The line numbers for warnings are reported on the old (pre-formatting) file. That means it is either hard to figure out where the issue is, or I need to run snakefmt again, to get the correct numbers reported in the re-formatted file.

Example:

# some things here to cause blank lines to be inserted
def my_function():
    return 1
rule call_variants:
    input:
        some_file,
        # some comment

First time running snakefmt:

[WARNING] In file "test.smk":  Keyword "input" at line 5 has comments under a value.
	PEP8 recommends block comments appear before what they describe
(see https://www.python.org/dev/peps/pep-0008/#id30)
[INFO] Writing formatted content to test.smk
[INFO] All done 🎉

which lists line 5 (input:) as where the issue is. However, the file was reformatted, and now looks like this:

# some things here to cause blank lines to be inserted
def my_function():
    return 1


rule call_variants:
    input:
        some_file,
        # some comment

So the reported line should be 7 instead, to match with the new file content. This is reported when running snakefmt again on the file, but that seems cumbersome.