Migrate to pytest

Dockerfile

@@ -9,7 +9,7 @@ RUN apt-get update && apt-get install -y \
     # Documentation build dependencies
     python3-sphinx python3-sphinx-rtd-theme python3-numpydoc \
     # Testing dependencies
-    python3-coverage python3-parameterized python3-pytest python3-pytest-cov \
+    python3-coverage python3-pytest python3-pytest-cov \
     # Optional NIFTy dependencies
     openmpi-bin libopenmpi-dev python3-mpi4py \
     # Packages needed for NIFTy

test/common.py

@@ -15,20 +15,12 @@
 #
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
-from builtins import str
+import pytest
 
-import numpy as np
-from parameterized import parameterized
 
-np.seterr(all='raise', under='ignore')
+def list2fixture(lst):
+    @pytest.fixture(params=lst)
+    def myfixture(request):
+        return request.param
 
-
-def _custom_name_func(testcase_func, param_num, param):
-    return "{}_{}".format(
-        testcase_func.__name__,
-        parameterized.to_safe_name("_".join(str(x) for x in param.args)),
-    )
-
-
-def expand(*args, **kwargs):
-    return parameterized.expand(*args, func=_custom_name_func, **kwargs)
+    return myfixture

test/test_energies/test_consistency.py

-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-# Copyright(C) 2013-2019 Max-Planck-Society
-#
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
-
-import unittest
-from itertools import product
-from test.common import expand
-
-import nifty5 as ift
-import numpy as np
-
-
-class Energy_Tests(unittest.TestCase):
-    def make_model(self, **kwargs):
-        np.random.seed(kwargs['seed'])
-        S = ift.ScalingOperator(1., kwargs['space'])
-        s = S.draw_sample()
-        return ift.MultiField.from_dict({kwargs['space_key']: s})
-
-    @expand(product(
-        [ift.GLSpace(15),
-         ift.RGSpace(64, distances=.789),
-         ift.RGSpace([32, 32], distances=.789)],
-        [4, 78, 23]
-        ))
-    def testGaussian(self, space, seed):
-        model = self.make_model(
-            space_key='s1', space=space, seed=seed)['s1']
-        energy = ift.GaussianEnergy(domain=space)
-        ift.extra.check_value_gradient_consistency(energy, model)
-
-#     @expand(product(
-#         [ift.GLSpace(15),
-#          ift.RGSpace(64, distances=.789),
-#          ift.RGSpace([32, 32], distances=.789)],
-#         [4, 78, 23]
-#         ))
-#     def testQuadratic(self, type1, space, seed):
-#         np.random.seed(seed)
-#         S = ift.ScalingOperator(1., space)
-#         s = [S.draw_sample() for _ in range(3)]
-#         energy = ift.QuadraticEnergy(s[0], ift.makeOp(s[1]), s[2])
-#         ift.extra.check_value_gradient_consistency(energy)
-
-    @expand(
-        product([
-            ift.GLSpace(15),
-            ift.RGSpace(64, distances=.789),
-            ift.RGSpace([32, 32], distances=.789)
-        ], [4, 78, 23]))
-    def testInverseGammaLikelihood(self, space, seed):
-        model = self.make_model(space_key='s1', space=space, seed=seed)['s1']
-        model = model.exp()
-        d = np.random.normal(10, size=space.shape)**2
-        d = ift.Field.from_global_data(space, d)
-        energy = ift.InverseGammaLikelihood(d)
-        ift.extra.check_value_gradient_consistency(energy, model, tol=1e-7)
-
-    @expand(product(
-        [ift.GLSpace(15),
-         ift.RGSpace(64, distances=.789),
-         ift.RGSpace([32, 32], distances=.789)],
-        [4, 78, 23]
-        ))
-    def testPoissonian(self, space, seed):
-        model = self.make_model(
-            space_key='s1', space=space, seed=seed)['s1']
-        model = model.exp()
-        d = np.random.poisson(120, size=space.shape)
-        d = ift.Field.from_global_data(space, d)
-        energy = ift.PoissonianEnergy(d)
-        ift.extra.check_value_gradient_consistency(energy, model, tol=1e-7)
-
-    @expand(product(
-        [ift.GLSpace(15),
-         ift.RGSpace(64, distances=.789),
-         ift.RGSpace([32, 32], distances=.789)],
-        [4, 78, 23]
-        ))
-    def testHamiltonian_and_KL(self, space, seed):
-        model = self.make_model(
-            space_key='s1', space=space, seed=seed)['s1']
-        model = model.exp()
-        lh = ift.GaussianEnergy(domain=space)
-        hamiltonian = ift.Hamiltonian(lh)
-        ift.extra.check_value_gradient_consistency(hamiltonian, model)
-        S = ift.ScalingOperator(1., space)
-        samps = [S.draw_sample() for i in range(3)]
-        kl = ift.SampledKullbachLeiblerDivergence(hamiltonian, samps)
-        ift.extra.check_value_gradient_consistency(kl, model)
-
-    @expand(product(
-        [ift.GLSpace(15),
-         ift.RGSpace(64, distances=.789),
-         ift.RGSpace([32, 32], distances=.789)],
-        [4, 78, 23]
-        ))
-    def testBernoulli(self, space, seed):
-        model = self.make_model(
-            space_key='s1', space=space, seed=seed)['s1']
-        model = model.positive_tanh()
-        d = np.random.binomial(1, 0.1, size=space.shape)
-        d = ift.Field.from_global_data(space, d)
-        energy = ift.BernoulliEnergy(d)
-        ift.extra.check_value_gradient_consistency(energy, model, tol=1e-6)

