-trial dynamics? | `python examples/paper/example03_psth_and_ssglm.py` | [Script](examples/paper/example03_psth_and_ssglm.py) · [Figures](docs/figures/example03/) |
+| Example 04 | ![Example 04](docs/figures/example04/fig01_example_cells_path_overlay.png) | Which receptive-field basis (Gaussian vs Zernike) better fits place cells? | `python examples/paper/example04_place_cells_continuous_stimulus.py` | [Script](examples/paper/example04_place_cells_continuous_stimulus.py) · [Figures](docs/figures/example04/) |
+| Example 05 | ![Example 05](docs/figures/example05/fig01_univariate_setup.png) | How well do adaptive/hybrid point-process filters decode stimulus and reach state? | `python examples/paper/example05_decoding_ppaf_pphf.py` | [Script](examples/paper/example05_decoding_ppaf_pphf.py) · [Figures](docs/figures/example05/) |
+
+Expanded paper-example index and figure gallery:
+- [docs/paper_examples.md](docs/paper_examples.md)
+
+Plot style policy:
+
+```python
+from nstat.plot_style import set_plot_style
+
+# Modern readability-focused plots (default)
+set_plot_style('modern')
+
+# Legacy visual style for strict reproduction
+set_plot_style('legacy')
+```
+
+Rendered help documentation (GitHub Pages):
+- https://cajigaslab.github.io/nSTAT-python/
+
+For mathematical and programmatic details of the toolbox, see:
+
+Cajigas I, Malik WQ, Brown EN. nSTAT: Open-source neural spike train analysis
+toolbox for Matlab. Journal of Neuroscience Methods 211: 245–264, Nov. 2012.
+- DOI: [10.1016/j.jneumeth.2012.08.009](https://doi.org/10.1016/j.jneumeth.2012.08.009)
+- PubMed: [22981419](https://pubmed.ncbi.nlm.nih.gov/22981419/)
+
+## Paper-Aligned Toolbox Map
+
+To keep terminology and workflows consistent with the 2012 toolbox paper,
+the documentation includes a dedicated mapping page:
+[docs/PaperOverview.md](docs/PaperOverview.md).
+
+This page ties the Python toolbox to the paper's workflow categories:
+
+- Class hierarchy and object model (`SignalObj`, `Covariate`, `Trial`,
+  `Analysis`, `FitResult`, `DecodingAlgorithms`)
+- Fitting and assessment workflow (GLM fitting, diagnostics, summaries)
+- Simulation workflow (conditional intensity and thinning examples)
+- Decoding workflow (univariate/bivariate and history-aware decoding)
+- Example-to-paper section mapping via `nSTATPaperExamples`
+
+If you use nSTAT in your work, please remember to cite the above paper in any publications.
+nSTAT is protected by the GPL v2 Open Source License.
+
+The code repository for the Python port of nSTAT is hosted on GitHub at
+https://github.com/cajigaslab/nSTAT-python.
+The paper-example dataset is distributed separately from the Git repository:
+- Figshare dataset DOI: https://doi.org/10.6084/m9.figshare.4834640.v3
+- Paper DOI: https://doi.org/10.1016/j.jneumeth.2012.08.009
+
+## Code audit (2026-03-11)
+
+The Python port was verified against the MATLAB reference through a comprehensive
+5-phase audit covering all 16 classes and 484 methods. **466 methods found in
+Python, 6 nominal (MATLAB-infrastructure) gaps.** Full class-level and behavioral
+parity verified.
+
+**Python bugs fixed during the port:**
+
+- `SignalObj.std()` used `ddof=0`; MATLAB uses `ddof=1` (N-1 normalization)
+- `CovariateCollection.isCovPresent()` off-by-one in boundary check
+- `SpikeTrainCollection.psthGLM()` was a stub; now wired to the full GLM path
+- `SpikeTrainCollection.getNSTnames()` / `getUniqueNSTnames()` ignored the
+  `selectorArray` filter parameter
+- `nspikeTrain.getNST()` missing resample check on retrieval
+
+**MATLAB bugs discovered (13 total, filed as GitHub issues):**
+
+- `FitResult.m` — KS test used `sampleRate` as bin width instead of
+  `1/sampleRate`, invalidating goodness-of-fit for any sampleRate != 1
+- `CIF.m` — `symvar()` reordered variables alphabetically, causing silent
+  argument mismatch for non-alphabetical variable names
+- `SignalObj.m` — `findPeaks('minima')` returned maxima; `findGlobalPeak('minima')`
+  crashed; handle aliasing mutated input signals in arithmetic
+- `DecodingAlgorithms.m` — `isa(condNum,'nan')` always false; `ExplambdaDeltaCubed`
+  used `.^2` instead of `.^3`
+- `Analysis.m` — Granger causality mask zeroed all columns instead of column `i`
+
+See [parity/report.md](parity/report.md) for the full audit.
+
+## MATLAB Toolbox
+
+The original MATLAB nSTAT toolbox lives in a separate repository:
+
+- https://github.com/cajigaslab/nSTAT
+
+That repository is MATLAB-focused and retains:
+
+- Original MATLAB class/source files
+- MATLAB helpfiles and help index (`helpfiles/helptoc.xml`)
+- MATLAB example workflows, including `.mlx` examples
+
+## Related Python projects
+
+> 📚 **Visual summary** with per-bridge cards, install matrix, and code snippets:
+> [`extras_summary.html`](https://cajigaslab.github.io/nSTAT-python/extras_summary.html).
+> **What's New** (per-iteration change summaries):
+> [`whats_new.html`](https://cajigaslab.github.io/nSTAT-python/whats_new.html).
+
+nstat ships **opt-in bridges** (`nstat.extras.*`) to libraries in the
+modern Python systems-neuroscience stack.  Install each via its
+optional-dep group:
+
+| Library | Use case | Bridge module | Install |
+|---|---|---|---|
+| [Neo](https://github.com/NeuralEnsemble/python-neo) | I/O for Spike2 / NEX / Blackrock / Plexon / TDT / NWB | `nstat.extras.interop.neo` | `pip install nstat-toolbox[neo]` |
+| [pynapple](https://github.com/pynapple-org/pynapple) | Time-series + epoch math, NWB-native | `nstat.extras.interop.pynapple` | `pip install nstat-toolbox[pynapple]` |
+| [pynwb](https://github.com/NeurodataWithoutBorders/pynwb) | BRAIN-Initiative NWB:N standard reader | `nstat.extras.interop.nwb` | `pip install nstat-toolbox[nwb]` |
+| [NeMoS](https://github.com/flatironinstitute/nemos) | JAX Poisson-GLM (cross-validation reference) | `nstat.extras.validation.nemos_bridge` | `pip install nstat-toolbox[nemos]` |
+| [pykalman](https://github.com/pykalman/pykalman) | Pure-NumPy Kalman (cross-validation reference) | `nstat.extras.validation.pykalman_bridge` | `pip install nstat-toolbox[test-parity]` |
+| [statsmodels](https://www.statsmodels.org) | Poisson GLM (IRLS — tightest cross-validation oracle, ~1e-9 agreement) | `nstat.extras.validation.statsmodels_bridge` | `pip install nstat-toolbox[test-parity]` |
+| [PySpike](https://github.com/mariomulansky/PySpike) | ISI / SPIKE-distance spike-train metrics | `nstat.extras.metrics.spike_distances` | `pip install nstat-toolbox[metrics]` |
+| [Dynamax](https://github.com/probml/dynamax) | EM-trained linear-Gaussian state-space models (foundation for unported MATLAB `KF_EM` / `PP_EM` / `mPPCO_EM`) | `nstat.extras.em.dynamax_bridge` | `pip install nstat-toolbox[dynamax]` (pulls JAX ~200 MB) |
+
+For ecosystem peers nstat does **not** wrap (spike sorting, calcium
+imaging, deep-learning decoders), see
+[`parity/integration_opportunities.md`](parity/integration_opportunities.md)
+for the rationale and recommended alternatives:
+
+- **[SpikeInterface](https://github.com/SpikeInterface/spikeinterface)** — spike sorting (nstat assumes pre-sorted data).
+- **[Elephant](https://github.com/NeuralEnsemble/elephant)** — overlapping spike-train statistics; Neo-typed.
+- **[ssqueezepy](https://github.com/OverLordGoldDragon/ssqueezepy)** — wavelet synchrosqueezing; planned `nstat.extras.spectral`.
+
+Install every bridge at once: `pip install nstat-toolbox[all-extras]`
+(does **not** include `[dynamax]` due to JAX install size — install
+that group separately if you need EM-trained state-space models).

