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# -*- coding: utf-8 -*-
# Author: Eric Larson <larson.eric.d@gmail.com>
#
# License: BSD-3-Clause
import importlib
import inspect
from inspect import getsource
import os.path as op
from pathlib import Path
from pkgutil import walk_packages
import re
import pytest
import mne
from mne.utils import requires_numpydoc, _pl, _record_warnings
public_modules = [
# the list of modules users need to access for all functionality
'mne',
'mne.baseline',
'mne.beamformer',
'mne.channels',
'mne.chpi',
'mne.cov',
'mne.cuda',
'mne.datasets',
'mne.datasets.brainstorm',
'mne.datasets.hf_sef',
'mne.datasets.sample',
'mne.decoding',
'mne.dipole',
'mne.export',
'mne.filter',
'mne.forward',
'mne.gui',
'mne.inverse_sparse',
'mne.io',
'mne.io.kit',
'mne.minimum_norm',
'mne.preprocessing',
'mne.report',
'mne.simulation',
'mne.source_estimate',
'mne.source_space',
'mne.surface',
'mne.stats',
'mne.time_frequency',
'mne.time_frequency.tfr',
'mne.viz',
]
def _func_name(func, cls=None):
"""Get the name."""
parts = []
if cls is not None:
module = inspect.getmodule(cls)
else:
module = inspect.getmodule(func)
if module:
parts.append(module.__name__)
if cls is not None:
parts.append(cls.__name__)
parts.append(func.__name__)
return '.'.join(parts)
# functions to ignore args / docstring of
docstring_ignores = {
'mne.fixes',
'mne.io.write',
'mne.io.meas_info.Info',
}
char_limit = 800 # XX eventually we should probably get this lower
tab_ignores = [
'mne.channels.tests.test_montage',
'mne.io.curry.tests.test_curry',
]
error_ignores = {
# These we do not live by:
'GL01', # Docstring should start in the line immediately after the quotes
'EX01', 'EX02', # examples failed (we test them separately)
'ES01', # no extended summary
'SA01', # no see also
'YD01', # no yields section
'SA04', # no description in See Also
'PR04', # Parameter "shape (n_channels" has no type
'RT02', # The first line of the Returns section should contain only the type, unless multiple values are being returned # noqa
# XXX should also verify that | is used rather than , to separate params
# XXX should maybe also restore the parameter-desc-length < 800 char check
}
error_ignores_specific = { # specific instances to skip
('regress_artifact', 'SS05'), # "Regress" is actually imperative
}
subclass_name_ignores = (
(dict, {'values', 'setdefault', 'popitems', 'keys', 'pop', 'update',
'copy', 'popitem', 'get', 'items', 'fromkeys', 'clear'}),
(list, {'append', 'count', 'extend', 'index', 'insert', 'pop', 'remove',
'sort'}),
(mne.fixes.BaseEstimator, {'get_params', 'set_params', 'fit_transform'}),
)
def check_parameters_match(func, cls=None):
"""Check docstring, return list of incorrect results."""
from numpydoc.validate import validate
name = _func_name(func, cls)
skip = (not name.startswith('mne.') or
any(re.match(d, name) for d in docstring_ignores))
if skip:
return list()
if cls is not None:
for subclass, ignores in subclass_name_ignores:
if issubclass(cls, subclass) and name.split('.')[-1] in ignores:
return list()
incorrect = ['%s : %s : %s' % (name, err[0], err[1])
for err in validate(name)['errors']
if err[0] not in error_ignores and
(name.split('.')[-1], err[0]) not in error_ignores_specific]
# Add a check that all public functions and methods that have "verbose"
# set the default verbose=None
if cls is None:
mod_or_class = importlib.import_module('.'.join(name.split('.')[:-1]))
else:
mod_or_class = importlib.import_module('.'.join(name.split('.')[:-2]))
mod_or_class = getattr(mod_or_class, cls.__name__.split('.')[-1])
callable_ = getattr(mod_or_class, name.split('.')[-1])
try:
sig = inspect.signature(callable_)
except ValueError as exc:
msg = str(exc)
# E ValueError: no signature found for builtin type
# <class 'mne.forward.forward.Forward'>
if inspect.isclass(callable_) and 'no signature found for buil' in msg:
pass
else:
raise
else:
if 'verbose' in sig.parameters:
verbose_default = sig.parameters['verbose'].default
if verbose_default is not None:
incorrect += [
f'{name} : verbose default is not None, '
f'got: {verbose_default}']
return incorrect
@pytest.mark.slowtest
@requires_numpydoc
def test_docstring_parameters():
"""Test module docstring formatting."""
