Merge pull request #47 from mplough-kobold/matt-refactor-tests-as-pytest

Remove nosetest and convert tests to pytest

Author: jcapriot

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

@@ -60,7 +60,7 @@ jobs:
 
     - name: Run Tests
       run: |
-        pytest --cov-config=.coveragerc --cov-report=xml --cov=pymatsolver -s -v
+        make coverage
 
     - name: Test Documentation
       if: ${{ (matrix.os == 'ubuntu-latest') && (matrix.python-version == '3.11') }}

.gitignore

@@ -1,3 +1,5 @@
+.coverage
+coverage.xml
 *.pyc
 *.so
 build/

Makefile

@@ -4,8 +4,7 @@ build:
 	python setup.py build_ext --inplace
 
 coverage:
-	nosetests --logging-level=INFO --with-coverage --cover-package=pymatsolver --cover-html
-	open cover/index.html
+	pytest --cov-config=.coveragerc --cov-report=xml --cov=pymatsolver -s -v
 
 lint:
 	pylint --output-format=html pymatsolver > pylint.html
@@ -14,7 +13,7 @@ graphs:
 	pyreverse -my -A -o pdf -p pymatsolver pymatsolver/**.py pymatsolver/**/**.py
 
 tests:
-	nosetests --logging-level=INFO
+	pytest
 
 docs:
 	cd docs;make html

README.rst

@@ -60,7 +60,7 @@ From a clean install on Ubuntu:
     ./miniconda.sh -b
     export PATH=/root/anaconda/bin:/root/miniconda/bin:$PATH
     conda update --yes conda
-    conda install --yes numpy scipy matplotlib cython ipython nose
+    conda install --yes numpy scipy matplotlib cython ipython pytest coverage
 
     git clone https://github.com/rowanc1/pymatsolver.git
     cd pymatsolver

pymatsolver/__init__.py

@@ -73,6 +73,8 @@
 from .direct import Solver
 from .direct import SolverLU
 
+from .solvers import PymatsolverAccuracyError
+
 BicgJacobi = BiCGJacobi  # backwards compatibility
 
 try:

pymatsolver/direct/pardiso.py

@@ -71,6 +71,7 @@ def factor(self, A=None):
         if not self._factored:
             self.solver.refactor(self.A)
             self._factored = True
+
     def _solveM(self, rhs):
         self.factor()
         sol = self.solver.solve(rhs)

pymatsolver/solvers.py

@@ -2,6 +2,10 @@
 import warnings
 
 
+class PymatsolverAccuracyError(Exception):
+    pass
+
+
 class Base():
     _accuracy_tol = 1e-6
     _check_accuracy = False
@@ -57,7 +61,7 @@ def _transposeClass(self):
     def T(self):
         "The transpose operator for this class"
         if self._transposeClass is None:
-            raise Exception(
+            raise NotImplementedError(
                 'The transpose for the {} class is not possible.'.format(
                     self.__name__
                 )
@@ -74,7 +78,7 @@ def _compute_accuracy(self, rhs, x):
             msg = 'Accuracy on solve is above tolerance: {0:e} > {1:e}'.format(
                 nrm, self.accuracy_tol
             )
-            raise Exception(msg)
+            raise PymatsolverAccuracyError(msg)
 
     def _solve(self, rhs):
 

tests/test_Basic.py

@@ -1,30 +1,25 @@
-import unittest
 import numpy as np
+import numpy.testing as npt
+import pytest
 import scipy.sparse as sp
 from pymatsolver import Diagonal
 
 TOL = 1e-12
 
 
-class TestBasic(unittest.TestCase):
+def test_DiagonalSolver():
 
-    def test_DiagonalSolver(self):
+    A = sp.identity(5)*2.0
+    rhs = np.c_[np.arange(1, 6), np.arange(2, 11, 2)]
+    X = Diagonal(A) * rhs
+    x = Diagonal(A) * rhs[:, 0]
 
-        A = sp.identity(5)*2.0
-        rhs = np.c_[np.arange(1, 6), np.arange(2, 11, 2)]
-        X = Diagonal(A) * rhs
-        x = Diagonal(A) * rhs[:, 0]
+    sol = rhs/2.0
 
-        sol = rhs/2.0
+    with pytest.raises(TypeError):
+        Diagonal(A, check_accuracy=np.array([1, 2, 3]))
+    with pytest.raises(TypeError):
+        Diagonal(A, accuracy_tol=0)
 
