Update312

.github/workflows/ci.yml

@@ -34,5 +34,7 @@ jobs:
       run: |
         pytest --cov=./ --cov-report=xml .
 
-    - name: Upload coverage
-      uses: codecov/codecov-action@v3
+    - name: Upload coverage to Codecov
+      uses: codecov/codecov-action@v4-beta
+      env:
+        CODECOV_TOKEN: ${{ secrets.CODECOV_TOKEN }}

codecov.yml

@@ -0,0 +1,4 @@
+coverage:
+  status:
+    project: off
+    patch: off

pyamg/aggregation/adaptive.py

@@ -219,7 +219,7 @@ def adaptive_sa_solver(A, initial_candidates=None, symmetry='hermitian',
         try:
             A = csr_matrix(A)
             warn('Implicit conversion of A to CSR', SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix or '
                             'bsr_matrix, or be convertible to csr_matrix') from e
 

pyamg/aggregation/aggregate.py

@@ -237,7 +237,7 @@ def pairwise_aggregation(A, matchings=2, theta=0.25,
         try:
             A = A.tocsr()
             warn('Implicit conversion of A to csr', sparse.SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Invalid matrix type, must be CSR or BSR.') from e
 
     index_type = A.indptr.dtype

pyamg/aggregation/aggregation.py

@@ -213,7 +213,7 @@ def smoothed_aggregation_solver(A, B=None, BH=None,
         try:
             A = csr_matrix(A)
             warn('Implicit conversion of A to CSR', SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix or bsr_matrix, '
                             'or be convertible to csr_matrix') from e
 

pyamg/aggregation/pairwise.py

@@ -87,7 +87,7 @@ def pairwise_solver(A,
         try:
             A = csr_matrix(A)
             warn('Implicit conversion of A to CSR', SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix or bsr_matrix, '
                             'or be convertible to csr_matrix') from e
 

pyamg/aggregation/rootnode.py

@@ -234,7 +234,7 @@ def rootnode_solver(A, B=None, BH=None,
             A = csr_matrix(A)
             warn('Implicit conversion of A to CSR',
                  SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix, '
                             'bsr_matrix, or be convertible to csr_matrix') from e
 

pyamg/aggregation/tests/test_aggregation.py

@@ -4,7 +4,6 @@
 from numpy.testing import TestCase, assert_approx_equal, \
     assert_array_almost_equal
 from scipy import sparse
-import scipy.linalg as sla
 from scipy.sparse import SparseEfficiencyWarning
 
 from pyamg.util.utils import diag_sparse
@@ -31,11 +30,9 @@ def run_cases(self, opts):
             b = A * np.random.rand(A.shape[0])
 
             residuals = []
-            x_sol = ml.solve(b, x0=x, maxiter=30, tol=1e-10,
-                             residuals=residuals)
+            x_sol = ml.solve(b, x0=x, maxiter=30, tol=1e-10, residuals=residuals)
             del x_sol
-            convergence_ratio =\
-                (residuals[-1] / residuals[0]) ** (1.0 / len(residuals))
+            convergence_ratio = (residuals[-1] / residuals[0])**(1.0 / len(residuals))
             assert convergence_ratio < 0.9
 
     def test_strength_of_connection(self):
@@ -110,11 +107,9 @@ def run_cases(self, opts):
             b = A * np.random.rand(A.shape[0])
             residuals = []
 
-            x_sol = ml.solve(b, x0=x, maxiter=30, tol=1e-10,
-                             residuals=residuals)
+            x_sol = ml.solve(b, x0=x, maxiter=30, tol=1e-10, residuals=residuals)
             del x_sol
-            convergence_ratio =\
-                (residuals[-1] / residuals[0]) ** (1.0 / len(residuals))
+            convergence_ratio = (residuals[-1] / residuals[0])**(1.0 / len(residuals))
             assert convergence_ratio < 0.9
 
