Pynwb

Enhancements and minor changes
- Fixed typos and added codespell GitHub action to check spelling in the future. yarikoptic [1648](https://github.com/NeurodataWithoutBorders/pynwb/pull/1648)

Documentation and tutorial enhancements
- Added `OnePhotonSeries` to [calcium imaging tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/domain/ophys.html#sphx-glr-tutorials-domain-ophys-py). bendichter [1658](https://github.com/NeurodataWithoutBorders/pynwb/pull/1658)
- Add tutorial for optogenetics. bendichter [1657](https://github.com/NeurodataWithoutBorders/pynwb/pull/1657)
- Update testing of gallery examples and disable testing of the allensdk tutorial.
[1680](https://github.com/NeurodataWithoutBorders/pynwb/pull/1680)
- Updated tutorials to follow best practices. bendichter [1656](https://github.com/NeurodataWithoutBorders/pynwb/pull/1656)

Bug fixes
- Fixed bug when initializing ``OnePhotonSeries`` with no value for ``binning``. bendichter [1660](https://github.com/NeurodataWithoutBorders/pynwb/pull/1660)
- Fixed bug in ``NWBHDF5IO.nwb_version`` property to support files written by third-party software with a fixed-length ``nwb_version`` attribute. oruebel [1669](https://github.com/NeurodataWithoutBorders/pynwb/pull/1669)
- Fixed search bar and missing jquery in ReadTheDocs documentation. rly [1671](https://github.com/NeurodataWithoutBorders/pynwb/pull/1671)
- Requires [HDMF 3.5.4](https://github.com/hdmf-dev/hdmf/releases/tag/3.5.4) which includes bug fixes. rly [#1672](https://github.com/NeurodataWithoutBorders/pynwb/pull/1672)
- Fixed issue with deprecated pkg_resources. rly [1678](https://github.com/NeurodataWithoutBorders/pynwb/pull/1678)

Bug fixes
- Fixed an issue where NWB files with version "2.0b" could not be read.
rly [1651](https://github.com/NeurodataWithoutBorders/pynwb/pull/1651)

Enhancements and minor changes
- Added support for NWB Schema 2.6.0. mavaylon1 [1636](https://github.com/NeurodataWithoutBorders/pynwb/pull/1636)
- Added a class and tests for the `OnePhotonSeries` new in NWB v2.6.0. CodyCBakerPhD [1593](https://github.com/NeurodataWithoutBorders/pynwb/pull/1593)(see also NWB Schema [#523](https://github.com/NeurodataWithoutBorders/nwb-schema/pull/523)
- `Subject.age` can be input as a `timedelta` type. bendichter [1590](https://github.com/NeurodataWithoutBorders/pynwb/pull/1590)
- Added `Subject.age__reference` field. bendichter ([1540](https://github.com/NeurodataWithoutBorders/pynwb/pull/1540))
- `IntracellularRecordingsTable.add_recording`: the `electrode` arg is now optional, and is automatically populated from the stimulus or response.
[1597](https://github.com/NeurodataWithoutBorders/pynwb/pull/1597)
- Added module `pynwb.testing.mock.icephys` and corresponding tests. bendichter
[1595](https://github.com/NeurodataWithoutBorders/pynwb/pull/1595)
- Removed redundant object mapper code. rly [1600](https://github.com/NeurodataWithoutBorders/pynwb/pull/1600)
- Fixed pending deprecations and issues in CI. rly [1594](https://github.com/NeurodataWithoutBorders/pynwb/pull/1594)
- Added ``NWBHDF5IO.nwb_version`` property to get the NWB version from an NWB HDF5 file oruebel [1612](https://github.com/NeurodataWithoutBorders/pynwb/pull/1612)
- Updated ``NWBHDF5IO.read`` to check NWB version before read and raise more informative error if an unsupported version is found oruebel [1612](https://github.com/NeurodataWithoutBorders/pynwb/pull/1612)
- Added the `driver` keyword argument to the `pynwb.validate` function as well as the corresponding namespace caching. CodyCBakerPhD [1588](https://github.com/NeurodataWithoutBorders/pynwb/pull/1588)
- Updated HDMF requirement to version 3.5.1. [1611](https://github.com/NeurodataWithoutBorders/pynwb/pull/1611)
- Increased the stacklevel of the warning from `_add_missing_timezone` in `pynwb.file` to make identification of which datetime field is missing a timezone easier. CodyCBakerPhD [1641](https://github.com/NeurodataWithoutBorders/pynwb/pull/1641)

