Merge pull request #53 from simpeg/0.4.0_updates

0.4.0 updates

Author: jcapriot

.github/workflows/python-package-conda.yml

@@ -1,14 +1,6 @@
 name: Testing
 
-on:
-  push:
-    branches:
-      - 'main'
-    tags:
-      - 'v*'
-  pull_request:
-    branches:
-      - '*'
+on: [push, pull_request]
 
 jobs:
   build-and-test:
@@ -20,10 +12,13 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        # NOTE: macOS-13 is the last Intel runner.
-        os: [ubuntu-latest, windows-latest, macOS-13, macOS-latest]
+        os: [ubuntu-latest, windows-latest, macOS-15-intel, macOS-latest]
         solver: [mumps, pardiso]
-        python-version : ['3.10', '3.11', '3.12']
+        python-version : ['3.11', '3.12', '3.13', '3.14']
+        include:
+          - os: ubuntu-latest
+            python-version: '3.13'
+            full-test: true
         exclude:
           - os: macOS-latest
             solver: pardiso
@@ -63,22 +58,22 @@ jobs:
         make coverage
 
     - name: Generate Source Distribution
-      if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == '3.11') }}
+      if: ${{ matrix.full-test }}
       run: |
         pip install build twine
         python -m build --sdist .
         twine check dist/*
 
     - name: Test Documentation
-      if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == '3.11') }}
+      if: ${{ matrix.full-test }}
       run: |
         pip install .[docs]
         cd docs
         make html
         cd ..
 
     - name: Upload coverage
-      if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version  == '3.11') }}
+      if: ${{ matrix.full-test }}
       uses: codecov/codecov-action@v4
       with:
         verbose: true # optional (default = false)
@@ -94,7 +89,7 @@ jobs:
       run:
         shell: bash -l {0}
     env:
-      PYTHON_VERSION: '3.11'
+      PYTHON_VERSION: '3.13'
 
     steps:
     - uses: actions/checkout@v4

pymatsolver/direct/mumps.py

@@ -28,22 +28,18 @@ class Mumps(Base):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments. If there are any left here a warning will be raised.
     """
     _transposed = False
 
-    def __init__(self, A, ordering=None, is_symmetric=None, is_positive_definite=False, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, ordering=None, is_symmetric=None, is_positive_definite=False, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         if not _available:
             raise ImportError(
                 "The Mumps solver requires the python-mumps package to be installed."
             )
         is_hermitian = kwargs.pop('is_hermitian', False)
-        super().__init__(A, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, is_hermitian=is_hermitian, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+        super().__init__(A, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, is_hermitian=is_hermitian, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
         if ordering is None:
             ordering = "metis"
         self.ordering = ordering

pymatsolver/direct/pardiso.py

@@ -32,20 +32,16 @@ class Pardiso(Base):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments. If there are any left here a warning will be raised.
     """
 
     _transposed = False
 
-    def __init__(self, A, n_threads=None, is_symmetric=None, is_positive_definite=False, is_hermitian=None, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, n_threads=None, is_symmetric=None, is_positive_definite=False, is_hermitian=None, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         if not _available:
             raise ImportError("Pardiso solver requires the pydiso package to be installed.")
-        super().__init__(A, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, is_hermitian=is_hermitian, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+        super().__init__(A, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, is_hermitian=is_hermitian, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
         self.solver = MKLPardisoSolver(
             self.A,
             matrix_type=self._matrixType(),

pymatsolver/iterative.py

@@ -21,9 +21,6 @@ class BiCGJacobi(Base):
     ----------
     A : matrix
         The matrix to solve, must have a ``diagonal()`` method.
-    symmetric: boolean, optional
-        .. deprecated:: 0.3.0
-            `symmetric` is deprecated. It is unused, and will be removed in pymatsolver 0.4.0.
     maxiter : int, optional
         The maximum number of BiCG iterations to perform.
     rtol : float, optional
@@ -36,21 +33,14 @@ class BiCGJacobi(Base):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments passed to the base class.
     """
 
