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Merge pull request #1580 from zm711/release-0.13.4
0.13.4 Release
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| ======================== | ||
| Neo 0.13.4 release notes | ||
| ======================== | ||
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| 21 October 2024 | ||
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| This release of Neo contains bug fixes across many IOs, a new IO for :code:`NeuroNexus`, drop of Python 3.8, NumPy 1.20 & 1.21, still with a focus on the planned 1.0 release. | ||
| Additionally Neo now supports Quantities >=16.1 which brings us closer to support for NumPy 2.0 +. At the :code:`RawIO` level a new :code:`buffer api` has been introduced | ||
| with the goal of better grouping streams of data together. This is an ongoing effort to provide better access to streams of data that are typically analyzed together without | ||
| changes to the public API. | ||
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| This point release will be the last release to not support Python 3.13 and NumPy > 2.0. | ||
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| See all `pull requests`_ included in this release and the `list of closed issues`_. | ||
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| Updated dependencies | ||
| -------------------- | ||
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| Neo has a limit of NumPy >= 1.22.4, < 2.0.0 | ||
| Neo now supports Python >= 3.9, <3.13 | ||
| Neo has a limit of Quantities >= 16.1 | ||
| Neo has a limit of dhn_med_py < 2.0.0 (for reading MED format) | ||
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| Deprecations | ||
| ------------ | ||
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| As Quantities has dropped support for the :code:`copy` argument when making Quantities arrays to be NumPy 2.0 compatible, the :code:`copy` argument | ||
| has also been deprecated in all Neo core objects (e.g. :code:`SpikeTrain`, etc.). For this version and the next version the default is now :code:`copy=None`. | ||
| If :code:`copy=True` or :code:`copy=False` are used an error will be raised. This also means that some functionality for rescaling and dtype conversion, which | ||
| required :code:`copy=True` are no longer possible. Appropriate errors are raised if the user tries these now impossible behaviors at construction. | ||
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| Additional changes that occurred in Quantities can be viewed at their changelog: | ||
| https://github.com/python-quantities/python-quantities/blob/master/CHANGES.txt | ||
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| Currently acceptable construction patterns can be found in the Neo test folder: | ||
| https://github.com/NeuralEnsemble/python-neo/blob/master/neo/test/coretest | ||
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| Many previous behaviors can still be achieved by using additional lines of code, e.g.: | ||
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| .. code-block:: python | ||
| >>> import quantities as pq | ||
| >>> import neo | ||
| # if we want to get a spiketrain in seconds, but we entered our times in ms | ||
| # we used to be able to autoconvert by specifying units. But now this will | ||
| # raise an error! | ||
| >>> times = [1,2,3] * 1 * pq.ms | ||
| >>> t_stop = 1 * pq.s | ||
| >>> spiketrain = neo.SpikeTrain(times, t_stop=t_stop, units='s') | ||
| ValueError: cannot rescale and return view | ||
| # so instead we need to rescale in a second step | ||
| >>> spiketrain = neo.SpikeTrain(times, t_stop=t_stop) | ||
| >>> spiketrain | ||
| <SpikeTrain(array[1, 2, 3] * ms, [0.0 ms, 1000.0 ms])> | ||
| >>> rescaled_spiketrain = spiketrain.rescale('s') | ||
| >>> rescaled_spiketrain | ||
| <SpikeTrain(array[0.001, 0.002, 0.003] * s, [0.0 s, 10.0 s])> | ||
| CI Additions/Changes | ||
| -------------------- | ||
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| Neo has sped up the testing suite by ~15% and added additional testing for IOs: :class:`NeuralynxIO` and | ||
| :class:`Plexon2IO`. | ||
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| Testing around :code:`copy` was removed from the core testing, since this argument is no longer possible. | ||
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| Addition of a New IO module | ||
| --------------------------- | ||
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| Neo now has support for reading NeuroNexus :code:`.xdat` files with the new :class:`NeuroNexusIO`. | ||
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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:`MaxwellIO`, :class:`NeuroNexusIO`, | ||
| :class:`IntanIO`, :class:`Plexon2IO`, :class:`IgorIO`, :class:`SpikeGadgetsIO`, :class:`PlexonIO`, | ||
| and :class:`BrainVisionRawIO`, and :class:`EDFIO` | ||
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| Buffer API | ||
| ---------- | ||
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| The motivation for this :code:`RawIO` was that many IOs have buffers of data (memmaps/hdf5) files, which allow for multiple unrelated streams of data to be packaged | ||
| together. This has led to some inconsistencies in how IOs access streams of data. For example, the :code:`PlexonIO` stores WideBand and Filtered versions of the same | ||
| data, but the end user likely wouldn't want to analyze them both at the same time as that would be duplication of information. :code:`SpikeGLX` also makes use of a sync | ||
| channel which is stored with the electrophysiological channels, but should not be analyzed as an ephys channel. The Buffer API will be an ongoing set of PRs at the | ||
| :code:`RawIO` level to better clarify how data enters and is mapped in Neo versus how the end-user might request streams of data. We hope that this process will allow | ||
| the end-user better access to the data they want without having unrelated data mixed in. Importantly the public API is not being affected by this process at all. The end-user | ||
| will still request their desired stream using :code:`stream_index` argument when interacting with a :code:`RawIO`. | ||
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| In this release, each IO was divided into whether it would fit with the buffer api requirements or not and the initial :code:`buffer_id` was applied to all IOs. This step | ||
| has not changed any behavior in Neo. But the :code:`RawIO.header` information will now have an additional field that will be used in future releases of Neo under-the-hood. | ||
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| We want to emphasize this is not a public API change and over the next version we hope to fully implement this new schema to allow for better interaction with data at the | ||
| :code:`RawIO` and :code:`IO` levels of Neo. | ||
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| This project has largely been spearheaded by Samuel Garcia and we thank him for his herculean efforts. | ||
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| Acknowledgements | ||
| ---------------- | ||
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| Thanks to Zach McKenzie, Heberto Mayorquin, Samuel Garcia, Andrew Davison, Alessio Buccino, Nikhil Chandra, and Peter Steinmetz for their contributions to this release. | ||
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| .. _`pull requests`: https://github.com/NeuralEnsemble/python-neo/pulls?q=is%3Apr+is%3Aclosed+milestone%3A0.13.4 | ||
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| .. _`list of closed issues`: https://github.com/NeuralEnsemble/python-neo/issues?q=is%3Aissue+is%3Aclosed+milestone%3A0.13.4 |
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