cajigaslab · iahncajigas · Feb 27, 2026 · Feb 27, 2026 · Feb 27, 2026 · Feb 27, 2026
diff --git a/.github/workflows/helpfiles-pages.yml b/.github/workflows/helpfiles-pages.yml
@@ -0,0 +1,51 @@
+name: Helpfiles Pages
+
+on:
+  workflow_dispatch:
+  push:
+    branches:
+      - master
+      - main
+    paths:
+      - "helpfiles/**"
+      - ".github/workflows/helpfiles-pages.yml"
+
+concurrency:
+  group: pages
+  cancel-in-progress: true
+
+permissions:
+  contents: read
+  pages: write
+  id-token: write
+
+jobs:
+  deploy:
+    runs-on: ubuntu-latest
+    environment:
+      name: github-pages
+      url: ${{ steps.deployment.outputs.page_url }}
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Configure Pages
+        uses: actions/configure-pages@v5
+
+      - name: Build Pages artifact from helpfiles
+        run: |
+          mkdir -p _site
+          cp -R helpfiles/. _site/
+          touch _site/.nojekyll
+          if [ ! -f _site/index.html ]; then
+            cp _site/NeuralSpikeAnalysis_top.html _site/index.html
+          fi
+
+      - name: Upload artifact
+        uses: actions/upload-pages-artifact@v3
+        with:
+          path: _site
+
+      - name: Deploy to GitHub Pages
+        id: deployment
+        uses: actions/deploy-pages@v4
diff --git a/.github/workflows/python-ci.yml b/.github/workflows/python-ci.yml
@@ -0,0 +1,34 @@
+name: Python CI
+
+on:
+  pull_request:
+  push:
+    branches:
+      - main
+      - master
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
+jobs:
+  test:
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+
+      - name: Setup Python
+        uses: actions/setup-python@v5
+        with:
+          python-version: "3.11"
+
+      - name: Install package and test dependencies
+        run: |
+          python -m pip install --upgrade pip
+          python -m pip install -e ./python[dev]
+
+      - name: Run pytest
+        run: |
+          cd python
+          python -m pytest -q
diff --git a/.gitignore b/.gitignore
@@ -2,3 +2,7 @@
 .svn
 __pycache__/
 *.pyc
+python/plots/
+
+python/docs/_build/
+python/.pytest_cache/
diff --git a/CIF.m b/CIF.m
@@ -1,9 +1,9 @@
-classdef CIF < handle
-    %CIF - Conditional Intensity function. 
-    %<a href="matlab: methods('CIF')">methods</a>
-    % 
-    %Reference page in Help browser
-    %<a href="matlab: doc('CIF')">doc CIF</a>
+classdef CIF < handle
+    %CIF - Conditional Intensity function. 
+    %<a href="matlab:nstatOpenHelpPage('PPSimExample.html')">CIF Example</a>
+    % 
+    %Reference page in Help browser
+    %<a href="matlab:nstatOpenHelpPage('PPSimExample.html')">CIF Reference Workflow</a>
 
 
     %

diff --git a/ConfidenceInterval.m b/ConfidenceInterval.m
@@ -1,9 +1,9 @@
-classdef ConfidenceInterval < SignalObj
-%ConfidenceInterval-represents the confidence interval for a time
-%series or <a href="matlab:help('Covariate')">Covariate</a>.
-% <a href="matlab: methods('ConfidenceInterval')">methods</a>
-% Reference page in Help browser
-% <a href="matlab: doc('ConfidenceInterval')">doc ConfidenceInterval</a>
+classdef ConfidenceInterval < SignalObj
+%ConfidenceInterval-represents the confidence interval for a time
+%series or <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate</a>.
+% <a href="matlab:nstatOpenHelpPage('ConfidenceIntervalOverview.html')">ConfidenceInterval Overview</a>
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('ConfidenceIntervalOverview.html')">ConfidenceInterval Reference</a>
 
 %
 % nSTAT v1 Copyright (C) 2012 Masschusetts Institute of Technology

diff --git a/ConfigColl.m b/ConfigColl.m
@@ -1,14 +1,14 @@
-classdef ConfigColl < handle
-%CONFIGCOLL - a collection of different configurations
-% <a href="matlab: methods('ConfigColl')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('ConfigCollExamples.html')">ConfigColl Examples</a> 
-%
-% see also <a href="matlab:help('TrialConfig')">TrialConfig</a>, <a
-% href="matlab:help('CovColl')">Trial</a>, <a
-% href="matlab:help('Analysis')">Analysis</a>
-%
-% Reference page in Help browser
-% <a href="matlab: doc('ConfigColl')">doc ConfigColl</a>
+classdef ConfigColl < handle
+%CONFIGCOLL - a collection of different configurations
+% <a href="matlab:nstatOpenHelpPage('ConfigCollExamples.html')">ConfigColl Reference</a>
+% <a href="matlab:nstatOpenHelpPage('ConfigCollExamples.html')">ConfigColl Examples</a> 
+%
+% see also <a href="matlab:nstatOpenHelpPage('TrialConfigExamples.html')">TrialConfig</a>, <a
+% href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl</a>, <a
+% href="matlab:nstatOpenHelpPage('AnalysisExamples.html')">Analysis</a>
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('ConfigCollExamples.html')">ConfigColl Reference</a>
 
