Update rapids-dependency-file-generator

[KyleFromNVIDIA]

This PR updates the rapids-dependency-file-generator hook to get rapidsai/dependency-file-generator#163.

[jameslamb]

🙌🏻 this caught something!

Traceback (most recent call last):
  File "/github/home/.cache/pre-commit/repoogqoa4r4/py_env-python3.13/bin/rapids-dependency-file-generator", line 7, in <module>
    sys.exit(main())
             ~~~~^^
  File "/github/home/.cache/pre-commit/repoogqoa4r4/py_env-python3.13/lib/python3.13/site-packages/rapids_dependency_file_generator/_cli.py", line 150, in main
    parsed_config = load_config_from_file(args.config)
  File "/github/home/.cache/pre-commit/repoogqoa4r4/py_env-python3.13/lib/python3.13/site-packages/rapids_dependency_file_generator/_config.py", line 264, in load_config_from_file
    return parse_config(yaml.safe_load(f), path)
  File "/github/home/.cache/pre-commit/repoogqoa4r4/py_env-python3.13/lib/python3.13/site-packages/rapids_dependency_file_generator/_config.py", line 241, in parse_config
    validate_dependencies(config)
    ~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
  File "/github/home/.cache/pre-commit/repoogqoa4r4/py_env-python3.13/lib/python3.13/site-packages/rapids_dependency_file_generator/_rapids_dependency_file_validator.py", line 44, in validate_dependencies
    warnings.warn(f'Dependency set "{dep}" is not referred to anywhere in "files:"', UnusedDependencySetWarning)
    ~~~~~~~~~~~~~^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
rapids_dependency_file_generator._warnings.UnusedDependencySetWarning: Dependency set "python_run_libwholegraph" is not referred to anywhere in "files:"

(build link)

[jameslamb]

Investigating that unused python_run_libwholegraph revealed more unused stuff that should also get removed here.

Since we'll have another commit and round of CI anyway, let's also add .pre-commit-config.yaml to the changed-files configurations too:

cugraph-gnn/.github/workflows/pr.yaml

Line 48 in e1ec288

files_yaml: |

[jameslamb]

Looks great!

[jameslamb]

Once we get #284 in, I'll manually re-trigger nightly tests. Hopefully those will pass and unblock the check-nightly-ci job here, and we'll be able to merge this normally.

[KyleFromNVIDIA]

/merge