diff --git a/doc/_templates/navbar.html b/doc/_templates/navbar.html new file mode 100644 index 000000000..36b5868c8 --- /dev/null +++ b/doc/_templates/navbar.html @@ -0,0 +1,16 @@ +{% extends "!navbar.html" %} + +{% block navbarsearch %} +
+ +{{ super() }} +{% endblock %} diff --git a/doc/conf.py b/doc/conf.py index 0b84d73fb..4c4360f9b 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -9,13 +9,6 @@ import mne_bids -# If extensions (or modules to document with autodoc) are in another directory, -# add these directories to sys.path here. If the directory is relative to the -# documentation root, use os.path.abspath to make it absolute, like shown here. -curdir = os.path.dirname(__file__) -sys.path.append(os.path.abspath(os.path.join(curdir, '..', 'mne_bids'))) -sys.path.append(os.path.abspath(os.path.join(curdir, 'sphinxext'))) - # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the @@ -88,6 +81,9 @@ html_theme = 'bootstrap' html_theme_path = sphinx_bootstrap_theme.get_html_theme_path() +# Add any paths that contain templates here, relative to this directory. +templates_path = ['_templates'] + # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. @@ -102,19 +98,21 @@ ("API", "api"), ("CLI", "generated/cli"), ("What's new", "whats_new"), - ("Github", "https://github.com/mne-tools/mne-bids", True), + ("GitHub", "https://github.com/mne-tools/mne-bids", True), ]} # Example configuration for intersphinx: refer to the Python standard library. intersphinx_mapping = { 'python': ('https://docs.python.org/3', None), - 'mne': ('https://mne.tools/stable/', None), + 'mne': ('https://mne.tools/dev', None), 'numpy': ('https://www.numpy.org/devdocs', None), 'scipy': ('https://scipy.github.io/devdocs', None), 'matplotlib': ('https://matplotlib.org', None), - 'nilearn': ('http://nilearn.github.io', None), + 'nilearn': ('https://nilearn.github.io', None), } +intersphinx_timeout = 5 + sphinx_gallery_conf = { 'examples_dirs': '../examples', diff --git a/doc/environment.yml b/doc/environment.yml index a46bcbc5a..adbe21e6a 100644 --- a/doc/environment.yml +++ b/doc/environment.yml @@ -20,7 +20,6 @@ dependencies: - pytest<5.4 - pytest-cov - pytest-sugar - - pytest-faulthandler - check-manifest - pydocstyle - sphinx diff --git a/environment.yml b/environment.yml index 184a5c513..1a8675887 100644 --- a/environment.yml +++ b/environment.yml @@ -19,7 +19,6 @@ dependencies: - pytest<5.4 - pytest-cov - pytest-sugar - - pytest-faulthandler - check-manifest - pydocstyle - sphinx diff --git a/examples/convert_empty_room.py b/examples/convert_empty_room.py index fdd6c0b21..48cd6d807 100644 --- a/examples/convert_empty_room.py +++ b/examples/convert_empty_room.py @@ -1,5 +1,5 @@ """ -.. _ex-convert-mne-sample: +.. _ex-convert-empty-room: ====================================== Storing empty room data in BIDS format diff --git a/examples/convert_group_studies.py b/examples/convert_group_studies.py index af1a7b577..ccb25a7a9 100644 --- a/examples/convert_group_studies.py +++ b/examples/convert_group_studies.py @@ -8,7 +8,7 @@ https://openneuro.org/datasets/ds000117 We recommend that you go through the more basic BIDS conversion example before -checking out this group conversion example: :ref:`_ex-convert-mne-sample` +checking out this group conversion example: :ref:`ex-convert-mne-sample` References ---------- diff --git a/mne_bids/write.py b/mne_bids/write.py index e9691b55e..c5d90a44d 100644 --- a/mne_bids/write.py +++ b/mne_bids/write.py @@ -1382,11 +1382,14 @@ def write_anat(bids_root, subject, t1w, session=None, acquisition=None, If True, deface with default parameters. `trans` and `raw` must not be `None` if True. If dict, accepts the following keys: - `inset`: how far back in millimeters to start defacing - relative to the nasion (default 20) - `theta`: is the angle of the defacing shear in degrees relative - to the normal to the plane passing through the anatomical - landmarks (default 35). + + - `inset`: how far back in millimeters to start defacing + relative to the nasion (default 20) + + - `theta`: is the angle of the defacing shear in degrees relative + to the normal to the plane passing through the anatomical + landmarks (default 35). + landmarks: instance of DigMontage | str The DigMontage or filepath to a DigMontage with landmarks that can be passed to provide information for defacing. Landmarks can be determined