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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.
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With 33a7c90 (snakemake-check-target: Adjust for upstream output,
2016-09-01), write-protected targets were no longer considered valid
targets.
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As of Snakemake v3.8.0, using a wildcard rule name signals a key error:
Traceback (most recent call last):
File "/usr/lib/python3.5/site-packages/snakemake/io.py", line 401, in format_match
value = wildcards[name]
KeyError: 'name'
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The approach from 7b210fc (Ignore standard error stream when digesting
output, 2016-09-01) does not work well because, depending on the
snakemake subcommand, the text of interest may be in the stderr stream.
Instead, use lines with spaces as a way to detect non-target lines.
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Avoid including warnings as targets.
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Include name and block type.
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With introduction of snakemake-graph-this-file, this variable isn't
restricted to rule names.
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Re: #9
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Re: #9
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snakemake-file-targets-at-point expects to be called from the original
directory.
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