test/test_energy_gradients.py

+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright(C) 2013-2019 Max-Planck-Society
+#
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
+
+import numpy as np
+import pytest
+
+import nifty5 as ift
+from itertools import product
+
+# Currently it is not possible to parametrize fixtures. But this will
+# hopefully be fixed in the future.
+# https://docs.pytest.org/en/latest/proposals/parametrize_with_fixtures.html
+
+SPACES = [
+    ift.GLSpace(15),
+    ift.RGSpace(64, distances=.789),
+    ift.RGSpace([32, 32], distances=.789)
+]
+SEEDS = [4, 78, 23]
+PARAMS = product(SEEDS, SPACES)
+
+
+@pytest.fixture(params=PARAMS)
+def field(request):
+    np.random.seed(request.param[0])
+    S = ift.ScalingOperator(1., request.param[1])
+    s = S.draw_sample()
+    return ift.MultiField.from_dict({'s1': s})['s1']
+
+
+def test_gaussian(field):
+    energy = ift.GaussianEnergy(domain=field.domain)
+    ift.extra.check_value_gradient_consistency(energy, field)
+
+
+def test_inverse_gamma(field):
+    field = field.exp()
+    space = field.domain
+    d = np.random.normal(10, size=space.shape)**2
+    d = ift.Field.from_global_data(space, d)
+    energy = ift.InverseGammaLikelihood(d)
+    ift.extra.check_value_gradient_consistency(energy, field, tol=1e-7)
+
+
+def testPoissonian(field):
+    field = field.exp()
+    space = field.domain
+    d = np.random.poisson(120, size=space.shape)
+    d = ift.Field.from_global_data(space, d)
+    energy = ift.PoissonianEnergy(d)
+    ift.extra.check_value_gradient_consistency(energy, field, tol=1e-7)
+
+
+def test_hamiltonian_and_KL(field):
+    field = field.exp()
+    space = field.domain
+    lh = ift.GaussianEnergy(domain=space)
+    hamiltonian = ift.Hamiltonian(lh)
+    ift.extra.check_value_gradient_consistency(hamiltonian, field)
+    S = ift.ScalingOperator(1., space)
+    samps = [S.draw_sample() for i in range(3)]
+    kl = ift.SampledKullbachLeiblerDivergence(hamiltonian, samps)
+    ift.extra.check_value_gradient_consistency(kl, field)
+
+
+def test_bernoulli(field):
+    field = field.positive_tanh()
+    space = field.domain
+    d = np.random.binomial(1, 0.1, size=space.shape)
+    d = ift.Field.from_global_data(space, d)
+    energy = ift.BernoulliEnergy(d)
+    ift.extra.check_value_gradient_consistency(energy, field, tol=1e-6)

test/test_energies/test_map.py → test/test_gaussian_metric.py

@@ -15,61 +15,67 @@
 #
 # NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
 
-import unittest
-from itertools import product
-from test.common import expand
+import numpy as np
+import pytest
 
 import nifty5 as ift
-import numpy as np
 
 
 def _flat_PS(k):
     return np.ones_like(k)
 
