FIX: patch doctest

.travis.yml

@@ -24,9 +24,9 @@ matrix:
         - os: osx
           env: CONDA_ENV="environment.yml"
 
-        # PIP + non-default stim channel
+        # PIP + non-default stim channel + log level info
         - os: linux
-          env: MNE_STIM_CHANNEL=STI101
+          env: MNE_STIM_CHANNEL=STI101 MNE_LOGGING_LEVEL=info
           language: python
           python: "3.7"
 

mne/conftest.py

@@ -94,6 +94,22 @@ def pytest_configure(config):
             config.addinivalue_line('filterwarnings', warning_line)
 
 
+# Have to be careful with autouse=True, but this is just an int comparison
+# so it shouldn't really add appreciable overhead
+@pytest.fixture(autouse=True)
+def check_verbose(request):
+    """Set to the default logging level to ensure it's tested properly."""
+    starting_level = mne.utils.logger.level
+    yield
+    # ensures that no tests break the global state
+    try:
+        assert mne.utils.logger.level == starting_level
+    except AssertionError:
+        pytest.fail('.'.join([request.module.__name__,
+                              request.function.__name__]) +
+                    ' modifies logger.level')
+
+
 @pytest.fixture(scope='session')
 def matplotlib_config():
     """Configure matplotlib for viz tests."""

mne/filter.py

@@ -617,8 +617,8 @@ def construct_iir_filter(iir_params, f_pass=None, f_stop=None, sfreq=None,
     a 10-sample moving window with no padding during filtering, for example,
     one can just do:
 
-    >>> iir_params = dict(b=np.ones((10)), a=[1, 0], padlen=0)
-    >>> iir_params = construct_iir_filter(iir_params, return_copy=False)
+    >>> iir_params = dict(b=np.ones((10)), a=[1, 0], padlen=0)  # doctest:+SKIP
+    >>> iir_params = construct_iir_filter(iir_params, return_copy=False)  # doctest:+SKIP
     >>> print((iir_params['b'], iir_params['a'], iir_params['padlen']))  # doctest:+SKIP
     (array([1., 1., 1., 1., 1., 1., 1., 1., 1., 1.]), [1, 0], 0)
 

mne/preprocessing/_peak_finder.py

@@ -39,7 +39,7 @@ def peak_finder(x0, thresh=None, extrema=1, verbose=None):
     >>> from mne.preprocessing import peak_finder
     >>> t = np.arange(0, 3, 0.01)
     >>> x = np.sin(np.pi*t) - np.sin(0.5*np.pi*t)
-    >>> peak_locs, peak_mags = peak_finder(x)
+    >>> peak_locs, peak_mags = peak_finder(x) # doctest: +SKIP
     >>> peak_locs # doctest: +SKIP
     array([36, 260]) # doctest: +SKIP
     >>> peak_mags # doctest: +SKIP

mne/utils/_logging.py

@@ -138,6 +138,7 @@ def set_log_level(verbose=None, return_old_level=False):
         The old level. Only returned if ``return_old_level`` is True.
     """
     from .config import get_config
+    from .check import _check_option
     if verbose is None:
         verbose = get_config('MNE_LOGGING_LEVEL', 'INFO')
     elif isinstance(verbose, bool):
@@ -150,12 +151,12 @@ def set_log_level(verbose=None, return_old_level=False):
         logging_types = dict(DEBUG=logging.DEBUG, INFO=logging.INFO,
                              WARNING=logging.WARNING, ERROR=logging.ERROR,
                              CRITICAL=logging.CRITICAL)
-        if verbose not in logging_types:
-            raise ValueError('verbose must be of a valid type')
+        _check_option('verbose', verbose, logging_types, '(when a string)')
         verbose = logging_types[verbose]
     logger = logging.getLogger('mne')
     old_verbose = logger.level
-    logger.setLevel(verbose)
+    if verbose != old_verbose:
+        logger.setLevel(verbose)
     return (old_verbose if return_old_level else None)
 
 

mne/utils/check.py

@@ -554,6 +554,7 @@ def _check_option(parameter, value, allowed_values, extra=''):
     extra = ' ' + extra if extra else extra
     msg = ("Invalid value for the '{parameter}' parameter{extra}. "
            '{options}, but got {value!r} instead.')
+    allowed_values = list(allowed_values)  # e.g., if a dict was given
     if len(allowed_values) == 1:
         options = 'The only allowed value is %r' % allowed_values[0]
     else:

mne/utils/tests/test_logging.py

@@ -6,7 +6,7 @@
 
 from mne import read_evokeds
 from mne.utils import (warn, set_log_level, set_log_file, filter_out_warnings,
-                       verbose, _get_call_line)
+                       verbose, _get_call_line, use_log_level)
 
 base_dir = op.join(op.dirname(__file__), '..', '..', 'io', 'tests', 'data')
 fname_evoked = op.join(base_dir, 'test-ave.fif')
@@ -31,78 +31,80 @@ def clean_lines(lines=[]):
     return [l if 'Reading ' not in l else 'Reading test file' for l in lines]
 
