Pynwb

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)

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)