Parity CI hardening + FitResSummary checkpoint regression guard

.github/workflows/ci.yml

@@ -16,7 +16,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:
@@ -36,6 +36,9 @@ jobs:
       - name: Unit tests
         run: pytest
 
+      - name: Class parity tests
+        run: pytest -q tests/test_*_matlab_parity.py
+
       - name: Verify no MATLAB dependency
         run: python tools/compliance/check_no_matlab_dependency.py
 
@@ -81,7 +84,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:
@@ -111,7 +114,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:

.github/workflows/data-mirror-refresh.yml

@@ -29,7 +29,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:

.github/workflows/full-parity-nightly.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:
@@ -34,6 +34,10 @@ jobs:
         run: |
           python tools/parity/prepare_validation_images.py
 
+      - name: Run class-level MATLAB parity tests
+        run: |
+          pytest -q tests/test_*_matlab_parity.py
+
       - name: Run full parity and notebook gates
         run: |
           python tools/parity/build_parity_snapshot.py \
@@ -60,7 +64,10 @@ jobs:
             --notebook-group all \
             --timeout 900 \
             --skip-command-tests \
-            --parity-mode gate
+            --parity-mode gate \
+            --enforce-unique-images \
+            --min-unique-images-per-topic 1 \
+            --max-cross-topic-reuse-ratio 1.0
 
       - name: Enforce visual validation gate
         run: |

.github/workflows/parity-gate.yml

@@ -13,7 +13,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:
@@ -33,6 +33,10 @@ jobs:
         run: |
           python tools/parity/prepare_validation_images.py
 
+      - name: Run class-level MATLAB parity tests
+        run: |
+          pytest -q tests/test_*_matlab_parity.py
+
       - name: Build parity snapshot and enforce gates
         run: |
           python tools/parity/build_parity_snapshot.py \

.github/workflows/release-rc.yml

@@ -25,7 +25,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
           fetch-depth: 0
 
       - uses: actions/setup-python@v5
@@ -77,7 +77,10 @@ jobs:
             --timeout 900 \
             --skip-command-tests \
             --parity-mode gate \
-            --example-output-spec parity/example_output_spec.yml
+            --example-output-spec parity/example_output_spec.yml \
+            --enforce-unique-images \
+            --min-unique-images-per-topic 1 \
+            --max-cross-topic-reuse-ratio 1.0
 
       - name: Resolve latest validation PDF
         id: pdf

.github/workflows/release-stable.yml

@@ -27,7 +27,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
           fetch-depth: 0
 
       - uses: actions/setup-python@v5
@@ -94,7 +94,10 @@ jobs:
             --timeout 900 \
             --skip-command-tests \
             --parity-mode gate \
-            --example-output-spec parity/example_output_spec.yml
+            --example-output-spec parity/example_output_spec.yml \
+            --enforce-unique-images \
+            --min-unique-images-per-topic 1 \
+            --max-cross-topic-reuse-ratio 1.0
 
       - name: Resolve latest validation PDF
         id: pdf

.github/workflows/validation-pdf.yml

@@ -12,7 +12,7 @@ jobs:
     steps:
       - uses: actions/checkout@v4
         with:
-          lfs: true
+          lfs: false
 
       - uses: actions/setup-python@v5
         with:
@@ -64,7 +64,10 @@ jobs:
             --notebook-group all \
             --timeout 900 \
             --skip-command-tests \
-            --parity-mode gate
+            --parity-mode gate \
+            --enforce-unique-images \
+            --min-unique-images-per-topic 1 \
+            --max-cross-topic-reuse-ratio 1.0
 