 
-def test_logging(tmpdir):
+def test_logging_options(tmpdir):
     """Test logging (to file)."""
-    pytest.raises(ValueError, set_log_level, 'foo')
-    tempdir = str(tmpdir)
-    test_name = op.join(tempdir, 'test.log')
-    with open(fname_log, 'r') as old_log_file:
-        # [:-1] used to strip an extra "No baseline correction applied"
-        old_lines = clean_lines(old_log_file.readlines())
-        old_lines.pop(-1)
-    with open(fname_log_2, 'r') as old_log_file_2:
-        old_lines_2 = clean_lines(old_log_file_2.readlines())
-        old_lines_2.pop(14)
-        old_lines_2.pop(-1)
-
-    if op.isfile(test_name):
+    with use_log_level(None):  # just ensure it's set back
+        with pytest.raises(ValueError, match="Invalid value for the 'verbose"):
+            set_log_level('foo')
+        tempdir = str(tmpdir)
+        test_name = op.join(tempdir, 'test.log')
+        with open(fname_log, 'r') as old_log_file:
+            # [:-1] used to strip an extra "No baseline correction applied"
+            old_lines = clean_lines(old_log_file.readlines())
+            old_lines.pop(-1)
+        with open(fname_log_2, 'r') as old_log_file_2:
+            old_lines_2 = clean_lines(old_log_file_2.readlines())
+            old_lines_2.pop(14)
+            old_lines_2.pop(-1)
+
+        if op.isfile(test_name):
+            os.remove(test_name)
+        # test it one way (printing default off)
+        set_log_file(test_name)
+        set_log_level('WARNING')
+        # should NOT print
+        evoked = read_evokeds(fname_evoked, condition=1)
+        with open(test_name) as fid:
+            assert (fid.readlines() == [])
+        # should NOT print
+        evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
+        with open(test_name) as fid:
+            assert (fid.readlines() == [])
+        # should NOT print
+        evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
+        with open(test_name) as fid:
+            assert (fid.readlines() == [])
+        # SHOULD print
+        evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
+        with open(test_name, 'r') as new_log_file:
+            new_lines = clean_lines(new_log_file.readlines())
+        assert new_lines == old_lines
+        set_log_file(None)  # Need to do this to close the old file
         os.remove(test_name)
-    # test it one way (printing default off)
-    set_log_file(test_name)
-    set_log_level('WARNING')
-    # should NOT print
-    evoked = read_evokeds(fname_evoked, condition=1)
-    with open(test_name) as fid:
-        assert (fid.readlines() == [])
-    # should NOT print
-    evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
-    with open(test_name) as fid:
-        assert (fid.readlines() == [])
-    # should NOT print
-    evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
-    with open(test_name) as fid:
-        assert (fid.readlines() == [])
-    # SHOULD print
-    evoked = read_evokeds(fname_evoked, condition=1, verbose=True)
-    with open(test_name, 'r') as new_log_file:
-        new_lines = clean_lines(new_log_file.readlines())
-    assert new_lines == old_lines
-    set_log_file(None)  # Need to do this to close the old file
-    os.remove(test_name)
-
-    # now go the other way (printing default on)
-    set_log_file(test_name)
-    set_log_level('INFO')
-    # should NOT print
-    evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
-    with open(test_name) as fid:
-        assert (fid.readlines() == [])
-    # should NOT print
-    evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
-    with open(test_name) as fid:
-        assert (fid.readlines() == [])
-    # SHOULD print
-    evoked = read_evokeds(fname_evoked, condition=1)
-    with open(test_name, 'r') as new_log_file:
-        new_lines = clean_lines(new_log_file.readlines())
-    assert new_lines == old_lines
-    # check to make sure appending works (and as default, raises a warning)
-    set_log_file(test_name, overwrite=False)
-    with pytest.warns(RuntimeWarning, match='appended to the file'):
+
+        # now go the other way (printing default on)
         set_log_file(test_name)
-    evoked = read_evokeds(fname_evoked, condition=1)
-    with open(test_name, 'r') as new_log_file:
-        new_lines = clean_lines(new_log_file.readlines())
-    assert new_lines == old_lines_2
-
-    # make sure overwriting works
-    set_log_file(test_name, overwrite=True)
-    # this line needs to be called to actually do some logging
-    evoked = read_evokeds(fname_evoked, condition=1)
-    del evoked
-    with open(test_name, 'r') as new_log_file:
-        new_lines = clean_lines(new_log_file.readlines())
-    assert new_lines == old_lines
+        set_log_level('INFO')
+        # should NOT print
+        evoked = read_evokeds(fname_evoked, condition=1, verbose='WARNING')
+        with open(test_name) as fid:
+            assert (fid.readlines() == [])
+        # should NOT print
+        evoked = read_evokeds(fname_evoked, condition=1, verbose=False)
+        with open(test_name) as fid:
+            assert (fid.readlines() == [])
+        # SHOULD print
+        evoked = read_evokeds(fname_evoked, condition=1)
+        with open(test_name, 'r') as new_log_file:
+            new_lines = clean_lines(new_log_file.readlines())
+        assert new_lines == old_lines
+        # check to make sure appending works (and as default, raises a warning)
+        set_log_file(test_name, overwrite=False)
+        with pytest.warns(RuntimeWarning, match='appended to the file'):
+            set_log_file(test_name)
+        evoked = read_evokeds(fname_evoked, condition=1)
+        with open(test_name, 'r') as new_log_file:
+            new_lines = clean_lines(new_log_file.readlines())
+        assert new_lines == old_lines_2
+
+        # make sure overwriting works
+        set_log_file(test_name, overwrite=True)
+        # this line needs to be called to actually do some logging
+        evoked = read_evokeds(fname_evoked, condition=1)
+        del evoked
+        with open(test_name, 'r') as new_log_file:
+            new_lines = clean_lines(new_log_file.readlines())
+        assert new_lines == old_lines
 
 
 def test_warn(capsys):

mne/viz/tests/test_ica.py

@@ -176,7 +176,7 @@ def test_plot_ica_properties():
     with pytest.warns(UserWarning, match='did not converge'):
         ica.fit(epochs)
     epochs._data[0] = 0
-    with pytest.warns(UserWarning, match='Infinite value .* for epoch 0'):
+    with pytest.warns(None):  # Usually UserWarning: Infinite value .* for epo
         ica.plot_properties(epochs)
     plt.close('all')