Line number of error is incorrect #1256
Description
Snakemake version: 6.10.0 installed via bioconda/mamba
Describe the bug
When a snakefile contains a syntax error or some other bug, snakemake reports the wrong line number of the error. More specifically, it seems to me that:
- The reported line number is consistently after the actual line number
- As the Snakefile becomes longer, the difference between reported and actual line number grows
- Earlier versions do not show this bug (e.g. v5.4.3 works)
This is quite a problem since it makes it difficult to locate bugs!
Minimal example
Here the syntax error is on line 9:
rule all:
input:
'done.txt',
rule trim_transcripts:
output:
done.txt,
run:
if 1 = 2: # Syntax error: It should be 1 == 2
print('foo')
Snakemake 6.10.0 reports the error on line 18:
snakemake -j 1 -n -s Snakefile2
SyntaxError in line 18 of /export/III-data/wcmp_bioinformatics/db291g/git_repos/wcip/20211109_kasia_asaj_snp/Snakefile2:
invalid syntax (Snakefile2, line 18)
Snakemake 5.4.3 is correct:
/export/projects/III-data/wcmp_bioinformatics/db291g/miniconda3/envs/20190312_andy_alba3_motifs/bin/snakemake -j 1 -n -s Snakefile2
SyntaxError in line 9 of /export/III-data/wcmp_bioinformatics/db291g/git_repos/wcip/20211109_kasia_asaj_snp/Snakefile2:
invalid syntax