MRG, MAINT: Change default role in conf.py (mne-tools#7841)

* WIP: Change default role to py:obj

* FIX: More

* FIX: Last ones

* FIX: gen_mne_ to mne

* STY: Flake

* FIX: gen_ [skip travis]

* DOC: Ticks and refs [skip travis]

doc/_includes/bem_model.rst

@@ -23,7 +23,7 @@ The watershed algorithm [Segonne *et al.*,
 2004] is part of the FreeSurfer software.
 The name of the program is mri_watershed .
 Its use in the MNE environment is facilitated by the script
-:ref:`gen_mne_watershed_bem`.
+:ref:`mne watershed_bem`.
 
 After ``mne watershed_bem`` has completed, the following files appear in the
 subject's :file:`bem/watershed` directory:
@@ -61,7 +61,7 @@ Creation of the BEM meshes using this method involves the following steps:
 
 - Creating a synthetic 5-degree flip angle FLASH volume, register
   it with the MPRAGE data, and run the segmentation and meshing program.
-  This step is accomplished by running the script :ref:`gen_mne_flash_bem`.
+  This step is accomplished by running the script :ref:`mne flash_bem`.
 
 - Inspecting the meshes with tkmedit, see :ref:`inspecting-meshes`.
 
@@ -88,10 +88,10 @@ Creating the surface tessellations
 ----------------------------------
 
 The BEM surface segmentation and tessellation is automated with the script
-:ref:`gen_mne_flash_bem`. It assumes that a FreeSurfer reconstruction for this
+:ref:`mne flash_bem`. It assumes that a FreeSurfer reconstruction for this
 subject is already in place.
 
-Before running :ref:`gen_mne_flash_bem` do the following:
+Before running :ref:`mne flash_bem` do the following:
 
 - Create symbolic links from the directories containing the 5-degree and
   30-degree flip angle FLASH series to ``flash05`` and ``flash30``,
@@ -161,6 +161,6 @@ Inspecting the meshes
 It is advisable to check the validity of the BEM meshes before
 using them. This can be done with:
 
-- the ``--view`` option of :ref:`gen_mne_flash_bem`
+- the ``--view`` option of :ref:`mne flash_bem`
 - calling :func:`mne.viz.plot_bem` directly
 - Using FreeSurfer tools ``tkmedit`` or ``freeview``

doc/_includes/channel_interpolation.rst

@@ -29,7 +29,7 @@ where the :math:`C = (c_{1}, ..., c_{N})^{T}` are constants which must be estima
 .. math:: g_{m}(x) = \frac{1}{4 \pi}\sum_{n=1}^{\infty} \frac{2n + 1}{(n(n + 1))^m}P_{n}(x)
    :label: legendre
 
-where :math:`P_{n}(x)` are `Legendre polynomials`_ of order `n`.
+where :math:`P_{n}(x)` are `Legendre polynomials`_ of order :math:`n`.
 
 .. _Legendre polynomials: https://en.wikipedia.org/wiki/Legendre_polynomials
 

doc/_includes/forward.rst

@@ -195,19 +195,19 @@ and
     | Transformation               | FreeSurfer                    | MNE                                             |
     +------------------------------+-------------------------------+-------------------------------------------------+
     | :math:`T_1`                  | Not present                   | | Measurement data files                        |
-    |                              |                               | | Forward solution files (`*fwd.fif`)           |
-    |                              |                               | | Inverse operator files (`*inv.fif`)           |
+    |                              |                               | | Forward solution files (``*fwd.fif``)         |
+    |                              |                               | | Inverse operator files (``*inv.fif``)         |
     +------------------------------+-------------------------------+-------------------------------------------------+
     | :math:`T_{s_1}\dots T_{s_n}` | Not present                   | Channel information in files                    |
     |                              |                               | containing :math:`T_1`.                         |
     +------------------------------+-------------------------------+-------------------------------------------------+
     | :math:`T_2`                  | Not present                   | | MRI description filesSeparate                 |
     |                              |                               | | Separate ``-trans.fif`` files                 |
-    |                              |                               | | from :ref:`gen_mne_coreg`                     |
+    |                              |                               | | from :ref:`mne coreg`                         |
     |                              |                               | | Forward solution files                        |
     |                              |                               | | Inverse operator files                        |
     +------------------------------+-------------------------------+-------------------------------------------------+
-    | :math:`T_3`                  | `mri/*mgz` files              | :class:`nibabel.freesurfer.mghformat.MGHImage`  |
+    | :math:`T_3`                  | ``mri/*mgz`` files            | :class:`nibabel.freesurfer.mghformat.MGHImage`  |
     +------------------------------+-------------------------------+-------------------------------------------------+
     | :math:`T_4`                  | mri/transforms/talairach.xfm  | Internal reading                                |
     +------------------------------+-------------------------------+-------------------------------------------------+

