MRG, MAINT: Tweak CIs

Makefile

@@ -97,7 +97,7 @@ upload-pipy:
 flake:
 	@if command -v flake8 > /dev/null; then \
 		echo "Running flake8"; \
-		flake8 --count mne examples tutorials setup.py; \
+		flake8 --count; \
 	else \
 		echo "flake8 not found, please install it!"; \
 		exit 1; \

doc/conf.py

@@ -71,12 +71,12 @@
 ]
 
 linkcheck_ignore = [
-    'https://doi.org/10.1088/0031-9155/57/7/1937',  # 403 Client Error: Forbidden for url: http://iopscience.iop.org/article/10.1088/0031-9155/57/7/1937/meta
-    'https://doi.org/10.1088/0031-9155/51/7/008',  # 403 Client Error: Forbidden for url: https://iopscience.iop.org/article/10.1088/0031-9155/51/7/008
-    'https://sccn.ucsd.edu/wiki/.*',  # HTTPSConnectionPool(host='sccn.ucsd.edu', port=443): Max retries exceeded with url: /wiki/Firfilt_FAQ (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)'),))
-    'https://docs.python.org/dev/howto/logging.html',  # ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
-    'https://docs.python.org/3/library/.*',  # ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
-    'https://hal.archives-ouvertes.fr/hal-01848442/',  # Sometimes: 503 Server Error: Service Unavailable for url: https://hal.archives-ouvertes.fr/hal-01848442/
+    'https://doi.org/10.1088/0031-9155/57/7/1937',  # noqa 403 Client Error: Forbidden for url: http://iopscience.iop.org/article/10.1088/0031-9155/57/7/1937/meta
+    'https://doi.org/10.1088/0031-9155/51/7/008',  # noqa 403 Client Error: Forbidden for url: https://iopscience.iop.org/article/10.1088/0031-9155/51/7/008
+    'https://sccn.ucsd.edu/wiki/.*',  # noqa HTTPSConnectionPool(host='sccn.ucsd.edu', port=443): Max retries exceeded with url: /wiki/Firfilt_FAQ (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:847)'),))
+    'https://docs.python.org/dev/howto/logging.html',  # noqa ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
+    'https://docs.python.org/3/library/.*',  # noqa ('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer'))
+    'https://hal.archives-ouvertes.fr/hal-01848442/',  # noqa Sometimes: 503 Server Error: Service Unavailable for url: https://hal.archives-ouvertes.fr/hal-01848442/
 ]
 linkcheck_anchors = False  # saves a bit of time
 
@@ -95,7 +95,7 @@
 source_suffix = '.rst'
 
 # The encoding of source files.
-#source_encoding = 'utf-8-sig'
+# source_encoding = 'utf-8-sig'
 
 # The master toctree document.
 master_doc = 'index'
@@ -120,13 +120,13 @@
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.
-#language = None
+# language = None
 
 # There are two options for replacing |today|: either, you set today to some
 # non-false value, then it is used:
-#today = ''
+# today = ''
 # Else, today_fmt is used as the format for a strftime call.
-#today_fmt = '%B %d, %Y'
+# today_fmt = '%B %d, %Y'
 
 # List of documents that shouldn't be included in the build.
 unused_docs = []
@@ -140,15 +140,15 @@
 default_role = "py:obj"
 
 # If true, '()' will be appended to :func: etc. cross-reference text.
-#add_function_parentheses = True
+# add_function_parentheses = True
 
 # If true, the current module name will be prepended to all description
 # unit titles (such as .. function::).
-#add_module_names = True
+# add_module_names = True
 
 # If true, sectionauthor and moduleauthor directives will be shown in the
 # output. They are ignored by default.
-#show_authors = False
+# show_authors = False
 
 # The name of the Pygments (syntax highlighting) style to use.
 pygments_style = 'default'
@@ -157,7 +157,7 @@
 modindex_common_prefix = ['mne.']
 
 # If true, keep warnings as "system message" paragraphs in the built documents.
-#keep_warnings = False
+# keep_warnings = False
 
 
 # -- Options for HTML output ----------------------------------------------
@@ -189,10 +189,10 @@
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
-#html_title = None
+# html_title = None
 
 # A shorter title for the navigation bar.  Default is the same as html_title.
-#html_short_title = None
+# html_short_title = None
 
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
@@ -220,27 +220,27 @@
 
 # If not '', a 'Last updated on:' timestamp is inserted at every page bottom,
 # using the given strftime format.
-#html_last_updated_fmt = '%b %d, %Y'
+# html_last_updated_fmt = '%b %d, %Y'
 
 # If true, SmartyPants will be used to convert quotes and dashes to
 # typographically correct entities.
-#html_use_smartypants = True
+# html_use_smartypants = True
 
 # Custom sidebar templates, maps document names to template names.
-#html_sidebars = {}
+# html_sidebars = {}
 
 # Additional templates that should be rendered to pages, maps page names to
 # template names.
-#html_additional_pages = {}
+# html_additional_pages = {}
 
