ENH: Improve MATLAB compat (#8515)

mne-tools · Nov 14, 2020 · c0d098e · c0d098e
1 parent 3a4d375
commit c0d098e
Show file tree

Hide file tree

Showing 15 changed files with 119 additions and 69 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -160,23 +160,23 @@ jobs:
                       python -c "import mne; print(mne.datasets.hf_sef.data_path(update_path=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_auditory.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.brainstorm.bst_auditory.data_path(update_path=True))" --accept-brainstorm-license;
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_auditory.data_path(update_path=True, accept=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_resting.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.brainstorm.bst_resting.data_path(update_path=True))" --accept-brainstorm-license;
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_resting.data_path(update_path=True, accept=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_raw.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.brainstorm.bst_raw.data_path(update_path=True))" --accept-brainstorm-license;
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_raw.data_path(update_path=True, accept=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_ctf.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_ctf.data_path(update_path=True))" --accept-brainstorm-license;
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_ctf.data_path(update_path=True, accept=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*brainstorm.*bst_phantom_elekta.*" | wc -l) -gt 0 ]]; then
-                      python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_elekta.data_path(update_path=True))" --accept-brainstorm-license;
+                      python -c "import mne; print(mne.datasets.brainstorm.bst_phantom_elekta.data_path(update_path=True, accept=True))";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*datasets.*hcp_mmp_parcellation.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.sample.data_path(update_path=True))";
-                      python -c "import mne; print(mne.datasets.fetch_hcp_mmp_parcellation(subjects_dir=mne.datasets.sample.data_path() + '/subjects'))" --accept-hcpmmp-license;
+                      python -c "import mne; print(mne.datasets.fetch_hcp_mmp_parcellation(subjects_dir=mne.datasets.sample.data_path() + '/subjects'), accept=True)";
                     fi;
                     if [[ $(cat $FNAME | grep -x ".*datasets.*misc.*" | wc -l) -gt 0 ]]; then
                       python -c "import mne; print(mne.datasets.misc.data_path(update_path=True))";

diff --git a/doc/changes/0.21.inc b/doc/changes/0.21.inc
@@ -7,11 +7,23 @@
    - "Bugs" for bug fixes
    - "API changes" for backward-incompatible changes
 
+.. _changes_0_21_2:
+
+Version 0.21.2
+--------------
+
+Bugs
+~~~~
+
+- Add option to disable TQDM entirely with ``MNE_TQDM='off'`` (:gh:`8515` by `Eric Larson`_)
+
+- Fix reading GDF files with excluded channels in :func:`mne.io.read_raw_gdf` (:gh:`8520` by `Clemens Brunner`_)
+
 
 .. _changes_0_21_1:
 
-Version 0.21.1 (unreleased)
----------------------------
+Version 0.21.1
+--------------
 
 .. |Eduard Ort| replace:: **Eduard Ort**
 
@@ -56,8 +68,6 @@ Bugs
 
 - When reading BrainVision raw data, the channel units and types were sometimes not inferred correctly by `Richard Höchenberger`_ (:gh:`8434`)
 
-- Fix reading GDF files with excluded channels in :func:`mne.io.read_raw_gdf` (:gh:`8520` by `Clemens Brunner`_)
-
 .. _changes_0_21:
 
 Version 0.21

diff --git a/mne/datasets/brainstorm/bst_auditory.py b/mne/datasets/brainstorm/bst_auditory.py
@@ -6,7 +6,7 @@
 
 from ...utils import verbose
 from ..utils import (has_dataset, _data_path, _get_version, _version_doc,
-                     _data_path_doc)
+                     _data_path_doc_accept)
 
 has_brainstorm_data = partial(has_dataset, name='brainstorm.bst_auditory')
 
@@ -29,15 +29,15 @@
 
 @verbose
 def data_path(path=None, force_update=False, update_path=True, download=True,
-              verbose=None):  # noqa: D103
+              *, accept=False, verbose=None):  # noqa: D103
     return _data_path(path=path, force_update=force_update,
                       update_path=update_path, name='brainstorm',
-                      download=download, archive_name='bst_auditory.tar.gz')
+                      download=download, archive_name='bst_auditory.tar.gz',
+                      accept=accept)
 
 
-_data_path_doc = _data_path_doc.format(name='brainstorm',
-                                       conf='MNE_DATASETS_BRAINSTORM_DATA'
-                                            '_PATH')
+_data_path_doc = _data_path_doc_accept.format(
+    name='brainstorm', conf='MNE_DATASETS_BRAINSTORM_DATA_PATH')
 _data_path_doc = _data_path_doc.replace('brainstorm dataset',
                                         'brainstorm (bst_auditory) dataset')
 data_path.__doc__ = _data_path_doc

diff --git a/mne/datasets/brainstorm/bst_phantom_ctf.py b/mne/datasets/brainstorm/bst_phantom_ctf.py
@@ -6,7 +6,7 @@
 
 from ...utils import verbose
 from ..utils import (has_dataset, _data_path, _get_version, _version_doc,
-                     _data_path_doc)
+                     _data_path_doc_accept)
 
 has_brainstorm_data = partial(has_dataset, name='brainstorm.bst_phantom_ctf')
 