 
 %

diff --git a/CovColl.m b/CovColl.m
@@ -8,14 +8,14 @@
 % the original covariates remain intact. The covariate collection
 % remembers the masked states, shifts, etc. so that these are applied
 % to the signal right before it is returned.
-% 
-% <a href="matlab: methods('CovColl')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl Examples</a> 
-%
-% see also <a href="matlab:help('SignalObj')">SignalObj</a>, <a href="matlab:help('Covariate')">Covariate</a>
-%
-% Reference page in Help browser
-% <a href="matlab: doc('CovColl')">doc CovColl</a>
+% 
+% <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl Reference</a>
+% <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl Examples</a> 
+%
+% see also <a href="matlab:nstatOpenHelpPage('SignalObjExamples.html')">SignalObj</a>, <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate</a>
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl Reference</a>
 % 
 
 %

diff --git a/Covariate.m b/Covariate.m
@@ -14,13 +14,13 @@
 % can also just use cov for the standard representation
 % cov.getSigRep('zero-mean') is a zero mean version of the Signal 
 %
-% <a href="matlab: methods('Covariate')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate Examples</a> 
-%
-% see also <a href="matlab:help('SignalObj')">SignalObj</a>, <a href="matlab:help('CovColl')">CovColl</a>  
-%
-% Reference page in Help browser
-% <a href="matlab: doc('Covariate')">doc Covariate</a>
+% <a href="matlab: methods('Covariate')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate Examples</a> 
+%
+% see also <a href="matlab:nstatOpenHelpPage('SignalObjExamples.html')">SignalObj</a>, <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl</a>  
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate Reference</a>
 
 %
 % nSTAT v1 Copyright (C) 2012 Masschusetts Institute of Technology

diff --git a/DecodingAlgorithms.m b/DecodingAlgorithms.m
@@ -2,12 +2,12 @@
 % DECODINGALGORITHMS A class that contains static functions for 
 % decoding the hidden states of linear discrete stochastic systems or 
 % hybrid linear discrete stochastic systems subject to gaussian noise. 
-% The observations can come from either a gaussian observation model 
-% or via a point process observation model.
-%
-% <a href="matlab: methods('DecodingAlgorithms')">methods</a>
-% Reference page in Help browser
-% <a href="matlab: doc('DecodingAlgorithms')">doc DecodingAlgorithms</a>
+% The observations can come from either a gaussian observation model 
+% or via a point process observation model.
+%
+% <a href="matlab:nstatOpenHelpPage('DecodingExample.html')">Decoding Algorithms Reference</a>
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('DecodingExample.html')">Decoding Algorithms Examples</a>
 
 
 %

diff --git a/Events.m b/Events.m
@@ -14,11 +14,11 @@
 %
 % The length of eventTimes and eventLabels must match for an Events
 % object to be successfully created.
-% <a href="matlab: methods('Events')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('EventsExamples.html')">Events Examples</a> 
-%
-% Reference page in Help browser
-% <a href="matlab: doc('Events')">doc Events</a>
+% <a href="matlab: methods('Events')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('EventsExamples.html')">Events Examples</a> 
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('EventsExamples.html')">Events Reference</a>
 
 
 %
@@ -186,4 +186,4 @@
 
 
 
-
+
diff --git a/FitResSummary.m b/FitResSummary.m
@@ -4,11 +4,11 @@
 % summary statistics across neurons. This is to allows visualization of
 % commonalities in the data across multiple neurons. 
 %
-% % <a href="matlab: methods('FitResSummary')">methods</a>
-% see also <a href="matlab:help('FitResult')">FitResult</a>
+% % <a href="matlab:nstatOpenHelpPage('FitResSummaryExamples.html')">FitResSummary Reference</a>
+% see also <a href="matlab:nstatOpenHelpPage('FitResultExamples.html')">FitResult</a>
 %
 % Reference page in Help browser
-% <a href="matlab:doc('FitResSummary')">doc FitResSummary</a>    
+% <a href="matlab:nstatOpenHelpPage('FitResSummaryExamples.html')">FitResSummary Reference</a>    
 
