Python 3.12 break f string inside Snakemake #2480
Description
Snakemake version
Tested with snakemake 7.34.2
(older version are affected, too. Tested down to 7.18.2)
Affected Python version: 3.12.0
(Last known good: Python 3.11.6)
Describe the bug
When snakemake is installed with python version 3.12.0, f-strings get unexpected extra space.
For example:
output: f'{PREFIX}.txt'will produce...
Logs
...this output in the log (note the unexpected extra spaces):
Building DAG of jobs...
File path ' SID23454678 .txt ' starts with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path ' SID23454678 .txt ' ends with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
When run on python 3.12.0
Minimal example
UnitTest.smk:
#!/usr/bin/env python3
PREFIX = 'SID23454678'
rule unit1:
input:
output:
f'{PREFIX}.txt'
run:
"sleep 1"Running with:
snakemake --dry-run -s UnitTest.smk --cores 1In this environment... :
mamba create -n snake-test -c conda-forge -c bioconda snakemake-minimal=7.32.4 python=3.11...everything work as expected:
[Thu Oct 12 15:55:02 2023]
rule unit1:
output: SID23454678.txt
jobid: 0
reason: Missing output files: SID23454678.txt
resources: tmpdir=/tmp
But in that environment...:
mamba create -n snake-test -c conda-forge -c bioconda snakemake-minimal=7.32.4 python=3.12...the bug is triggered:
Building DAG of jobs...
File path ' SID23454678 .txt ' starts with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
File path ' SID23454678 .txt ' ends with whitespace. This is likely unintended. It can also lead to inconsistent results of the file-matching approach used by Snakemake.
Additional context
Apparently, the f-string have been completely overhauled as part of python 3.12. I suspect the new f-string parser somehow clashes with the parse of snakemake files.