 
-class Energy_Tests(unittest.TestCase):
-    @expand(product([ift.GLSpace(15),
-                     ift.RGSpace(64, distances=.789),
-                     ift.RGSpace([32, 32], distances=.789)],
-                    ["tanh", "exp", ""],
-                    [1, 1e-2, 1e2],
-                    [4, 78, 23]))
-    def testGaussianEnergy(self, space, nonlinearity, noise, seed):
-        np.random.seed(seed)
-        dim = len(space.shape)
-        hspace = space.get_default_codomain()
-        ht = ift.HarmonicTransformOperator(hspace, target=space)
-        binbounds = ift.PowerSpace.useful_binbounds(hspace, logarithmic=False)
-        pspace = ift.PowerSpace(hspace, binbounds=binbounds)
-        Dist = ift.PowerDistributor(target=hspace, power_space=pspace)
-        xi0 = ift.Field.from_random(domain=hspace, random_type='normal')
-        xi0_var = ift.Linearization.make_var(xi0)
+pmp = pytest.mark.parametrize
 
-        def pspec(k): return 1 / (1 + k**2)**dim
-        pspec = ift.PS_field(pspace, pspec)
-        A = Dist(ift.sqrt(pspec))
-        N = ift.ScalingOperator(noise, space)
-        n = N.draw_sample()
-        s = ht(ift.makeOp(A)(xi0_var))
-        R = ift.ScalingOperator(10., space)
 
-        def d_model():
-            if nonlinearity == "":
-                return R(ht(ift.makeOp(A)))
-            else:
-                tmp = ht(ift.makeOp(A))
-                nonlin = getattr(tmp, nonlinearity)()
-                return R(nonlin)
+@pmp('space', [
+    ift.GLSpace(15),
+    ift.RGSpace(64, distances=.789),
+    ift.RGSpace([32, 32], distances=.789)
+])
+@pmp('nonlinearity', ["tanh", "exp", ""])
+@pmp('noise', [1, 1e-2, 1e2])
+@pmp('seed', [4, 78, 23])
+def test_gaussian_energy(space, nonlinearity, noise, seed):
+    np.random.seed(seed)
+    dim = len(space.shape)
+    hspace = space.get_default_codomain()
+    ht = ift.HarmonicTransformOperator(hspace, target=space)
+    binbounds = ift.PowerSpace.useful_binbounds(hspace, logarithmic=False)
+    pspace = ift.PowerSpace(hspace, binbounds=binbounds)
+    Dist = ift.PowerDistributor(target=hspace, power_space=pspace)
+    xi0 = ift.Field.from_random(domain=hspace, random_type='normal')
+    # FIXME Needed?
+    xi0_var = ift.Linearization.make_var(xi0)
 
-        d = d_model()(xi0) + n
+    def pspec(k):
+        return 1/(1 + k**2)**dim
 
-        if noise == 1:
-            N = None
+    pspec = ift.PS_field(pspace, pspec)
+    A = Dist(ift.sqrt(pspec))
+    N = ift.ScalingOperator(noise, space)
+    n = N.draw_sample()
+    # FIXME Needed?
+    s = ht(ift.makeOp(A)(xi0_var))
+    R = ift.ScalingOperator(10., space)
 
-        energy = ift.GaussianEnergy(d, N)(d_model())
+    def d_model():
         if nonlinearity == "":
-            ift.extra.check_value_gradient_metric_consistency(
-                energy, xi0, ntries=10)
+            return R(ht(ift.makeOp(A)))
         else:
-            ift.extra.check_value_gradient_consistency(
-                energy, xi0, ntries=10, tol=5e-8)
+            tmp = ht(ift.makeOp(A))
+            nonlin = getattr(tmp, nonlinearity)()
+            return R(nonlin)
+
+    d = d_model()(xi0) + n
+
+    if noise == 1:
+        N = None
+
+    energy = ift.GaussianEnergy(d, N)(d_model())
+    if nonlinearity == "":
+        ift.extra.check_value_gradient_metric_consistency(
+            energy, xi0, ntries=10)
+    else:
+        ift.extra.check_value_gradient_consistency(
+            energy, xi0, ntries=10, tol=5e-8)

