starting transition to pytest and flake8

Author: pancetta

pySDC/core/Sweeper.py

@@ -264,7 +264,6 @@ def compute_residual(self):
 
         # get current level and problem description
         L = self.level
-        P = L.prob
 
         # check if there are new values (e.g. from a sweep)
         # assert L.status.updated

pySDC/implementations/problem_classes/acoustic_helpers/standard_integrators.py

@@ -1,5 +1,5 @@
 import math
-from decimal import *
+from decimal import Decimal
 
 import numpy as np
 import scipy.sparse as sp

pySDC/implementations/problem_classes/boussinesq_helpers/standard_integrators.py

@@ -1,5 +1,5 @@
 import math
-from decimal import *
+from decimal import Decimal
 
 import numpy as np
 import scipy.sparse as sp

pySDC/tests/test_Q_transfer.py

@@ -1,27 +1,17 @@
-import nose
+import pytest
 import numpy as np
 from numpy.polynomial.polynomial import polyval
 
 import pySDC.helpers.transfer_helper as th
 from pySDC.core.Collocation import CollBase
 from pySDC.tests.test_helpers import get_derived_from_in_package
 
-classes = []
+classes = get_derived_from_in_package(CollBase, 'pySDC/implementations/collocation_classes')
+t_start = np.random.rand(1) * 0.2
+t_end = 0.8 + np.random.rand(1) * 0.2
 
-def setup():
-    global classes, t_start, t_end
-
-    # generate random boundaries for the time slice with 0.0 <= t_start < 0.2 and 0.8 <= t_end < 1.0
-    t_start = np.random.rand(1) * 0.2
-    t_end = 0.8 + np.random.rand(1) * 0.2
-    classes = get_derived_from_in_package(CollBase, 'pySDC/implementations/collocation_classes')
-
-@nose.tools.with_setup(setup)
-def test_Q_transfer():
-    for collclass in classes:
-        yield check_Q_transfer, collclass
-
-def check_Q_transfer(collclass):
+@pytest.mark.parametrize("collclass", classes)
+def test_Q_transfer(collclass):
     """
     A simple test program to check the order of the Q interpolation/restriction
     """
@@ -61,13 +51,8 @@ def check_Q_transfer(collclass):
                 else:
                     assert err_inter > 2E-15, "ERROR: Q-interpolation order is higher than expected, got %s" % polyorder
 
-
-@nose.tools.with_setup(setup)
-def test_Q_transfer_minimal():
-    for collclass in classes:
-        yield check_Q_transfer_minimal, collclass
-
-def check_Q_transfer_minimal(collclass):
+@pytest.mark.parametrize("collclass", classes)
+def test_Q_transfer_minimal(collclass):
     """
     A simple test program to check the order of the Q interpolation/restriction for only 2 coarse nodes
     """

pySDC/tests/test_collocation.py

@@ -1,39 +1,23 @@
-import nose
+import pytest
 import numpy as np
 
 from pySDC.core.Collocation import CollBase
 from pySDC.tests.test_helpers import get_derived_from_in_package
 
-classes = []
-t_start = None
-t_end = None
+classes = get_derived_from_in_package(CollBase, 'pySDC/implementations/collocation_classes')
+t_start = np.random.rand(1) * 0.2
+t_end = 0.8 + np.random.rand(1) * 0.2
 
-def setup():
-    global classes, t_start, t_end
-
-    # generate random boundaries for the time slice with 0.0 <= t_start < 0.2 and 0.8 <= t_end < 1.0
-    t_start = np.random.rand(1)[0] * 0.2
-    t_end = 0.8 + np.random.rand(1)[0] * 0.2
-    classes = get_derived_from_in_package(CollBase, 'pySDC/implementations/collocation_classes')
-
-
-# TEST 1:
-  # Check that the quadrature rule integrates polynomials up to order p-1 exactly
-  # -----------------------------------------------------------------------------
-@nose.tools.with_setup(setup)
-def test_canintegratepolynomials():
-    for collclass in classes:
-        yield check_canintegratepolynomials, collclass, t_start, t_end
-
-def check_canintegratepolynomials(collclass,t_start,t_end):
+@pytest.mark.parametrize("collclass", classes)
+def test_canintegratepolynomials(collclass):
 
     for M in range(2,13):
 
         coll = collclass(M, t_start, t_end)
 
         # some basic consistency tests
-        assert np.size(coll.nodes)==np.size(coll.weights), "For node type " + type[0] + ", number of entries in nodes and weights is different"
-        assert np.size(coll.nodes)==M, "For node type " + type[0] + ", requesting M nodes did not produce M entries in nodes and weights"
+        assert np.size(coll.nodes)==np.size(coll.weights), "For node type " + coll.__class__.__name__ + ", number of entries in nodes and weights is different"
+        assert np.size(coll.nodes)==M, "For node type " + coll.__class__.__name__ + ", requesting M nodes did not produce M entries in nodes and weights"
 