 # If false, no module index is generated.
-#html_domain_indices = True
+# html_domain_indices = True
 
 # If false, no index is generated.
-#html_use_index = True
+# html_use_index = True
 
 # If true, the index is split into individual pages for each letter.
-#html_split_index = False
+# html_split_index = False
 
 # If true, links to the reST sources are added to the pages.
 html_show_sourcelink = False
@@ -250,12 +250,12 @@
 html_show_sphinx = False
 
 # If true, "(C) Copyright ..." is shown in the HTML footer. Default is True.
-#html_show_copyright = True
+# html_show_copyright = True
 
 # If true, an OpenSearch description file will be output, and all pages will
 # contain a <link> tag referring to it.  The value of this option must be the
 # base URL from which the finished HTML is served.
-#html_use_opensearch = ''
+# html_use_opensearch = ''
 
 # variables to pass to HTML templating engine
 build_dev_html = bool(int(os.environ.get('BUILD_DEV_HTML', False)))
@@ -264,7 +264,7 @@
                 'use_media_buttons': True, 'build_dev_html': build_dev_html}
 
 # This is the file name suffix for HTML files (e.g. ".xhtml").
-#html_file_suffix = None
+# html_file_suffix = None
 
 # Output file base name for HTML help builder.
 htmlhelp_basename = 'mne-doc'
@@ -282,8 +282,8 @@
 # (source start file, target name, title, author, documentclass
 # [howto/manual]).
 latex_documents = [
-#    ('index', 'MNE.tex', u'MNE Manual',
-#     u'MNE Contributors', 'manual'),
+    # ('index', 'MNE.tex', u'MNE Manual',
+    #  u'MNE Contributors', 'manual'),
 ]
 
 # The name of an image file (relative to this directory) to place at the top of
@@ -463,7 +463,7 @@ def reset_warnings(gallery_conf, fname):
                 'scipy.* is deprecated and will be removed in',  # dipy
                 r'Converting `np\.character` to a dtype is deprecated',  # vtk
                 r'sphinx\.util\.smartypants is deprecated',
-               'is a deprecated alias for the builtin',  # NumPy
+                'is a deprecated alias for the builtin',  # NumPy
                 ):
         warnings.filterwarnings(  # deal with other modules having bad imports
             'ignore', message=".*%s.*" % key, category=DeprecationWarning)
@@ -622,7 +622,6 @@ def reset_warnings(gallery_conf, fname):
     'n_elp', 'n_pts', 'n_tris', 'n_nodes', 'n_nonzero', 'n_events_out',
     'n_segments', 'n_orient_inv', 'n_orient_fwd', 'n_orient', 'n_dipoles_lcmv',
     'n_dipoles_fwd',
-
     # Undocumented (on purpose)
     'RawKIT', 'RawEximia', 'RawEGI', 'RawEEGLAB', 'RawEDF', 'RawCTF', 'RawBTi',
     'RawBrainVision', 'RawCurry', 'RawNIRX', 'RawGDF',

doc/conftest.py

@@ -1 +1 @@
-from mne.conftest import *
+from mne.conftest import *  # noqa

doc/sphinxext/flow_diagram.py

@@ -149,8 +149,8 @@ def generate_flow_diagram(app):
     del node
     g.get_node('legend').attr.update(shape='plaintext', margin=0, rank='sink')
     # put legend in same rank/level as inverse
-    l = g.add_subgraph(['legend', 'inv'], name='legendy')
-    l.graph_attr['rank'] = 'same'
+    leg = g.add_subgraph(['legend', 'inv'], name='legendy')
+    leg.graph_attr['rank'] = 'same'
 
     g.layout('dot')
     g.draw(out_fname, format='svg')

environment.yml

@@ -4,7 +4,6 @@ channels:
 dependencies:
 - python>=3.5
 - pip
-- mkl
 - numpy
 - scipy
 - matplotlib
@@ -33,8 +32,7 @@ dependencies:
   - mne
   - https://github.com/numpy/numpydoc/archive/master.zip
   - imageio-ffmpeg>=0.4.1
-  - vtk<8.2; platform_system == "Darwin"
-  - vtk; platform_system != "Darwin"
+  - vtk>=9.0.1
   - pyvista>=0.24
   - pyvistaqt
   - https://github.com/enthought/mayavi/archive/master.zip

mne/beamformer/_compute_beamformer.py

@@ -12,6 +12,7 @@
 from scipy import linalg
 
 from ..cov import Covariance, make_ad_hoc_cov
+from ..fixes import dict_
 from ..forward.forward import is_fixed_orient, _restrict_forward_to_src_sel
 from ..io.proj import make_projector, Projection
 from ..minimum_norm.inverse import _get_vertno, _prepare_forward
@@ -406,7 +407,7 @@ def _compute_power(Cm, W, n_orient):
     return source_power
 
 
-class Beamformer(dict):
+class Beamformer(dict_):
     """A computed beamformer.
 