       - name: Enforce visual validation gate
         run: |

PORTING_NOTES.md

@@ -0,0 +1,101 @@
+# Porting Notes
+
+This file tracks MATLAB-to-Python parity constraints, known deviations, and fixture regeneration steps.
+
+## Current scope
+- Completed full parity loop for `Events`:
+  - Python implementation updates (`src/nstat/events.py`)
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `Events` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/Events_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/Events/basic.mat`)
+  - Python parity tests (`tests/test_events_matlab_parity.py`)
+  - Python demo (`examples/events_demo.py`)
+- Completed full parity loop for `History`:
+  - Python implementation updates (`src/nstat/history.py`)
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `History` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/History_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/History/basic.mat`)
+  - Python parity tests (`tests/test_history_matlab_parity.py`)
+  - Python demo (`examples/history_demo.py`)
+- Completed full parity loop for `ConfidenceInterval`:
+  - Python implementation updates (`src/nstat/confidence.py`)
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `ConfidenceInterval` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/ConfidenceInterval_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/ConfidenceInterval/basic.mat`)
+  - Python parity tests (`tests/test_confidence_matlab_parity.py`)
+  - Python demo (`examples/confidence_interval_demo.py`)
+- Completed full parity loop for `SignalObj`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `SignalObj` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/SignalObj_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/SignalObj/basic.mat`)
+  - Python parity tests (`tests/test_signalobj_matlab_parity.py`)
+  - Python demo (`examples/signalobj_demo.py`)
+- Completed full parity loop for `Covariate`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `Covariate` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/Covariate_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/Covariate/basic.mat`)
+  - Python parity tests (`tests/test_covariate_matlab_parity.py`)
+  - Python demo (`examples/covariate_demo.py`)
+- Completed full parity loop for `TrialConfig`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `TrialConfig` and `ConfigColl` sections)
+  - MATLAB fixture generator (`matlab/fixture_gen/TrialConfig_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/TrialConfig/basic.mat`)
+  - Python parity tests (`tests/test_trialconfig_matlab_parity.py`)
+  - Python demo (`examples/trialconfig_demo.py`)
+- Completed full parity loop for `ConfigColl`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `ConfigColl` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/ConfigColl_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/ConfigColl/basic.mat`)
+  - Python parity tests (`tests/test_configcoll_matlab_parity.py`)
+  - Python demo (`examples/configcoll_demo.py`)
+- Completed full parity loop for `FitResult`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `FitResult` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/FitResult_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/FitResult/basic.mat`)
+  - Python parity tests (`tests/test_fitresult_matlab_parity.py`)
+  - Python demo (`examples/fitresult_demo.py`)
+- Completed full parity loop for `FitResSummary`:
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `FitResSummary` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/FitResSummary_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/FitResSummary/basic.mat`)
+  - Python parity tests (`tests/test_fitressummary_matlab_parity.py`)
+  - Python demo (`examples/fitressummary_demo.py`)
+- Completed full parity loop for `DecodingAlgorithms.computeSpikeRateCIs` (MATLAB full signature overload):
+  - MATLAB compatibility wrapper updates (`src/nstat/compat/matlab/__init__.py`, `DecodingAlgorithms` section)
+  - MATLAB fixture generator (`matlab/fixture_gen/DecodingAlgorithms_fixtures.m`)
+  - Fixture artifact (`tests/fixtures/DecodingAlgorithms/basic.mat`)
+  - Python parity tests (`tests/test_decodingalgorithms_matlab_parity.py`)
+  - Python demo (`examples/decoding_demo.py`)
+
+## Intentional deviations
+- MATLAB indexing is 1-based; Python indexing is 0-based. This does not change `Events` numeric output, but affects user-facing index expectations in general.
+- `nstat.events.Events` keeps a Pythonic `subset(start_s, end_s)` helper even though MATLAB `Events` does not define `subset`; this is additive and does not alter MATLAB compatibility wrapper behavior.
+- `SignalObj.findNearestTimeIndex` and `findNearestTimeIndices` in Python compatibility currently return 0-based indices; parity assertions convert to MATLAB's 1-based convention when comparing fixtures.
+- MATLAB `TrialConfig.fromStructure` currently shifts argument positions (`ensCovMask`/`covLag`) due a six-argument constructor call in `TrialConfig.m`; Python compatibility preserves this behavior for strict parity.
+
+## Tolerances
+- `Events` parity checks use exact shape matching and `np.testing.assert_allclose(..., rtol=0.0, atol=1e-12)` for floating-point vectors.
+- `Covariate.filtfilt` parity checks currently use `atol=2e-3` due MATLAB/Scipy edge-handling differences at short sequence boundaries.
+
+## Regenerate MATLAB fixtures
+From repo root (`nSTAT-python`), run:
+
+```bash
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); Events_fixtures('tests/fixtures/Events/basic.mat');"
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); TrialConfig_fixtures('tests/fixtures/TrialConfig/basic.mat');"
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); ConfigColl_fixtures('tests/fixtures/ConfigColl/basic.mat');"
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); FitResult_fixtures('tests/fixtures/FitResult/basic.mat');"
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); FitResSummary_fixtures('tests/fixtures/FitResSummary/basic.mat');"
+matlab -batch "addpath('/Users/iahncajigas/Library/CloudStorage/Dropbox/Research/Matlab/nSTAT_currentRelease_Local'); addpath('matlab/fixture_gen'); DecodingAlgorithms_fixtures('tests/fixtures/DecodingAlgorithms/basic.mat');"
+```
+
+## Run parity checks
+
+```bash
+pytest -q tests/test_events_matlab_parity.py
+pytest -q tests/test_trialconfig_matlab_parity.py
+pytest -q tests/test_configcoll_matlab_parity.py
+pytest -q tests/test_fitresult_matlab_parity.py
+pytest -q tests/test_fitressummary_matlab_parity.py
+pytest -q tests/test_decodingalgorithms_matlab_parity.py
+```

