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Release notes for 0.13.0
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| ======================== | ||
| Neo 0.13.0 release notes | ||
| ======================== | ||
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| 2nd February 2024 | ||
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| This release of Neo sees a lot of changes and improvements, with a documentation rewrite, | ||
| final tweaks and refinements to the object model (in anticipation of a 1.0 release in the next few months), | ||
| a new approach to filtering objects of interest from complex datasets, | ||
| and a large number of bug fixes and performance improvements in IO modules. | ||
| 23 people contributed to this release, which is a new record for Neo! | ||
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| See all `pull requests`_ included in this release and the `list of closed issues`_. | ||
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| Refinements to the Neo object model | ||
| ----------------------------------- | ||
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| In order to simplify the structure of Neo datasets, and make a clearer distinction between the Block-Segment-data | ||
| hierarchy and the more flexible data-grouping functionality, we no longer allow Groups to contain Segments. | ||
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| We have made the handling of RegionOfInterest subclasses consistent with :class:`ChannelView`, | ||
| i.e., just as a :class:`ChannelView` gives a view of a subset of the channels in a multi-channel :class:`AnalogSignal`, | ||
| so the :class:`RegionOfInterest`` subclasses give views of a subset of the pixels in an :class:`ImageSequence`. | ||
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| Neo now has automatic handling of relationships between objects. | ||
| In previous versions, the child-parent relationships between objects had to be handled manually, | ||
| for example when you added a :class:`SpikeTrain` to a :class:`Segment`, this created a parent-child relationship, | ||
| but the reverse child-parent relationship was not automatically created, leading to potential inconsistencies. | ||
| Now these relationships are created automatically, as the various child lists | ||
| (``Segment.spiketrains``, ``Segment.analogsignals``, ``Block.segments``, etc.) | ||
| are now represented by pseudo-list objects which take care of the book-keeping behind the scenes. | ||
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| As a convenience, all Neo containers (:class:`Block`, :class:`Segment`, :class:`Group`) | ||
| now have an :meth:`add()` method that automatically puts the object in the correct list, for example:: | ||
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| segment.add(signal1, event2, spiketrain3) | ||
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| instead of:: | ||
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| segment.analogsignals.append(signal1) | ||
| segment.events.append(event2) | ||
| segment.spiketrains.append(spiketrain3) | ||
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| Documentation rewrite and new theme | ||
| ----------------------------------- | ||
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| The Neo documentation has had a complete overhaul, | ||
| with a rewrite aimed at providing different entry points to the documentation for different_ user_ needs_, | ||
| using the Sphinx IPython extension to ensure code snippets are always up-to-date, | ||
| and a switch to the `PyData Sphinx theme`_. | ||
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| Improved filtering | ||
| ------------------ | ||
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| For complex datasets, it is often necessary to extract subsets of the data from a Neo object tree by filtering | ||
| based on object types, names, and annotations. | ||
| Neo's filtering capabilities have been improved, with the addition of a new :mod:`filters` module. | ||
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| For example, suppose we have a dataset from an animal performing a behavioural task. | ||
| Our objective is to retain only the trials where the animal performed correctly, | ||
| for one of the four trial types in the experiment, and where the recordings met certain quality criteria. | ||
| Based on an annotated Neo dataset, we can extract the spike trains of interest in a single step, | ||
| without for loops or complex list comprehensions, as follows: | ||
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| .. code-block:: python | ||
| import neo.core.filters as nf | ||
| # ... load data, `trial` is a Segment object ... | ||
| sua_spiketrains = trial.filter( | ||
| objects=neo.SpikeTrain, | ||
| targdict=[ | ||
| {"sua": True}, # only single-unit activity | ||
| {"electrode_reject_HFC": False}, # } exclude different types | ||
| {"electrode_reject_LFC": False}, # } of artefacts | ||
| {"electrode_reject_IFC": False}, # } or markers of poor-quality | ||
| {"noise": False}, # } recordings | ||
| {"spike_count": nf.FilterGreaterThan(10000)} # only use neurons with a sufficiently high firing rate | ||
| ] | ||
| ) | ||
| New IO modules | ||
| -------------- | ||
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| Neo now supports MED_ format, with the new :class:`MedIO` and :class:`MedRawIO` classes. | ||
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| Bug fixes and improvements in IO modules | ||
| ---------------------------------------- | ||
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| Bug fixes and/or improvements have been made to :class:`AsciiSignalIO`, :class:`BCI2000IO`, :class:`BiocamIO`, | ||
| :class:`BlackrockIO`, :class:`IgorIO`, :class:`IntanIO`, :class:`KlustaKwikIO`, :class:`MaxwellIO`, :class:`MEArecIO`, | ||
| :class:`NeoMatlabIO`, :class:`NeuralynxIO`, :class:`NixIO`, :class:`NWBIO`, :class:`OpenEphysIO`, :class:`PlexonIO`, | ||
| :class:`Plexon2IO`, :class:`SpikeGLXIO`, and :class:`TdtIO`. | ||
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| Other changes | ||
| ------------- | ||
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| - RawIO classes have a method :meth:`parse_header` that extracts all the information from the formats | ||
| and therefore is usually a computationally heavy process. | ||
| A flag ``is_header_parsed`` has now been added, to avoid re-extracting the header information | ||
| if it is already available. This can produce significant speed ups. | ||
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| - Type hints have been added to the :mod:`baseio`, :mod:`baserawio`, and :mod:`exampleio` modules, | ||
| with the aim of helping developers who wish to add a new IO module. | ||
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| - All of the code is now formatted with black_. | ||
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| - The continuous integration (CI) pipeline has been sped up. | ||
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| Updated dependencies | ||
| -------------------- | ||
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| Neo now requires NumPy version >=1.20.3. | ||
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| Acknowledgements | ||
| ---------------- | ||
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| Thanks to Julia Sprenger, Andrew Davison, Zach McKenzie, Alessio Buccino, Moritz Alexander Kern, | ||
| Samuel Garcia, Heberto Mayorquin, Joscha Schmiedt, Daniel Crepeau, Divyansh Gupta, Nate Dolensek, | ||
| Peter N. Steinmetz, Philipp Hornauer, Robert Wolff, Jules Lebert, Kyle Johnsen, Benjamin Heasly, | ||
| Baptiste Grimaud, Cody Baker, Daniel P. Crepeau, Fernando J. Chaure, @Filipe, and Matthias Klumpp | ||
| for their contributions to this release. | ||
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| .. generated with git shortlog --since=2023-02-17 -sne then checking Github for PRs merged since the last release but with commits before then | ||
| .. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+milestone%3A0.13.0+is%3Aclosed | ||
| .. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+merged%3A%3E2023-02-17+milestone%3A0.13.0 | ||
| .. _`latest recommendations`: https://packaging.python.org/en/latest/ | ||
| .. _black: https://black.readthedocs.io | ||
| .. _`PyData Sphinx theme`: https://pydata-sphinx-theme.readthedocs.io | ||
| .. _MED: https://medformat.org | ||
| .. _different: https://neo.readthedocs.io/en/latest/read_and_analyze.html | ||
| .. _user: https://neo.readthedocs.io/en/latest/share_data.html | ||
| .. _needs: https://neo.readthedocs.io/en/latest/use_neo_as_dependency.html |
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