MAINT/TST: update tests to use pytest

.coveragerc

@@ -5,6 +5,7 @@ include = */pywt/*
 omit =
     */version.py
     */pywt/tests/*
+    */pywt/_doc_utils.py*
     */pywt/data/create_dat.py
     *.pxd
     stringsource

.travis.yml

@@ -56,7 +56,7 @@ before_install:
   - pip install $NUMPYSPEC
   - pip install $MATPLOTLIBSPEC
   - pip install $CYTHONSPEC
-  - pip install nose coverage codecov futures
+  - pip install pytest pytest-cov coverage codecov futures
   - set -o pipefail
   - if [ "${USE_WHEEL}" == "1" ]; then pip install wheel; fi
   - |
@@ -72,23 +72,26 @@ script:
         pip wheel . -v
         pip install PyWavelets*.whl -v
         pushd demo
-        nosetests pywt
+        pytest --pyargs pywt
         python ../pywt/tests/test_doc.py
         popd
     elif [ "${USE_SDIST}" == "1" ]; then
         python setup.py sdist
         # Move out of source directory to avoid finding local pywt
         pushd dist
         pip install PyWavelets* -v
-        nosetests pywt
+        pytest --pyargs pywt
         python ../pywt/tests/test_doc.py
         popd
     elif [ "${REFGUIDE_CHECK}" == "1" ]; then
         pip install -e . -v
         python util/refguide_check.py --doctests
     else
         CFLAGS="--coverage" python setup.py build --build-lib build/lib/ --build-temp build/tmp/
-        nosetests build/lib/ --tests pywt/tests
+        CFLAGS="--coverage" pip install -e . -v
+        pushd demo
+        pytest --pyargs pywt --cov=pywt
+        popd
     fi
 
 after_success:

LICENSE

@@ -1,5 +1,5 @@
 Copyright (c) 2006-2012 Filip Wasilewski <http://en.ig.ma/>
-Copyright (c) 2012-2017 The PyWavelets Developers <https://github.com/PyWavelets/pywt>
+Copyright (c) 2012-2019 The PyWavelets Developers <https://github.com/PyWavelets/pywt>
 
 Permission is hereby granted, free of charge, to any person obtaining a copy of
 this software and associated documentation files (the "Software"), to deal in
@@ -18,3 +18,15 @@ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
 SOFTWARE.
+
+
+The PyWavelets repository and source distributions bundle some code that is
+adapted from compatibly licensed projects. We list these here.
+
+Name: NumPy
+Files:  pywt/_pytesttester.py
+License: 3-clause BSD
+
+Name: SciPy
+Files:  setup.py, util/*
+License: 3-clause BSD

appveyor.yml

@@ -23,11 +23,13 @@ install:
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install
      numpy --cache-dir c:\\tmp\\pip-cache"
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install
-     Cython nose coverage matplotlib futures --cache-dir c:\\tmp\\pip-cache"
+     Cython pytest coverage matplotlib futures --cache-dir c:\\tmp\\pip-cache"
 
 test_script:
-  - "util\\appveyor\\build.cmd %PYTHON%\\python.exe setup.py build --build-lib build\\lib\\"
-  - "%PYTHON%\\Scripts\\nosetests build\\lib --tests pywt\\tests"
+  - "util\\appveyor\\build.cmd %PYTHON%\\python.exe -m pip install -e . -v"
+  - "cd demo"
+  - "%PYTHON%\\Scripts\\pytest --pyargs pywt"
+  - "cd .."
 
 after_test:
   - "util\\appveyor\\build.cmd %PYTHON%\\python.exe setup.py bdist_wheel"

doc/source/dev/testing.rst

@@ -23,13 +23,22 @@ does not break the build.
 Running tests locally
 ---------------------
 
-Tests are implemented with `nose`_, so use one of:
+Tests are implemented with `pytest`_, so use one of:
 
-    $ nosetests pywt
+    $ pytest --pyargs pywt -v
 
-    >>> pywt.test()  # doctest: +SKIP
+There are also older doctests that can be run by performing the following from
+the root of the project source.
 
-Note doctests require `Matplotlib`_ in addition to the usual dependencies.
+    $ python pywt/tests/test_doc.py
+    $ cd doc
+    $ make doctest
+
+Additionally the examples in the demo subfolder can be checked by running:
+
+    $ python util/refguide_check.py
+
+Note: doctests require `Matplotlib`_ in addition to the usual dependencies.
 
 
 Running tests with Tox
@@ -43,6 +52,6 @@ To for example run tests for Python 3.5 and 3.6 use::
 For more information see the `Tox`_ documentation.
 