-    def __init__(self, A, symmetric=None, maxiter=1000, rtol=1E-6, atol=0.0, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
-        if symmetric is not None:
-            warnings.warn(
-                "The symmetric keyword argument is unused and is deprecated. It will be removed in pymatsolver 0.4.0.",
-                FutureWarning, stacklevel=2
-            )
-        super().__init__(A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+    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
         self.rtol = rtol

pymatsolver/solvers.py

@@ -36,10 +36,6 @@ class Base(ABC):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments. If there are any left here a warning will be raised.
     """
@@ -50,7 +46,7 @@ class Base(ABC):
     _is_conjugate = False
 
     def __init__(
-            self, A, is_symmetric=None, is_positive_definite=False, is_hermitian=None, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs
+            self, A, is_symmetric=None, is_positive_definite=False, is_hermitian=None, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs
     ):
         # don't make any assumptions on what A is, let the individual solvers handle that
         shape = A.shape
@@ -61,13 +57,8 @@ def __init__(
         self._A = A
         self._dtype = np.dtype(A.dtype)
 
-        if accuracy_tol is not None:
-            warnings.warn(
-                "accuracy_tol is deprecated and will be removed in v0.4.0, use check_rtol and check_atol.",
-                FutureWarning,
-                stacklevel=3
-            )
-            check_rtol = accuracy_tol
+        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
@@ -341,14 +332,6 @@ def solve(self, rhs):
                 rhs = rhs.conjugate()
             x = self._solve_single(rhs)
         else:
-            if ndim == 2 and rhs.shape[-1] == 1:
-                warnings.warn(
-                    "In Future pymatsolver v0.4.0, passing a vector of shape (n, 1) to the solve method "
-                    "will return an array with shape (n, 1), instead of always returning a flattened array. "
-                    "This is to be consistent with numpy.linalg.solve broadcasting.",
-                    FutureWarning,
-                    stacklevel=2
-                )
             if rhs.shape[-2] != n:
                 raise ValueError(f'Second to last dimension should be {n}, got {rhs.shape}')
             do_broadcast = rhs.ndim > 2
@@ -377,10 +360,6 @@ def solve(self, rhs):
         if self.check_accuracy:
             self._compute_accuracy(rhs, x)
 
-        #TODO remove this in v0.4.0.
-        if x.size == n:
-            x = x.reshape(-1)
-
         if self._is_conjugate:
             x = x.conjugate()
         return x
@@ -449,15 +428,11 @@ class Diagonal(Base):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments passed to the base class.
     """
 
-    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         try:
             self._diagonal = np.asarray(A.diagonal())
             if not np.all(self._diagonal):
@@ -469,7 +444,7 @@ def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, accur
         is_hermitian = kwargs.pop("is_hermitian", None)
         is_positive_definite = kwargs.pop("is_positive_definite", None)
         super().__init__(
-            A, is_symmetric=True, is_hermitian=False, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs
+            A, is_symmetric=True, is_hermitian=False, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs
         )
         if is_positive_definite is None:
             if self.is_real:
@@ -510,23 +485,19 @@ class Triangle(Base):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments passed to the base class.
     """
 
-    def __init__(self, A, lower=True, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, lower=True, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         # pop off unneeded keyword arguments.
         is_hermitian = kwargs.pop("is_hermitian", False)
         is_symmetric = kwargs.pop("is_symmetric", False)
         is_positive_definite = kwargs.pop("is_positive_definite", False)
         if not (sp.issparse(A) and A.format in ['csr', 'csc']):
             A = sp.csc_matrix(A)
         A.sum_duplicates()
-        super().__init__(A, is_hermitian=is_hermitian, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+        super().__init__(A, is_hermitian=is_hermitian, is_symmetric=is_symmetric, is_positive_definite=is_positive_definite, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
 
         self.lower = lower
 
@@ -565,17 +536,13 @@ class Forward(Triangle):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments passed to the base class.
     """
 
