Mumps solver updates

.gitignore

@@ -1,4 +1,5 @@
 *.pyc
+.coverage
 *.so
 build/
 dist/

Makefile

@@ -4,8 +4,9 @@ build:
 	python setup.py build_ext --inplace
 
 coverage:
-	nosetests --logging-level=INFO --with-coverage --cover-package=pymatsolver --cover-html
-	open cover/index.html
+	coverage run --source pymatsolver -m pytest
+	coverage report -m
+	coverage html
 
 lint:
 	pylint --output-format=html pymatsolver > pylint.html
@@ -14,7 +15,7 @@ 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

@@ -9,7 +9,7 @@ pymatsolver
     :target: https://github.com/simpeg/pymatsolver/blob/master/LICENSE
     :alt: MIT license.
 
-.. image:: https://img.shields.io/travis/rowanc1/pymatsolver.svg
+.. image:: https://img.shields.io/travis/simpeg/pymatsolver.svg
     :target: https://travis-ci.org/simpeg/pymatsolver
     :alt: Travis CI build status
 
@@ -64,9 +64,9 @@ 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
+    git clone https://github.com/simpeg/pymatsolver.git
     cd pymatsolver
     make mumps
 
@@ -79,7 +79,7 @@ This assumes that you have Brew and some python installed (numpy, scipy):
 
     brew install mumps --with-scotch5 --without-mpi
 
-    git clone https://github.com/rowanc1/pymatsolver.git
+    git clone https://github.com/simpeg/pymatsolver.git
     cd pymatsolver
     make mumps_mac
 

pymatsolver/__init__.py

@@ -71,31 +71,31 @@
     AvailableSolvers['Pardiso'] = True
     PardisoSolver = Pardiso  # backwards compatibility
 except ImportError:
-    SolverHelp['Pardiso'] = """Pardiso is not working
+    SolverHelp['Pardiso'] = """Pardiso is not working.
 
 Ensure that you have pydiso installed, which may also require Python
 to be installed through conda.
 """
 
-# try:
-#     from pymatsolver.mumps import Mumps
-#     AvailableSolvers['Mumps'] = True
-#     MumpsSolver = Mumps  # backwards compatibility
-# except Exception:
-#     SolverHelp['Mumps'] = """Mumps is not working.
-#
-# Ensure that you have Mumps installed, and know where the path to it is.
-# Try something like:
-#     cd pymatsolver/mumps
-#     make
-#
-# When that doesn't work, you may need to edit the make file, to modify the
-# path to the mumps installation, or any other compiler flags.
-# If you find a good way of doing it, please share.
-#
-# brew install mumps --with-scotch5 --without-mpi
-# mpicc --showme
-# """
+try:
+    from pymatsolver.mumps import Mumps
+    AvailableSolvers['Mumps'] = True
+    MumpsSolver = Mumps  # backwards compatibility
+except ImportError:
+    SolverHelp['Mumps'] = """Mumps is not working.
+
+Ensure that you have Mumps installed, and know where the path to it is.
+Try something like:
+    cd pymatsolver/mumps
+    make
+
+When that doesn't work, you may need to edit the make file, to modify the
+path to the mumps installation, or any other compiler flags.
+If you find a good way of doing it, please share.
+
+brew install mumps --with-scotch5 --without-mpi
+mpicc --showme
+"""
 
 __version__ = '0.2.0'
 __author__ = 'Rowan Cockett'

pymatsolver/mumps/Makefile

@@ -43,4 +43,4 @@ clean:
 	rm -rf *.dSYM
 
 test:
-	cd ..;nosetests
+	cd ../..;pytest

pymatsolver/mumps/mumps_cmplx_p.f90

@@ -229,17 +229,11 @@ subroutine solve( mumps_par, nrhs, rhs, x, transpose )
       mumps_par%icntl(9) = 1  ! for solving Ax = b
    end if
 
-   if (transpose) then
-      mumps_par%RHS = conjg(mumps_par%RHS)
-   end if
 
    mumps_par%JOB = 3  ! Solve the system.
    CALL ZMUMPS(mumps_par)
    ! At this point mumps_par%RHS (rhs) contains the solution.
 
