Distribute tests

.pypirc

@@ -1,6 +1,12 @@
 [distutils]
-index-servers=pypi
+index-servers=
+    pypi
+    pypitest
 
 [pypi]
-repository = https://pypi.python.org/pypi
-username = kohr-h
+repository = https://upload.pypi.org/legacy
+username = odlgroup
+
+[pypitest]
+repository = https://test.pypi.org/legacy
+username = kohr-h

.travis.yml

@@ -50,7 +50,7 @@ before_script:
 
 script:
   # Run tests, including PEP8 check, and produce a coverage report
-  - py.test --doctest-modules --cov --cov-report term-missing --pep8
+  - py.test --doctest-modules --cov --cov-report term-missing --pep8 $TRAVIS_BUILD_DIR/odl
   # Build the Sphinx doc (only for Python 3.5 and the master branch)
   - if [[ "$TRAVIS_PYTHON_VERSION" == "3.5" && "$TRAVIS_BRANCH" == "master" ]]; then
       cd $TRAVIS_BUILD_DIR/doc/source && python generate_doc.py && cd -;

MANIFEST.in

@@ -5,3 +5,6 @@ include requirements.txt
 include setup.cfg
 include setup.py
 include test_requirements.txt
+include odl/pytest.ini
+exclude pytest.ini
+recursive-include odl/test test*.py *test.py

conda/meta.yaml

@@ -1,11 +1,11 @@
 package:
     name: odl
-    version: "0.5.0"
+    version: "0.5.1"
 
 source:
     git_url: https://github.com/odlgroup/odl
-    git_rev: master  # for testing, put any branch here
-    # git_rev: v0.5.0  # release
+    # git_rev: master  # for testing, put any branch here
+    git_rev: v0.5.1  # release
 
 build:
     noarch_python: True
@@ -30,6 +30,8 @@ requirements:
 test:
     imports:
         - odl
+    commands:
+        - python -c "import odl; odl.test()"
 
 about:
     home: https://github.com/odlgroup/odl

doc/source/getting_started/installing.rst

@@ -408,7 +408,7 @@ After that, follow the `build instructions there <https://github.com/odlgroup/od
 
 ASTRA for X-ray tomography
 ==========================
-To calculate fast forward and backward projections for image reconstruction in X-ray tomography, install the `ASTRA tomography toolbox`_.
+To calculate fast forward and backward projections for image reconstruction in X-ray tomography, install the `ASTRA tomography toolbox <https://github.com/astra-toolbox/astra-toolbox>`_.
 ASTRA projectors are fully supported in ODL.
 
 You can try using the conda package, but we can give no guarantee that it works out of the box:
@@ -417,7 +417,7 @@ You can try using the conda package, but we can give no guarantee that it works
 
     $ conda install -c astra-toolbox astra-toolbox
 
-For further instructions, check `the ASTRA GitHub page <ASTRA tomography toolbox>`_.
+For further instructions, check `the ASTRA GitHub page <https://github.com/astra-toolbox/astra-toolbox>`_.
 
 
 STIR for emission tomography
@@ -467,5 +467,5 @@ If that does not help, `make an issue on GitHub <https://github.com/odlgroup/odl
 .. _CVXPY: http://www.cvxpy.org/en/latest/
 .. _odlcuda: https://github.com/odlgroup/odlcuda
 .. _CUDA toolkit: https://developer.nvidia.com/cuda-toolkit
-.. _ASTRA tomography toolbox: https://github.com/astra-toolbox/astra-toolbox
+.. _ASTRA: https://github.com/astra-toolbox/astra-toolbox
 .. _STIR: https://github.com/UCL/STIR

doc/source/release_notes.rst

@@ -9,6 +9,12 @@ Release Notes
 Next release
 ============
 
+ODL 0.5.1 Release Notes (2016-10-22)
+====================================
+
+This is a maintenance release since the test suite was not bundled with PyPI and Conda packages as intended already in 0.5.0.
+From this version on, users can run ``python -c "import odl; odl.test()"`` with all types of installations (from PyPI, Conda or from source).
+
 
 ODL 0.5.0 Release Notes (2016-10-21)
 ====================================

odl/__init__.py

@@ -25,7 +25,7 @@
 
 from __future__ import absolute_import
 
-__version__ = '0.5.0'
+__version__ = '0.5.1'
 __all__ = ('diagnostics', 'discr', 'operator', 'set', 'space', 'solvers',
            'tomo', 'trafos', 'util', 'phantom', 'deform')
 

odl/test/test_doc.py

@@ -33,6 +33,12 @@
 from doctest import IGNORE_EXCEPTION_DETAIL, ELLIPSIS, NORMALIZE_WHITESPACE
 import os
 import pytest
+try:
+    import matplotlib
+    matplotlib.use('Agg')  # To avoid the backend freezing
+    import matplotlib.pyplot as plt
+except ImportError:
+    pass
 
 # Modules to be added to testing globals
 import numpy
@@ -69,13 +75,14 @@ def doc_src_file(request):
     return request.param
 