doc/_includes/inverse.rst

@@ -119,7 +119,7 @@ where
 
 is the spatially whitened gain matrix. We arrive at the whitened inverse
 operator equation :eq:`inv_m_tilde` by making the substitution for
-`G` from :eq:`inv_g_tilde` in :eq:`inv_m` as
+:math:`G` from :eq:`inv_g_tilde` in :eq:`inv_m` as
 
 .. math::
 

doc/changes/0.10.inc

@@ -100,9 +100,9 @@ API
 
 - Rename and deprecate ``mne.viz.plot_topo`` for ``mne.viz.plot_evoked_topo`` by `Jaakko Leppakangas`_
 
-- Deprecated :class: `mne.decoding.transformer.ConcatenateChannels` and replaced by :class: `mne.decoding.transformer.EpochsVectorizer` by `Romain Trachel`_
+- Deprecated ``mne.decoding.transformer.ConcatenateChannels`` and replaced by ``mne.decoding.EpochsVectorizer`` by `Romain Trachel`_
 
-- Deprecated `lws` and renamed `ledoit_wolf` for the ``reg`` argument in :class:`mne.decoding.CSP` by `Romain Trachel`_
+- Deprecated ``lws`` and renamed ``ledoit_wolf`` for the ``reg`` argument in :class:`mne.decoding.CSP` by `Romain Trachel`_
 
 - Redesigned and rewrote :meth:`mne.Epochs.plot` (no backwards compatibility) during the GSOC 2015 by `Jaakko Leppakangas`_, `Mainak Jas`_, `Federico Raimondo`_ and `Denis Engemann`_
 

doc/changes/0.12.inc

@@ -109,7 +109,7 @@ BUG
 
 - Fix bug in :class:`mne.Evoked` type setting in :func:`mne.stats.linear_regression_raw` by `Eric Larson`_
 
-- Fix bug in :class: `mne.io.edf.RawEDF` highpass filter setting to take max highpass to match warning message by `Teon Brooks`_
+- Fix bug in ``mne.io.edf.RawEDF`` highpass filter setting to take max highpass to match warning message by `Teon Brooks`_
 
 - Fix bugs with coordinane frame adjustments in ``mne.viz.plot_trans`` by `Eric Larson`_
 
