Modernizations and bug fixes

[Zeitsperre]

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)
• Documentation has been added / updated (for bug fixes / features)
• HISTORY.rst has been updated (with summary of main changes)

What kind of change does this PR introduce?:

• 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• Several tests marked "outdated" have been removed.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?:

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:

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

[Zeitsperre]

@cehbrecht This PR is ready to go.

There are several things that clisops could benefit from in the Ouranosinc cookiecutter, but I intend to do that migration later, after the clisops-core has been split out. Work in progress: roocs/clisops-core#6.

There's need to tag a new version very soon. I'll leave some time for you to check this over, but we're aiming for a Monday release (2026-06-08). Please let me know if I've made any changes that should be reverted.

Thanks!

[cehbrecht]

@cehbrecht This PR is ready to go.

There are several things that clisops could benefit from in the Ouranosinc cookiecutter, but I intend to do that migration later, after the clisops-core has been split out. Work in progress: roocs/clisops-core#6.

There's need to tag a new version very soon. I'll leave some time for you to check this over, but we're aiming for a Monday release (2026-06-08). Please let me know if I've made any changes that should be reverted.

Thanks!

@Zeitsperre looks all fine to me. I'm currently also updating rook and can make use of the latest clisops.