 
-.. _nose: http://nose.readthedocs.org/en/latest/
-.. _Tox: http://tox.testrun.org/
-.. _Matplotlib: http://matplotlib.org
+.. _pytest: https://pytest.org
+.. _Tox: https://tox.readthedocs.io/en/latest/
+.. _Matplotlib: https://matplotlib.org

pytest.ini

@@ -0,0 +1,15 @@
+[pytest]
+addopts = -l
+norecursedirs = doc tools pywt/_extensions
+doctest_optionflags = NORMALIZE_WHITESPACE ELLIPSIS ALLOW_UNICODE ALLOW_BYTES
+
+filterwarnings =
+    error
+# Filter out annoying import messages.
+    ignore:Not importing directory
+    ignore:numpy.dtype size changed
+    ignore:numpy.ufunc size changed
+    ignore::UserWarning:cpuinfo,
+
+env =
+    PYTHONHASHSEED=0

pywt/__init__.py

@@ -35,11 +35,6 @@
 
 from pywt.version import version as __version__
 
-import numpy as np
-if np.lib.NumpyVersion(np.__version__) >= '1.14.0':
-    from ._utils import is_nose_running
-    if is_nose_running():
-        np.set_printoptions(legacy='1.13')
-
-from numpy.testing import Tester
-test = Tester().test
+from ._pytesttester import PytestTester
+test = PytestTester(__name__)
+del PytestTester

pywt/_pytest.py

@@ -0,0 +1,68 @@
+"""common test-related code."""
+import os
+import sys
+import multiprocessing
+import numpy as np
+import pytest
+
+
+__all__ = ['uses_matlab',   # skip if pymatbridge and Matlab unavailable
+           'uses_futures',  # skip if futures unavailable
+           'uses_pymatbridge',  # skip if no PYWT_XSLOW environment variable
+           'uses_precomputed',  # skip if PYWT_XSLOW environment variable found
+           'matlab_result_dict_cwt',   # dict with precomputed Matlab dwt data
+           'matlab_result_dict_dwt',   # dict with precomputed Matlab cwt data
+           'futures',      # the futures module or None
+           'max_workers',  # the number of workers available to futures
+           'size_set',     # the set of Matlab tests to run
+           ]
+
+try:
+    if sys.version_info[0] == 2:
+        import futures
+    else:
+        from concurrent import futures
+    max_workers = multiprocessing.cpu_count()
+    futures_available = True
+except ImportError:
+    futures_available = False
+    futures = None
+
+# check if pymatbridge + MATLAB tests should be run
+matlab_result_dict_dwt = None
+matlab_result_dict_cwt = None
+matlab_missing = True
+use_precomputed = True
+size_set = 'reduced'
+if 'PYWT_XSLOW' in os.environ:
+    try:
+        from pymatbridge import Matlab
+        mlab = Matlab()
+        matlab_missing = False
+        use_precomputed = False
+        size_set = 'full'
+    except ImportError:
+        print("To run Matlab compatibility tests you need to have MathWorks "
+              "MATLAB, MathWorks Wavelet Toolbox and the pymatbridge Python "
+              "package installed.")
+if use_precomputed:
+    # load dictionaries of precomputed results
+    data_dir = os.path.join(os.path.dirname(__file__), 'tests', 'data')
+    matlab_data_file_cwt = os.path.join(
+        data_dir, 'cwt_matlabR2015b_result.npz')
+    matlab_result_dict_cwt = np.load(matlab_data_file_cwt)
+
+    matlab_data_file_dwt = os.path.join(
+        data_dir, 'dwt_matlabR2012a_result.npz')
+    matlab_result_dict_dwt = np.load(matlab_data_file_dwt)
+
+uses_futures = pytest.mark.skipif(
+    not futures_available, reason='futures not available')
+uses_matlab = pytest.mark.skipif(
+    matlab_missing, reason='pymatbridge and/or Matlab not available')
+uses_pymatbridge = pytest.mark.skipif(
+    use_precomputed,
+    reason='PYWT_XSLOW set: skipping tests against precomputed Matlab results')
+uses_precomputed = pytest.mark.skipif(
+    not use_precomputed,
+    reason='PYWT_XSLOW not set: test against precomputed matlab tests')