@@ -18,15 +18,15 @@
 
 @verbose
 def data_path(path=None, force_update=False, update_path=True, download=True,
-              verbose=None):  # noqa: D103
+              *, accept=False, verbose=None):  # noqa: D103
     return _data_path(path=path, force_update=force_update,
                       update_path=update_path, name='brainstorm',
-                      download=download, archive_name='bst_phantom_ctf.tar.gz')
+                      download=download, archive_name='bst_phantom_ctf.tar.gz',
+                      accept=accept)
 
 
-_data_path_doc = _data_path_doc.format(name='brainstorm',
-                                       conf='MNE_DATASETS_BRAINSTORM_DATA'
-                                            '_PATH')
+_data_path_doc = _data_path_doc_accept.format(
+    name='brainstorm', conf='MNE_DATASETS_BRAINSTORM_DATA_PATH')
 _data_path_doc = _data_path_doc.replace('brainstorm dataset',
                                         'brainstorm (bst_phantom_ctf) dataset')
 data_path.__doc__ = _data_path_doc

diff --git a/mne/datasets/brainstorm/bst_phantom_elekta.py b/mne/datasets/brainstorm/bst_phantom_elekta.py
@@ -6,7 +6,7 @@
 
 from ...utils import verbose
 from ..utils import (has_dataset, _data_path, _get_version, _version_doc,
-                     _data_path_doc)
+                     _data_path_doc_accept)
 
 has_brainstorm_data = partial(has_dataset,
                               name='brainstorm.bst_phantom_elekta')
@@ -19,16 +19,16 @@
 
 @verbose
 def data_path(path=None, force_update=False, update_path=True, download=True,
-              verbose=None):  # noqa: D103
+              *, accept=False, verbose=None):  # noqa: D103
     return _data_path(path=path, force_update=force_update,
                       update_path=update_path, name='brainstorm',
                       download=download,
-                      archive_name='bst_phantom_elekta.tar.gz')
+                      archive_name='bst_phantom_elekta.tar.gz',
+                      accept=accept)
 
 
-_data_path_doc = _data_path_doc.format(name='brainstorm',
-                                       conf='MNE_DATASETS_BRAINSTORM_DATA'
-                                            '_PATH')
+_data_path_doc = _data_path_doc_accept.format(
+    name='brainstorm', conf='MNE_DATASETS_BRAINSTORM_DATA_PATH')
 _data_path_doc = _data_path_doc.replace('brainstorm dataset',
                                         'brainstorm (bst_phantom_elekta) '
                                         'dataset')

diff --git a/mne/datasets/brainstorm/bst_raw.py b/mne/datasets/brainstorm/bst_raw.py
@@ -6,7 +6,7 @@
 
 from ...utils import verbose, get_config
 from ..utils import (has_dataset, _data_path, _get_version, _version_doc,
-                     _data_path_doc)
+                     _data_path_doc_accept)
 
 has_brainstorm_data = partial(has_dataset, name='brainstorm.bst_raw')
 
@@ -27,15 +27,15 @@
 
 @verbose
 def data_path(path=None, force_update=False, update_path=True, download=True,
-              verbose=None):    # noqa: D103
+              *, accept=False, verbose=None):    # noqa: D103
     return _data_path(path=path, force_update=force_update,
                       update_path=update_path, name='brainstorm',
-                      download=download, archive_name='bst_raw.tar.gz')
+                      download=download, archive_name='bst_raw.tar.gz',
+                      accept=accept)
 
 
-_data_path_doc = _data_path_doc.format(name='brainstorm',
-                                       conf='MNE_DATASETS_BRAINSTORM_DATA'
-                                            '_PATH')
+_data_path_doc = _data_path_doc_accept.format(
+    name='brainstorm', conf='MNE_DATASETS_BRAINSTORM_DATA_PATH')
 _data_path_doc = _data_path_doc.replace('brainstorm dataset',
                                         'brainstorm (bst_raw) dataset')
 data_path.__doc__ = _data_path_doc

diff --git a/mne/datasets/brainstorm/bst_resting.py b/mne/datasets/brainstorm/bst_resting.py
@@ -6,7 +6,7 @@
 
 from ...utils import verbose
 from ..utils import (has_dataset, _data_path, _get_version, _version_doc,
-                     _data_path_doc)
+                     _data_path_doc_accept)
 
 has_brainstorm_data = partial(has_dataset, name='brainstorm.bst_resting')
 
