TST: Fix largescale pytest mark issue

We change the command-line option to a version recommended in
the pytest docs:
https://docs.pytest.org/en/latest/example/markers.html#custom-marker-and-command-line-option-to-control-test-runs

- A global `suite(name)` mark is registered, that takes a
  name and marks a test as belonging to a specific suite.
- These special suites are opt-in, i.e., not run by default.
- To enable a suite, one adds `-S name` to the pytest
  command-line options.
- Since function-scoped fixtures are handled stricter now,
  the workaround in tensors_test.py didn't work any longer
  (see pytest-dev/pytest#6497).
- We thus set the minimum pytest version to 5.4.0, where the
  fix for the issue is implemented.

Closes: odlgroup#1514

doc/source/dev/testing.rst

@@ -11,7 +11,7 @@ ODL tests are run using pytest_, and there are several types:
 Name            Command                    Description
 ==============  =========================  =======
 Unit tests      ``pytest``                 Test "micro-features" of the code
-Large-scale     ``pytest --largescale``    Unit tests with large inputs and more cases
+Large-scale     ``pytest -S largescale``   Unit tests with large inputs and more cases
 Doctests        ``pytest``                 Validate usage examples in docstrings
 Examples        ``pytest --examples``      Run all examples in the `examples`_ folder
 Documentation   ``pytest --doctest-doc``   Run the doctest examples in the Sphinx documentation
@@ -33,7 +33,7 @@ For more information consult the `pytest`_ documentation and look at existing te
 
 
     def myfunction(x):
-        """Convert ``x`` to a integer and add 1"""
+        """Convert ``x`` to a integer and add 1."""
         return int(x) + 1
 
 

odl/pytest.ini

@@ -1,15 +1,11 @@
 [pytest]
-minversion = 3.0.3
-markers = not benchmark and not largescale
+minversion = 5.4.0
 testpaths = odl
 doctest_optionflags = NORMALIZE_WHITESPACE IGNORE_EXCEPTION_DETAIL ELLIPSIS
-addopts = --doctest-modules
+addopts = --doctest-modules --strict-markers
 xfail_strict=true
 
 # PEP8
 pep8ignore =
     E402
 pep8maxlinelength = 79
-# Temporary fix for https://github.com/odlgroup/odl/issues/1514, works with pytest<5.1
-filterwarnings =
-    ignore::pytest.PytestDeprecationWarning

odl/test/largescale/solvers/nonsmooth/default_functionals_slow_test.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2019 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -16,14 +16,13 @@
 
 import odl
 from odl.solvers.functional.functional import FunctionalDefaultConvexConjugate
-from odl.util.testutils import (
-    all_almost_equal, noise_element, simple_fixture, skip_if_no_largescale)
-
+from odl.util.testutils import all_almost_equal, noise_element, simple_fixture
 
 # --- pytest fixtures --- #
 
 
-pytestmark = skip_if_no_largescale
+# Global pytest mark
+pytestmark = pytest.mark.suite('largescale')
 
 
 stepsize = simple_fixture('stepsize', [0.1, 1.0, 10.0])
@@ -72,8 +71,11 @@ def functional(request, linear_offset, quadratic_offset, dual):
                                        outer_exp=outer_exp,
                                        singular_vector_exp=singular_vector_exp)
     elif name == 'quadratic':
-        func = odl.solvers.QuadraticForm(operator=odl.IdentityOperator(space),
-                                         vector=space.one(), constant=0.623)
+        func = odl.solvers.QuadraticForm(
+            operator=odl.IdentityOperator(space),
+            vector=space.one(),
+            constant=0.623,
+        )
     elif name == 'linear':
         func = odl.solvers.QuadraticForm(vector=space.one(), constant=0.623)
     elif name == 'huber':
@@ -91,7 +93,8 @@ def functional(request, linear_offset, quadratic_offset, dual):
 
         quadratic_coeff = 1.32
         func = odl.solvers.FunctionalQuadraticPerturb(
-            func, quadratic_coeff=quadratic_coeff, linear_term=g)
+            func, quadratic_coeff=quadratic_coeff, linear_term=g
+        )
 
     elif linear_offset:
         g = noise_element(space)
@@ -279,4 +282,4 @@ def test_proximal_convex_conj_kl_cross_entropy_solving_opt_problem():
 
 
 if __name__ == '__main__':
-    odl.util.test_file(__file__, ['--largescale'])
+    odl.util.test_file(__file__, ['-S', 'slow'])

odl/test/largescale/space/tensor_space_slow_test.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2019 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -14,14 +14,13 @@
 import pytest
 
 import odl
-from odl.util.testutils import (
-    all_almost_equal, dtype_tol, noise_elements, skip_if_no_largescale)
-
+from odl.util.testutils import all_almost_equal, dtype_tol, noise_elements
 
 # --- pytest fixtures --- #
 
 
-pytestmark = skip_if_no_largescale
+# Global pytest mark
+pytestmark = pytest.mark.suite('largescale')
 
 
 spc_params = ['rn', '1d', '3d']
@@ -333,4 +332,4 @@ def idiv_aliased(x):
 
 
 if __name__ == '__main__':
-    odl.util.test_file(__file__)
+    odl.util.test_file(__file__, ['-S', 'largescale'])

odl/test/largescale/tomo/analytic_slow_test.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2017 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -17,13 +17,13 @@
 import odl.tomo as tomo
 from odl.tomo.util.testutils import (
     skip_if_no_astra, skip_if_no_astra_cuda, skip_if_no_skimage)
-from odl.util.testutils import simple_fixture, skip_if_no_largescale
-
+from odl.util.testutils import simple_fixture
 
