Eelbrain

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* API:

- Plotting parameters ``ncol`` and ``nrow`` have been renamed to ``columns`` and ``rows``.
- :class:`Factor` cells that are not specified in ``labels`` are now ordered by their first ocurrence in ``x`` (previously order was alphabetic).
- The ``pool_error`` argument is replaced by ``within_subject_error``.

* :func:`boosting`:

- Now accepts data with ragged trials (trials of different lengths).
- Now stores both the l1 and l2 loss of the final fit.
- Due to optimization, results may be numerically different from earlier versions.


* Pipeline:

- :class:`pipeline.RawICA` preprocessing pipe now allows setting ``fit_kwargs``.
- The default :attr:`pipeline.MneExperiment.subject_re` pattern for finding subjects is now more general.

* Permutation tests:

- Due to a change in randomization algorithm, the permutation distribution for vector-based tests may be slightly different (old and new versions are both valid randomizations).

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* :class:`testnd.LM` now supports permutation-based significance testing.
* New :class:`NDVar` functions for time series and an auditory model: :func:`pad`, :func:`gammatone_bank`, :func:`edge_detector`
* API:

- The common ``ds`` parameter has been renamed to ``data`` to be more consistent with other packages.
- The evaluation context for :class:`Dataset` does not include ``from numpy import *`` anymore, to avoid overwriting builtins like :func:`abs`; instead, NumPy is accessible as ``numpy``.
- :class:`testnd.LM`: The default number of permutations is now 10000 and the argument order has changed slightly to be consistent with other :mod:`testnd` tests. To use :class:`testnd.LM` for two-stage tests, set ``samples=0``.
- :class:`plot.Barplot` parameter ``c`` renamed to ``color``.

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* :func:`boosting` optimized (as a consequence, the progress bar has been disabled).

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* ICA-GUI (:func:`gui.select_components`): Sort noisy epochs by dominant components - makes it easier to find components that capture specific artifacts.
* API: :func:`load.mne.events` now loads events from all stim-channels. To use a subset, use the ``stim_channel`` parameter.
* New plot: :class:`plot.SensorMap3d`.
* :func:`plot.styles_for_twoway` to quickly generate different color and line-style combinations.
* New function :func:`set_connectivity` to set the neighborhood structure of an :class:`NDVar`.
* :class:`pipeline.MneExperiment`:

- :meth:`pipeline.MneExperiment.plot_evoked`: plot sensor data with corresponding source estimates
- API: By default, events are now loaded from all stim-channels. To only use a subset of stim-channels, use the new :attr:`pipeline.MneExperiment.stim_channel` attribute.

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* Preview cross-validation data partitions with :func:`plot.preview_partitions`.
* :meth:`BoostingResult.partition_result_data` method to retrieve results from different partitions.

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* ICA GUI (:func:`gui.select_components`; :meth:`pipeline.MneExperiment.make_ica_selection`):

- In the source time-course window, display the range of the data before and after cleaning in real-time.
- New keyboard shortcut: ``alt + arrow`` keys to go to the beginning/end.
- New context-menu commands: find top component for an epoch.

* Mark pairwise comparisons individually with :meth:`plot.Barplot.mark_pair` and :meth:`plot.Boxplot.mark_pair`.
* :meth:`NDVar.dot` generalized to multiple dimensions.