@@ -20,15 +20,15 @@
 
 @verbose
 def data_path(path=None, force_update=False, update_path=True, download=True,
-              verbose=None):  # noqa: D103
+              *, accept=False, verbose=None):  # noqa: D103
     return _data_path(path=path, force_update=force_update,
                       update_path=update_path, name='brainstorm',
-                      download=download, archive_name='bst_resting.tar.gz')
+                      download=download, archive_name='bst_resting.tar.gz',
+                      accept=accept)
 
 
-_data_path_doc = _data_path_doc.format(name='brainstorm',
-                                       conf='MNE_DATASETS_BRAINSTORM_DATA'
-                                            '_PATH')
+_data_path_doc = _data_path_doc_accept.format(
+    name='brainstorm', conf='MNE_DATASETS_BRAINSTORM_DATA_PATH')
 _data_path_doc = _data_path_doc.replace('brainstorm dataset',
                                         'brainstorm (bst_resting) dataset')
 data_path.__doc__ = _data_path_doc

diff --git a/mne/datasets/utils.py b/mne/datasets/utils.py
@@ -22,7 +22,7 @@
 from .. import __version__ as mne_version
 from ..label import read_labels_from_annot, Label, write_labels_to_annot
 from ..utils import (get_config, set_config, _fetch_file, logger, warn,
-                     verbose, get_subjects_dir, hashfunc, _pl)
+                     verbose, get_subjects_dir, hashfunc, _pl, _safe_input)
 from ..utils.docs import docdict
 from ..externals.doccer import docformat
 
@@ -55,7 +55,12 @@
     path : str
         Path to {name} dataset directory.
 """
+_data_path_doc_accept = _data_path_doc.split('%(verbose)s')
+_data_path_doc_accept[-1] = '%(verbose)s' + _data_path_doc_accept[-1]
+_data_path_doc_accept.insert(1, '    %(accept)s')
+_data_path_doc_accept = ''.join(_data_path_doc_accept)
 _data_path_doc = docformat(_data_path_doc, docdict)
+_data_path_doc_accept = docformat(_data_path_doc_accept, docdict)
 
 _version_doc = """Get version of the local {name} dataset.
 
@@ -204,7 +209,7 @@ def _do_path_update(path, update_path, key, name):
                 msg = ('Do you want to set the path:\n    %s\nas the default '
                        '%s dataset path in the mne-python config [y]/n? '
                        % (path, name))
-                answer = input(msg)
+                answer = _safe_input(msg, alt='pass update_path=True')
             if answer.lower() == 'n':
                 update_path = False
 
@@ -215,7 +220,7 @@ def _do_path_update(path, update_path, key, name):
 
 def _data_path(path=None, force_update=False, update_path=True, download=True,
                name=None, check_version=False, return_version=False,
-               archive_name=None):
+               archive_name=None, accept=False):
     """Aux function."""
     key = {
         'fake': 'MNE_DATASETS_FAKE_PATH',
@@ -381,10 +386,13 @@ def _data_path(path=None, force_update=False, update_path=True, download=True,
         for f in folder_path:
             logger.debug('  Exists: %s: %s' % (f, op.exists(f)))
         if name == 'brainstorm':
-            if '--accept-brainstorm-license' in sys.argv:
+            if accept or '--accept-brainstorm-license' in sys.argv:
                 answer = 'y'
             else:
-                answer = input('%sAgree (y/[n])? ' % _bst_license_text)
+                # If they don't have stdin, just accept the license
+                # https://github.com/mne-tools/mne-python/issues/8513#issuecomment-726823724  # noqa: E501
+                answer = _safe_input(
+                    '%sAgree (y/[n])? ' % _bst_license_text, use='y')
             if answer.lower() != 'y':
                 raise RuntimeError('You must agree to the license to use this '
                                    'dataset')
@@ -590,15 +598,11 @@ def _download_all_example_data(verbose=True):
     kiloword.data_path()
     phantom_4dbti.data_path()
     refmeg_noise.data_path()
-    sys.argv += ['--accept-brainstorm-license']
-    try:
-        brainstorm.bst_raw.data_path()
-        brainstorm.bst_auditory.data_path()
-        brainstorm.bst_resting.data_path()
-        brainstorm.bst_phantom_elekta.data_path()
-        brainstorm.bst_phantom_ctf.data_path()
-    finally:
-        sys.argv.pop(-1)
+    brainstorm.bst_raw.data_path(accept=True)
+    brainstorm.bst_auditory.data_path(accept=True)
+    brainstorm.bst_resting.data_path(accept=True)
+    brainstorm.bst_phantom_elekta.data_path(accept=True)
+    brainstorm.bst_phantom_ctf.data_path(accept=True)
     eegbci.load_data(1, [6, 10, 14], update_path=True)
     for subj in range(4):
         eegbci.load_data(subj + 1, runs=[3], update_path=True)
@@ -607,11 +611,8 @@ def _download_all_example_data(verbose=True):
     # If the user has SUBJECTS_DIR, respect it, if not, set it to the EEG one
     # (probably on CircleCI, or otherwise advanced user)
     fetch_fsaverage(None)
-    sys.argv += ['--accept-hcpmmp-license']
-    try:
-        fetch_hcp_mmp_parcellation(subjects_dir=sample_path + '/subjects')
-    finally:
-        sys.argv.pop(-1)
+    fetch_hcp_mmp_parcellation(
+        subjects_dir=sample_path + '/subjects', accept=True)
     limo.load_data(subject=1, update_path=True)
 
