Merge pull request #48 from simpeg/consistent_refactor

Refactor base class

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

@@ -3,7 +3,7 @@ name: Testing
 on:
   push:
     branches:
-      - '*'
+      - 'main'
     tags:
       - 'v*'
   pull_request:
@@ -75,6 +75,8 @@ jobs:
       uses: codecov/codecov-action@v4
       with:
         verbose: true # optional (default = false)
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}
 
   distribute:
     name: Distributing from 3.8

pymatsolver/__init__.py

@@ -24,6 +24,7 @@
 .. autosummary::
   :toctree: generated/
 
+  Triangle
   Forward
   Backward
 
@@ -60,9 +61,9 @@
 }
 
 # Simple solvers
-from .solvers import Diagonal, Forward, Backward
-from .wrappers import WrapDirect
-from .wrappers import WrapIterative
+from .solvers import Diagonal, Triangle, Forward, Backward
+from .wrappers import wrap_direct, WrapDirect
+from .wrappers import wrap_iterative, WrapIterative
 
 # Scipy Iterative solvers
 from .iterative import SolverCG

pymatsolver/direct/mumps.py

@@ -2,64 +2,106 @@
 from mumps import Context
 
 class Mumps(Base):
-    """
-    Mumps solver
+    """The MUMPS direct solver.
+
+    This solver uses the python-mumps wrappers to factorize a sparse matrix, and use that factorization for solving.
+
+    Parameters
+    ----------
+    A
+        Matrix to solve with.
+    ordering : str, default 'metis'
+        Which ordering algorithm to use. See the `python-mumps` documentation for more details.
+    is_symmetric : bool, optional
+        Whether the matrix is symmetric. By default, it will perform some simple tests to check for symmetry, and
+        default to ``False`` if those fail.
+    is_positive_definite : bool, optional
+        Whether the matrix is positive definite.
+    check_accuracy : bool, optional
+        Whether to check the accuracy of the solution.
+    check_rtol : float, optional
+        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
-    ordering = ''
 
-    def __init__(self, A, **kwargs):
-        self.set_kwargs(**kwargs)
+    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):
+        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)
+        if ordering is None:
+            ordering = "metis"
+        self.ordering = ordering
         self.solver = Context()
-        self._set_A(A)
-        self.A = A
+        self._set_A(self.A)
 
     def _set_A(self, A):
         self.solver.set_matrix(
             A,
             symmetric=self.is_symmetric,
-            # positive_definite=self.is_positive_definite  # doesn't (yet) support setting positive definiteness
         )
 
     @property
     def ordering(self):
-        return getattr(self, '_ordering', "metis")
+        """The ordering algorithm to use.
+
+        Returns
+        -------
+        str
+        """
+        return self._ordering
 
     @ordering.setter
     def ordering(self, value):
-        self._ordering = value
+        self._ordering = str(value)
 
     @property
     def _factored(self):
         return self.solver.factored
 
-    @property
+    def get_attributes(self):
+        attrs = super().get_attributes()
+        attrs['ordering'] = self.ordering
+        return attrs
+
     def transpose(self):
         trans_obj = Mumps.__new__(Mumps)
-        trans_obj.A = self.A
+        trans_obj._A = self.A
+        for attr, value in self.get_attributes().items():
+            setattr(trans_obj, attr, value)
         trans_obj.solver = self.solver
-        trans_obj.is_symmetric = self.is_symmetric
-        trans_obj.is_positive_definite = self.is_positive_definite
-        trans_obj.ordering = self.ordering
         trans_obj._transposed = not self._transposed
         return trans_obj
 
-    T = transpose
-
     def factor(self, A=None):
-        reuse_analysis = False
-        if A is not None:
-            self._set_A(A)
-            self.A = A
+        """(Re)factor the A matrix.
+
+        Parameters
+        ----------
+        A : scipy.sparse.spmatrix
+            The matrix to be factorized. If a previous factorization has been performed, this will
+            reuse the previous factorization's analysis.
+        """
+        reuse_analysis = self._factored
+        do_factor = not self._factored
+        if A is not None and A is not self.A:
             # if it was previously factored then re-use the analysis.
-            reuse_analysis = self._factored
-        if not self._factored:
+            self._set_A(A)
+            self._A = A
+            do_factor = True
+        if do_factor:
             pivot_tol = 0.0 if self.is_positive_definite else 0.01
             self.solver.factor(
                 ordering=self.ordering, reuse_analysis=reuse_analysis, pivot_tol=pivot_tol
             )
 