-   if (transpose) then
-      mumps_par%RHS = conjg(mumps_par%RHS)
-   end if
 
 return
 end subroutine solve

pymatsolver/solvers.py

@@ -87,13 +87,16 @@ def _solve(self, rhs):
         else:
             x = self._solveM(rhs)
 
+        if nrhs == 1:
+            x = x.flatten()
+        elif nrhs > 1:
+            x = x.reshape((n, nrhs), order='F')
+
         if self.check_accuracy:
             self._compute_accuracy(rhs, x)
 
-        if nrhs == 1:
-            return x.flatten()
-        elif nrhs > 1:
-            return x.reshape((n, nrhs), order='F')
+        return x
+
 
     def clean(self):
         pass

setup.py

@@ -5,8 +5,7 @@
 
 """
 
-from distutils.core import setup
-from setuptools import find_packages
+from setuptools import find_packages, setup
 
 CLASSIFIERS = [
     'Development Status :: 4 - Beta',
@@ -42,7 +41,7 @@
     license="MIT",
     keywords="matrix solver",
     url="http://simpeg.xyz/",
-    download_url="http://github.com/rowanc1/pymatsolver",
+    download_url="http://github.com/simpeg/pymatsolver",
     classifiers=CLASSIFIERS,
     platforms=["Windows", "Linux", "Solaris", "Mac OS-X", "Unix"],
     use_2to3=False

tests/test_Basic.py

@@ -1,30 +1,25 @@
-import unittest
+import pytest
 import numpy as np
 import scipy.sparse as sp
 from pymatsolver import Diagonal
 
 TOL = 1e-12
 
 
-class TestBasic(unittest.TestCase):
+class TestBasic:
 
     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]
 
         sol = rhs/2.0
 
-        with self.assertRaises(TypeError):
+        with pytest.raises(TypeError):
             Diagonal(A, check_accuracy=np.array([1, 2, 3]))
-        with self.assertRaises(TypeError):
+        with pytest.raises(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()
+        assert np.linalg.norm(sol-X, np.inf) < TOL
+        assert np.linalg.norm(sol[:, 0]-x, np.inf) < TOL

tests/test_BicgJacobi.py

@@ -1,14 +1,14 @@
-import unittest
 from pymatsolver import BicgJacobi
 import numpy as np
 import scipy.sparse as sp
 
 TOL = 1e-6
 
 
-class TestBicgJacobi(unittest.TestCase):
+class TestBicgJacobi:
 
-    def setUp(self):
+    @classmethod
+    def setup_class(cls):
 
         nSize = 100
         A = sp.rand(nSize, nSize, 0.05, format='csr', random_state=100)
@@ -19,9 +19,9 @@ def setUp(self):
         sol = np.random.rand(nSize, 4)
         rhs = A.dot(sol)
 
-        self.A = A
-        self.rhs = rhs
-        self.sol = sol
+        cls.A = A
+        cls.rhs = rhs
+        cls.sol = sol
 
     def test(self):
         rhs = self.rhs
@@ -30,7 +30,7 @@ def test(self):
         for i in range(3):
             err = np.linalg.norm(
                 self.A*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
+            assert err < TOL
         Ainv.clean()
 
     def test_T(self):
@@ -42,13 +42,14 @@ def test_T(self):
         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)
+            assert err < TOL
         Ainv.clean()
 
 
-class TestPardisoComplex(unittest.TestCase):
+class TestBicgJacobiComplex:
 
-    def setUp(self):
+    @classmethod
+    def setup_class(cls):
         nSize = 100
         A = sp.rand(nSize, nSize, 0.05, format='csr', random_state=100)
         A.data = A.data + 1j*np.random.rand(A.nnz)
@@ -59,9 +60,9 @@ def setUp(self):
         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
+        cls.A = A
+        cls.rhs = rhs
+        cls.sol = sol
 
     def test(self):
         rhs = self.rhs
@@ -70,7 +71,7 @@ def test(self):
         for i in range(3):
             err = np.linalg.norm(
                 self.A*solb[:, i] - rhs[:, i]) / np.linalg.norm(rhs[:, i])
-            self.assertLess(err, TOL)
+            assert err < TOL
         Ainv.clean()
 
     def test_T(self):
@@ -82,9 +83,5 @@ def test_T(self):
         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)
+            assert err < TOL
         Ainv.clean()
-
-
-if __name__ == '__main__':
-    unittest.main()