Documentation and tutorial enhancements:
- Adjusted [ecephys tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/domain/ecephys.html) to create fake data with proper dimensions bendichter [#1581](https://github.com/NeurodataWithoutBorders/pynwb/pull/1581)
- Refactored testing documentation, including addition of section on ``pynwb.testing.mock`` submodule. bendichter
[1583](https://github.com/NeurodataWithoutBorders/pynwb/pull/1583)
- Updated round trip tutorial to the newer ``NWBH5IOMixin`` and ``AcquisitionH5IOMixin`` classes. bendichter
[1586](https://github.com/NeurodataWithoutBorders/pynwb/pull/1586)
- Added more informative error message for common installation error. bendichter, rly
[1591](https://github.com/NeurodataWithoutBorders/pynwb/pull/1591)
- Updated citation for PyNWB in docs and duecredit to use the eLife NWB paper. oruebel [1604](https://github.com/NeurodataWithoutBorders/pynwb/pull/1604)
- Fixed docs build warnings due to use of hardcoded links. oruebel [1604](https://github.com/NeurodataWithoutBorders/pynwb/pull/1604)
- Updated the [iterative write tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/iterative_write.html) to reference the new ``GenericDataChunkIterator`` functionality and use the new ``H5DataIO.dataset`` property to simplify the custom I/O section. oruebel [#1633](https://github.com/NeurodataWithoutBorders/pynwb/pull/1633)
- Updated the [parallel I/O tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/advanced_io/parallelio.html) to use the new ``H5DataIO.dataset`` feature to set up an empty dataset for parallel write. oruebel [#1633](https://github.com/NeurodataWithoutBorders/pynwb/pull/1633)

Bug fixes
- Added shape constraint to `PatchClampSeries.data`. bendichter
[1596](https://github.com/NeurodataWithoutBorders/pynwb/pull/1596)
- Updated the [images tutorial](https://pynwb.readthedocs.io/en/stable/tutorials/domain/images.html) to provide example usage of an ``IndexSeries``
with a reference to ``Images``. bendichter [1602](https://github.com/NeurodataWithoutBorders/pynwb/pull/1602)
- Fixed an issue with the `tox` tool when upgrading to tox 4. rly [1608](https://github.com/NeurodataWithoutBorders/pynwb/pull/1608)
- Fixed an issue where `Images` were not allowed as stimulus templates. rly [1638](https://github.com/NeurodataWithoutBorders/pynwb/pull/1638)

Enhancements and minor changes
- Enhanced `pynwb.validate` API function to accept a list of file paths as well as the ability to operate on cached
namespaces. Also adjusted the validate CLI to directly use the API function. CodyCBakerPhD
[1511](https://github.com/NeurodataWithoutBorders/pynwb/pull/1511)

Internal enhancements
- Moved CI to GitHub Actions. rly [1560](https://github.com/NeurodataWithoutBorders/pynwb/pull/1560),
[1566](https://github.com/NeurodataWithoutBorders/pynwb/pull/1566)

Bug fixes
- Fixed bug in ``pynwb.testing.mock.file.mock_NWBFile`` to identifier UUID to string. oruebel
[1557](https://github.com/NeurodataWithoutBorders/pynwb/pull/1557)
- Minor fixes to test suite to prevent warnings. rly
[1571](https://github.com/NeurodataWithoutBorders/pynwb/pull/1571)
- Made build wheel python 3 only. mavaylon1
[1572](https://github.com/NeurodataWithoutBorders/pynwb/pull/1572)
- Updated README.rst. mavaylon1
[1573](https://github.com/NeurodataWithoutBorders/pynwb/pull/1573)

Documentation and tutorial enhancements:
- Added support for explicit ordering of sphinx gallery tutorials in the docs. oruebel
[1504](https://github.com/NeurodataWithoutBorders/pynwb/pull/1504), bdichter
[1495](https://github.com/NeurodataWithoutBorders/pynwb/pull/1495)
- Added developer guide on how to create a new tutorial. oruebel
[1504](https://github.com/NeurodataWithoutBorders/pynwb/pull/1504)
- Added images tutorial. weiglszonja
[1470](https://github.com/NeurodataWithoutBorders/pynwb/pull/1470)
- Added example code for fsspec in the streaming tutorial. bdichter
[1499](https://github.com/NeurodataWithoutBorders/pynwb/pull/1499)
- Add voxel_mask tutorial. codycbakerphd (1544)

