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2022-02-21Rework copyright linesKyle Meyer
public-inbox has started to drop dates from its copyright lines, pointing to the recommendation at https://www.linuxfoundation.org/blog/copyright-notices-in-open-source-software-projects/ I regularly fail to keep copyright lines up to date, so I'll gladly follow suit. Drop the dates and change the copyright holder to (almost match) the variants recommended in the above article.
2020-02-21Update copyright yearsKyle Meyer
2018-09-01Prefer https linksKyle Meyer
2018-01-20Update copyright yearsKyle Meyer
2018-01-20snakemake-test.el: Remove email for copyright lineKyle Meyer
2017-03-26Update copyright yearsKyle 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.
2016-10-31tests: Run snakemake-check-target with rule targetsKyle Meyer
2016-10-31tests: Use write-region instead of with-temp-fileKyle 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.
2016-09-01Change 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.
2016-05-24indentation: Account for trailing commentsKyle Meyer
2016-05-24Fix indentation for continued lines under naked ruleKyle Meyer
2016-05-11Extend snakemake-block-bounds functionKyle Meyer
Include name and block type.
2016-05-11Define function for add-log-current-defun-functionKyle Meyer
2016-05-11Define defun navigation commandsKyle Meyer
2016-05-11Add snakemake-block-bounds functionKyle Meyer
2016-05-11Rework indentationKyle Meyer
The previous implementation did not support some legal syntax: * spaces between rule lines * indented rule blocks (e.g., a rule defined under an if-statement) * top-level commands like "include" when the value started on the second line (re: #16)
2016-05-03Be more lenient with spacing in regexpsKyle Meyer
2016-04-17Filter out anonymous rules from rule listsKyle Meyer
2016-04-17snakemake-rule-at-point: Fix anonymous rule checkKyle Meyer
2016-04-15mode: Unset indent-region-functionKyle Meyer
Don't use python-indent-region for indent-region-function. At first glance, setting indent-region-function to nil (that is, running indent-according-to-mode on each line) seems to indent rule blocks fine, though it will probably fail on more complex "run" values. However, this does mean that python-indent-region is no longer used when indent-region is called with a region that doesn't include a rule block, so it's probably worth adding a snakemake-indent-region function that calls python-indent-region in this case. Re: #8
2016-03-04popup: Consider file targets in regionKyle Meyer
2016-02-28Fix rule recognition at beginning of bufferKyle Meyer
2016-02-28tests: Change naming schemeKyle Meyer
2016-02-28Rename test file for MELPA filteringKyle Meyer
MELPA excludes test.el, tests.el, *-test.el, and *-tests.el.