 
-@pytest.mark.skipif("not pytest.config.getoption('--documentation')",
-                    reason='Need --documentation option to run')
+@pytest.mark.skipif("not pytest.config.getoption('--doctest-doc')",
+                    reason='Need --doctest-doc option to run')
 def test_file(doc_src_file):
     doctest.testfile(doc_src_file, module_relative=False, report=True,
                      extraglobs=doctest_extraglobs, verbose=True,
                      optionflags=doctest_optionflags)
+    plt.close('all')
 
 
 if __name__ == '__main__':
-    pytest.main([str(__file__.replace('\\', '/')), '-v', '--documentation'])
+    pytest.main([str(__file__.replace('\\', '/')), '-v', '--doctest-doc'])

odl/test/test_examples.py

@@ -64,7 +64,7 @@ def example(request):
                     reason='Need --examples option to run')
 def test_example(example):
     imp.load_source('tmp', example)
-    plt.close("all")
+    plt.close('all')
 
 
 if __name__ == '__main__':

odl/util/__init__.py

@@ -36,4 +36,7 @@
 from .numerics import *
 __all__ += numerics.__all__
 
+from .vectorization import *
+__all__ += vectorization.__all__
+
 from . import ufuncs

conftest.py → odl/util/pytest_plugins.py

@@ -23,17 +23,26 @@
 
 import numpy as np
 import operator
-import pytest
+import os
 
 import odl
 from odl.trafos.backends import PYFFTW_AVAILABLE, PYWT_AVAILABLE
-from odl.util import dtype_repr
+from odl.util import dtype_repr, OptionalArgDecorator
+
+try:
+    from pytest import fixture
+except ImportError:
+    # Make trivial decorator
+    class fixture(OptionalArgDecorator):
+        @staticmethod
+        def _wrapper(f, *a, **kw):
+            return f
 
 
 # --- Add numpy and ODL to all doctests ---
 
 
-@pytest.fixture(autouse=True)
+@fixture(autouse=True)
 def add_doctest_np_odl(doctest_namespace):
     doctest_namespace['np'] = np
     doctest_namespace['odl'] = odl
@@ -42,14 +51,19 @@ def add_doctest_np_odl(doctest_namespace):
 # --- Files to be ignored by the tests ---
 
 
-collect_ignore = ['setup.py']
+this_dir = os.path.dirname(__file__)
+odl_root = os.path.abspath(os.path.join(this_dir, os.pardir, os.pardir))
+collect_ignore = [os.path.join(odl_root, 'setup.py')]
 
 if not PYFFTW_AVAILABLE:
-    collect_ignore.append('odl/trafos/backends/pyfftw_bindings.py')
+    collect_ignore.append(
+        os.path.join(odl_root, 'odl/trafos/backends/pyfftw_bindings.py'))
 if not PYWT_AVAILABLE:
-    collect_ignore.append('odl/trafos/backends/pywt_bindings.py')
+    collect_ignore.append(
+        os.path.join(odl_root, 'odl/trafos/backends/pywt_bindings.py'))
     # Currently `pywt` is the only implementation
-    collect_ignore.append('odl/trafos/wavelet.py')
+    collect_ignore.append(
+        os.path.join(odl_root, 'odl/trafos/wavelet.py'))
 
 
 def pytest_addoption(parser):
@@ -62,7 +76,7 @@ def pytest_addoption(parser):
     parser.addoption('--examples', action='store_true',
                      help='Run examples')
 
-    parser.addoption('--documentation', action='store_true',
+    parser.addoption('--doctest-doc', action='store_true',
                      help='Run doctests in the documentation')
 
 
@@ -71,7 +85,7 @@ def pytest_addoption(parser):
 fn_impl_ids = [" impl='{}' ".format(p) for p in fn_impl_params]
 
 
-@pytest.fixture(scope="module", ids=fn_impl_ids, params=fn_impl_params)
+@fixture(scope="module", ids=fn_impl_ids, params=fn_impl_params)
 def fn_impl(request):
     """String with an available `FnBase` implementation name."""
     return request.param
@@ -80,8 +94,7 @@ def fn_impl(request):
 ntuples_impl_ids = [" impl='{}' ".format(p) for p in ntuples_impl_params]
 
 
-@pytest.fixture(scope="module", ids=ntuples_impl_ids,
-                params=ntuples_impl_params)
+@fixture(scope="module", ids=ntuples_impl_ids, params=ntuples_impl_params)
 def ntuples_impl(request):
     """String with an available `NtuplesBase` implementation name."""
     return request.param
@@ -92,8 +105,7 @@ def ntuples_impl(request):
                       for dt in floating_dtype_params]
 
 
-@pytest.fixture(scope="module", ids=floating_dtype_ids,
-                params=floating_dtype_params)
+@fixture(scope="module", ids=floating_dtype_ids, params=floating_dtype_params)
 def floating_dtype(request):
     """Floating point (real or complex) dtype."""
     return request.param
@@ -106,8 +118,7 @@ def floating_dtype(request):
                     for dt in scalar_dtype_params]
 
 
-@pytest.fixture(scope="module", ids=scalar_dtype_ids,
-                params=scalar_dtype_params)
+@fixture(scope="module", ids=scalar_dtype_ids, params=scalar_dtype_params)
 def scalar_dtype(request):
     """Scalar (integers or real or complex) dtype."""
     return request.param
@@ -117,7 +128,7 @@ def scalar_dtype(request):
 ufunc_ids = [' ufunc={} '.format(p[0]) for p in ufunc_params]
 
 
-@pytest.fixture(scope="module", ids=ufunc_ids, params=ufunc_params)
+@fixture(scope="module", ids=ufunc_ids, params=ufunc_params)
 def ufunc(request):
     """Tuple with information on a ufunc.
 
