Eelbrain

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* Transition to `Python 3.6 <https://docs.python.org/3.6/>`_
* API changes:

- :class:`testnd.ANOVA`: The ``match`` parameter is now determined
automatically and does not need to be specified anymore in most cases.
- :attr:`testnd.TTestOneSample.diff` renamed to
:attr:`testnd.TTestOneSample.difference`.
- :class:`plot.Histogram`: following :mod:`matplotlib`, the ``normed``
parameter was renamed to ``density``.
- Previously capitalized argument and attribute names ``Y``, ``X`` and ``Xax``
are now lowercase.
- Topomap-plot argument order changed to provide consistency between different
plots.

* :class:`NDVar` and :class:`Var` support for ``round(x)``
* :class:`~pipeline.MneExperiment` pipeline:

- Independent measures t-test

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* API changes:

- To change the parcellation of an :class:`NDVar` with source-space data,
use the new function :func:`set_parc`. The :meth:`SourceSpace.set_parc`
method has been removed because dimension objects should be treated
as immutable, as they can be shared between different :class:`NDVar`
instances. Analogously, :meth:`UTS.set_tmin` is now :func:`set_tmin`.
- :func:`table.frequencies`: If the input ``y`` is a :class:`Var` object, the
output will also be a :class:`Var` (was :class:`Factor`).
- :meth:`NDVar.smooth`: window-based smoothing now uses a symmetric window,
which can lead to slightly different results.

* :func:`concatenate`: concatenate multiple :class:`NDVar` objects to form a
new dimension.
* :meth:`NDVar.ols`: regress on a dimension.
* :class:`plot.brain.SequencePlotter` to plot multiple anatomical images on one
figure.
* New functions and objects:

- :func:`complete_source_space`
- :func:`psd_welch`
- :func:`frequency_response`
- :class:`test.Correlation`, :func:`test.pairwise_correlations`
- :func:`xhemi`

* New methods:

- :meth:`Dataset.zip`, :meth:`Dataset.tile`
- :meth:`Factor.sort_cells`

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* API changes:

- A new global :func:`configure` function replaces module-level configuration
functions.
- :class:`Dataset`: when a one-dimensional array is assigned to an unused
key, the array is now automatically converted to a :class:`Var` object.
- :attr:`SourceSpace.vertno` has been renamed to
:attr:`SourceSpace.vertices`.

* Plotting:

- The new ``name`` argument allows setting the window title without adding a
title to the figure.
- Plots that reresent time have a new method to synchronize the time axis on
multiple plots: :meth:`~plot.Butterfly.link_time_axis`.
- Plot source space time series: :func:`plot.brain.butterfly`

* ANOVAs now support mixed models with between- and within-subjects factors
(see examples at :class:`test.ANOVA`).
* :mod:`load.mne`: when generating epochs from raw data, a new ``tstop``
argument allows specifying the time interval exclusive of the last sample.
* New functions:

- :func:`table.cast_to_ndvar`
- :func:`test.TTestIndependent`

* New methods:

- :meth:`NDVar.log`
- :meth:`NDVar.smooth`

* :class:`~pipeline.MneExperiment` pipeline:

- :meth:`pipeline.MneExperiment.reset` (replacing :meth:`pipeline.MneExperiment.store_state`
and :meth:`pipeline.MneExperiment.restore_state`)
- New :attr:`pipeline.MneExperiment.auto_delete_results` attribute to control whether
invalidated results are automatically deleted.
- :attr:`pipeline.MneExperiment.screen_log_level`

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* Installation with ``conda`` (see :doc:`installing`) and ``$ eelbrain`` launch
script (see :doc:`getting_started`).
* API:

- :class:`NDVar` objects now inherit names through operations.
- Assignment to a :class:`Dataset` overwrites variable ``.name`` attributes,
unless the :class:`Dataset` key is a pythonified version of ``.name``.

* GUI/plotting:

- When using iPython 5 or later, GUI start and stop is now automatic. It is
possible to revert to the old behavior with :func:`plot.configure`.
- There are new hotkeys for most plots (see the individual plots' help for
details).
- Plots automatically rescale when the window is resized.

* :class:`MneExperiment`:

- A new :attr:`pipeline.MneExperiment.sessions` attribute replaces
``defaults['experiment']``, with support for multiple sessions in one
experiment (see :ref:`MneExperiment-filestructure`).
- The :attr:`pipeline.MneExperiment.epochs` parameter ``sel_epoch`` has been removed,
use ``base`` instead.
- The setting ``raw='clm'`` has been renamed to ``raw='raw'``.
- Custom preprocessing pipelines (see :attr:`pipeline.MneExperiment.raw`).
- The ``model`` parameter for ANOVA tests is now optional (see
:attr:`pipeline.MneExperiment.tests`).

* Deconvolution using :func:`boosting`.
* Loading and saving ``*.wav`` files (:func:`load.wav` and :func:`save.wav`).

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* API:

- :class:`pipeline.MneExperiment`: For data from the NYU New York system converted
with :mod:`mne` < 0.13, the :attr:`pipeline.MneExperiment.meg_system` attribute needs
to be set to ``"KIT-157"`` to distinguish it from data collected with the
KIT UMD system.
- :meth:`~testnd.TTestRelated.masked_parameter_map` method of cluster-based test
results: use of ``pmin=None`` is deprecated, use ``pmin=1`` instead.

* New test: :class:`test.TTestRelated`.
* :meth:`pipeline.MneExperiment.make_report_rois` includes corrected p-values in reports
for tests in more than one ROI
* :meth:`pipeline.MneExperiment.make_rej` now has a ``decim`` parameter to improve
display performance.
* :class:`pipeline.MneExperiment`: BEM-solution files are now created dynamically with
:mod:`mne` and are not cached any more. This can lead to small changes
in results due to improved numerical precision. Delete old files to free up
space with ``mne_experiment.rm('bem-sol-file', subject='*')``.
* New :meth:`pipeline.MneExperiment.make_report_coreg` method.
* New :class:`pipeline.MneExperiment`: analysis parameter
:ref:`state-connectivity`
* :class:`plot.TopoButterfly`: press ``Shift-T`` for a large topo-map with
sensor names.

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* API :func:`plot.colors_for_twoway` and :func:`plot.colors_for_categorial`:
new color model, different options.
* :class:`testnd.TContrastRelated` contrasts can contain ``*`` to include the
average of multiple cells.
* New :class:`NDVar` methods: :meth:`NDVar.envelope`, :meth:`NDVar.fft`.