From 7a8e675848939dd3214f49e40a767bc18ad27881 Mon Sep 17 00:00:00 2001
From: Thomas Prest <thomas.prest@pqshield.com>
Date: Thu, 9 Jul 2026 23:44:02 +0200
Subject: [PATCH] Fix extended battery rejecting correct samplers on its
 default path

UnivariateSamples.run_extended_battery() called without an explicit `samples=`
argument rebuilt the sample list from the histogram:

    samples = [z for z in self.histogram for _ in range(self.histogram[z])]

which is *sorted*. The three sequence tests -- Ljung-Box, runs, block
homogeneity -- measure ordering, so they saw a perfectly monotone stream and
rejected at p ~ 0. Any correct sampler therefore failed the default battery
(all_pass=False, is_valid_extended=False).

The class already receives the ordered samples in __init__ and threw them away.
Keep them (by reference, no memory cost) and use them as the default.

Verified on 20k samplerz draws: default path went from ljung_box/runs/
block_homogeneity all at p=0.0000 to p=0.26/0.72/0.90, all_pass=True.

The suite never caught this because every test passed `samples=` explicitly, so
the default path was unexercised -- the same blind spot as the earlier nan bug.
Added test_extended_battery_default_samples, which exercises the default path
and fails on all six good vectors without this fix.

Co-Authored-By: Claude Opus 4.8 <noreply@anthropic.com>
---
 code/saga.py                  | 17 ++++++++++++++---
 code/tests/test_univariate.py | 17 +++++++++++++++++
 2 files changed, 31 insertions(+), 3 deletions(-)

diff --git a/code/saga.py b/code/saga.py
index 88d4467..718bba3 100644
--- a/code/saga.py
+++ b/code/saga.py
@@ -122,6 +122,11 @@ def __init__(self, mu, sigma, list_samples, tau=14, chi2_bucket=10, pmin=0.001):
                 "over Z), but received non-integer values. For continuous "
                 "multivariate data, MultivariateSamples skips the "
                 "per-coordinate discrete channel automatically.")
+        # Keep the samples in their original order (by reference -- do not
+        # mutate them afterwards). The sequence tests of the extended battery
+        # (Ljung-Box, runs, block homogeneity) measure ordering, so they cannot
+        # be run on a histogram-reconstructed sample list, which is sorted.
+        self.samples = list_samples
         self.histogram = dict()
         self.outlier = 0
         # Initialize histogram
@@ -152,11 +157,17 @@ def __init__(self, mu, sigma, list_samples, tau=14, chi2_bucket=10, pmin=0.001):
 
 
     def run_extended_battery(self, samples=None, mc_B=1000):
-        """Run the extended test battery (Phase 3 tests)."""
+        """
+        Run the extended test battery (Phase 3+4 tests).
+
+        `samples` defaults to the ordered samples this object was built from.
+        It must never be reconstructed from the histogram: that yields a sorted
+        sequence, and the sequence tests (Ljung-Box, runs, block homogeneity)
+        would then reject any correct sampler with p ~ 0.
+        """
         from univariate_tests import run_extended_battery
         if samples is None:
-            samples = [z for z in self.histogram
-                       for _ in range(self.histogram[z])]
+            samples = self.samples
         self._extended = run_extended_battery(
             self.exp_mu, self.exp_sigma, samples,
             tau=self.tau, alpha=self.pmin, mc_B=mc_B,
diff --git a/code/tests/test_univariate.py b/code/tests/test_univariate.py
index 6c77a4d..3c2a110 100644
--- a/code/tests/test_univariate.py
+++ b/code/tests/test_univariate.py
@@ -49,6 +49,23 @@ def test_extended_battery_passes(self, good_univariate_vector):
                         if isinstance(r, dict) and not r.get("passes", True))
         )
 
+    def test_extended_battery_default_samples(self, good_univariate_vector):
+        """The default (no `samples=`) path must use the ordered samples.
+
+        It once rebuilt them from the histogram, i.e. sorted, which made the
+        sequence tests reject every correct sampler at p ~ 0.
+        """
+        v = good_univariate_vector
+        uv = UnivariateSamples(v["params"]["mu"], v["params"]["sigma"], v["samples"])
+        ext = uv.run_extended_battery(mc_B=200)          # no samples= argument
+        for name in ("ljung_box", "runs_test", "block_homogeneity"):
+            assert ext[name]["passes"], (
+                f"Good vector {v['label']}: {name} rejects on the default "
+                f"path (p={ext[name]['pvalue']:.6f}) -- samples were "
+                f"probably reordered")
+        assert ext["all_pass"]
+        assert uv.is_valid_extended
+
 
 class TestBadVectors:
     """Flawed distributions must be detected by chi-square or extended battery."""