@@ -136,9 +136,9 @@ BUG
 API
 ~~~
 
-- The default `picks=None` in :func:`mne.viz.plot_epochs_image` now only plots the first 5 channels, not all channels, by `Jona Sassenhagen`_
+- The default ``picks=None`` in :func:`mne.viz.plot_epochs_image` now only plots the first 5 channels, not all channels, by `Jona Sassenhagen`_
 
-- The ``mesh_color`` parameter in :func:`mne.viz.plot_dipole_locations` has been removed (use `brain_color` instead), by `Marijn van Vliet`_
+- The ``mesh_color`` parameter in :func:`mne.viz.plot_dipole_locations` has been removed (use ``brain_color`` instead), by `Marijn van Vliet`_
 
 - Deprecated functions ``mne.time_frequency.compute_raw_psd`` and ``mne.time_frequency.compute_epochs_psd``, replaced by :func:`mne.time_frequency.psd_welch` by `Chris Holdgraf`_
 
@@ -164,7 +164,7 @@ API
 
 - Subselecting channels can now emit a warning if many channels have been subselected from projection vectors. We recommend only computing projection vertors for and applying projectors to channels that will be used in the final analysis. However, after picking a subset of channels, projection vectors can be renormalized with :func:`mne.Info.normalize_proj` if necessary to avoid warnings about subselection. Changes by `Eric Larson`_ and `Alex Gramfort`_.
 
-- Rename and deprecate ``mne.Epochs.drop_bad_epochs`` to :func:`mne.Epochs.drop_bad`, and `mne.Epochs.drop_epochs`` to :func:`mne.Epochs.drop` by `Alex Gramfort`_.
+- Rename and deprecate ``mne.Epochs.drop_bad_epochs`` to :func:`mne.Epochs.drop_bad`, and ``mne.Epochs.drop_epochs`` to :func:`mne.Epochs.drop` by `Alex Gramfort`_.
 
 - The C wrapper ``mne.do_forward_solution`` has been deprecated in favor of the native Python version :func:`mne.make_forward_solution` by `Eric Larson`_
 

doc/changes/0.13.inc

@@ -42,9 +42,9 @@ Changelog
 
 - Add the option to plot brain surfaces and source spaces to :func:`viz.plot_bem` by `Christian Brodbeck`_
 
-- Add the ``--filterchpi`` option to :ref:`mne browse_raw <gen_mne_browse_raw>`, by `Felix Raimundo`_
+- Add the ``--filterchpi`` option to :ref:`mne browse_raw`, by `Felix Raimundo`_
 
-- Add the ``--no-decimate`` option to :ref:`mne make_scalp_surfaces <gen_mne_make_scalp_surfaces>` to skip the high-resolution surface decimation step, by `Eric Larson`_
+- Add the ``--no-decimate`` option to :ref:`mne make_scalp_surfaces` to skip the high-resolution surface decimation step, by `Eric Larson`_
 
 - Add new class :class:`mne.decoding.EMS` to transform epochs with the event-matched spatial filters and add 'cv' parameter to :func:`mne.decoding.compute_ems`, by `Jean-Remi King`_
 
@@ -64,7 +64,7 @@ Changelog
 
 - Adds new function :func:`mne.viz.plot_compare_evokeds` to show multiple evoked time courses at a single location, or the mean over a ROI, or the GFP, automatically averaging and calculating a CI if multiple subjects are given, by `Jona Sassenhagen`_
 
-- Added `transform_into` parameter into :class:`mne.decoding.CSP` to retrieve the average power of each source or the time course of each source, by `Jean-Remi King`_
+- Added ``transform_into`` parameter into :class:`mne.decoding.CSP` to retrieve the average power of each source or the time course of each source, by `Jean-Remi King`_
 
 - Added support for reading MaxShield (IAS) evoked data (e.g., from the acquisition machine) in :func:`mne.read_evokeds` by `Eric Larson`_
 
@@ -194,7 +194,7 @@ API
 
 - ``mne.decoding.EpochsVectorizer`` has been deprecated in favor of :class:`mne.decoding.Vectorizer` by `Asish Panda`_
 
-- The `epochs_data` parameter has been deprecated in :class:`mne.decoding.CSP`, in favour of the ``X`` parameter to comply to scikit-learn API, by `Jean-Remi King`_
+- The ``epochs_data`` parameter has been deprecated in :class:`mne.decoding.CSP`, in favour of the ``X`` parameter to comply to scikit-learn API, by `Jean-Remi King`_
 
 - Deprecated ``mne.time_frequency.cwt_morlet`` and ``mne.time_frequency.single_trial_power`` in favour of :func:`mne.time_frequency.tfr_morlet` with parameter average=False, by `Jean-Remi King`_ and `Alex Gramfort`_
 

doc/changes/0.14.inc

@@ -24,7 +24,7 @@ Changelog
 
 - Add convenient default values to :meth:`mne.io.Raw.apply_hilbert` and :meth:`mne.io.Raw.apply_function` by `Denis Engemann`_
 
-- Remove MNE-C requirement for :ref:`mne make_scalp_surfaces <gen_mne_make_scalp_surfaces>` by `Eric Larson`_
+- Remove MNE-C requirement for :ref:`mne make_scalp_surfaces` by `Eric Larson`_
 
 - Add support for FastTrack Polhemus ``.mat`` file outputs in ``hsp`` argument of ``mne.channels.read_dig_montage`` by `Eric Larson`_
 
@@ -196,15 +196,15 @@ API
 
 - An ``overwrite=False`` default parameter has been added to :func:`write_source_spaces` to protect against accidental overwrites, by `Eric Larson`_
 
-- The :class:`mne.decoding.LinearModel` class will no longer support `plot_filters` and `plot_patterns`, use :class:`mne.EvokedArray` with :func:`mne.decoding.get_coef` instead, by `Jean-Remi King`_
+- The :class:`mne.decoding.LinearModel` class will no longer support ``plot_filters`` and ``plot_patterns``, use :class:`mne.EvokedArray` with :func:`mne.decoding.get_coef` instead, by `Jean-Remi King`_
 
 - Made functions :func:`mne.time_frequency.tfr_array_multitaper`, :func:`mne.time_frequency.tfr_array_morlet`, :func:`mne.time_frequency.tfr_array_stockwell`, :func:`mne.time_frequency.psd_array_multitaper` and :func:`mne.time_frequency.psd_array_welch` public to allow computing TFRs and PSDs on numpy arrays by `Jaakko Leppakangas`_
 
 - :meth:`mne.preprocessing.ICA.fit` now rejects data annotated bad by default. Turn off with ``reject_by_annotation=False``, by `Jaakko Leppakangas`_
 
 - :func:`mne.io.read_raw_egi` now names channels with pattern 'E<idx>'. This behavior can be changed with parameter ``channel_naming`` by `Jaakko Leppakangas`_
 
-- the `name`` parameter in :class:`mne.Epochs` is deprecated, by `Jaakko Leppakangas`_
+- the ``name`` parameter in :class:`mne.Epochs` is deprecated, by `Jaakko Leppakangas`_
 
 Authors
 ~~~~~~~