         # generate random set of polynomial coefficients
         poly_coeff = np.random.rand(coll.order-1)
@@ -49,37 +33,22 @@ def check_canintegratepolynomials(collclass,t_start,t_end):
         assert abs(int_ex - int_coll) < 1e-13, "For node type " + coll.__class__.__name__ + ", failed to integrate polynomial of degree " + str(coll.order-1) + " exactly. Error: %5.3e" % abs(int_ex - int_coll)
 
 
-# TEST 2:
-# Check that the Qmat entries are equal to the sum of Smat entries
-# ----------------------------------------------------------------
-@nose.tools.with_setup(setup)
-def test_relateQandSmat():
-    for collclass in classes:
-        yield check_relateQandSmat, collclass, t_start, t_end
-
-
-def check_relateQandSmat(collclass,t_start,t_end):
+@pytest.mark.parametrize("collclass", classes)
+def test_relateQandSmat(collclass):
     for M in range(2, 13):
         coll = collclass(M, t_start, t_end)
         Q = coll.Qmat[1:,1:]
         S = coll.Smat[1:,1:]
-        assert np.shape(Q) == np.shape(S), "For node type " + type[0] + ", Qmat and Smat have different shape"
+        assert np.shape(Q) == np.shape(S), "For node type " + coll.__class__.__name__ + ", Qmat and Smat have different shape"
         shape = np.shape(Q)
-        assert shape[0] == shape[1], "For node type " + type[0] + ", Qmat / Smat are not quadratic"
+        assert shape[0] == shape[1], "For node type " + coll.__class__.__name__ + ", Qmat / Smat are not quadratic"
         SSum = np.cumsum(S[:,:],axis=0)
         for i in range(0,M):
           assert np.linalg.norm( Q[i,:] - SSum[i,:] ) < 1e-15, "For node type " + coll.__class__.__name__ + ", Qmat and Smat did not satisfy the expected summation property."
 
 
-# TEST 3:
-# Check that the partial quadrature rules from Qmat entries have order equal to number of nodes M
-# -----------------------------------------------------------------------------------------------
-@nose.tools.with_setup(setup)
-def test_partialquadrature():
-    for collclass in classes:
-        yield check_partialquadraturewithQ, collclass, t_start, t_end
-
-def check_partialquadraturewithQ(collclass, t_start, t_end):
+@pytest.mark.parametrize("collclass", classes)
+def test_partialquadraturewithQ(collclass):
     for M in range(2, 13):
         coll = collclass(M, t_start, t_end)
         Q = coll.Qmat[1:,1:]
@@ -93,15 +62,9 @@ def check_partialquadraturewithQ(collclass, t_start, t_end):
             int_coll = np.dot(poly_vals, Q[i,:])
             assert abs(int_ex - int_coll)<1e-12, "For node type " + coll.__class__.__name__ + ", partial quadrature from Qmat rule failed to integrate polynomial of degree M-1 exactly for M = " + str(M)
 
-# TEST 3:
-# Check that the partial quadrature rules from Smat entries have order equal to number of nodes M
-# -----------------------------------------------------------------------------------------------
-@nose.tools.with_setup(setup)
-def test_partialquadraturewithS():
-    for collclass in classes:
-        yield check_partialquadraturewithS, collclass, t_start, t_end
 
-def check_partialquadraturewithS(collclass, t_start, t_end):
+@pytest.mark.parametrize("collclass", classes)
+def test_partialquadraturewithS(collclass):
     for M in range(2, 13):
         coll = collclass(M, t_start, t_end)
         S = coll.Smat[1:,1:]

pySDC/tests/test_pep8.py

@@ -1,14 +1,17 @@
 # coding=utf-8
 import os
 import os.path
+import pytest
 
 import nose.tools
 import pep8
 
-BASE_PATH = os.path.abspath(os.path.join(__file__, '..', '..', '..'))
+dir = ['pySDC/core', 'pySDC/implementations', 'pySDC/helpers', 'pySDC/tutorial', 'pySDC/projects']
 
+@pytest.mark.parametrize("dir", dir)
+def test_files(dir):
+    BASE_PATH = os.path.abspath(os.path.join(__file__, '..', '..', '..'))
 
-def check_files(dir):
     style = pep8.StyleGuide()
     style.options.max_line_length = 120
     style.options.ignore = 'E402'
@@ -21,7 +24,3 @@ def check_files(dir):
         report.print_statistics()
         nose.tools.assert_equal(report.total_errors, 0, "File %s has some PEP8 errors: %d" % (file, report.total_errors))
 
-
-def test_pep8():
-    for dir in ['pySDC/core', 'pySDC/implementations', 'pySDC/helpers', 'pySDC/tutorial', 'pySDC/projects']:
-        yield check_files, dir

requirements.txt

@@ -6,7 +6,7 @@ dill>=0.2.6
 matplotlib>=1.5.3
 numba>=0.35
 sympy>=1.0
-nose>=1.3.7
+pytest
 pep8
 # These packages are required for some of the more involved examples (and data types etc.), can be omitted
 petsc4py>=3.10.0