 
@@ -648,7 +649,8 @@ def fetch_aparc_sub_parcellation(subjects_dir=None, verbose=None):
 
 
 @verbose
-def fetch_hcp_mmp_parcellation(subjects_dir=None, combine=True, verbose=None):
+def fetch_hcp_mmp_parcellation(subjects_dir=None, combine=True, *,
+                               accept=False, verbose=None):
     """Fetch the HCP-MMP parcellation.
 
     This will download and install the HCP-MMP parcellation
@@ -664,6 +666,7 @@ def fetch_hcp_mmp_parcellation(subjects_dir=None, combine=True, verbose=None):
         If True, also produce the combined/reduced set of 23 labels per
         hemisphere as ``HCPMMP1_combined.annot``
         :footcite:`GlasserEtAl2016supp`.
+    %(accept)s
     %(verbose)s
 
     Notes
@@ -684,10 +687,10 @@ def fetch_hcp_mmp_parcellation(subjects_dir=None, combine=True, verbose=None):
     hashes = dict(lh='46a102b59b2fb1bb4bd62d51bf02e975',
                   rh='75e96b331940227bbcb07c1c791c2463')
     if not all(op.isfile(fname) for fname in fnames):
-        if '--accept-hcpmmp-license' in sys.argv:
+        if accept or '--accept-hcpmmp-license' in sys.argv:
             answer = 'y'
         else:
-            answer = input('%s\nAgree (y/[n])? ' % _hcp_mmp_license_text)
+            answer = _safe_input('%s\nAgree (y/[n])? ' % _hcp_mmp_license_text)
         if answer.lower() != 'y':
             raise RuntimeError('You must agree to the license to use this '
                                'dataset')

diff --git a/mne/report.py b/mne/report.py
@@ -25,7 +25,7 @@
 from .io.pick import _DATA_CH_TYPES_SPLIT
 from .source_space import _mri_orientation
 from .utils import (logger, verbose, get_subjects_dir, warn,
-                    fill_doc, _check_option, _validate_type)
+                    fill_doc, _check_option, _validate_type, _safe_input)
 from .viz import (plot_events, plot_alignment, plot_cov, plot_projs_topomap,
                   plot_compare_evokeds)
 from .viz.misc import _plot_mri_contours, _get_bem_plotting_surfaces
@@ -1586,7 +1586,7 @@ def save(self, fname=None, open_browser=True, overwrite=False):
             msg = ('Report already exists at location %s. '
                    'Overwrite it (y/[n])? '
                    % fname)
-            answer = input(msg)
+            answer = _safe_input(msg, alt='pass overwrite=True')
             if answer.lower() == 'y':
                 overwrite = True
 

diff --git a/mne/utils/__init__.py b/mne/utils/__init__.py
@@ -17,7 +17,7 @@
                     _check_path_like, _check_src_normal, _check_stc_units,
                     _check_pyqt5_version, _check_sphere, _check_time_format,
                     _check_freesurfer_home, _suggest, _require_version,
-                    _on_missing)
+                    _on_missing, _safe_input)
 from .config import (set_config, get_config, get_config_path, set_cache_dir,
                      set_memmap_min_size, get_subjects_dir, _get_stim_channel,
                      sys_info, _get_extra_data_path, _get_root_dir,

diff --git a/mne/utils/check.py b/mne/utils/check.py
@@ -4,6 +4,7 @@
 #
 # License: BSD (3-clause)
 
+from builtins import input  # no-op here but facilitates testing
 from difflib import get_close_matches
 from distutils.version import LooseVersion
 import operator
@@ -730,3 +731,14 @@ def _on_missing(on_missing, msg):
         warn(msg)
     else:  # Ignore
         assert on_missing == 'ignore'
+
+
+def _safe_input(msg, *, alt=None, use=None):
+    try:
+        return input(msg)
+    except EOFError:  # MATLAB or other non-stdin
+        if use is not None:
+            return use
+        raise RuntimeError(
+            f'Could not use input() to get a response to:\n{msg}\n'
+            f'You can {alt} to avoid this error.')