TST: Fix largescale pytest mark issue

doc/source/dev/testing.rst

@@ -7,15 +7,15 @@ Testing in ODL
 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
-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
-==============  =========================  =======
+==============  ==========================  =======
+Name            Command                     Description
+==============  ==========================  =======
+Unit tests      ``pytest``                  Test "micro-features" of the code
+Large-scale     ``pytest -S largescale``    Unit tests with large inputs and more cases
+Doctests        ``pytest``                  Validate usage examples in docstrings
+Examples        ``pytest -S examples``      Run all examples in the `examples`_ folder
+Documentation   ``pytest -S doc_doctests``  Run the doctest examples in the Sphinx documentation
+==============  ==========================  =======
 
 Unit tests
 ~~~~~~~~~~
@@ -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
 
 
@@ -116,7 +116,7 @@ Examples
 Examples, while not technically tests in the traditional sense, still constitute a part of the test framework for ODL by showing how different parts of ODL work together and by ensuring that functions that depend on each other work as expected.
 The main purpose of the examples is however to show ODL from a users perspective and particular care should be taken to keep them readable and working since this is often the first thing users see when they start using ODL.
 
-It is even possible to run all examples as part of the test suite by running ``pytest --examples``, but be aware that this requires all ODL dependencies to be installed and that plotting windows can be opened during execution.
+It is even possible to run all examples as part of the test suite by running ``pytest -S examples``, but be aware that this requires all ODL dependencies to be installed and can take a long time.
 
 Consult the `examples`_ directory for an impression of the style in which ODL examples are written.
 

odl/pytest.ini

@@ -1,15 +1,10 @@
 [pytest]
-minversion = 3.0.3
-markers = not benchmark and not largescale
 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', 'largescale'])

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

@@ -93,10 +93,7 @@ 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
 
@@ -108,7 +105,7 @@ def tspace(odl_floating_dtype, odl_tspace_impl):
     return odl.tensor_space(shape=(3, 4), dtype=dtype, impl=impl)
 
 
-# --- Space classes --- #
+# --- Tests --- #
 
 
 def test_init_npy_tspace():
@@ -451,8 +448,8 @@ 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/test_doc.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2018 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -16,26 +16,26 @@
 """
 
 from __future__ import division
+
 import doctest
-from doctest import IGNORE_EXCEPTION_DETAIL, ELLIPSIS, NORMALIZE_WHITESPACE
 import os
+from doctest import ELLIPSIS, IGNORE_EXCEPTION_DETAIL, NORMALIZE_WHITESPACE
+
+import numpy
 import pytest
+
+import odl
+from odl.util.testutils import simple_fixture
+
 try:
     import matplotlib
-    matplotlib.use('Agg')  # To avoid the backend freezing
+    matplotlib.use('agg')  # prevent backend from freezing
     import matplotlib.pyplot as plt
 except ImportError:
     pass
 
-# Modules to be added to testing globals
-import numpy
-import odl
-try:
-    import proximal
-except ImportError:
-    proximal = None
 
-doctest_extraglobs = {'odl': odl, 'np': numpy, 'proximal': proximal}
+doctest_extraglobs = {'odl': odl, 'np': numpy}
 
 root_dir = os.path.join(os.path.abspath(os.path.dirname(__file__)),
                         os.pardir, os.pardir, 'doc', 'source')
@@ -55,13 +55,10 @@
                 doc_src_files.append(os.path.join(path, filename))
 
 
-@pytest.fixture(scope="module", ids=doc_src_files, params=doc_src_files)
-def doc_src_file(request):
-    return request.param
+doc_src_file = simple_fixture("doc_src_file", doc_src_files)
 
 
-@pytest.mark.skipif("not pytest.config.getoption('--doctest-doc')",
-                    reason='Need --doctest-doc option to run')
+@pytest.mark.suite("doc_doctests")
 def test_file(doc_src_file):
     # FIXXXME: This doesn't seem to actually test the file :-(
     doctest.testfile(doc_src_file, module_relative=False, report=True,

odl/test/test_examples.py

@@ -1,4 +1,4 @@
-# Copyright 2014-2017 The ODL contributors
+# Copyright 2014-2020 The ODL contributors
 #
 # This file is part of ODL.
 #
@@ -19,10 +19,14 @@
 """
 
 from __future__ import division
+
 import os
-import pytest
 import sys
+
+import pytest
+
 import odl
+from odl.util.testutils import simple_fixture
 
 try:
     import matplotlib
@@ -36,23 +40,18 @@
 # Make a fixture for all examples
 here = os.path.dirname(os.path.abspath(__file__))
 examples_path = os.path.join(here, os.path.pardir, os.path.pardir, 'examples')
-example_ids = []
 example_params = []
 for dirpath, dirnames, filenames in os.walk(examples_path):
     for filename in [f for f in filenames
                      if f.endswith('.py') and
                      not any(f.startswith(pre) for pre in ignore_prefix)]:
         example_params.append(os.path.join(dirpath, filename))
-        example_ids.append(filename[:-3])  # skip .py
 
 
-@pytest.fixture(scope="module", ids=example_ids, params=example_params)
-def example(request):
-    return request.param
+example = simple_fixture("example", example_params)
 
 
-@pytest.mark.skipif("not pytest.config.getoption('--examples')",
-                    reason='Need --examples option to run')
+@pytest.mark.suite("examples")
 def test_example(example):
     if (sys.version_info.major, sys.version_info.minor) <= (3, 3):
         # The `imp` module is deprecated since 3.4