Enhancements and minor changes
- Updated coverage workflow, report separate unit vs integration coverage. rly
[1509](https://github.com/NeurodataWithoutBorders/pynwb/pull/1509)
- Deleted test files generated from running sphinx gallery examples. rly
[1517](https://github.com/NeurodataWithoutBorders/pynwb/pull/1517)
- Enabled passing an S3File created through s3fs, which provides a method for reading an NWB file directly
from s3 that is an alternative to ros3. This required relaxing of `NWBHDF5IO` input validation. The `path`
arg is not needed if `file` is provided. `mode` now has a default value of "r".
bendichter
[1499](https://github.com/NeurodataWithoutBorders/pynwb/pull/1499)
- Added a method to `NWBMixin` that only raises an error when a check is violated on instance creation,
otherwise throws a warning when reading from a file. The new checks in `ImageSeries` when `external_file`
is provided is used with this method to ensure that that files with invalid data can be read, but prohibits
the user from creating new instances when these checks are violated. weiglszonja
[1516](https://github.com/NeurodataWithoutBorders/pynwb/pull/1516)
- Created a GitHub Actions workflow to generate test files for testing backward compatibility. rly
[1548](https://github.com/NeurodataWithoutBorders/pynwb/pull/1548)
- Updated requirements, including allowing numpy 1.23. rly
[1550](https://github.com/NeurodataWithoutBorders/pynwb/pull/1550)
- Enhanced docs for ``LabMetaData`` to clarify its usage. oruebel
[1546](https://github.com/NeurodataWithoutBorders/pynwb/pull/1546)
- Add testing/mock, which provides mock neurodata objects for testing. bendichter
[1454](https://github.com/NeurodataWithoutBorders/pynwb/pull/1454)

Breaking changes:
- Updated ``TimeIntervals`` to use the new ``TimeSeriesReferenceVectorData`` type. This does not alter the overall
structure of ``TimeIntervals`` in a major way aside from changing the value of the ``neurodata_type`` attribute of the
``TimeIntervals.timeseries`` column from ``VectorData`` to ``TimeSeriesReferenceVectorData``. This change facilitates
creating common functionality around ``TimeSeriesReferenceVectorData``. For NWB files with version 2.4.0 and earlier,
the ``TimeIntervals.timeseries`` column is automatically migrated on read in the ``TimeIntervalsMap``
object mapper class to use the ``TimeSeriesReferenceVectorData`` container class, so that users are presented a
consistent API for existing and new files. This change affects all existing ``TimeIntervals`` tables
e.g., ``NBWFile.epochs``, ``NWBFile.trials``, and ``NWBFile.invalid_times``. While this is technically a breaking
change, the impact user codes should be minimal as this change primarily adds functionality while the overall
behavior of the API is largely consistent with existing behavior. oruebel, rly (1390)

Enhancements and minor changes
- A warning is now raised if `SpatialSeries.data` has more than 3 columns. bendichter, rly (1455, 1480)
- The arguments x, y, z, imp, location, filtering are no longer required in the electrodes table.
h-mayorquin, rly (1448)
- Added `cell_id` attribute to `IntracellularElectrode`. bendichter (1459)
- Added `offset` field to `TimeSeries` and its subtypes. codycbakerphd (1424)
- Added support for NWB 2.5.0.
- Added support for updated ``IndexSeries`` type, new ``order_of_images`` field in ``Images``, and new neurodata_type
``ImageReferences``. rly (1483)
- Added support for HDMF 3.3.1. This is now the minimum version of HDMF supported. Importantly, HDMF 3.3 introduces
warnings when the constructor of a class mapped to an HDMF-common data type or an autogenerated data type class
is passed positional arguments instead of all keyword arguments. rly (1484)
- Moved logic that checks the 0th dimension of TimeSeries data equals the length of timestamps to a private method in the
``TimeSeries`` class. This is to avoid raising a warning when an ImageSeries is used with external file.
weiglszonja (1486)
- Improved warning text when dimensions are not matched in `TimeSeries`, `ElectricalSeries`, and `RoiResponseSeries`.
rly (1491)

Documentation and tutorial enhancements:
- Added tutorial on annotating data via ``TimeIntervals``. oruebel (1390)
- Added copy button to code blocks. weiglszonja (1460)
- Created behavioral tutorial. weiglszonja (1464)
- Enhanced display of icephys pandas tutorial by using ``dataframe_image`` to render and display large tables
as images. oruebel (1469)
- Created tutorial about reading and exploring an existing `NWBFile`. weiglszonja (1453)
- Added new logo for PyNWB. oruebel (1461)
- Minor text fixes. oruebel bendichter (1443, 1462, 1463, 1466, 1472, 1473)

Bug fixes:
- Fixed input data types to allow only `float` for fields `conversion` and `offset` in definition of
``TimeSeries``. codycbakerphd (1424)
- Fixed incorrect warning in `RoiResponseSeries.__init__` about mismatch between the second dimension of data and
the length of rois. rly (1491)