TEST: Drop nose for pytest

.azure-pipelines/windows.yml

@@ -11,6 +11,7 @@ jobs:
   variables:
     EXTRA_WHEELS: "https://5cf40426d9f06eb7461d-6fe47d9331aba7cd62fc36c7196769e4.ssl.cf2.rackcdn.com"
     DEPENDS: numpy scipy matplotlib h5py pydicom
+    CHECK_TYPE: test
   strategy:
     matrix:
       ${{ insert }}: ${{ parameters.matrix }}
@@ -29,19 +30,20 @@ jobs:
       displayName: 'Update build tools'
     - script: |
         python -m pip install --find-links %EXTRA_WHEELS% %DEPENDS%
-        python -m pip install nose mock coverage codecov pytest
       displayName: 'Install dependencies'
     - script: |
-        python -m pip install .
+        python -m pip install .[$(CHECK_TYPE)]
         SET NIBABEL_DATA_DIR=%CD%\\nibabel-data
       displayName: 'Install nibabel'
     - script: |
         mkdir for_testing
         cd for_testing
         cp ../.coveragerc .
-        nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
-      displayName: 'Nose tests'
+        pytest --doctest-modules --cov nibabel -v --pyargs nibabel
+      displayName: 'Pytest tests'
+      condition: and(succeeded(), eq(variables['CHECK_TYPE'], 'test'))
     - script: |
+        python -m pip install codecov
         cd for_testing
         codecov
       displayName: 'Upload To Codecov'

.gitignore

@@ -85,3 +85,4 @@ doc/source/reference
 venv/
 .buildbot.patch
 .vscode
+for_testing/

.travis.yml

@@ -4,11 +4,11 @@
 # for it to be on multiple physical lines, so long as you remember: - There
 # can't be any leading "-"s - All newlines will be removed, so use ";"s
 
+os: linux
 dist: xenial
-sudo: true
 language: python
-
 cache: pip
+
 env:
     global:
         - SETUP_REQUIRES="pip setuptools>=30.3.0 wheel"
@@ -25,7 +25,7 @@ python:
     - 3.7
     - 3.8
 
-matrix:
+jobs:
   include:
     # Basic dependencies only
     - python: 3.5
@@ -143,7 +143,7 @@ script:
           mkdir for_testing
           cd for_testing
           cp ../.coveragerc .
-          nosetests --with-doctest --with-coverage --cover-package nibabel nibabel
+          pytest --doctest-modules --cov nibabel -v --pyargs nibabel
       else
           false
       fi

dev-requirements.txt

@@ -1,3 +1,3 @@
 # Requirements for running tests
 -r requirements.txt
-nose
+pytest

doc/source/devel/advanced_testing.rst

@@ -25,7 +25,7 @@ Long-running tests
 Long-running tests are not enabled by default, and can be resource-intensive. To run these tests:
 
 * Set environment variable ``NIPY_EXTRA_TESTS=slow``;
-* Run ``nosetests``.
+* Run ``pytest nibabel``.
 
 Note that some tests may require a machine with >4GB of RAM.
 

doc/source/devel/make_release.rst

@@ -79,7 +79,7 @@ Release checklist
 
 * Make sure all tests pass (from the nibabel root directory)::
 
-    nosetests --with-doctest nibabel
+    pytest --doctest-modules nibabel
 
 * Make sure you are set up to use the ``try_branch.py`` - see
   https://github.com/nipy/nibotmi/blob/master/install.rst#trying-a-set-of-changes-on-the-buildbots

doc/source/installation.rst

@@ -90,7 +90,7 @@ Requirements
 *  h5py_ (optional, for MINC2 support)
 *  PyDICOM_ 0.9.9 or greater (optional, for DICOM support)
 *  `Python Imaging Library`_ (optional, for PNG conversion in DICOMFS)
-*  nose_ 0.11 or greater and pytest_ (optional, to run the tests)
+*  pytest_ (optional, to run the tests)
 *  sphinx_ (optional, to build the documentation)
 
 Get the development sources
@@ -128,7 +128,7 @@ module to see if everything is fine.  It should look something like this::
     >>>
 
 
-To run the nibabel test suite, from the terminal run ``nosetests nibabel`` or
+To run the nibabel test suite, from the terminal run ``pytest nibabel`` or
 ``python -c "import nibabel; nibabel.test()``.
 
 To run an extended test suite that validates ``nibabel`` for long-running and

nibabel/__init__.py

@@ -36,29 +36,6 @@
 For more detailed information see the :ref:`manual`.
 """
 
-# Package-wide test setup and teardown
-_test_states = {
-    # Numpy changed print options in 1.14; we can update docstrings and remove
-    # these when our minimum for building docs exceeds that
-    'legacy_printopt': None,
-    }
-
-def setup_package():
-    """ Set numpy print style to legacy="1.13" for newer versions of numpy """
-    import numpy as np
-    from distutils.version import LooseVersion
-    if LooseVersion(np.__version__) >= LooseVersion('1.14'):
-        if _test_states.get('legacy_printopt') is None:
-            _test_states['legacy_printopt'] = np.get_printoptions().get('legacy')
-        np.set_printoptions(legacy="1.13")
-
-def teardown_package():
-    """ Reset print options when tests finish """
-    import numpy as np
-    if _test_states.get('legacy_printopt') is not None:
-        np.set_printoptions(legacy=_test_states.pop('legacy_printopt'))
-
-
 # module imports
 from . import analyze as ana
 from . import spm99analyze as spm99
@@ -92,13 +69,101 @@ def teardown_package():
 from . import streamlines
 from . import viewers
 