test/test_minimization/test_minimizers.py

-# This program is free software: you can redistribute it and/or modify
-# it under the terms of the GNU General Public License as published by
-# the Free Software Foundation, either version 3 of the License, or
-# (at your option) any later version.
-#
-# This program is distributed in the hope that it will be useful,
-# but WITHOUT ANY WARRANTY; without even the implied warranty of
-# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
-# GNU General Public License for more details.
-#
-# You should have received a copy of the GNU General Public License
-# along with this program.  If not, see <http://www.gnu.org/licenses/>.
-#
-# Copyright(C) 2013-2019 Max-Planck-Society
-#
-# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
-
-import unittest
-from itertools import product
-from test.common import expand
-
-import nifty5 as ift
-import numpy as np
-from unittest import SkipTest
-from numpy.testing import assert_allclose, assert_equal
-
-IC = ift.GradientNormController(tol_abs_gradnorm=1e-5, iteration_limit=1000)
-
-spaces = [ift.RGSpace([1024], distances=0.123), ift.HPSpace(32)]
-
-minimizers = ['ift.VL_BFGS(IC)',
-              'ift.NonlinearCG(IC, "Polak-Ribiere")',
-              # 'ift.NonlinearCG(IC, "Hestenes-Stiefel"),
-              'ift.NonlinearCG(IC, "Fletcher-Reeves")',
-              'ift.NonlinearCG(IC, "5.49")',
-              'ift.L_BFGS_B(ftol=1e-10, gtol=1e-5, maxiter=1000)',
-              'ift.L_BFGS(IC)',
-              'ift.NewtonCG(IC)']
-
-newton_minimizers = ['ift.RelaxedNewton(IC)']
-quadratic_only_minimizers = ['ift.ConjugateGradient(IC)',
-                             'ift.ScipyCG(tol=1e-5, maxiter=300)']
-slow_minimizers = ['ift.SteepestDescent(IC)']
-
-
-class Test_Minimizers(unittest.TestCase):
-
-    @expand(product(minimizers + newton_minimizers +
-                    quadratic_only_minimizers + slow_minimizers, spaces))
-    def test_quadratic_minimization(self, minimizer, space):
-        np.random.seed(42)
-        starting_point = ift.Field.from_random('normal', domain=space)*10
-        covariance_diagonal = ift.Field.from_random(
-                                  'uniform', domain=space) + 0.5
-        covariance = ift.DiagonalOperator(covariance_diagonal)
-        required_result = ift.full(space, 1.)
-
-        try:
-            minimizer = eval(minimizer)
-            energy = ift.QuadraticEnergy(A=covariance, b=required_result,
-                                         position=starting_point)
-
-            (energy, convergence) = minimizer(energy)
-        except NotImplementedError:
-            raise SkipTest
-
-        assert_equal(convergence, IC.CONVERGED)
-        assert_allclose(energy.position.local_data,
-                        1./covariance_diagonal.local_data,
-                        rtol=1e-3, atol=1e-3)
-
-    @expand(product(minimizers+newton_minimizers))
-    def test_rosenbrock(self, minimizer):
-        try:
-            from scipy.optimize import rosen, rosen_der, rosen_hess_prod
-        except ImportError:
-            raise SkipTest
-        np.random.seed(42)
-        space = ift.DomainTuple.make(ift.UnstructuredDomain((2,)))
-        starting_point = ift.Field.from_random('normal', domain=space)*10
-
-        class RBEnergy(ift.Energy):
-            def __init__(self, position):
-                super(RBEnergy, self).__init__(position)
-
-            @property
-            def value(self):
-                return rosen(self._position.to_global_data_rw())
-
-            @property
-            def gradient(self):
-                inp = self._position.to_global_data_rw()
-                out = ift.Field.from_global_data(space, rosen_der(inp))
-                return out
-
-            @property
-            def metric(self):
-                class RBCurv(ift.EndomorphicOperator):
-                    def __init__(self, loc):
-                        self._loc = loc.to_global_data_rw()
-                        self._capability = self.TIMES
-                        self._domain = space
-
-                    def apply(self, x, mode):
-                        self._check_input(x, mode)
-                        inp = x.to_global_data_rw()
-                        out = ift.Field.from_global_data(