doc/changes/0.15.inc

@@ -82,7 +82,7 @@ Changelog
 
 - Add support for :class:`numpy.random.RandomState` argument to ``seed`` in :mod:`statistical clustering functions <mne.stats>` and better documentation of exact 1-sample tests by `Eric Larson`_
 
-- Extend :func:`mne.viz.plot_epochs_image`/:meth:`mne.Epochs.plot_image` with regards to grouping by or aggregating over channels. See the new example at `examples/visualization/plot_roi_erpimage_by_rt.py` by `Jona Sassenhagen`_
+- Extend :func:`mne.viz.plot_epochs_image`/:meth:`mne.Epochs.plot_image` with regards to grouping by or aggregating over channels. See the new example at ``examples/visualization/plot_roi_erpimage_by_rt.py`` by `Jona Sassenhagen`_
 
 - Add bootstrapped confidence intervals to :func:`mne.viz.plot_compare_evokeds` by `Jona Sassenhagen`_ and `Denis Engemann`_
 
@@ -120,7 +120,7 @@ BUG
 
 - :meth:`mne.concatenate_epochs` now maintains the relative position of events during concatenation by `Alexandre Barachant`_
 
-- Fix bug in script `mne make_scalp_surfaces` by `Denis Engemann`_ (this bug prevented creation of high-resolution meshes when they were absent in the first place.)
+- Fix bug in script ``mne make_scalp_surfaces`` by `Denis Engemann`_ (this bug prevented creation of high-resolution meshes when they were absent in the first place.)
 
 - Fix writing of raw files with empty set of annotations by `Jaakko Leppakangas`_
 

doc/changes/0.16.inc

@@ -111,7 +111,7 @@ Bug
 
 - Fix bug with events when saving split files using :meth:`mne.Epochs.save` by `Eric Larson`_
 
-- Fix bug in :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` to allow :func:`mne.decoding.cross_val_multiscore` to automatically detect whether the `base_estimator` is a classifier and use a `StratifiedKFold` instead of a `KFold` when `cv` is not specified, by `Jean-Remi King`_
+- Fix bug in :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` to allow :func:`mne.decoding.cross_val_multiscore` to automatically detect whether the ``base_estimator`` is a classifier and use a ``StratifiedKFold`` instead of a ``KFold`` when ``cv`` is not specified, by `Jean-Remi King`_
 
 - Fix bug in :func:`mne.set_eeg_reference` to remove an average reference projector when setting the reference to ``[]`` (i.e. do not change the existing reference) by `Clemens Brunner`_
 

doc/changes/0.17.inc

@@ -36,7 +36,7 @@ Changelog
 
 - Add possibility to save :class:`mne.VolSourceEstimate` and :class:`mne.MixedSourceEstimate` to HDF5 format (file extension .h5) with :meth:`mne.VolSourceEstimate.save` and :meth:`mne.MixedSourceEstimate.save` by `Alex Gramfort`_
 
-- Add `replace` parameter to :meth:`mne.io.Raw.add_events` to allow adding events while removing the old ones on the stim channel by `Alex Gramfort`_
+- Add ``replace`` parameter to :meth:`mne.io.Raw.add_events` to allow adding events while removing the old ones on the stim channel by `Alex Gramfort`_
 
 - Add ability to pass ``axes`` to ``ts_args`` and ``topomap_args`` of :meth:`mne.viz.plot_evoked_joint` by `Jona Sassenhagen`_
 
