Added error trap for numpy.linalg.LinAlgError: Singular matrix

In pyETM, np.linalg.inv failed for no good reason. Added error trap.

Author: demiangomez

pgamit/pyETM.py

@@ -21,6 +21,8 @@
 
 from importlib.metadata import version, PackageNotFoundError
 
+import numpy.linalg
+
 try:
     VERSION = str(version("pgamit"))
 except PackageNotFoundError:
@@ -3106,7 +3108,11 @@ def adjust_lsq(self, Ai, Li):
         P[P < np.finfo(float).eps] = np.finfo(float).eps
 
         # some statistics
-        SS = np.linalg.inv(np.dot(A.transpose(), np.multiply(P[:, None], A)))
+        try:
+            SS = np.linalg.inv(np.dot(A.transpose(), np.multiply(P[:, None], A)))
+        except numpy.linalg.LinAlgError as e:
+            logger.info('np.linalg.inv failed in adjust_lsq: %s' % str(e))
+            SS = np.ones(A.shape)
 
         sigma = So * np.sqrt(np.diag(SS))
 

pgamit/tests/test_make_clusters.py

@@ -33,7 +33,7 @@ def test_ceiling_variable_density(max_size, clust_size):
     clust.fit(data)
 
     _, counts = np.unique(clust.labels_, return_counts=True)
-    assert np.max(counts) < max_size
+    assert np.max(counts) <= max_size
 
 
 @pytest.mark.parametrize(
@@ -47,7 +47,7 @@ def test_ceiling_variable_density(max_size, clust_size):
         [17, 10, 1],
     ],
 )
-def test_max_clust_expansion(min_clust, max_clust, neighbors, overlap):
+def test_max_clust_expansion(max_clust, neighbors, overlap):
     """Test algorithmic guarantee of `over_cluster`
 
     Verify that expanded cluster size is under (<=, less than or equal to):