Pynwb

Enhancements and minor changes
- Added `bounds` field to `SpatialSeries` to set optional boundary range (min, max) for each dimension of data. mavaylon1 [1869](https://github.com/NeurodataWithoutBorders/pynwb/pull/1869/files)
- Added support for NWB schema 2.7.0. See [2.7.0 release notes](https://nwb-schema.readthedocs.io/en/latest/format_release_notes.html) for details
- Deprecated `ImagingRetinotopy` neurodata type. rly [1813](https://github.com/NeurodataWithoutBorders/pynwb/pull/1813)
- Modified `OptogeneticSeries` to allow 2D data, primarily in extensions of `OptogeneticSeries`. rly [1812](https://github.com/NeurodataWithoutBorders/pynwb/pull/1812)
- Support `stimulus_template` as optional predefined column in `IntracellularStimuliTable`. stephprince [1815](https://github.com/NeurodataWithoutBorders/pynwb/pull/1815)
- Support `NWBDataInterface` and `DynamicTable` in `NWBFile.stimulus`. rly [1842](https://github.com/NeurodataWithoutBorders/pynwb/pull/1842)
- Added support for python 3.12 and upgraded dependency versions. This also includes infrastructure updates for developers. mavaylon1 [1853](https://github.com/NeurodataWithoutBorders/pynwb/pull/1853)
- Added `grid_spacing`, `grid_spacing_unit`, `origin_coords`, `origin_coords_unit` to `ImagingPlane` fields. h-mayorquin [1892](https://github.com/NeurodataWithoutBorders/pynwb/pull/1892)
- Added `mock_Units` for generating Units tables. h-mayorquin [1875](https://github.com/NeurodataWithoutBorders/pynwb/pull/1875) and [#1883](https://github.com/NeurodataWithoutBorders/pynwb/pull/1883)
- Allow datetimes without a timezone and without a time. rly [1886](https://github.com/NeurodataWithoutBorders/pynwb/pull/1886)
- No longer automatically set the timezone to the local timezone when not provided. [1886](https://github.com/NeurodataWithoutBorders/pynwb/pull/1886)
- Updated testing to not install in editable mode and not run `coverage` by default. [1897](https://github.com/NeurodataWithoutBorders/pynwb/pull/1897)

Bug fixes
- Fix bug with reading file with linked `TimeSeriesReferenceVectorData` rly [1865](https://github.com/NeurodataWithoutBorders/pynwb/pull/1865)
- Fix bug where extra keyword arguments could not be passed to `NWBFile.add_{x}_column` for use in custom `VectorData` classes. rly [1861](https://github.com/NeurodataWithoutBorders/pynwb/pull/1861)

Enhancements and minor changes
- For `NWBHDF5IO()`, change the default of arg `load_namespaces` from `False` to `True`. bendichter [1748](https://github.com/NeurodataWithoutBorders/pynwb/pull/1748)
- Add `NWBHDF5IO.can_read()`. bendichter [1703](https://github.com/NeurodataWithoutBorders/pynwb/pull/1703)
- Add `pynwb.get_nwbfile_version()`. bendichter [1703](https://github.com/NeurodataWithoutBorders/pynwb/pull/1703)
- Fix usage of the `validate` function in the `pynwb.testing.testh5io` classes and cache the spec by default in those classes. rly [1782](https://github.com/NeurodataWithoutBorders/pynwb/pull/1782)
- Updated timeseries data checks to warn instead of error when reading invalid files. stephprince [1793](https://github.com/NeurodataWithoutBorders/pynwb/pull/1793) and [#1809](https://github.com/NeurodataWithoutBorders/pynwb/pull/1809)
- Expose the offset, conversion and channel conversion parameters in `mock_ElectricalSeries`. h-mayorquin [1796](https://github.com/NeurodataWithoutBorders/pynwb/pull/1796)
- Expose `starting_time` in `mock_ElectricalSeries`. h-mayorquin [1805](https://github.com/NeurodataWithoutBorders/pynwb/pull/1805)
- Enhance `get_data_in_units()` to work with objects that have a `channel_conversion` attribute like the `ElectricalSeries`. h-mayorquin [1806](https://github.com/NeurodataWithoutBorders/pynwb/pull/1806)
- Refactor validation CLI tests to use `{sys.executable} -m coverage` to use the same Python version and run correctly on Debian systems. yarikoptic [1811](https://github.com/NeurodataWithoutBorders/pynwb/pull/1811)
- Fixed tests to address newly caught validation errors. rly [1839](https://github.com/NeurodataWithoutBorders/pynwb/pull/1839)

