Maint/deprecations

pymatsolver/__init__.py

@@ -79,8 +79,24 @@
     "Mumps": _mumps_available,
 }
 
-BicgJacobi = BiCGJacobi  # backwards compatibility
-PardisoSolver = Pardiso  # backwards compatibility
+_DEPRECATED_ALIASES = {
+    "BicgJacobi": ("BiCGJacobi", BiCGJacobi),
+    "PardisoSolver": ("Pardiso", Pardiso),
+}
+
+
+def __getattr__(name):
+    if name in _DEPRECATED_ALIASES:
+        new_name, obj = _DEPRECATED_ALIASES[name]
+        import warnings
+        warnings.warn(
+            f"pymatsolver.{name} is deprecated and will be removed in v0.6.0, "
+            f"use pymatsolver.{new_name} instead.",
+            FutureWarning,
+            stacklevel=2,
+        )
+        return obj
+    raise AttributeError(f"module {__name__!r} has no attribute {name!r}")
 
 if not AvailableSolvers["Pardiso"]:
     SolverHelp['Pardiso'] = """Pardiso is not working

pymatsolver/iterative.py

@@ -7,9 +7,9 @@
 from .wrappers import WrapIterative
 from .solvers import Base
 
-# The tol kwarg was removed from bicgstab in scipy 1.14.0.
+# The rtol kwarg was added to bicgstab in scipy 1.12.0 (deprecating tol), and tol was removed in 1.14.0.
 # See https://docs.scipy.org/doc/scipy-1.12.0/reference/generated/scipy.sparse.linalg.bicgstab.html
-RTOL_ARG_NAME = "rtol" if Version(scipy.__version__) >= Version("1.14.0") else "tol"
+RTOL_ARG_NAME = "rtol" if Version(scipy.__version__) >= Version("1.12.0") else "tol"
 
 SolverCG = WrapIterative(cg, name="SolverCG")
 SolverBiCG = WrapIterative(bicgstab, name="SolverBiCG")
@@ -38,8 +38,6 @@ class BiCGJacobi(Base):
     """
 
     def __init__(self, A, maxiter=1000, rtol=1E-6, atol=0.0, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
-        if "symmetric" in kwargs:
-            raise TypeError("The symmetric keyword argument was been removed in pymatsolver 0.4.0.")
         super().__init__(A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
         self._factored = False
         self.maxiter = maxiter

pymatsolver/solvers.py

@@ -40,7 +40,6 @@ class Base(ABC):
         Extra keyword arguments. If there are any left here a warning will be raised.
     """
 
-    __numpy_ufunc__ = True
     __array_ufunc__ = None
 
     _is_conjugate = False
@@ -57,9 +56,6 @@ def __init__(
         self._A = A
         self._dtype = np.dtype(A.dtype)
 
-        if 'accuracy_tol' in kwargs:
-            raise TypeError("'accuracy_tol' was removed in v0.4.0, use 'check_rtol' and 'check_atol'.")
-
         self.check_accuracy = check_accuracy
         self.check_rtol = check_rtol
         self.check_atol = check_atol

tests/test_Basic.py

@@ -88,9 +88,6 @@ def test_errors_and_warnings():
     with pytest.raises(ValueError, match="A is not a square matrix."):
         IdentitySolver(np.full((3, 5), 1))
 
-    with pytest.raises(TypeError, match=r"'accuracy_tol' was removed.*"):
-        IdentitySolver(np.full((4, 4), 1), accuracy_tol=0.41)
-
     with pytest.warns(UnusedArgumentWarning, match="Unused keyword arguments.*"):
         IdentitySolver(np.full((4, 4), 1), not_an_argument=4)
 
@@ -228,3 +225,10 @@ def test_diagonal_inferance():
     assert Ainv.is_symmetric
     assert not Ainv.is_hermitian
     assert not Ainv.is_positive_definite
+
+
+@pytest.mark.parametrize("old_name, new_name", [("BicgJacobi", "BiCGJacobi"), ("PardisoSolver", "Pardiso")])
+def test_deprecated_aliases(old_name, new_name):
+    with pytest.warns(FutureWarning, match=f"pymatsolver.{old_name} is deprecated"):
+        obj = getattr(pymatsolver, old_name)
+    assert obj is getattr(pymatsolver, new_name)

tests/test_BicgJacobi.py

@@ -1,4 +1,4 @@
-from pymatsolver import BicgJacobi
+from pymatsolver import BiCGJacobi
 import numpy as np
 import numpy.testing as npt
 import scipy.sparse as sp
@@ -30,29 +30,26 @@ def test_solve(test_mat_data, dtype, transpose, symmetric):
         A = D @ A
     rhs = A @ sol
     if transpose:
-        Ainv = BicgJacobi(A.T, is_symmetric=symmetric).T
+        Ainv = BiCGJacobi(A.T, is_symmetric=symmetric).T
     else:
-        Ainv = BicgJacobi(A, is_symmetric=symmetric)
+        Ainv = BiCGJacobi(A, is_symmetric=symmetric)
     Ainv.maxiter = 2000
     solb = Ainv * rhs
     npt.assert_allclose(rhs, A @ solb, rtol=RTOL)
 
 def test_errors_and_warnings(test_mat_data):
     A, sol = test_mat_data
-    with pytest.raises(TypeError, match="The symmetric keyword.*"):
-        Ainv = BicgJacobi(A, symmetric=True)
-
     with pytest.raises(ValueError):
-        Ainv = BicgJacobi(A, rtol=0.0)
+        Ainv = BiCGJacobi(A, rtol=0.0)
 
     with pytest.raises(ValueError):
-        Ainv = BicgJacobi(A, atol=-1.0)
+        Ainv = BiCGJacobi(A, atol=-1.0)
 
 def test_shallow_copy(test_mat_data):
     A, sol = test_mat_data
-    Ainv = BicgJacobi(A, maxiter=100, rtol=1.0E-3, atol=1.0E-16)
+    Ainv = BiCGJacobi(A, maxiter=100, rtol=1.0E-3, atol=1.0E-16)
 
     attrs = Ainv.get_attributes()
 
-    new_Ainv = BicgJacobi(A, **attrs)
+    new_Ainv = BiCGJacobi(A, **attrs)
     assert attrs == new_Ainv.get_attributes()

tests/test_Pardiso.py

@@ -142,6 +142,11 @@ def test_pardiso_fdem():
 
     A = sp.csr_matrix((data, indices, indptr), shape=(13872, 13872))
     rhs = np.load(os.path.join(base_path, 'RHS.npy'))
+    # The rhs has many exact zeros, which would compare round-off against zero in the
+    # element-wise check below. Offset every entry by a small fraction of its column's largest
+    # magnitude, along the entry's own phase (angle(0) == 0), so no entry is shifted towards zero.
+    offset = 1e-3 * np.abs(rhs).max(axis=0)
+    rhs = rhs + offset * np.exp(1j * np.angle(rhs))
 
     Ainv = pymatsolver.Pardiso(A, check_accuracy=True)
     print(Ainv.is_symmetric)