 
 %

diff --git a/History.m b/History.m
@@ -9,10 +9,10 @@
 %           them in order and use them to specify windows in which we are
 %           interested in computing the history;
 %        
-% <a href="matlab: methods('History')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('HistoryExamples.html')">History Examples</a> 
-% Reference page in Help browser
-% <a href="matlab: doc('History')">doc History</a>
+% <a href="matlab: methods('History')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('HistoryExamples.html')">History Examples</a> 
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('HistoryExamples.html')">History Reference</a>
 
 
 %

diff --git a/README.md b/README.md
@@ -12,12 +12,36 @@ Although created with neural signal processing in mind, nSTAT can be used as a g
 
 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 version of nSTAT can be downloaded from http://www.neurostat.mit.edu/nstat .
+The current release version of nSTAT can be downloaded from https://www.neurostat.mit.edu/nstat .
+Lab websites:
+- Neuroscience Statistics Research Laboratory: https://www.neurostat.mit.edu
+- RESToRe Lab: https://www.med.upenn.edu/cajigaslab/
+
+Rendered help documentation (GitHub Pages):
+- https://cajigaslab.github.io/nSTAT/
 
 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
 http://doi.org/10.1016/j.jneumeth.2012.08.009
+PMID: 22981419
+
+Paper-aligned toolbox map
+-------------------------
+
+To keep terminology and workflows consistent with the 2012 toolbox paper,
+the MATLAB help system includes a dedicated mapping page:
+
+- `helpfiles/PaperOverview.m` (published as `PaperOverview.html`)
+
+This page ties major toolbox components 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.

diff --git a/SignalObj.m b/SignalObj.m
@@ -50,11 +50,11 @@
 %              number of components in the data. 
 %
 %
-% <a href="matlab: methods('SignalObj')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('SignalObjExamples.html')">SignalObj Examples</a> 
-%
-% Reference page in Help browser
-% <a href="matlab:doc('SignalObj')">doc SignalObj</a>
+% <a href="matlab: methods('SignalObj')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('SignalObjExamples.html')">SignalObj Examples</a> 
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('SignalObj.html')">SignalObj Reference</a>
 
 
 %

diff --git a/Trial.m b/Trial.m
@@ -9,16 +9,16 @@
 %           covarColl:  CovColl Object. Required.
 %           nspikeColl: nstColl Obj
 %
-% <a href="matlab: methods('Trial')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('TrialExamples.html')">Trial Examples</a> 
-%
-% see also <a href="matlab:help('CovColl')">CovColl</a>, 
-% <a href="matlab:help('Covariate')">Covariate</a>, 
-% <a href="matlab:help('SignalObj')">SignalObj</a>,
-% <a href="matlab:help('nspikeTrain')">nspikeTrain</a>
-%
-% Reference page in Help browser
-% <a href="matlab: doc('Trial')">doc Trial</a>
+% <a href="matlab: methods('Trial')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('TrialExamples.html')">Trial Examples</a> 
+%
+% see also <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl</a>, 
+% <a href="matlab:nstatOpenHelpPage('CovariateExamples.html')">Covariate</a>, 
+% <a href="matlab:nstatOpenHelpPage('SignalObjExamples.html')">SignalObj</a>,
+% <a href="matlab:nstatOpenHelpPage('nSpikeTrainExamples.html')">nspikeTrain</a>
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('TrialExamples.html')">Trial Reference</a>
 
 %
 % nSTAT v1 Copyright (C) 2012 Masschusetts Institute of Technology

diff --git a/TrialConfig.m b/TrialConfig.m
@@ -4,15 +4,15 @@
 % >>tcObj=TrialConfig(covMask,sampleRate, history,ensCovHist,covLag,name)
 %
 % All parameters are optional
-% <a href="matlab: methods('TrialConfig')">methods</a>
-% <a href="matlab:nstatOpenHelpPage('TrialConfigExamples.html')">TrialConfig Examples</a> 
-%
-% see also <a href="matlab:help('Trial')">Trial</a>, 
-% <a href="matlab:help('CovColl')">CovColl</a>, 
-% <a href="matlab:help('nstColl')">nstColl</a>
-%
-% Reference page in Help browser
-% <a href="matlab: doc('TrialConfig')">doc TrialConfig</a>
+% <a href="matlab: methods('TrialConfig')">methods</a>
+% <a href="matlab:nstatOpenHelpPage('TrialConfigExamples.html')">TrialConfig Examples</a> 
+%
+% see also <a href="matlab:nstatOpenHelpPage('TrialExamples.html')">Trial</a>, 
+% <a href="matlab:nstatOpenHelpPage('CovCollExamples.html')">CovColl</a>, 
+% <a href="matlab:nstatOpenHelpPage('nstCollExamples.html')">nstColl</a>
+%
+% Reference page in Help browser
+% <a href="matlab:nstatOpenHelpPage('TrialConfigExamples.html')">TrialConfig Reference</a>
 
 %
 % nSTAT v1 Copyright (C) 2012 Masschusetts Institute of Technology