 # --- pytest fixtures --- #
 
 
-pytestmark = skip_if_no_largescale
+# Global pytest mark
+pytestmark = pytest.mark.suite('largescale')
 
 
 filter_type = simple_fixture(
@@ -230,4 +230,4 @@ def test_fbp_reconstruction_filters(filter_type, frequency_scaling, weighting):
 
 
 if __name__ == '__main__':
-    odl.util.test_file(__file__, ['--largescale'])
+    odl.util.test_file(__file__, ['-S', 'largescale'])

odl/test/largescale/tomo/ray_transform_slow_test.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2019 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -17,13 +17,13 @@
 import odl
 from odl.tomo.util.testutils import (
     skip_if_no_astra, skip_if_no_astra_cuda, skip_if_no_skimage)
-from odl.util.testutils import simple_fixture, skip_if_no_largescale
-
+from odl.util.testutils import all_almost_equal, simple_fixture
 
 # --- pytest fixtures --- #
 
 
-pytestmark = skip_if_no_largescale
+# Global pytest mark
+pytestmark = pytest.mark.suite('largescale')
 
 
 dtype_params = ['float32', 'float64', 'complex64']
@@ -212,7 +212,7 @@ def test_adjoint_of_adjoint(projector):
     proj_adj_adj_adj = projector.adjoint.adjoint.adjoint(proj)
 
     # Verify A^*(y) == ((A^*)^*)^*(x)
-    assert proj_adj == proj_adj_adj_adj
+    assert all_almost_equal(proj_adj, proj_adj_adj_adj)
 
 
 def test_reconstruction(projector):
@@ -243,4 +243,4 @@ def test_reconstruction(projector):
 
 
 if __name__ == '__main__':
-    odl.util.test_file(__file__, ['--largescale'])
+    odl.util.test_file(__file__, ['-S', 'largescale'])

odl/test/largescale/trafos/fourier_slow_test.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2019 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -18,14 +18,13 @@
 import pytest
 
 import odl
-from odl.util.testutils import (
-    simple_fixture, skip_if_no_largescale, skip_if_no_pyfftw)
-
+from odl.util.testutils import simple_fixture, skip_if_no_pyfftw
 
 # --- pytest fixtures --- #
 
 
-pytestmark = skip_if_no_largescale
+# Global pytest mark
+pytestmark = pytest.mark.suite('largescale')
 
 
 impl = simple_fixture(
@@ -85,4 +84,4 @@ def charfun_freq_ball(x):
 
 
 if __name__ == '__main__':
-    odl.util.test_file(__file__, ['--largescale'])
+    odl.util.test_file(__file__, ['-S', 'largescale'])

odl/test/space/tensors_test.py

@@ -93,22 +93,21 @@ def _weighting_cls(impl, kind):
 weight_ids = [' weight=1.0 ', ' weight=0.5 ', ' weight=<array> ']
 
 
-# scope='module' removed due to pytest issue, see
-# https://github.com/pytest-dev/pytest/issues/6497
-# TODO: re-introduce when fixed
-@pytest.fixture(params=weight_params, ids=weight_ids)
+@pytest.fixture(scope='module', params=weight_params, ids=weight_ids)
 def weight(request):
     return request.param
 
 
 @pytest.fixture(scope='module')
-def tspace(odl_floating_dtype, odl_tspace_impl):
+def tspace(odl_floating_dtype, odl_tspace_impl, weight):
     impl = odl_tspace_impl
     dtype = odl_floating_dtype
-    return odl.tensor_space(shape=(3, 4), dtype=dtype, impl=impl)
+    return odl.tensor_space(
+        shape=(3, 4), dtype=dtype, impl=impl, weighting=weight
+    )
 
 
-# --- Space classes --- #
+# --- Tests --- #
 
 
 def test_init_npy_tspace():
@@ -451,8 +450,8 @@ def test_lincomb_discontig(odl_tspace_impl):
             _test_lincomb(tspace, a, b, discontig=True)
 
 
-def test_lincomb_raise(tspace):
-    """Test if lincomb raises correctly for bad input."""
+def test_lincomb_exceptions(tspace):
+    """Test whether lincomb raises correctly for bad output element."""
     other_space = odl.rn((4, 3), impl=tspace.impl)
 
     other_x = other_space.zero()

odl/test/util/normalize_test.py

@@ -22,10 +22,6 @@
 length = simple_fixture('length', [1, 2])
 
 
-# For this and other fixtures below:
-# scope='module' removed due to pytest issue, see
-# https://github.com/pytest-dev/pytest/issues/6497
-# TODO: re-introduce when fixed
 single_conv_params = [(-1.0, float),
                       (2, float),
                       ('10', float),
@@ -41,7 +37,7 @@
                    for p in single_conv_params]
 
 
-@pytest.fixture(ids=single_conv_ids, params=single_conv_params)
+@pytest.fixture(scope='module', ids=single_conv_ids, params=single_conv_params)
 def single_conv(request):
     return request.param
 
@@ -64,7 +60,7 @@ def single_conv(request):
                 for p in seq_conv_params]
 
 
-@pytest.fixture(ids=seq_conv_ids, params=seq_conv_params)
+@pytest.fixture(scope='module', ids=seq_conv_ids, params=seq_conv_params)
 def seq_conv(request):
     return request.param
 
@@ -82,7 +78,7 @@ def seq_conv(request):
                  for axis in axes_conv_params]
 
 
-@pytest.fixture(ids=axes_conv_ids, params=axes_conv_params)
+@pytest.fixture(scope='module', ids=axes_conv_ids, params=axes_conv_params)
 def axes_conv(request):
     return request.param