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author | Kyle Meyer <kyle@kyleam.com> | 2016-10-31 20:08:31 -0400 |
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committer | Kyle Meyer <kyle@kyleam.com> | 2016-11-01 22:04:11 -0400 |
commit | 82afce155a22c5b93a165945cc17e095485d6b7e (patch) | |
tree | 18e0d09b24dd78317e5e32c09d3c00ce2b0a12f8 /.gitignore | |
parent | 13620417f99495f74b17cd2d9ca3c37551dbb120 (diff) | |
download | snakemake-mode-82afce155a22c5b93a165945cc17e095485d6b7e.tar.gz |
Change approach for detecting invalid targets
Initially (7374840), snakemake-check-target only used regular
expressions to detect invalid targets based on the presence of a
MissingRuleException or RuleException in Snakemake's output. The target
was assumed to be valid if these exceptions weren't found. If there was
a non-zero exit status for another reason, it bubbled up to the compile
call where it was visible to the user.
33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01)
restricted the invalid target check to calls with an exit status of
zero. This makes the regular expression check useless because snakemake
should always exit with a non-zero status if a MissingRuleException or
RuleException is thrown. Due to this change, snakemake-check-target
classified all non-zero exits as invalid and all zero exits as valid.
While this often gives the right answer, it doesn't in cases where the
non-zero exit is unrelated to an invalid target.
2bceb7f (snakemake-check-target: Recognize protected items, 2016-09-05)
addressed one case.
To deal with other cases (such as an ambiguous rule error or a syntax
error in the Snakefile), use the following approach.
* An exit status of zero indicates a valid target.
* A non-zero exit status indicates an invalid target if
snakemake-all-rules has an exit status of zero. Otherwise,
snakemake-all-rules will signal an error and display the Snakemake
output.
The main downside of this approach is the need to call snakemake twice.
The output of snakmake-all-rules is cached, so this is only the case on
the first call to snakemake-check-target for a given version of a
Snakefile.
Diffstat (limited to '.gitignore')
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