-    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         kwargs.pop("lower", None)
-        super().__init__(A, lower=True, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+        super().__init__(A, lower=True, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
 
 
 class Backward(Triangle):
@@ -591,19 +558,15 @@ class Backward(Triangle):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments passed to the base class.
     """
 
     _transpose_class = Forward
 
-    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, check_accuracy=False, check_rtol=1e-6, check_atol=0, **kwargs):
         kwargs.pop("lower", None)
-        super().__init__(A, lower=False, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol, **kwargs)
+        super().__init__(A, lower=False, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, **kwargs)
 
 
 Forward._transpose_class = Backward

pymatsolver/wrappers.py

@@ -72,9 +72,9 @@ def wrap_direct(fun, factorize=True, name=None):
     >>> SolverLU = pymatsolver.WrapDirect(splu, factorize=True)
     """
 
-    def __init__(self, A, check_accuracy=False, check_rtol=1E-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, check_accuracy=False, check_rtol=1E-6, check_atol=0, **kwargs):
         Base.__init__(
-            self, A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol,
+            self, A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol,
         )
         self.kwargs = kwargs
         if factorize:
@@ -137,34 +137,20 @@ def clean(self):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments which will attempted to be passed to the wrapped function.
     """
     return WrappedClass
 
 
-def wrap_iterative(fun, check_accuracy=None, accuracy_tol=None, name=None):
+def wrap_iterative(fun, name=None):
     """
     Wraps an iterative Solver.
 
     Parameters
     ----------
     fun : callable
         The iterative Solver function.
-    check_accuracy : bool, optional
-        .. deprecated:: 0.3.0
-            The `check_accuracy` argument was previously unused. This will be
-            removed in a `pymatsolver` 0.4.0. Pass the relevant accuracy check parameters
-            to the wrapped class.
-    accuracy_tol : bool, optional
-        .. deprecated:: 0.3.0
-            The `check_accuracy` argument was previously unused. This will be
-            removed in a `pymatsolver` 0.4.0. Pass the relevant accuracy check parameters
-            to the wrapped class.
     name : string, optional
         The name of the wrapper class to construct. Defaults to the name of `fun`.
 
@@ -185,14 +171,10 @@ def wrap_iterative(fun, check_accuracy=None, accuracy_tol=None, name=None):
     >>> SolverCG = pymatsolver.WrapIterative(cg)
 
     """
-    if check_accuracy is not None or accuracy_tol is not None:
-        warnings.warn('check_accuracy and accuracy_tol were unused and are now deprecated. They '
-                      'will be removed in pymatsolver v0.4.0. Please pass the keyword arguments `check_rtol` '
-                      'and check_atol directly to the wrapped solver class.', FutureWarning, stacklevel=2)
 
-    def __init__(self, A, check_accuracy=False, check_rtol=1E-6, check_atol=0, accuracy_tol=None, **kwargs):
+    def __init__(self, A, check_accuracy=False, check_rtol=1E-6, check_atol=0, **kwargs):
         Base.__init__(
-            self, A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol, accuracy_tol=accuracy_tol,
+            self, A, check_accuracy=check_accuracy, check_rtol=check_rtol, check_atol=check_atol,
         )
         self.kwargs = kwargs
 
@@ -245,10 +227,6 @@ def _solve_multiple(self, rhs):
         The relative tolerance to check against for accuracy.
     check_atol : float, optional
         The absolute tolerance to check against for accuracy.
-    accuracy_tol : float, optional
-        Relative accuracy tolerance.
-        .. deprecated:: 0.3.0
-            `accuracy_tol` will be removed in pymatsolver 0.4.0. Use `check_rtol` and `check_atol` instead.
     **kwargs
         Extra keyword arguments which will attempted to be passed to the wrapped function.
     """