     def test_strength_of_connection(self):
@@ -400,12 +395,7 @@ def test_coarse_solver_opts(self):
                                     'gauss_seidel'))
         coarse_solver_pairs.append(('gauss_seidel', 'jacobi'))
         coarse_solver_pairs.append(('cg', ('cg', {'tol': 10.0})))
-        # scipy >= 1.7: pinv takes 'rtol'
-        # scipy <  1.7: pinv takes 'cond'
-        kword = 'rtol'
-        if kword not in sla.pinv.__code__.co_varnames:
-            kword = 'cond'
-        coarse_solver_pairs.append(('pinv', ('pinv', {kword: 1.0})))
+        coarse_solver_pairs.append(('pinv', ('pinv', {'rtol': 1.0})))
 
         for coarse1, coarse2 in coarse_solver_pairs:
             r1 = []

pyamg/aggregation/tests/test_rootnode.py

@@ -2,7 +2,6 @@
 import warnings
 import numpy as np
 from scipy import sparse
-import scipy.linalg as sla
 from scipy.sparse import SparseEfficiencyWarning
 
 from numpy.testing import TestCase, assert_approx_equal, \
@@ -388,12 +387,7 @@ def test_coarse_solver_opts(self):
                                      {'iterations': 30}), 'gauss_seidel'))
         coarse_solver_pairs.append(('gauss_seidel', 'jacobi'))
         coarse_solver_pairs.append(('cg', ('cg', {'tol': 10.0})))
-        # scipy >= 1.7: pinv takes 'rtol'
-        # scipy <  1.7: pinv takes 'cond'
-        kword = 'rtol'
-        if kword not in sla.pinv.__code__.co_varnames:
-            kword = 'cond'
-        coarse_solver_pairs.append(('pinv', ('pinv', {kword: 1.0})))
+        coarse_solver_pairs.append(('pinv', ('pinv', {'rtol': 1.0})))
 
         for coarse1, coarse2 in coarse_solver_pairs:
             r1 = []

pyamg/blackbox.py

@@ -37,7 +37,7 @@ def make_csr(A):
         try:
             A = csr_matrix(A)
             print('Implicit conversion of A to CSR in pyamg.blackbox.make_csr')
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix or '
                             'bsr_matrix, or be convertible to csr_matrix') from e
 
@@ -201,7 +201,7 @@ def solver(A, config):
                                         presmoother=config['presmoother'],
                                         postsmoother=config['postsmoother'],
                                         keep=config['keep'])
-    except BaseException as e:
+    except Exception as e:
         raise TypeError('Failed generating smoothed_aggregation_solver') from e
 
 

pyamg/classical/classical.py

@@ -96,7 +96,7 @@ def ruge_stuben_solver(A,
             A = csr_matrix(A)
             warn('Implicit conversion of A to CSR',
                  SparseEfficiencyWarning)
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Argument A must have type csr_matrix, '
                             'or be convertible to csr_matrix') from e
     # preprocess A

pyamg/classical/interpolate.py

@@ -215,7 +215,7 @@ def injection_interpolation(A, splitting):
             warn('Implicit conversion of A to csr', SparseEfficiencyWarning)
             n = A.shape[0]
             blocksize = 1
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Invalid matrix type, must be CSR or BSR.') from e
 
     P_rowptr = np.append(np.array([0], dtype=A.indptr.dtype),
@@ -286,7 +286,7 @@ def one_point_interpolation(A, C, splitting, by_val=False):
             warn('Implicit conversion of A to csr', SparseEfficiencyWarning)
             n = A.shape[0]
             blocksize = 1
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Invalid matrix type, must be CSR or BSR.') from e
 
     nc = np.sum(splitting)
@@ -376,7 +376,7 @@ def local_air(A, splitting, theta=0.1, norm='abs', degree=1,
             warn('Implicit conversion of A to csr', SparseEfficiencyWarning)
             C = classical_strength_of_connection(A=A, theta=theta, block=False, norm=norm)
             blocksize = 1
-        except BaseException as e:
+        except Exception as e:
             raise TypeError('Invalid matrix type, must be CSR or BSR.') from e
 
