MRG: Minor fixes for 3.7 (#5831)

* FIX: Deprecations for 3.7 from other modules

Author: larsoner

.travis.yml

@@ -1,5 +1,5 @@
 language: c
-dist: trusty
+dist: xenial
 sudo: false
 cache:
   apt: true
@@ -9,7 +9,7 @@ env:
     # OPENBLAS_NUM_THREADS=1 avoid slowdowns:
     # https://github.com/xianyi/OpenBLAS/issues/731
     global: PYTHON_VERSION=3.6 DISPLAY=:99.0 MNE_LOGGING_LEVEL=warning TEST_LOCATION=src
-            PIP_DEPENDENCIES="codecov pytest-faulthandler pytest-sugar pytest-timeout nitime" OPTION=""
+            PIP_DEPENDENCIES="codecov pytest-faulthandler pytest-sugar pytest-timeout nitime"
             TRAVIS_PYTHON_VERSION=3.6 CONDA_VERSION=">=4.3.27"
             OPENBLAS_NUM_THREADS=1
 
@@ -20,7 +20,6 @@ matrix:
           env: DEPS=nodata MNE_DONTWRITE_HOME=true MNE_FORCE_SERIAL=true MNE_SKIP_NETWORK_TEST=1
                CONDA_DEPENDENCIES="numpy scipy matplotlib sphinx pytest pytest-cov"
                PIP_DEPENDENCIES="flake8 numpydoc codespell git+git://github.com/PyCQA/pydocstyle.git codecov check-manifest pytest-faulthandler pytest-sugar pytest-timeout"
-               OPTION="--doctest-ignore-import-errors"
 
         # Linux
         - os: linux
@@ -33,8 +32,9 @@ matrix:
         # PIP + non-default stim channel
         - os: linux
           env: MNE_STIM_CHANNEL=STI101
+               PYTHON_VERSION=3.7
           language: python
-          python: "3.6"
+          python: "3.7"
 
         # Old dependencies
         - os: linux
@@ -165,8 +165,8 @@ script:
           fi;
         done;
       fi;
-    - echo py.test -m "${CONDITION}" ${OPTION} ${USE_DIRS} --cov=mne;
-    - py.test -m "${CONDITION}" ${OPTION} ${USE_DIRS} --cov=mne;
+    - echo pytest -m "${CONDITION}" ${USE_DIRS} --cov=mne;
+    - pytest -m "${CONDITION}" ${USE_DIRS} --cov=mne;
     - if [ "${DEPS}" == "nodata" ]; then
         make pep;
       fi;

conftest.py

@@ -4,9 +4,19 @@
 # License: BSD (3-clause)
 
 import pytest
+import warnings
+# For some unknown reason, on Travis-xenial there are segfaults caused on
+# the line pytest -> pdb.Pdb.__init__ -> "import readline". Forcing an
+# import here seems to prevent them (!?). This suggests a potential problem
+# with some other library stepping on memory where it shouldn't. It only
+# seems to happen on the Linux runs that install Mayavi. Anectodally,
+# @larsoner has had problems a couple of years ago where a mayavi import
+# seemed to corrupt SciPy linalg function results (!), likely due to the
+# associated VTK import, so this could be another manifestation of that.
+import readline  # noqa
 
 
-@pytest.fixture(scope='package')
+@pytest.fixture(scope='session')
 def matplotlib_config():
     """Configure matplotlib for viz tests."""
     import matplotlib
@@ -18,3 +28,10 @@ def matplotlib_config():
     # functionality)
     plt.ioff()
     plt.rcParams['figure.dpi'] = 100
+    try:
+        with warnings.catch_warnings(record=True):  # traits
+            from mayavi import mlab
+    except Exception:
+        pass
+    else:
+        mlab.options.backend = 'test'

mne/tests/test_docstring_parameters.py

@@ -135,9 +135,10 @@ def test_docstring_parameters():
                 continue
             with pytest.warns(None) as w:
                 cdoc = docscrape.ClassDoc(cls)
-            if len(w):
-                raise RuntimeError('Error for __init__ of %s in %s:\n%s'
-                                   % (cls, name, w[0]))
+            for ww in w:
+                if 'Using or importing the ABCs' not in str(ww.message):
+                    raise RuntimeError('Error for __init__ of %s in %s:\n%s'
+                                       % (cls, name, ww))
             if hasattr(cls, '__init__'):
                 incorrect += check_parameters_match(cls.__init__, cdoc)
             for method_name in cdoc.methods:

mne/utils.py

@@ -1264,7 +1264,6 @@ def wrapper(func):
 _mayavi_call = """
 with warnings.catch_warnings(record=True):  # traits
     from mayavi import mlab
-mlab.options.backend = 'test'
 """
 
 _mne_call = """

requirements.txt

@@ -16,6 +16,7 @@ pytest
 pytest-cov
 pytest-sugar
 pytest-timeout
+pytest-faulthandler
 joblib
 psutil
 dipy

setup.cfg

@@ -33,13 +33,15 @@ filterwarnings =
     ignore:joblib not installed:RuntimeWarning
     ignore:Using a non-tuple sequence for multidimensional indexing:FutureWarning
     ignore:using a non-integer number instead of an integer will result in an error:DeprecationWarning
-    ignore:Importing from numpy.testing.decorators is deprecated, import from numpy.testing instead:DeprecationWarning
+    ignore:Importing from numpy.testing.decorators is deprecated:DeprecationWarning
     ignore:np.loads is deprecated, use pickle.loads instead:DeprecationWarning
     ignore:The oldnumeric module will be dropped:DeprecationWarning
     ignore:Collection picker None could not be converted to float:UserWarning
     ignore:covariance is not positive-semidefinite:RuntimeWarning
     ignore:Can only plot ICA components:RuntimeWarning
     ignore:Matplotlib is building the font cache using fc-list:UserWarning
+    ignore:Using or importing the ABCs from 'collections':DeprecationWarning
+    ignore:`formatargspec` is deprecated:DeprecationWarning
 
 [flake8]
 exclude = __init__.py,*externals*,constants.py,fixes.py