from numpydoc import docscrape
incorrect = []
for name in public_modules:
# Assert that by default we import all public names with `import mne`
if name not in ('mne', 'mne.gui'):
extra = name.split('.')[1]
assert hasattr(mne, extra)
with _record_warnings(): # traits warnings
module = __import__(name, globals())
for submod in name.split('.')[1:]:
module = getattr(module, submod)
classes = inspect.getmembers(module, inspect.isclass)
for cname, cls in classes:
if cname.startswith('_'):
continue
incorrect += check_parameters_match(cls)
cdoc = docscrape.ClassDoc(cls)
for method_name in cdoc.methods:
method = getattr(cls, method_name)
incorrect += check_parameters_match(method, cls=cls)
if hasattr(cls, '__call__') and \
'of type object' not in str(cls.__call__) and \
'of ABCMeta object' not in str(cls.__call__):
incorrect += check_parameters_match(cls.__call__, cls)
functions = inspect.getmembers(module, inspect.isfunction)
for fname, func in functions:
if fname.startswith('_'):
continue
incorrect += check_parameters_match(func)
incorrect = sorted(list(set(incorrect)))
msg = '\n' + '\n'.join(incorrect)
msg += '\n%d error%s' % (len(incorrect), _pl(incorrect))
if len(incorrect) > 0:
raise AssertionError(msg)
def test_tabs():
"""Test that there are no tabs in our source files."""
for _, modname, ispkg in walk_packages(mne.__path__, prefix='mne.'):
# because we don't import e.g. mne.tests w/mne
if not ispkg and modname not in tab_ignores:
try:
mod = importlib.import_module(modname)
except Exception: # e.g., mne.export not having pybv
continue
source = getsource(mod)
assert '\t' not in source, ('"%s" has tabs, please remove them '
'or add it to the ignore list'
% modname)
documented_ignored_mods = (
'mne.fixes',
'mne.io.write',
'mne.utils',
'mne.viz.utils',
)
documented_ignored_names = """
BaseEstimator
ContainsMixin
CrossSpectralDensity
FilterMixin
GeneralizationAcrossTime
RawFIF
TimeMixin
ToDataFrameMixin
TransformerMixin
UpdateChannelsMixin
activate_proj
adjust_axes
apply_maxfilter
apply_trans
channel_type
combine_kit_markers
combine_tfr
combine_transforms
design_mne_c_filter
detrend
dir_tree_find
fast_cross_3d
fiff_open
find_source_space_hemi
find_tag
get_score_funcs
get_version
invert_transform
is_power2
is_fixed_orient
kit2fiff
label_src_vertno_sel
make_eeg_average_ref_proj
make_projector
mesh_dist
mesh_edges
next_fast_len
parallel_func
pick_channels_evoked
plot_epochs_psd
plot_epochs_psd_topomap
plot_raw_psd_topo
plot_source_spectrogram
prepare_inverse_operator
read_fiducials
read_tag
rescale
setup_proj
source_estimate_quantification
tddr
whiten_evoked
write_fiducials
write_info
""".split('\n')
def test_documented():
"""Test that public functions and classes are documented."""
doc_dir = op.abspath(op.join(op.dirname(__file__), '..', '..', 'doc'))
doc_file = op.join(doc_dir, 'python_reference.rst')
if not op.isfile(doc_file):
pytest.skip('Documentation file not found: %s' % doc_file)
api_files = (
'covariance', 'creating_from_arrays', 'datasets',
'decoding', 'events', 'file_io', 'forward', 'inverse', 'logging',
'most_used_classes', 'mri', 'preprocessing', 'reading_raw_data',
'realtime', 'report', 'sensor_space', 'simulation', 'source_space',
'statistics', 'time_frequency', 'visualization', 'export')
known_names = list()
for api_file in api_files:
with open(op.join(doc_dir, f'{api_file}.rst'), 'rb') as fid:
for line in fid:
line = line.decode('utf-8')
if not line.startswith(' '): # at least two spaces
continue
line = line.split()
if len(line) == 1 and line[0] != ':':
known_names.append(line[0].split('.')[-1])
known_names = set(known_names)
missing = []
for name in public_modules:
with _record_warnings(): # traits warnings
module = __import__(name, globals())
for submod in name.split('.')[1:]:
module = getattr(module, submod)
classes = inspect.getmembers(module, inspect.isclass)
functions = inspect.getmembers(module, inspect.isfunction)
checks = list(classes) + list(functions)
for name, cf in checks:
if not name.startswith('_') and name not in known_names:
from_mod = inspect.getmodule(cf).__name__
if (from_mod.startswith('mne') and
not any(from_mod.startswith(x)
for x in documented_ignored_mods) and
name not in documented_ignored_names and
not hasattr(cf, '_deprecated_original')):
missing.append('%s (%s.%s)' % (name, from_mod, name))
if len(missing) > 0:
raise AssertionError('\n\nFound new public members missing from '
'doc/python_reference.rst:\n\n* ' +
'\n* '.join(sorted(set(missing))))
def test_docdict_order():
"""Test that docdict is alphabetical."""
from mne.utils.docs import docdict
# read the file as text, and get entries via regex
docs_path = Path(__file__).parent.parent / 'utils' / 'docs.py'
assert docs_path.is_file(), docs_path
with open(docs_path, 'r', encoding='UTF-8') as fid:
docs = fid.read()
entries = re.findall(r'docdict\[["\'](.+)["\']\] = ', docs)
# test length & uniqueness
assert len(docdict) == len(entries)
# test order
assert sorted(entries) == entries
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