-    def _solveM(self, rhs):
+    def _solve_multiple(self, rhs):
         self.factor()
         if self._transposed:
             self.solver.mumps_instance.icntl[9] = 0
@@ -68,4 +110,4 @@ def _solveM(self, rhs):
         sol = self.solver.solve(rhs)
         return sol
 
-    _solve1 = _solveM
+    _solve_single = _solve_multiple

pymatsolver/direct/pardiso.py

@@ -3,27 +3,50 @@
 from pydiso.mkl_solver import set_mkl_pardiso_threads, get_mkl_pardiso_max_threads
 
 class Pardiso(Base):
+    """The Pardiso direct solver.
+
+    This solver uses the `pydiso` Intel MKL wrapper to factorize a sparse matrix, and use that
+    factorization for solving.
+
+    Parameters
+    ----------
+    A : scipy.sparse.spmatrix
+        Matrix to solve with.
+    n_threads : int, optional
+        Number of threads to use for the `Pardiso` routine in Intel's MKL.
+    is_symmetric : bool, optional
+        Whether the matrix is symmetric. By default, it will perform some simple tests to check for symmetry, and
+        default to ``False`` if those fail.
+    is_positive_definite : bool, optional
+        Whether the matrix is positive definite.
+    is_hermitian : bool, optional
+        Whether the matrix is hermitian. By default, it will perform some simple tests to check, and default to
+        ``False`` if those fail.
+    check_accuracy : bool, optional
+        Whether to check the accuracy of the solution.
+    check_rtol : float, optional
+        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.
     """
-    Pardiso Solver
 
-        https://github.com/simpeg/pydiso
+    _transposed = False
 
-
-    documentation::
-
-        http://www.pardiso-project.org/
-    """
-
-    _factored = False
-
-    def __init__(self, A, **kwargs):
-        self.A = A
-        self.set_kwargs(**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, accuracy_tol=None, **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, accuracy_tol=accuracy_tol, **kwargs)
         self.solver = MKLPardisoSolver(
             self.A,
             matrix_type=self._matrixType(),
             factor=False
         )
+        if n_threads is not None:
+            self.n_threads = n_threads
 
     def _matrixType(self):
         """
@@ -65,28 +88,45 @@ def _matrixType(self):
                 return 13
 
     def factor(self, A=None):
-        if A is not None:
-            self._factored = False
-            self.A = A
-        if not self._factored:
+        """(Re)factor the A matrix.
+
+        Parameters
+        ----------
+        A : scipy.sparse.spmatrix
+            The matrix to be factorized. If a previous factorization has been performed, this will
+            reuse the previous factorization's analysis.
+        """
+        if A is not None and self.A is not A:
+            self._A = A
             self.solver.refactor(self.A)
-            self._factored = True
 
-    def _solveM(self, rhs):
-        self.factor()
-        sol = self.solver.solve(rhs)
+    def _solve_multiple(self, rhs):
+        sol = self.solver.solve(rhs, transpose=self._transposed)
         return sol
 
+    def transpose(self):
+        trans_obj = Pardiso.__new__(Pardiso)
+        trans_obj._A = self.A
+        for attr, value in self.get_attributes().items():
+            setattr(trans_obj, attr, value)
+        trans_obj.solver = self.solver
+        trans_obj._transposed = not self._transposed
+        return trans_obj
+
     @property
     def n_threads(self):
-        """
-        Number of threads to use for the Pardiso solver routine. This property
-        is global to all Pardiso solver objects for a single python process.
+        """Number of threads to use for the Pardiso solver routine.
+
+        This property is global to all Pardiso solver objects for a single python process.
+
+        Returns
+        -------
+        int
         """
         return get_mkl_pardiso_max_threads()
 
     @n_threads.setter
     def n_threads(self, n_threads):
         set_mkl_pardiso_threads(n_threads)
 
-    _solve1 = _solveM
+    _solve_single = _solve_multiple