Modernize: Drop py39, add py313 compatibility, switch to uv

[dalito]

py313 is not a typo. This repo was never "renovated" in term of devops like linkml and linkml-runtime.

With the changes tests can also be run locally with tox again.

Core Changes (Poetry → uv)

• pyproject.toml — Rewritten from [tool.poetry] to PEP 621 [project] with hatchling backend,
  uv-dynamic-versioning, [dependency-groups], and inline [tool.tox] config
• tox.ini — Deleted (config moved into pyproject.toml)
• poetry.lock — Deleted (replaced by uv.lock)
• uv.lock — Generated via uv lock
• Makefile — All poetry references replaced with uv equivalents
• README.md — Updated installation instructions from poetry to uv

New Files

• .pre-commit-config.yaml — Standard hooks (end-of-file-fixer, check-yaml, check-toml,
  trailing-whitespace) + codespell

GitHub Actions Workflows

• main.yaml — Restructured with quality-checks job (uv lock --check, pre-commit) + test job
  (matrix: py3.10+3.13 × ubuntu+windows)
• build-publish-documentation.yaml — Replaced poetry with uv throughout
• release.yaml — Split into build + pypi-publish (new: trusted publishing) + deploy-docs jobs
  ⚠️@sierra-moxon or someone with permissions on pypi needs to change the config (Sierra did it for linkml repo)
• validate-yaml-syntax.yaml — Added setup-uv, installs yamllint via uv pip install --system

Pre-commit Whitespace Fixes

~100 files auto-fixed by the new pre-commit hooks (trailing whitespace, missing final newlines).
These are existing issues in the repo, not introduced by the migration.

[matentzn]

Awesome, thanks! Maybe combine with #235?

[dalito]

Yes that would make sense. I wanted to ask you on that one. So we close #235 and do all "renovation" here if you agree.

@matentzn - Have you seen the current action error before (e.g. on #235)?

ValueError: The ifabsent value default_range of the range slot could not be processed

[matentzn]

@dalito I closed #235 in favour of this one here. Do you want me to migrate uv or do you want to do the honors? I am fine either way, but since it is your PR I thought I'd leave you the say :)

[matentzn]

I might reach out to you regarding trusted publishing @dalito but I think I remember how to set it up