pywt/_pytesttester.py

@@ -0,0 +1,164 @@
+"""
+Pytest test running.
+
+This module implements the ``test()`` function for NumPy modules. The usual
+boiler plate for doing that is to put the following in the module
+``__init__.py`` file::
+
+    from pywt._pytesttester import PytestTester
+    test = PytestTester(__name__).test
+    del PytestTester
+
+
+Warnings filtering and other runtime settings should be dealt with in the
+``pytest.ini`` file in the pywt repo root. The behavior of the test depends on
+whether or not that file is found as follows:
+
+* ``pytest.ini`` is present (develop mode)
+    All warnings except those explicily filtered out are raised as error.
+* ``pytest.ini`` is absent (release mode)
+    DeprecationWarnings and PendingDeprecationWarnings are ignored, other
+    warnings are passed through.
+
+In practice, tests run from the PyWavelets repo are run in develop mode. That
+includes the standard ``python runtests.py`` invocation.
+
+"""
+from __future__ import division, absolute_import, print_function
+
+import sys
+import os
+
+__all__ = ['PytestTester']
+
+
+def _show_pywt_info():
+    import pywt
+    from pywt._c99_config import _have_c99_complex
+    print("PyWavelets version %s" % pywt.__version__)
+    if _have_c99_complex:
+        print("Compiled with C99 complex support.")
+    else:
+        print("Compiled without C99 complex support.")
+
+
+class PytestTester(object):
+    """
+    Pytest test runner.
+
+    This class is made available in ``pywt.testing``, and a test function
+    is typically added to a package's __init__.py like so::
+
+      from pywt.testing import PytestTester
+      test = PytestTester(__name__).test
+      del PytestTester
+
+    Calling this test function finds and runs all tests associated with the
+    module and all its sub-modules.
+
+    Attributes
+    ----------
+    module_name : str
+        Full path to the package to test.
+
+    Parameters
+    ----------
+    module_name : module name
+        The name of the module to test.
+
+    """
+    def __init__(self, module_name):
+        self.module_name = module_name
+
+    def __call__(self, label='fast', verbose=1, extra_argv=None,
+                 doctests=False, coverage=False, durations=-1, tests=None):
+        """
+        Run tests for module using pytest.
+
+        Parameters
+        ----------
+        label : {'fast', 'full'}, optional
+            Identifies the tests to run. When set to 'fast', tests decorated
+            with `pytest.mark.slow` are skipped, when 'full', the slow marker
+            is ignored.
+        verbose : int, optional
+            Verbosity value for test outputs, in the range 1-3. Default is 1.
+        extra_argv : list, optional
+            List with any extra arguments to pass to pytests.
+        doctests : bool, optional
+            .. note:: Not supported
+        coverage : bool, optional
+            If True, report coverage of NumPy code. Default is False.
+            Requires installation of (pip) pytest-cov.
+        durations : int, optional
+            If < 0, do nothing, If 0, report time of all tests, if > 0,
+            report the time of the slowest `timer` tests. Default is -1.
+        tests : test or list of tests
+            Tests to be executed with pytest '--pyargs'
+
+        Returns
+        -------
+        result : bool
+            Return True on success, false otherwise.
+
+        Examples
+        --------
+        >>> result = np.lib.test() #doctest: +SKIP
+        ...
+        1023 passed, 2 skipped, 6 deselected, 1 xfailed in 10.39 seconds
+        >>> result
+        True
+
+        """
+        import pytest
+
+        module = sys.modules[self.module_name]
+        module_path = os.path.abspath(module.__path__[0])
+
+        # setup the pytest arguments
+        pytest_args = ["-l"]
+
+        # offset verbosity. The "-q" cancels a "-v".
+        pytest_args += ["-q"]
+
+        # Filter out annoying import messages. Want these in both develop and
+        # release mode.
+        pytest_args += [
+            "-W ignore:Not importing directory",
+            "-W ignore:numpy.dtype size changed",
+            "-W ignore:numpy.ufunc size changed", ]
+
+        if doctests:
+            raise ValueError("Doctests not supported")
+
+        if extra_argv:
+            pytest_args += list(extra_argv)
+
+        if verbose > 1:
+            pytest_args += ["-" + "v"*(verbose - 1)]
+
+        if coverage:
+            pytest_args += ["--cov=" + module_path]
+
+        if label == "fast":
+            pytest_args += ["-m", "not slow"]
+        elif label != "full":
+            pytest_args += ["-m", label]
+
+        if durations >= 0:
+            pytest_args += ["--durations=%s" % durations]
+
+        if tests is None:
+            tests = [self.module_name]
+
+        pytest_args += ["--pyargs"] + list(tests)
+
+        # run tests.
+        _show_pywt_info()
+
+        try:
+            code = pytest.main(pytest_args)
+        except SystemExit as exc:
+            code = exc.code
+
+        return code == 0