Line number of error is incorrect

[dariober]

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

[Linkrw12]

This also exists in Snakemake 6.12.1

[dariober]

I think it's been fixed in v6.12.3 (thanks!) - please correct me if I'm wrong...

[yardimcilab]

This error persists in version 8.0.1.