@@ -54,7 +54,7 @@ Changelog
 
 - Add support for raw PSD plots in :meth:`mne.Report.parse_folder` via ``raw_psd`` argument of :class:`mne.Report` by `Eric Larson`_
 
-- Add `trig_shift_by_type` parameter in :func:`mne.io.read_raw_brainvision` to allow to specify offsets for arbitrary marker types by `Henrich Kolkhorst`_
+- Add ``trig_shift_by_type`` parameter in :func:`mne.io.read_raw_brainvision` to allow to specify offsets for arbitrary marker types by `Henrich Kolkhorst`_
 
 - Add progress bar support to :class:`mne.decoding.SlidingEstimator` and :class:`mne.decoding.GeneralizingEstimator` by `Eric Larson`_
 
@@ -66,7 +66,7 @@ Changelog
 
 - Add handling in :func:`mne.combine_evoked` and :func:`mne.grand_average` for input with the same channels in different orders, if required, by `Jona Sassenhagen`_
 
-- Add `split_naming` parameter to the `Raw.save` method to allow for BIDS-compatible raw file name construction by `Teon Brooks`_
+- Add ``split_naming`` parameter to the `mne.io.Raw.save` method to allow for BIDS-compatible raw file name construction by `Teon Brooks`_
 
 - Add ``origin`` parameter to :meth:`mne.Evoked.interpolate_bads` and related methods by `Eric Larson`_
 
@@ -100,7 +100,7 @@ Changelog
 
 - Handle different time vectors in topography plots using :func:`mne.viz.plot_evoked_topo` by `Jussi Nurminen`_
 
-- Speed up :func:`mne.inverse_sparse.mixed_norm` if the :solver: parameter is set to `bcd` using :func:`scipy.linalg.get_blas_funcs` by `Quentin Bertrand`_
+- Speed up :func:`mne.inverse_sparse.mixed_norm` if the ``solver`` parameter is set to ``bcd`` using :func:`scipy.linalg.get_blas_funcs` by `Quentin Bertrand`_
 
 Bug
 ~~~
@@ -145,7 +145,7 @@ Bug
 
 - Fix bug in :func:`mne.io.read_raw_edf` where GDF files had ``info['highpass']`` and ``info['lowpass']`` set to NaN and ``info['meas_date']`` set incorrectly, by `Eric Larson`_
 
-- Fix bug in :func:`mne.preprocessing.ICA.apply` to handle arrays as `exclude` property by `Joan Massich`_
+- Fix bug in :func:`mne.preprocessing.ICA.apply` to handle arrays as ``exclude`` property by `Joan Massich`_
 
 - Fix bug in ``method='eLORETA'`` for :func:`mne.minimum_norm.apply_inverse` when using a sphere model and saved ``inv`` by `Eric Larson`_
 
@@ -236,7 +236,7 @@ API
 
 - Calling :meth:``mne.io.pick.pick_info`` removing channels that are needed by compensation matrices (``info['comps']``) no longer raises ``RuntimeException`` but instead logs an info level message. By `Luke Bloy`_
 
-- :meth:`mne.Epochs.save` now has the parameter `fmt` to specify the desired format (precision) saving epoched data, by `Stefan Repplinger`_, `Eric Larson`_ and `Alex Gramfort`_
+- :meth:`mne.Epochs.save` now has the parameter ``fmt`` to specify the desired format (precision) saving epoched data, by `Stefan Repplinger`_, `Eric Larson`_ and `Alex Gramfort`_
 
 - Deprecated ``mne.SourceEstimate.morph_precomputed``, ``mne.SourceEstimate.morph``, ``mne.compute_morph_matrix``, ``mne.morph_data_precomputed`` and ``mne.morph_data`` in favor of :func:`mne.compute_source_morph`, by `Tommy Clausner`_
 
@@ -256,7 +256,7 @@ API
 
 - Deprecated save_stc_as_volume function in favor of :meth:`mne.VolSourceEstimate.as_volume` and :meth:`mne.VolSourceEstimate.save_as_volume` by `Alex Gramfort`_
 
-- `src.kind` now equals to `'mixed'` (and not `'combined'`) for a mixed source space (made of surfaces and volume grids) by `Alex Gramfort`_
+- ``src.kind`` now equals to ``'mixed'`` (and not ``'combined'``) for a mixed source space (made of surfaces and volume grids) by `Alex Gramfort`_
 
 - Deprecation of :attr:`mne.io.Raw.annotations` property in favor of :meth:`mne.io.Raw.set_annotations` by `Joan Massich`_