-        with self.assertRaises(TypeError):
-            Diagonal(A, check_accuracy=np.array([1, 2, 3]))
-        with self.assertRaises(TypeError):
-            Diagonal(A, accuracy_tol=0)
-
-        self.assertLess(np.linalg.norm(sol-X, np.inf), TOL)
-        self.assertLess(np.linalg.norm(sol[:, 0]-x, np.inf), TOL)
-
-
-if __name__ == '__main__':
-    unittest.main()
+    npt.assert_allclose(sol, X, atol=TOL)
+    npt.assert_allclose(sol[:, 0], x, atol=TOL)

tests/test_BicgJacobi.py

@@ -1,90 +1,36 @@
-import unittest
 from pymatsolver import BicgJacobi
 import numpy as np
+import numpy.testing as npt
 import scipy.sparse as sp
-
-TOL = 1e-6
-
-
-class TestBicgJacobi(unittest.TestCase):
-
-    def setUp(self):
-
-        nSize = 100
-        A = sp.rand(nSize, nSize, 0.05, format='csr', random_state=100)
-        A = A + sp.spdiags(np.ones(nSize), 0, nSize, nSize)
-        A = A.T*A
-        A = A.tocsr()
-        np.random.seed(1)
-        sol = np.random.rand(nSize, 4)
-        rhs = A.dot(sol)
-
-        self.A = A
-        self.rhs = rhs
-        self.sol = sol
-
-    def test(self):
-        rhs = self.rhs
-        Ainv = BicgJacobi(self.A, symmetric=True)
-        solb = Ainv*rhs
-        for i in range(3):
-            err = np.linalg.norm(
-                self.A*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
-        Ainv.clean()
-
-    def test_T(self):
-        rhs = self.rhs
-        Ainv = BicgJacobi(self.A, symmetric=True)
-        Ainv.maxIter = 2000
-        AinvT = Ainv.T
-        solb = AinvT*rhs
-        for i in range(3):
-            err = np.linalg.norm(
-                self.A.T*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
-        Ainv.clean()
-
-
-class TestBicgJacobiComplex(unittest.TestCase):
-
-    def setUp(self):
-        nSize = 100
-        A = sp.rand(nSize, nSize, 0.05, format='csr', random_state=100)
-        A.data = A.data + 1j*np.random.rand(A.nnz)
-        A = A.T.dot(A) + sp.spdiags(np.ones(nSize), 0, nSize, nSize)
-        A = A.tocsr()
-
-        np.random.seed(1)
-        sol = np.random.rand(nSize, 5) + 1j*np.random.rand(nSize, 5)
-        rhs = A.dot(sol)
-
-        self.A = A
-        self.rhs = rhs
-        self.sol = sol
-
-    def test(self):
-        rhs = self.rhs
-        Ainv = BicgJacobi(self.A, symmetric=True)
-        solb = Ainv*rhs
-        for i in range(3):
-            err = np.linalg.norm(
-                self.A*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
-        Ainv.clean()
-
-    def test_T(self):
-        rhs = self.rhs
-        Ainv = BicgJacobi(self.A, symmetric=True)
-        Ainv.maxIter = 2000
-        AinvT = Ainv.T
-        solb = AinvT*rhs
-        for i in range(3):
-            err = np.linalg.norm(
-                self.A.T*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
-        Ainv.clean()
-
-
-if __name__ == '__main__':
-    unittest.main()
+import pytest
+
+TOL = 1e-5
+
+@pytest.fixture()
+def test_mat_data():
+    nSize = 100
+    A = sp.rand(nSize, nSize, 0.05, format='csr', random_state=100)
+    A = A + sp.spdiags(np.ones(nSize), 0, nSize, nSize)
+    A = A.T*A
+    A = A.tocsr()
+    np.random.seed(1)
+    sol = np.random.rand(nSize, 4)
+    rhs = A.dot(sol)
+    return A, sol, rhs
+
+
+@pytest.mark.parametrize('transpose', [True, False])
+@pytest.mark.parametrize('dtype', [np.float64, np.complex128])
+def test_solve(test_mat_data, dtype, transpose):
+    A, rhs, sol = test_mat_data
+    A = A.astype(dtype)
+    rhs = rhs.astype(dtype)
+    sol = sol.astype(dtype)
+    if transpose:
+        A = A.T
+        Ainv = BicgJacobi(A, symmetric=True).T
+    else:
+        Ainv = BicgJacobi(A, symmetric=True)
+    Ainv.maxiter = 2000
+    solb = Ainv * rhs
+    npt.assert_allclose(rhs, A @ solb, atol=TOL)

tests/test_Mumps.py

@@ -1,83 +1,61 @@
-import unittest
 import numpy as np
 import scipy.sparse as sp
 import pymatsolver
+import pytest
+import numpy.testing as npt
 