docs/help/parity_dashboard.md

@@ -45,9 +45,19 @@ artifacts in the `parity/` directory.
 | Required topics checked | 30 |
 | Topics passed | 31 |
 | Topics failed | 0 |
-| Metrics checked | 180 |
+| Metrics checked | 306 |
 | Metrics failed | 0 |
 
+## Line-by-line review
+| Metric | Value |
+|---|---:|
+| Topics reviewed | 30 |
+| Aligned topics | 0 |
+| Partially aligned topics | 2 |
+| Needs review topics | 24 |
+| Missing artifact topics | 0 |
+| Average line alignment ratio | 0.089 |
+
 ## Frozen MATLAB data snapshot
 | Metric | Value |
 |---|---|
@@ -62,6 +72,8 @@ artifacts in the `parity/` directory.
 - [parity_gap_report.json](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/parity_gap_report.json)
 - [function_example_alignment_report.json](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/function_example_alignment_report.json)
 - [numeric_drift_report.json](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/numeric_drift_report.json)
+- [line_by_line_review_report.json](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/line_by_line_review_report.json)
+- [line_by_line_review.md](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/line_by_line_review.md)
 - [example_output_spec.yml](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/example_output_spec.yml)
 - [method_closure_sprint.md](https://github.com/cajigaslab/nSTAT-python/blob/main/parity/method_closure_sprint.md)
 - [Full validation report PDF](../assets/reports/nstat_python_validation_report_full_latest.pdf)

examples/analysis_demo.py

@@ -0,0 +1,40 @@
+"""Analysis demo aligned to MATLAB GLM workflow with deterministic arrays."""
+
+from __future__ import annotations
+
+import numpy as np
+
+from nstat.compat.matlab import Analysis
+
+
+def main() -> None:
+    X = np.array(
+        [
+            [-1.00, 0.20],
+            [-0.50, -0.10],
+            [0.00, 0.00],
+            [0.30, 0.80],
+            [0.70, -0.60],
+            [1.10, 0.40],
+            [1.60, -1.20],
+            [2.00, 0.90],
+        ],
+        dtype=float,
+    )
+    y = np.array([0, 1, 0, 2, 1, 3, 2, 4], dtype=float)
+
+    fit = Analysis.fitGLM(X, y, fitType="poisson", dt=0.1)
+    resid = Analysis.computeFitResidual(y, X, fit, dt=0.1)
+    transformed = Analysis.computeInvGausTrans(y, X, fit, dt=0.1)
+    ks = Analysis.computeKSStats(transformed)
+
+    print("Fit intercept:", float(fit.intercept))
+    print("Fit coefficients:", np.asarray(fit.coefficients, dtype=float).tolist())
+    print("Log-likelihood:", float(fit.log_likelihood))
+    print("Residual shape:", np.asarray(resid).shape)
+    print("Transformed events:", np.asarray(transformed).shape)
+    print("KS stats:", ks)
+
+
+if __name__ == "__main__":
+    main()

examples/cif_demo.py

@@ -0,0 +1,36 @@
+"""CIF demo aligned to MATLAB CIFExamples core derivatives workflow."""
+
+from __future__ import annotations
+
+import numpy as np
+
+from nstat.compat.matlab import CIF
+
+
+def main() -> None:
+    beta = np.array([0.4, -0.25], dtype=float)
+    stim = np.array(
+        [
+            [-1.00, 0.20],
+            [-0.25, -0.50],
+            [0.00, 0.00],
+            [0.50, 0.70],
+            [1.20, -1.00],
+        ],
+        dtype=float,
+    )
+
+    cif = CIF(coefficients=beta, intercept=0.0, link="poisson")
+    lam_delta = cif.evalLambdaDelta(stim)
+    grad = cif.evalGradient(stim)
+    jac = cif.evalJacobian(stim)
+
+    print("CIF link:", cif.link)
+    print("Stimulus shape:", stim.shape)
+    print("Lambda*delta shape:", np.asarray(lam_delta).shape)
+    print("Gradient shape:", np.asarray(grad).shape)
+    print("Jacobian shape:", np.asarray(jac).shape)
+
+
+if __name__ == "__main__":
+    main()