@@ -139,7 +150,7 @@ def ufunc(request):
 reduction_ids = [' reduction={} '.format(p[0]) for p in reduction_params]
 
 
-@pytest.fixture(scope="module", ids=reduction_ids, params=reduction_params)
+@fixture(scope="module", ids=reduction_ids, params=reduction_params)
 def reduction(request):
     """Tuple with information on a reduction.
 
@@ -164,7 +175,7 @@ def reduction(request):
                      ' += ', ' /= ', ' *= ', ' -= ']
 
 
-@pytest.fixture(ids=arithmetic_op_ids, params=arithmetic_op_par)
+@fixture(ids=arithmetic_op_ids, params=arithmetic_op_par)
 def arithmetic_op(request):
     """An arithmetic operator, e.g. +, -, // etc."""
     return request.param

odl/util/testutils.py

@@ -589,13 +589,18 @@ def test(arguments=None):
                           '\nRun `$ pip install [--user] odl[testing]` in '
                           'order to install `pytest`.')
 
+    from .pytest_plugins import collect_ignore
+
     this_dir = os.path.dirname(__file__)
     odl_root = os.path.abspath(os.path.join(this_dir, os.pardir, os.pardir))
-    base_args = ['-x', '{root}/odl'.format(root=odl_root)]
-    if arguments is None:
-        args = base_args
-    else:
-        args = base_args + list(arguments)
+
+    args = ['-x', '{root}/odl'.format(root=odl_root)]
+
+    ignores = ['--ignore={}'.format(file) for file in collect_ignore]
+    args.extend(ignores)
+
+    if arguments is not None:
+        args.extend(arguments)
 
     pytest.main(args)
 

odl/util/vectorization.py

@@ -28,7 +28,8 @@
 
 
 __all__ = ('is_valid_input_array', 'is_valid_input_meshgrid',
-           'out_shape_from_meshgrid', 'out_shape_from_array', 'vectorize')
+           'out_shape_from_meshgrid', 'out_shape_from_array',
+           'OptionalArgDecorator', 'vectorize')
 
 
 def is_valid_input_array(x, ndim=None):

setup.py

@@ -30,17 +30,12 @@
 import sys
 
 
-if os.environ.get('READTHEDOCS', None) == 'True':
-    # Mock requires in conf.py
-    requires = ''
-    test_requires = []
-else:
-    requires = open(
-        os.path.join(os.path.dirname(__file__),
-                     'requirements.txt')).readlines()
-    test_requires = open(
-        os.path.join(os.path.dirname(__file__),
-                     'test_requirements.txt')).readlines()
+root_path = os.path.dirname(__file__)
+
+
+requires = open(os.path.join(root_path, 'requirements.txt')).readlines()
+test_requires = open(
+    os.path.join(root_path, 'test_requirements.txt')).readlines()
 
 
 class PyTest(TestCommand):
@@ -61,6 +56,23 @@ def run_tests(self):
         errno = pytest.main(self.pytest_args)
         sys.exit(errno)
 
+
+test_path = os.path.join(root_path, 'odl', 'test')
+
+
+def find_tests():
+    tests = []
+    for path, _, filenames in os.walk(os.path.join(root_path, test_path)):
+        for filename in filenames:
+            basename, suffix = os.path.splitext(filename)
+            if (suffix == '.py' and
+                    (basename.startswith('test_') or
+                     basename.endswith('_test'))):
+                tests.append(os.path.join(path, filename))
+
+    return tests
+
+
 long_description = """
 Operator Discretization Library (ODL) is a Python library for fast prototyping focusing on (but not restricted to) inverse problems. ODL is being developed at `KTH Royal Institute of Technology <https://www.kth.se/en/sci/institutioner/math>`_.
 
@@ -89,7 +101,7 @@ def run_tests(self):
 setup(
     name='odl',
 
-    version='0.5.0',
+    version='0.5.1',
 
     description='Operator Discretization Library',
     long_description=long_description,
@@ -124,8 +136,11 @@ def run_tests(self):
 
     keywords='research development mathematics prototyping imaging tomography',
 
-    packages=find_packages(exclude=['*test*']),
+    packages=find_packages(),
     package_dir={'odl': 'odl'},
+    package_data={'odl': find_tests() + ['odl/pytest.ini']},
+    include_package_data=True,
+    entry_points={'pytest11': ['odl_plugins = odl.util.pytest_plugins']},
 
     install_requires=[requires],
     tests_require=['pytest'],