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2017-03-26snakemake-compile-targets: Remove an unnecessary let*Kyle Meyer
2017-03-26snakemake-read-file-target: Fix a docstring typoKyle Meyer
2017-03-26Update copyright yearsKyle Meyer
2016-11-24Fix doc-string typoKyle Meyer
2016-11-01Change approach for detecting invalid targetsKyle Meyer
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.
2016-11-01Display unexpected errors from snakemake callsKyle Meyer
2016-10-26cosmetics: Use zerop instead of (= 0 ...)Kyle Meyer
2016-09-13snakemake-check-target: Recognize protected itemsKyle Meyer
With 33a7c90 (snakemake-check-target: Adjust for upstream output, 2016-09-01), write-protected targets were no longer considered valid targets.
2016-09-01snakemake-check-target: Adjust for upstream outputKyle Meyer
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'
2016-09-01Change approach to handling errorsKyle Meyer
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.
2016-09-01snakemake-check-target: Relax output order assumptionKyle Meyer
2016-09-01snakemake-check-target: Pull out regexpKyle Meyer
2016-09-01Ignore standard error stream when digesting outputKyle Meyer
Avoid including warnings as targets.
2016-06-13snakemake-compile-targets: Update compile-historyKyle Meyer
2016-05-11Extend snakemake-block-bounds functionKyle Meyer
Include name and block type.
2016-05-11Add snakemake-block-bounds functionKyle Meyer
2016-04-19Rename snakemake-graph-rule to snakemake-graph-idKyle Meyer
With introduction of snakemake-graph-this-file, this variable isn't restricted to rule names.
2016-04-19Add snakemake-graph-this-file commandKyle Meyer
2016-04-19snakemake-graph: Fix docstring line breakKyle Meyer
2016-04-19graph: Correct docstringsKyle Meyer
2016-04-17Add helper for splitting rule listsKyle Meyer
2016-04-17Filter out anonymous rules from rule listsKyle Meyer
2016-04-17snakemake-rule-at-point: Fix anonymous rule checkKyle Meyer
2016-04-17commentary: Mention how Snakefile is locatedKyle Meyer
2016-04-17commentary: Add graph commandsKyle Meyer
2016-04-17Add snakemake-graph-save commandKyle Meyer
Re: #9
2016-04-17Add snakemake-graph commandKyle Meyer
Re: #9
2016-04-16Support anonymous rule blocksKyle Meyer
2016-03-04popup: Consider file targets in regionKyle Meyer
2016-02-29snakemake-compile: Fix target pathKyle Meyer
snakemake-file-targets-at-point expects to be called from the original directory.
2016-02-28popup: Add --allowed-rulesKyle Meyer
2016-02-28snakemake-all-rules: New commandKyle Meyer
2016-02-28Add popup interface for compilationKyle Meyer