     Cpts = np.array(np.where(splitting == 1)[0], dtype=A.indptr.dtype)

pyamg/krylov/tests/test_scipy.py

@@ -1,4 +1,5 @@
 """Test scipy methods."""
+import inspect
 from functools import partial
 
 import numpy as np
@@ -37,20 +38,24 @@ def cb(x, normb):
             x0 = case['x0']
             tol = case['tol']
 
+            kwargs = dict(tol=tol, restart=3, maxiter=2)
+
             mgsres = []
-            _ = gmres_mgs(A, b, x0, residuals=mgsres,
-                          tol=tol, restart=3, maxiter=2)
+            _ = gmres_mgs(A, b, x0, residuals=mgsres, **kwargs)
 
             hhres = []
-            _ = gmres_householder(A, b, x0, residuals=hhres,
-                                  tol=tol, restart=3, maxiter=2)
+            _ = gmres_householder(A, b, x0, residuals=hhres, **kwargs)
 
             scipyres = []
             normb = np.linalg.norm(b)
             callback = partial(cb, normb=normb)
 
-            _ = sla.gmres(A, b, x0, callback=callback, callback_type='pr_norm',
-                          tol=tol, atol=0, restart=3, maxiter=2)
+            # check if scipy gmres has rtol
+            kwargs['atol'] = 0
+            if 'rtol' in inspect.getfullargspec(sla.gmres).args:
+                kwargs['rtol'] = kwargs.pop(tol)
+
+            _ = sla.gmres(A, b, x0, callback=callback, callback_type='pr_norm', **kwargs)
 
             assert_array_almost_equal(mgsres[1:], scipyres)
             assert_array_almost_equal(hhres[1:], scipyres)

pyamg/multilevel.py

@@ -1,4 +1,5 @@
 """Generic AMG solver."""
+import inspect
 
 from warnings import warn
 
@@ -457,7 +458,6 @@ def solve(self, b, x0=None, tol=1e-5, maxiter=100, cycle='V', accel=None,
                     accel = getattr(krylov, accel)
                 else:
                     accel = getattr(sla, accel)
-                    kwargs['atol'] = 'legacy'
 
             M = self.aspreconditioner(cycle=cycle)
 
@@ -485,7 +485,13 @@ def callback_wrapper(x):
                 else:
                     callback_wrapper = callback
 
-                x, info = accel(A, b, x0=x0, tol=tol, maxiter=maxiter, M=M,
+                # for scipy solvers, see if rtol is available
+                kwargs['tol'] = tol
+                kwargs['atol'] = 0
+                if 'rtol' in inspect.getfullargspec(accel).args:
+                    kwargs['rtol'] = kwargs.pop(tol)
+
+                x, info = accel(A, b, x0=x0, maxiter=maxiter, M=M,
                                 callback=callback_wrapper, **kwargs)
                 if return_info:
                     return x, info

pyamg/tests/test_multilevel.py

@@ -1,4 +1,6 @@
 """Test MultilevelSolver class."""
+import inspect
+
 import numpy as np
 from numpy.testing import TestCase, assert_almost_equal, assert_equal
 from scipy import sparse
@@ -53,9 +55,13 @@ def test_aspreconditioner(self):
 
         ml = smoothed_aggregation_solver(A)
 
+        kwargs = dict(tol=1e-8, maxiter=30, atol=0)
+        if 'rtol' in inspect.getfullargspec(cg).args:
+            kwargs['rtol'] = kwargs.pop('tol')
+
         for cycle in ['V', 'W', 'F']:
             M = ml.aspreconditioner(cycle=cycle)
-            x, info = cg(A, b, tol=1e-8, maxiter=30, M=M, atol='legacy')
+            x, info = cg(A, b, M=M, **kwargs)
             # cg satisfies convergence in the preconditioner norm
             assert precon_norm(b - A*x, ml) < 1e-8*precon_norm(b, ml)
 
@@ -78,24 +84,16 @@ def test_accel(self):
 
