roocs / clisops / 27145410268
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Modernizations and bug fixes (#498)

<!--Please ensure the PR fulfills the following requirements! -->
### Pull Request Checklist:
- [ ] This PR addresses an already opened issue (for bug fixes /
features)
  - This PR fixes issue #xyz
- [ ] Tests for the changes have been added (for bug fixes / features)
- [x] Documentation has been added / updated (for bug fixes / features)
- [x] HISTORY.rst has been updated (with summary of main changes)

### What kind of change does this PR introduce?: <!--(Bug fix, feature,
docs update, etc.)-->

* `numpy` is no longer pinned below v2.3.0.
* Updates several development dependencies
* Fixes a handful of issues with the documentation builds.
* GitHub Workflows now use more secure token and permissions defaults.
* Enables Python3.14 builds specifically for Conda.
* Replaces `pre-commit` with `prek`.
* Updates `pytest` to v9.0; enables `pytest-timeout` with 300 second
limit.
* Updates the ReadTheDocs base image versions to modern defaults.
* Fixes the HISTORY.txt
* Adjusts the `tox.ini` for better compatibility with `tox-gh`, ahead of
movement to `tox.toml`.
* License metadata is now PEP 639 compliant.
* Several tests marked "outdated" have been removed.

### Does this PR introduce a breaking change?: <!--(Has there been an
API change? New dependencies?)-->

Yes:
* Several dependencies have been updated.
* `pytest` configuration is now v9.0+ only.
* `numcodecs` has been pinned below v0.16.0 to ensure compatibility with
`zarr` v2.0.

### Other information: <!--(Relevant discussion threads? Outside
documentation pages?)-->

https://prek.j178.dev/
https://peps.python.org/pep-0639/

3208 of 3692 relevant lines covered (86.89%)

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Jobs
ID Job ID Ran Files Coverage
1 run-Python3.12-conda - 27145410268.1 32
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2 run-Python3.13-conda - 27145410268.2 32
86.89
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3 run-Python3.14-conda - 27145410268.3 32
86.89
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4 run-Python3.11-conda - 27145410268.4 32
86.89
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Source Files on build 27145410268