Bug fixes
- Fix bug where namespaces were loaded in "w-" mode. h-mayorquin [1795](https://github.com/NeurodataWithoutBorders/pynwb/pull/1795)
- Fix bug where pynwb version was reported as "unknown" to readthedocs stephprince [1810](https://github.com/NeurodataWithoutBorders/pynwb/pull/1810)
- Fixed bug to allow linking of `TimeSeries.data` by setting the `data` constructor argument to another `TimeSeries`. oruebel [1766](https://github.com/NeurodataWithoutBorders/pynwb/pull/1766)
- Fix recursion error in html representation generation in jupyter notebooks. stephprince [1831](https://github.com/NeurodataWithoutBorders/pynwb/pull/1831)

Documentation and tutorial enhancements
- Add RemFile to streaming tutorial. bendichter [1761](https://github.com/NeurodataWithoutBorders/pynwb/pull/1761)
- Fix typos and improve clarify throughout tutorials. zm711 [1825](https://github.com/NeurodataWithoutBorders/pynwb/pull/1825)
- Fix internal links in docstrings and tutorials. stephprince [1827](https://github.com/NeurodataWithoutBorders/pynwb/pull/1827)
- Add Zarr IO tutorial bendichter [1834](https://github.com/NeurodataWithoutBorders/pynwb/pull/1834)

Enhancements and minor changes
- Added `TimeSeries.get_timestamps()`. bendichter [1741](https://github.com/NeurodataWithoutBorders/pynwb/pull/1741)
- Added `TimeSeries.get_data_in_units()`. bendichter [1745](https://github.com/NeurodataWithoutBorders/pynwb/pull/1745)
- Updated `ExternalResources` name change to `HERD`, along with HDMF 3.9.0 being the new minimum. mavaylon1 [1754](https://github.com/NeurodataWithoutBorders/pynwb/pull/1754)

Documentation and tutorial enhancements
- Updated streaming tutorial to ensure code is run on tests and clarify text. bendichter [1760](https://github.com/NeurodataWithoutBorders/pynwb/pull/1760) oruebel [#1762](https://github.com/NeurodataWithoutBorders/pynwb/pull/1762)
- Fixed minor documentation build warnings and broken links to `basic_trials` tutorial oruebel [1762](https://github.com/NeurodataWithoutBorders/pynwb/pull/1762)

- Stop running validation tests as part of integration tests. They cause issues in CI and can be run separately. rly [1740](https://github.com/NeurodataWithoutBorders/pynwb/pull/1740)

Enhancements and minor changes
- Added support for `ExternalResources`. mavaylon1 [1684](https://github.com/NeurodataWithoutBorders/pynwb/pull/1684)
- Updated links for making a release. mavaylon1 [1720](https://github.com/NeurodataWithoutBorders/pynwb/pull/1720)

Bug fixes
- Fixed sphinx-gallery setting to correctly display index in the docs with sphinx-gallery>=0.11. oruebel [1733](https://github.com/NeurodataWithoutBorders/pynwb/pull/1733)

Documentation and tutorial enhancements
- Added thumbnail for Optogentics tutorial. oruebel [1729](https://github.com/NeurodataWithoutBorders/pynwb/pull/1729)
- Updated and fixed errors in tutorials. bendichter oruebel

Enhancements and minor changes
- Add testing support for Python 3.11. rly [1687](https://github.com/NeurodataWithoutBorders/pynwb/pull/1687)
- Add CI testing of NWB files on DANDI. rly [1695](https://github.com/NeurodataWithoutBorders/pynwb/pull/1695)

Bug fixes
- Remove unused, deprecated `codecov` package from dev installation requirements. rly
[1688](https://github.com/NeurodataWithoutBorders/pynwb/pull/1688)
- Remove references to discontinued `requires.io` service in documentation. rly
[1690](https://github.com/NeurodataWithoutBorders/pynwb/pull/1690)
- Update `requirements-doc.txt` to resolve Python 3.7 incompatibility. rly
[1694](https://github.com/NeurodataWithoutBorders/pynwb/pull/1694)
- Fixed test battery to show and check for warnings appropriately. rly
[1698](https://github.com/NeurodataWithoutBorders/pynwb/pull/1698)