         # cg halts based on the preconditioner norm
         for accel in ['cg', cg]:
-            x = ml.solve(b, maxiter=30, tol=1e-8, accel=accel)
-            assert precon_norm(b - A*x, ml) < 1e-8*precon_norm(b, ml)
             residuals = []
-            x = ml.solve(b, maxiter=30, tol=1e-8, residuals=residuals,
-                         accel=accel)
+            x = ml.solve(b, maxiter=30, tol=1e-8, residuals=residuals, accel=accel)
             assert precon_norm(b - A*x, ml) < 1e-8*precon_norm(b, ml)
-            # print residuals
             assert_almost_equal(precon_norm(b - A*x, ml), residuals[-1])
 
         # cgs and bicgstab use the Euclidean norm
         for accel in ['bicgstab', 'cgs', bicgstab]:
-            x = ml.solve(b, maxiter=30, tol=1e-8, accel=accel)
-            assert np.linalg.norm(b - A*x) < 1e-8*np.linalg.norm(b)
             residuals = []
-            x = ml.solve(b, maxiter=30, tol=1e-8, residuals=residuals,
-                         accel=accel)
+            x = ml.solve(b, maxiter=30, tol=1e-8, residuals=residuals, accel=accel)
             assert np.linalg.norm(b - A*x) < 1e-8*np.linalg.norm(b)
-            # print residuals
             assert_almost_equal(np.linalg.norm(b - A*x), residuals[-1])
 
     def test_cycle_complexity(self):

pyamg/util/tests/test_utils.py

@@ -1,4 +1,6 @@
 """Test utils."""
+import inspect
+
 import numpy as np
 from scipy.sparse import (csr_matrix, csc_matrix, isspmatrix,
                           bsr_matrix, isspmatrix_bsr,
@@ -167,8 +169,12 @@ def test_profile_solver(self):
 
         opts = []
         opts.append({})
-        opts.append({'accel': cg, 'atol': 'legacy'})
-        opts.append({'accel': cg, 'tol': 1e-10, 'atol': 'legacy'})
+
+        # does cg have rtol?
+        nextopt = dict(accel=cg, tol=1e-10, atol=0)
+        if 'rtol' in inspect.getfullargspec(cg).args:
+            nextopt['rtol'] = nextopt.pop('tol')
+        opts.append(nextopt)
 
         for kwargs in opts:
             residuals = profile_solver(ml, **kwargs)
@@ -1194,8 +1200,12 @@ def test_profile_solver(self):
 
         opts = []
         opts.append({})
-        opts.append({'accel': cg, 'atol': 'legacy'})
-        opts.append({'accel': cg, 'tol': 1e-10, 'atol': 'legacy'})
+
+        # does cg have rtol?
+        nextopt = dict(accel=cg, tol=1e-10, atol=0)
+        if 'rtol' in inspect.getfullargspec(cg).args:
+            nextopt['rtol'] = nextopt.pop('tol')
+        opts.append(nextopt)
 
         for kwargs in opts:
             residuals = profile_solver(ml, **kwargs)

pyamg/vis/vis_coarse.py

@@ -279,4 +279,4 @@ def check_input(V=None, E2V=None, AggOp=None, A=None, splitting=None, mesh_type=
     if mesh_type is not None:
         valid_mesh_types = ('vertex', 'tri', 'quad', 'tet', 'hex')
         if mesh_type not in valid_mesh_types:
-            raise ValueError(f'mesh_type should be {" or ".join(valid_mesh_types)}')
+            raise ValueError(f'mesh_type should one of {valid_mesh_types}')

requirements-dev.txt

@@ -1,5 +1,5 @@
 numpy
-scipy>=1.7.0
+scipy>=1.8.0
 pytest
 pep8-naming
 flake8-quotes

requirements.txt

@@ -1,2 +1,2 @@
 numpy
-scipy>=1.7.0
+scipy>=1.8.0

setup.cfg

@@ -41,8 +41,8 @@ packages = find:
 platforms = any
 python_requires = >=3.8
 install_requires =
-    numpy>=1.7.0
-    scipy>=1.7.0
+    numpy
+    scipy>=1.8.0
 tests_require =
     pytest>=2