dfg does not clean up nonexistent lists in dependencies.yaml

[vyasr]

The pyproject.toml support is based on overwriting the file in place. If a particular table/key that was previously being overwritten is removed altogether from dependencies.yaml, however, the resulting list will not be removed from the file. For instance, if all test dependencies were to be removed from a dependencies.yaml file, the project.optional-dependencies.test key would continue to exist in the pyproject.toml file.

Currently this problem is fairly academic since there are almost no cases where a project has 0 dependencies in any section, and it is even less likely that a project with nonzero dependencies removes all of them. I am documenting this issue for now, but there is no immediate rush to fix it. The solution would likely be to erase all dependency-related keys at the beginning of every run, similar to how the cli cleans up files.

[jameslamb]

there are almost no cases where a project has 0 dependencies in any section

Just observed one of these! Linking here for context: rapidsai/cudf#16681 (comment)