snakemake --lint mistakes regex for path #3001
Description
Hi,
Snakemake version
8.16.0
Describe the bug
with this submodule in a workflow
import os
from pathlib import Path
import sys
from itertools import product
import pandas as pd
from snakemake.remote import FTP
from snakemake.utils import validate
from snakemake.exceptions import WorkflowError
validate(config, schema="../schemas/config.schema.yaml")
samples = (
pd.read_csv(
os.path.join(
os.path.realpath(os.path.dirname(workflow.configfiles[0])),
config["samples"],
),
sep=r"\s+",
dtype={"sample": str, "condition": str, "condition2": str, "batch_effect": str},
header=0,
comment="#",
)
.set_index("sample", drop=False)
.sort_index()
)
...Logs
I get this in the CI logs:
Lints for snakefile /github/workspace/workflow/rules/commons.smk:
* Path composition with '+' in line 19:
This becomes quickly unreadable. Usually, it is better to endure some
redundancy against having a more readable workflow. Hence, just repeat
common prefixes. If path composition is unavoidable, use pathlib or
(python >= 3.6) string formatting with f"...".
Also see:
Additional context
On the command line with snakefmt version 0.10.2 and black (internally used, version 24.4.2), I get no error.
Apparently, sep=r"\s+" is considered path concatenation, which it isn't.
We could use \t instead for a while, but this is semantically not identical.
Cheers,
Christian