Fix to_json() crashing on the test batteries' numpy scalars

code/saga.py

@@ -16,7 +16,7 @@
 # Distributions
 from scipy.stats import chi2, norm
 # Numpy stuff
-from numpy import cov, set_printoptions, diag, array, mean
+from numpy import cov, set_printoptions, diag, array, mean, ndarray, generic
 from numpy.linalg import matrix_rank, inv, eig, eigh
 import matplotlib.pyplot as plt
 
@@ -62,6 +62,25 @@
 set_printoptions(precision=4)
 
 
+def _jsonable(obj):
+    """
+    Recursively convert numpy scalars and arrays to plain Python types.
+
+    The test batteries return numpy scalars (np.bool_ for `passes`, np.float64
+    for statistics), which json.dumps refuses. Applying this to the output of
+    to_dict() keeps both to_dict() and to_json() usable for batch analysis.
+    """
+    if isinstance(obj, dict):
+        return {key: _jsonable(value) for key, value in obj.items()}
+    if isinstance(obj, (list, tuple)):
+        return [_jsonable(value) for value in obj]
+    if isinstance(obj, ndarray):
+        return _jsonable(obj.tolist())
+    if isinstance(obj, generic):        # any numpy scalar (bool_, int64, ...)
+        return obj.item()
+    return obj
+
+
 def gaussian(x, mu, sigma):
     """
     Gaussian function of center mu and "standard deviation" sigma.
@@ -235,7 +254,7 @@ def effect_sizes(self):
 
     def to_dict(self):
         es = self.effect_sizes()
-        return {
+        return _jsonable({
             "test": "univariate",
             "params": {
                 "mu": self.exp_mu, "sigma": self.exp_sigma,
@@ -260,7 +279,7 @@ def to_dict(self):
             "effect_sizes": es,
             "extended_tests": self._extended,
             "is_valid_extended": getattr(self, 'is_valid_extended', None),
-        }
+        })
 
     def to_json(self):
         return json.dumps(self.to_dict(), indent=2)
@@ -403,7 +422,7 @@ def __repr__(self):
         return rep
 
     def to_dict(self):
-        return {
+        return _jsonable({
             "test": "multivariate",
             "params": {"sigma": self.exp_si, "dim": self.dim, "n": self.nsamples},
             "doornik_hansen": {"stat": float(self.DH), "pvalue": float(self.PO)},
@@ -415,7 +434,7 @@ def to_dict(self):
                 "total": self.dim,
                 "applicable": self.is_integer},
             "extended_tests": self._mv_extended,
-        }
+        })
 
     def to_json(self):
         return json.dumps(self.to_dict(), indent=2)

code/tests/test_multivariate.py

@@ -1,4 +1,5 @@
 """Test SAGA multivariate analysis against generated test vectors."""
+import json
 import sys
 import os
 
@@ -50,6 +51,16 @@ def test_extended_battery_passes(self, good_multivariate_vector):
                         if isinstance(r, dict) and not r.get("passes", True))
         )
 
+    def test_to_json_after_battery(self, good_multivariate_vector):
+        """to_dict()/to_json() must survive the battery's numpy scalars."""
+        v = good_multivariate_vector
+        mv = MultivariateSamples(v["params"]["sigma"], v["samples"])
+        mv.run_multivariate_battery()
+        parsed = json.loads(mv.to_json())
+        assert parsed["test"] == "multivariate"
+        assert parsed["extended_tests"]["all_pass"] is True
+        json.dumps(mv.to_dict())  # a user dumping to_dict() directly also works
+
     def test_per_coordinate_channel(self, good_multivariate_vector):
         """Integer (discrete-Gaussian) good vectors must light up the
         per-coordinate discrete channel; continuous vectors skip it."""

code/tests/test_univariate.py

@@ -1,4 +1,5 @@
 """Test SAGA univariate analysis against generated test vectors."""
+import json
 import sys
 import os
 
@@ -66,6 +67,17 @@ def test_extended_battery_default_samples(self, good_univariate_vector):
         assert ext["all_pass"]
         assert uv.is_valid_extended
 
+    def test_to_json_after_battery(self, good_univariate_vector):
+        """to_dict()/to_json() must survive the battery's numpy scalars."""
+        v = good_univariate_vector
+        uv = UnivariateSamples(v["params"]["mu"], v["params"]["sigma"], v["samples"])
+        uv.run_extended_battery(samples=v["samples"], mc_B=100)
+        # to_dict() must be plain Python, to_json() must not raise
+        parsed = json.loads(uv.to_json())
+        assert parsed["test"] == "univariate"
+        assert parsed["extended_tests"]["all_pass"] is True
+        json.dumps(uv.to_dict())  # a user dumping to_dict() directly also works
+
 
 class TestBadVectors:
     """Flawed distributions must be detected by chi-square or extended battery."""