     Notes

mne/bem.py

@@ -33,7 +33,7 @@
 from .utils import (verbose, logger, run_subprocess, get_subjects_dir, warn,
                     _pl, _validate_type, _TempDir, _check_freesurfer_home,
                     _check_fname, has_nibabel)
-from .fixes import einsum
+from .fixes import einsum, dict_
 
 
 # ############################################################################
@@ -47,7 +47,7 @@
 #
 
 
-class ConductorModel(dict):
+class ConductorModel(dict_):
     """BEM or sphere model."""
 
     def __repr__(self):  # noqa: D105

mne/conftest.py

@@ -297,14 +297,8 @@ def _check_skip_backend(name):
 def renderer_notebook():
     """Verify that pytest_notebook is installed."""
     from mne.viz.backends.renderer import _use_test_3d_backend
-    try:
-        with warnings.catch_warnings():
-            warnings.filterwarnings("ignore", category=DeprecationWarning)
-            from pytest_notebook import execution
-    except ImportError:
-        pytest.skip("Test skipped, requires pytest-notebook")
     with _use_test_3d_backend('notebook'):
-        yield execution
+        yield
 
 
 @pytest.fixture(scope='function', params=[testing._pytest_param()])

mne/cov.py

@@ -40,7 +40,7 @@
 from . import viz
 
 from .fixes import (BaseEstimator, EmpiricalCovariance, _logdet,
-                    empirical_covariance, log_likelihood)
+                    empirical_covariance, log_likelihood, dict_)
 
 
 def _check_covs_algebra(cov1, cov2):
@@ -63,7 +63,7 @@ def _get_tslice(epochs, tmin, tmax):
     return tslice
 
 
-class Covariance(dict):
+class Covariance(dict_):
     """Noise covariance matrix.
 
     .. warning:: This class should not be instantiated directly, but

mne/fixes.py

@@ -1091,3 +1091,61 @@ def mean(array, axis):
     @contextmanager
     def nullcontext(enter_result=None):
         yield enter_result
+
+
+###############################################################################
+# Work around autosummary making bad :class: links
+
+class dict_(dict):
+
+    def clear(self):
+        """D.clear() -> None
+
+        Remove all items from D.
+        """
+        return super().clear()
+
+    def copy(self):
+        """D.copy() -> dict
+
+        a shallow copy of D."""
+        return super().copy()
+
+    def items(self):
+        """D.items() -> object
+
+        A set-like object providing a view on D's items.
+        """
+        return super().items()
+
+    def keys(self):
+        """D.keys() -> object
+
+        A set-like object providing a view on D's keys.
+        """
+        return super().keys()
+
+    def pop(self, k, *args, **kwargs):
+        """D.pop(k[,d]) -> object
+
+        Remove specified key and return the corresponding value.
+        If key is not found, d is returned if given, otherwise KeyError is raised.
+        """
+        return super().pop(k, *args, **kwargs)
+
+    def update(self, *E, **F):
+        """D.update([E, ]**F) -> None
+
+        Update D from dict/iterable E and F.
+        If E is present and has a .keys() method, then does:  for k in E: D[k] = E[k]
+        If E is present and lacks a .keys() method, then does:  for k, v in E: D[k] = v
+        In either case, this is followed by: for k in F:  D[k] = F[k]
+        """
+        return super().update(*E, **F)
+
+    def values(self):
+        """D.values() -> object
+
+        An object providing a view on D's values.
+        """
+        return super().values()

mne/forward/forward.py

@@ -47,10 +47,10 @@
                      _validate_type, _check_compensation_grade, _check_option,
                      _check_stc_units, _stamp_to_dt)
 from ..label import Label
-from ..fixes import einsum
+from ..fixes import einsum, dict_
 
 
-class Forward(dict):
+class Forward(dict_):
     """Forward class to represent info from forward solution.
 
     Attributes

mne/io/meas_info.py

@@ -17,6 +17,7 @@
 import numpy as np
 from scipy import linalg
 
+from ..fixes import dict_
 from .pick import channel_type, pick_channels, pick_info
 from .constants import FIFF
 from .open import fiff_open
@@ -192,7 +193,7 @@ def _format_trans(obj, key):
 
 
 # XXX Eventually this should be de-duplicated with the MNE-MATLAB stuff...
-class Info(dict, MontageMixin):
+class Info(dict_, MontageMixin):
     """Measurement information.
 
     This data structure behaves like a dictionary. It contains all metadata

mne/io/proj.py

@@ -19,10 +19,11 @@
 from .write import (write_int, write_float, write_string, write_name_list,
                     write_float_matrix, end_block, start_block)
 from ..defaults import _BORDER_DEFAULT, _EXTRAPOLATE_DEFAULT
+from ..fixes import dict_
 from ..utils import logger, verbose, warn, fill_doc
 
 
-class Projection(dict):
+class Projection(dict_):
     """Projection vector.
 
     A basic class to proj a meaningful print for projection vectors.