-                            space, rosen_hess_prod(self._loc.copy(), inp))
-                        return out
-
-                t1 = ift.GradientNormController(tol_abs_gradnorm=1e-5,
-                                                iteration_limit=1000)
-                return ift.InversionEnabler(RBCurv(self._position), t1)
-
-            def apply_metric(self, x):
-                inp = x.to_global_data_rw()
-                pos = self._position.to_global_data_rw()
-                return ift.Field.from_global_data(
-                    space, rosen_hess_prod(pos, inp))
-
-        try:
-            minimizer = eval(minimizer)
-            energy = RBEnergy(position=starting_point)
-
-            (energy, convergence) = minimizer(energy)
-        except NotImplementedError:
-            raise SkipTest
-
-        assert_equal(convergence, IC.CONVERGED)
-        assert_allclose(energy.position.local_data, 1.,
-                        rtol=1e-3, atol=1e-3)
-
-    @expand(product(minimizers+slow_minimizers))
-    def test_gauss(self, minimizer):
-        space = ift.UnstructuredDomain((1,))
-        starting_point = ift.Field.full(space, 3.)
-
-        class ExpEnergy(ift.Energy):
-            def __init__(self, position):
-                super(ExpEnergy, self).__init__(position)
-
-            @property
-            def value(self):
-                x = self.position.to_global_data()[0]
-                return -np.exp(-(x**2))
-
-            @property
-            def gradient(self):
-                x = self.position.to_global_data()[0]
-                return ift.Field.full(self.position.domain,
-                                      2*x*np.exp(-(x**2)))
-
-            def apply_metric(self, x):
-                p = self.position.to_global_data()[0]
-                v = (2 - 4*p*p)*np.exp(-p**2)
-                return ift.DiagonalOperator(
-                    ift.Field.full(self.position.domain, v))(x)
-
-        try:
-            minimizer = eval(minimizer)
-            energy = ExpEnergy(position=starting_point)
-
-            (energy, convergence) = minimizer(energy)
-        except NotImplementedError:
-            raise SkipTest
-
-        assert_equal(convergence, IC.CONVERGED)
-        assert_allclose(energy.position.local_data, 0.,
-                        atol=1e-3)
-
-    @expand(product(minimizers+newton_minimizers+slow_minimizers))
-    def test_cosh(self, minimizer):
-        space = ift.UnstructuredDomain((1,))
-        starting_point = ift.Field.full(space, 3.)
-
-        class CoshEnergy(ift.Energy):
-            def __init__(self, position):
-                super(CoshEnergy, self).__init__(position)
-
-            @property
-            def value(self):
-                x = self.position.to_global_data()[0]
-                return np.cosh(x)
-
-            @property
-            def gradient(self):
-                x = self.position.to_global_data()[0]
-                return ift.Field.full(self.position.domain, np.sinh(x))
-
-            @property
-            def metric(self):
-                x = self.position.to_global_data()[0]
-                v = np.cosh(x)
-                return ift.DiagonalOperator(
-                    ift.Field.full(self.position.domain, v))
-
-            def apply_metric(self, x):
-                p = self.position.to_global_data()[0]
-                v = np.cosh(p)
-                return ift.DiagonalOperator(
-                    ift.Field.full(self.position.domain, v))(x)
-
-        try:
-            minimizer = eval(minimizer)
-            energy = CoshEnergy(position=starting_point)
-
-            (energy, convergence) = minimizer(energy)
-        except NotImplementedError:
-            raise SkipTest
-
-        assert_equal(convergence, IC.CONVERGED)
-        assert_allclose(energy.position.local_data, 0., atol=1e-3)

test/test_minimizers.py

+# This program is free software: you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation, either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License
+# along with this program.  If not, see <http://www.gnu.org/licenses/>.
+#
+# Copyright(C) 2013-2019 Max-Planck-Society
+#
+# NIFTy is being developed at the Max-Planck-Institut fuer Astrophysik.
+
+from unittest import SkipTest
+