betaMixPy 0.2.1__tar.gz → 0.2.2__tar.gz

{betamixpy-0.2.1 → betamixpy-0.2.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: betaMixPy
-Version: 0.2.1
+Version: 0.2.2
 Summary: A Python package to find strong correlations among P variables, each with N observations.
 Home-page: https://pypi.org/project/betaMixPy/
 Author: Haim Bar
@@ -152,6 +152,8 @@ Two strategies:
 
 See [NEWS.md](NEWS.md) for the full changelog.  Highlights:
 
+- **0.2.2**: `getAdjMat(nodes=...)` uses the same inclusive threshold;
+  constant columns never get edges
 - **0.2.1**: `getAdjMat` edge count now matches `betaMix()`; fixed a
   `plotFittedBetaMix` crash; unused dependencies removed; full test suite
 

{betamixpy-0.2.1 → betamixpy-0.2.2}/README.md

@@ -126,6 +126,8 @@ Two strategies:
 
 See [NEWS.md](NEWS.md) for the full changelog.  Highlights:
 
+- **0.2.2**: `getAdjMat(nodes=...)` uses the same inclusive threshold;
+  constant columns never get edges
 - **0.2.1**: `getAdjMat` edge count now matches `betaMix()`; fixed a
   `plotFittedBetaMix` crash; unused dependencies removed; full test suite
 

betamixpy-0.2.2/betaMixPy/__init__.py

@@ -0,0 +1,3 @@
+__version__ = "0.2.2"  # single source of truth; setup.py reads this line
+
+from .betaMixPy import *

{betamixpy-0.2.1 → betamixpy-0.2.2}/betaMixPy/betaMixPy.py

@@ -118,13 +118,16 @@ def betaMix(M, tol=1e-4, calcAcc=1e-9, ppr=0.05, maxalpha=1e-4,
     if msg:
         print("Generating the z_ij statistics...")
 
-    # Correlation matrix P×P (rowvar=False: each column is a variable)
-    if method == "spearman":
-        from scipy.stats import rankdata
-        ranked = np.apply_along_axis(rankdata, 0, M)
-        corM = np.corrcoef(ranked, rowvar=False)
-    else:
-        corM = np.corrcoef(M, rowvar=False)
+    # Correlation matrix P×P (rowvar=False: each column is a variable).
+    # Constant columns divide by zero here; the resulting NaNs are reported
+    # by the warnings above/below, so numpy's own RuntimeWarning is suppressed.
+    with np.errstate(divide="ignore", invalid="ignore"):
+        if method == "spearman":
+            from scipy.stats import rankdata
+            ranked = np.apply_along_axis(rankdata, 0, M)
+            corM = np.corrcoef(ranked, rowvar=False)
+        else:
+            corM = np.corrcoef(M, rowvar=False)
 
     if np.any(np.isnan(corM)):
         n_nans = int(np.sum(np.isnan(corM)))
@@ -277,7 +280,11 @@ def getAdjMat(res, ppthr=None, signed=False, nodes=None):
     signed -- if True, -1 for negative correlations (default False).
     nodes  -- list of node indices (0-based) for a sparse submatrix (default None).
 
-    Returns a P×P numpy array (or submatrix when nodes is given).
+    Returns a P×P numpy array (or submatrix when nodes is given).  A pair is
+    an edge when 1 - r^2 <= ppthr, so with the default threshold the edge
+    count equals res['edges'].  Pairs with r == 0 exactly (which only arise
+    from zero-variance columns) are never edges, so constant columns stay
+    isolated even when ppthr = 1.
     """
     if ppthr is None:
         ppthr = res["ppthr"]
@@ -290,14 +297,16 @@ def getAdjMat(res, ppthr=None, signed=False, nodes=None):
             raise ValueError(f"getAdjMat: 'nodes' must be in [0, {P-1}]")
         # Find all neighbors of the requested nodes
         rows = corM[nodes, :]        # shape (len(nodes), P)
-        is_edge = (1.0 - rows ** 2) < ppthr  # bool, shape (len(nodes), P)
+        is_edge = ((1.0 - rows ** 2) <= ppthr) & (rows != 0)  # bool, shape (len(nodes), P)
         nbr_mask = np.any(is_edge, axis=0)
         selected = np.sort(np.union1d(nodes, np.where(nbr_mask)[0]))
         corM = corM[np.ix_(selected, selected)]
 
     # Use <= so the boundary pair (z_j == ppthr) is included, matching the
-    # edge count reported by betaMix() which also uses <=.
-    A = (1.0 - corM ** 2) <= ppthr
+    # edge count reported by betaMix() which also uses <=.  r == 0 exactly
+    # only arises from zero-variance columns (correlation set to 0); exclude
+    # it so such nodes stay isolated even when ppthr = 1.
+    A = ((1.0 - corM ** 2) <= ppthr) & (corM != 0)
     if signed:
         A = A.astype(float)
         neg = (corM < 0) & (A > 0)

{betamixpy-0.2.1 → betamixpy-0.2.2}/betaMixPy.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: betaMixPy
-Version: 0.2.1
+Version: 0.2.2
 Summary: A Python package to find strong correlations among P variables, each with N observations.
 Home-page: https://pypi.org/project/betaMixPy/
 Author: Haim Bar
@@ -152,6 +152,8 @@ Two strategies:
 
 See [NEWS.md](NEWS.md) for the full changelog.  Highlights:
 
+- **0.2.2**: `getAdjMat(nodes=...)` uses the same inclusive threshold;
+  constant columns never get edges
 - **0.2.1**: `getAdjMat` edge count now matches `betaMix()`; fixed a
   `plotFittedBetaMix` crash; unused dependencies removed; full test suite
 

{betamixpy-0.2.1 → betamixpy-0.2.2}/tests/test_betaMixPy.py

@@ -178,6 +178,26 @@ class TestGetAdjMat:
         with pytest.raises(ValueError, match="nodes"):
             bx.getAdjMat(dry_res, nodes=[9999])
 
+    def test_node_submatrix_includes_boundary_neighbour(self, dry_res):
+        # Threshold exactly at node 0's strongest pair: that neighbour must be
+        # selected (<=, not <), giving a 2×2 submatrix with one edge.
+        z_row = 1.0 - dry_res["angleMat"][0, 1:] ** 2
+        A = bx.getAdjMat(dry_res, ppthr=z_row.min(), nodes=[0])
+        assert A.shape == (2, 2)
+        assert A[0, 1] == 1.0
+
+    def test_constant_column_isolated_at_ppthr_one(self, tiny_M):
+        M = tiny_M.copy()
+        M[:, 2] = 0.0
+        with pytest.warns(UserWarning):
+            res = bx.betaMix(M, msg=False)
+        A = bx.getAdjMat(res, ppthr=1.0)
+        assert np.all(A[2, :] == 0) and np.all(A[:, 2] == 0)
+        # non-constant pairs are all edges at ppthr = 1
+        others = [0, 1, 3]
+        sub = A[np.ix_(others, others)]
+        assert np.all(sub[~np.eye(3, dtype=bool)] == 1.0)
+
 
 # ---------------------------------------------------------------------------
 # clusteringCoef

betamixpy-0.2.1/betaMixPy/__init__.py

@@ -1,3 +0,0 @@
-__version__ = "0.2.1"  # single source of truth; setup.py reads this line
-
-from .betaMixPy import *