Cookiecutter update

[Zeitsperre]

Pull Request Checklist:

• This PR addresses an already opened issue (for bug fixes / features)
  • This PR closes [pre-commit.ci] pre-commit autoupdate #291 (redundant)
• (If applicable) Documentation has been added / updated (for bug fixes / features).
• (If applicable) Tests have been added.
• CHANGELOG.rst has been updated (with summary of main changes).
  • Link to issue (:issue:number) and pull request (:pull:number) has been added.

What kind of change does this PR introduce?

• Added support and CI builds for Python3.13
• Removed several unnecessary dependencies listed in pyproject.toml
• Migrates optional-dependencies to dependency-groups
• Sets token-based workflows to run within an automation environment
• Updates dependencies
• pre-commit has been replaced by prek
• Makefile now handles some dependency installation logic
• Configuration issues in tox.toml have been resolved

Does this PR introduce a breaking change?

Yes.

• Many dependencies that are implicitly installed and never called but listed in the pyproject.toml have been removed. Many of these dependencies are bundled and only called within the xscen codebase.
• The new method for installing dependencies is to either use the Makefile commands or the new command invocation.
• tox has been undergoing significant overhaul to its configuration language. The previous config settings were not working as intended, but it now implements most features from the ini format in the toml spec. There are likely some neat new goodies that we can make use of for specialized testing.
• ESMF_VERSION no longer requires a preceding v when using tox.

Other information:

dependency-groups are a way to ensure that development-time dependencies are not published with distributions of packages, which is great for packages that do not bundle code, or for preventing end-users from installing tools they will never require when using the package.

Example invocation:

$ pip install --group lint,test

A dependency-group is only available when examining the source code of the library and allows developers to only install the dependencies without needing to install the library itself (great for linting). It also supports installing the library or nesting of other dependency-groups/optional-dependencies, if desired. Testing and other miscellaneous development libraries are also suggested to be listed under dependency-groups.

https://peps.python.org/pep-0735/