nstat_toolbox-0.4.1/nstat/ConfidenceInterval.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .confidence_interval import ConfidenceInterval
+
+__all__ = ["ConfidenceInterval"]

nstat_toolbox-0.4.1/nstat/ConfigColl.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .trial import ConfigCollection as ConfigColl
+
+__all__ = ["ConfigColl"]

nstat_toolbox-0.4.1/nstat/CovColl.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .trial import CovariateCollection as CovColl
+
+__all__ = ["CovColl"]

nstat_toolbox-0.4.1/nstat/Covariate.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .core import Covariate
+
+__all__ = ["Covariate"]

nstat_toolbox-0.4.1/nstat/DecodingAlgorithms.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .decoding_algorithms import DecodingAlgorithms
+
+__all__ = ["DecodingAlgorithms"]

nstat_toolbox-0.4.1/nstat/FitResSummary.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .fit import FitResSummary
+
+__all__ = ["FitResSummary"]

nstat_toolbox-0.4.1/nstat/FitResult.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .fit import FitResult
+
+__all__ = ["FitResult"]

nstat_toolbox-0.4.1/nstat/SignalObj.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .core import SignalObj
+
+__all__ = ["SignalObj"]

nstat_toolbox-0.4.1/nstat/TrialConfig.py

@@ -0,0 +1,5 @@
+from __future__ import annotations
+
+from .trial import TrialConfig
+
+__all__ = ["TrialConfig"]