-from numpy.testing import Tester
-test = Tester().test
-bench = Tester().bench
-del Tester
-
 from .pkg_info import get_pkg_info as _get_pkg_info
 
 
 def get_info():
     return _get_pkg_info(os.path.dirname(__file__))
+
+
+def test(label=None, verbose=1, extra_argv=None,
+         doctests=False, coverage=False, raise_warnings=None,
+         timer=False):
+    """
+    Run tests for nibabel using pytest
+
+    The protocol mimics the ``numpy.testing.NoseTester.test()``.
+    Not all features are currently implemented.
+
+    Parameters
+    ----------
+    label : None
+        Unused.
+    verbose: int, optional
+        Verbosity value for test outputs. Positive values increase verbosity, and
+        negative values decrease it. Default is 1.
+    extra_argv : list, optional
+        List with any extra arguments to pass to pytest.
+    doctests: bool, optional
+        If True, run doctests in module. Default is False.
+    coverage: bool, optional
+        If True, report coverage of NumPy code. Default is False.
+        (This requires the
+        `coverage module <https://nedbatchelder.com/code/modules/coveragehtml>`_).
+    raise_warnings : None
+        Unused.
+    timer : False
+        Unused.
+
+    Returns
+    -------
+    code : ExitCode
+        Returns the result of running the tests as a ``pytest.ExitCode`` enum
+    """
+    import pytest
+    args = []
+
+    if label is not None:
+        raise NotImplementedError("Labels cannot be set at present")
+
+    verbose = int(verbose)
+    if verbose > 0:
+        args.append("-" + "v" * verbose)
+    elif verbose < 0:
+        args.append("-" + "q" * -verbose)
+
+    if extra_argv:
+        args.extend(extra_argv)
+    if doctests:
+        args.append("--doctest-modules")
+    if coverage:
+        args.extend(["--cov", "nibabel"])
+    if raise_warnings is not None:
+        raise NotImplementedError("Warning filters are not implemented")
+    if timer:
+        raise NotImplementedError("Timing is not implemented")
+
+    args.extend(["--pyargs", "nibabel"])
+
+    return pytest.main(args=args)
+
+
+def bench(label=None, verbose=1, extra_argv=None):
+    """
+    Run benchmarks for nibabel using pytest
+
+    The protocol mimics the ``numpy.testing.NoseTester.bench()``.
+    Not all features are currently implemented.
+
+    Parameters
+    ----------
+    label : None
+        Unused.
+    verbose: int, optional
+        Verbosity value for test outputs. Positive values increase verbosity, and
+        negative values decrease it. Default is 1.
+    extra_argv : list, optional
+        List with any extra arguments to pass to pytest.
+
+    Returns
+    -------
+    code : ExitCode
+        Returns the result of running the tests as a ``pytest.ExitCode`` enum
+    """
+    from pkg_resources import resource_filename
+    config = resource_filename("nibabel", "benchmarks/pytest.benchmark.ini")
+    args = []
+    if extra_argv is not None:
+        args.extend(extra_argv)
+    args.extend(["-c", config])
+    return test(label, verbose, extra_argv=args)

nibabel/benchmarks/bench_array_to_file.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_array_to_file.py
 """
 
 import sys

nibabel/benchmarks/bench_arrayproxy_slicing.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_arrayproxy_slicing.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_arrayproxy_slicing.py
 """
 
 from timeit import timeit

nibabel/benchmarks/bench_fileslice.py

@@ -3,13 +3,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_fileslice.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_fileslice.py
 """
 
 import sys

nibabel/benchmarks/bench_finite_range.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_finite_range
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_finite_range.py
 """
 
 import sys

nibabel/benchmarks/bench_load_save.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also
-run the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_load_save.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_load_save.py
 """
 
 import sys

nibabel/benchmarks/bench_streamlines.py

@@ -5,13 +5,9 @@
     import nibabel as nib
     nib.bench()
 
-If you have doctests enabled by default in nose (with a noserc file or
-environment variable), and you have a numpy version <= 1.6.1, this will also run
-the doctests, let's hope they pass.
+Run this benchmark with::
 
-Run this benchmark with:
-
-    nosetests -s --match '(?:^|[\\b_\\.//-])[Bb]ench' /path/to/bench_streamlines.py
+    pytest -c <path>/benchmarks/pytest.benchmark.ini <path>/benchmarks/bench_streamlines.py
 """
 
 import numpy as np

nibabel/benchmarks/pytest.benchmark.ini

@@ -0,0 +1,4 @@
+[pytest]
+python_files = bench_*.py
+python_functions = bench_*
+addopts = --capture=no