-TOL = 1e-11
-
-if pymatsolver.AvailableSolvers['Mumps']:
-    class TestMumps(unittest.TestCase):
-
-            def setUp(self):
-                n = 5
-                irn = np.r_[0, 1, 3, 4, 1, 0, 4, 2, 1, 2, 0, 2]
-                jcn = np.r_[1, 2, 2, 4, 0, 0, 1, 3, 4, 1, 2, 2]
-                a = np.r_[
-                    3.0, -3.0, 2.0, 1.0, 3.0, 2.0,
-                    4.0, 2.0, 6.0, -1.0, 4.0, 1.0
-                ]
-                rhs = np.r_[20.0, 24.0, 9.0, 6.0, 13.0]
-                rhs = np.c_[rhs, 10*rhs, 100*rhs]
-                sol = np.r_[1., 2., 3., 4., 5.]
-                sol = np.c_[sol, 10*sol, 100*sol]
-                A = sp.coo_matrix((a, (irn, jcn)), shape=(n, n))
-                self.A = A
-                self.rhs = rhs
-                self.sol = sol
-
-            def test_1to5(self):
-                rhs = self.rhs
-                sol = self.sol
-                Ainv = pymatsolver.Mumps(self.A)
-                for i in range(3):
-                    self.assertLess(
-                        np.linalg.norm(Ainv * rhs[:, i] - sol[:, i]), TOL
-                    )
-                self.assertLess(np.linalg.norm(Ainv * rhs - sol, np.inf), TOL)
-
-            def test_1to5_cmplx(self):
-                rhs = self.rhs.astype(complex)
-                sol = self.sol.astype(complex)
-                self.A = self.A.astype(complex)
-                Ainv = pymatsolver.Mumps(self.A)
-                for i in range(3):
-                    self.assertLess(
-                        np.linalg.norm(Ainv * rhs[:, i] - sol[:, i]), TOL
-                    )
-                self.assertLess(np.linalg.norm(Ainv * rhs - sol, np.inf), TOL)
+if not pymatsolver.AvailableSolvers['Mumps']:
+    pytest.skip(reason="MUMPS solver is not installed", allow_module_level=True)
 
-            def test_1to5_T(self):
-                rhs = self.rhs
-                sol = self.sol
-                Ainv = pymatsolver.Mumps(self.A)
-                AinvT = Ainv.T
-                for i in range(3):
-                    self.assertLess(
-                        np.linalg.norm(AinvT.T * rhs[:, i] - sol[:, i]), TOL
-                    )
-                self.assertLess(np.linalg.norm(AinvT.T * rhs - sol, np.inf), TOL)
-
-            # def test_singular(self):
-            #     A = sp.identity(5).tocsr()
-            #     A[-1, -1] = 0
-            #     self.assertRaises(Exception, pymatsolver.Mumps, A)
-
-            def test_multiFactorsInMem(self):
-                n = 100
-                A = sp.rand(n, n, 0.7)+sp.identity(n)
-                x = np.ones((n, 10))
-                rhs = A * x
-                solvers = [pymatsolver.Mumps(A) for _ in range(20)]
-
-                for Ainv in solvers:
-                    self.assertLess(
-                        np.linalg.norm(Ainv * rhs - x)/np.linalg.norm(rhs), TOL)
-                    Ainv.clean()
-
-                for Ainv in solvers:
-                    self.assertLess(
-                        np.linalg.norm(Ainv * rhs - x)/np.linalg.norm(rhs), TOL
-                    )
+TOL = 1e-11
 
-if __name__ == '__main__':
-    unittest.main()
+@pytest.fixture()
+def test_mat_data():
+    n = 5
+    irn = np.r_[0, 1, 3, 4, 1, 0, 4, 2, 1, 2, 0, 2]
+    jcn = np.r_[1, 2, 2, 4, 0, 0, 1, 3, 4, 1, 2, 2]
+    a = np.r_[
+        3.0, -3.0, 2.0, 1.0, 3.0, 2.0,
+        4.0, 2.0, 6.0, -1.0, 4.0, 1.0
+    ]
+    rhs = np.r_[20.0, 24.0, 9.0, 6.0, 13.0]
+    rhs = np.c_[rhs, 10 * rhs, 100 * rhs]
+    sol = np.r_[1., 2., 3., 4., 5.]
+    sol = np.c_[sol, 10 * sol, 100 * sol]
+    A = sp.coo_matrix((a, (irn, jcn)), shape=(n, n))
+    return A, rhs, sol
+
+@pytest.mark.parametrize('transpose', [True, False])
+@pytest.mark.parametrize('dtype', [np.float64, np.complex128])
+def test_solve(test_mat_data, dtype, transpose):
+    A, rhs, sol = test_mat_data
+    sol = sol.astype(dtype)
+    rhs = rhs.astype(dtype)
+    A = A.astype(dtype)
+    if transpose:
+        Ainv = pymatsolver.Mumps(A.T).T
+    else:
+        Ainv = pymatsolver.Mumps(A)
+    for i in range(3):
+        npt.assert_allclose(Ainv * rhs[:, i], sol[:, i], atol=TOL)
+    npt.assert_allclose(Ainv * rhs, sol, atol=TOL)
+
+
+# def test_singular(self):
+#     A = sp.identity(5).tocsr()
+#     A[-1, -1] = 0
+#     self.assertRaises(Exception, pymatsolver.Mumps, A)
+
+def test_multiFactorsInMem():
+    n = 100
+    A = sp.rand(n, n, 0.7)+sp.identity(n)
+    x = np.ones((n, 10))
+    rhs = A * x
+    solvers = [pymatsolver.Mumps(A) for _ in range(20)]
+
+    for Ainv in solvers:
+        npt.assert_allclose(Ainv * rhs, x, rtol=TOL)
+        Ainv.clean()
+
+    for Ainv in solvers:
+        npt.assert_allclose(Ainv * rhs, x, rtol=TOL)