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2022-02-22mode: Add support for new module syntaxKyle Meyer
Snakemake 6.0 introduced a module syntax that looks like this: module other_workflow: snakefile: "other_workflow/Snakefile" use rule * from other_workflow as other_* Give the new module block the same indentation and fontification as other blocks by adding "module" to the list of words that mark a named rule. For the "use rule" line, highlight "use rule" as a keyword, leaving the rest of the line to be highlighted by python.el.
2022-02-22Delete snakemake-compile compatibility aliasKyle Meyer
2022-02-22mode: Add support for some newer keywordsKyle Meyer
I'm not sure if containerized can be used as a field too, but I only see it used as a top-level command in the examples.
2022-02-21Increase minimum required Emacs version to 26.1Kyle Meyer
26.1 was released in 2018 and is in the current Debian oldstable (Buster). I'm unlikely to build an older Emacs version than that in order to investigate and work around any incompatibilities that are reported, so mark it as the minimum. Message-Id: <20220222043213.218747-1-kyle@kyleam.com>
2022-02-21transient: Replace --jobs with --coresKyle Meyer
--cores was added as a synonym for --jobs in v3.10.0 (2012), and, as of v6.5.0, --cores and --jobs are distinct things for cloud/cluster jobs. Wait to add --jobs until it's requested. Message-Id: <20220222030207.204401-3-kyle@kyleam.com>
2022-02-21Rewrite snakemake-popup as a transientKyle Meyer
Magit switched to Transient for its popups a while go. Magit Popup is still around for third-party libraries that may use it, but it's not actively developed. At the moment, this switch is trading one external library for another (improved) one. However, Transient will ship with Emacs starting with the upcoming 28.1 release. Message-Id: <20220222030207.204401-2-kyle@kyleam.com>
2020-12-24mode: Add "name" to the list of field keysKyle Meyer
2020-11-08Release 1.8.0v1.8.0Kyle Meyer
2020-11-01mode: Add "container" and "envmodules" keywordsKyle Meyer
Register "container" as both a field key and a top-level command because an example of both is present in the Snakemake docs. Reported-by: Nicholas Knoblauch <knoblauch.nicholas@gene.com> Message-Id: <87eelcak64.fsf@kyleam.com>
2020-11-01NEWS: Reformat entry about new keywordsKyle Meyer
More are on the way.
2020-07-19mode: Add "envvars" to list of top-level commandsKyle Meyer
2020-04-17mode: Add "cache" to the list of field keysKyle Meyer
2020-02-22Release 1.7.0v1.7.0Kyle Meyer
2020-02-21font-lock: Adjust python-font-lock-keywords handling for Emacs 27Kyle Meyer
In Emacs 27, specifically 36b64e087e (Add 'font-lock-maximum-decoration' levels for Python, 2018-07-19), python-font-lock-keywords was changed to a list of symbols that define different fontification levels, so we can no longer simply tack snakemake-font-lock-keywords onto it. Instead define a set of levels that mirrors Python mode's. For Snakemake mode, the same decoration is used for all levels, but at least we will honor the level of decoration that the user has set for Python. Reported-by: Nicholas Knoblauch <nwknoblauch@gmail.com> Closes #29.
2020-02-21mode: Add "multiext" to list of built-insKyle Meyer
2020-02-21NEWS: Delete second-level headingsKyle Meyer
There are few enough entries in each release that this extra structure isn't really helpful. Plus, some things that are labeled as "new features", like recognizing keywords for fontification, seem a bit silly to call a feature, but I can't think of a better heading for them.
2019-09-11Release 1.6.0v1.6.0Kyle Meyer
2019-04-11mode: Add checkpoint supportKyle Meyer
2018-10-07Release 1.5.0v1.5.0Kyle Meyer
2018-10-04mode: Add "report" to list of field keys and built-insKyle Meyer
2018-10-04mode: Add "localrules" as to the list of top-level commandsKyle Meyer
This has been around forever.
2018-09-22snakemake-popup: Add --use-condaKyle Meyer
2018-09-18mode: Add "group" to the list of field keysKyle Meyer
2018-08-16Release 1.4.0v1.4.0Kyle Meyer
2018-08-16mode: Add "pipe" to the list of built-insKyle Meyer
2018-08-16mode: Add "directory" to the list of built-insKyle Meyer
2018-08-16Change Emacs requirement for Emacs 24 to Emacs 24.5Kyle Meyer
python.el changed its indentation engine in Emacs 24.5. We rely on a python-indent-calculate-indentation that is specific for the newer version. Re: #28
2018-05-19mode: Add "ancient" as to the list of built-insKyle Meyer
This has been around since Snakemake 3.9.0.
2018-03-20mode: Add "cwl" to the list of field keysKyle Meyer
2018-01-28Bump versionv1.3.0Kyle Meyer
2018-01-25mode: Add "singularity" to the list of field keysKyle Meyer
Closes #24.
2017-10-10mode: Add ".smk" as a file suffixKyle Meyer
Closes #22.
2017-04-06Bump versionv1.2.0Kyle Meyer
2017-03-26Add a terminal interface for running SnakemakeKyle Meyer
Snakemake commands are currently executed through compile. In general, this works fine, but it doesn't work well when Snakemake should be executed in a different environment than the one in which the current Emacs session was started. For example, Guix commands like 'guix environment ...' manipulate environmental variables to expose particular software. With the current setup, snakemake-program could be set to a wrapper script that creates the environment and then calls Snakemake: guix environment -l manifest.scm --ad-hoc snakemake --pure \ -- snakemake $@ But the disadvantage of this approach is that it adds the environmental setup time to _each_ Snakemake call. To work better with tools like Guix, let's add an alternative interface that allows commands to be executed in a terminal session. Instead of the above script, snakemake-shell-file-name can be set to a script with guix environment -l manifest.scm --ad-hoc snakemake --pure Now the environmental setup cost is limited to starting the terminal.
2016-11-22Bump versionv1.1.0Kyle Meyer
2016-11-15Support 'conda' keywordKyle Meyer
2016-11-10Bump versionv1.0.0Kyle Meyer
2016-10-31NEWS: Touch up spacingKyle Meyer
2016-09-02Support 'wildcard_constraints' keywordKyle Meyer
wildcard_constraints was added in Snakemake v3.8.0 (feb6aee).
2016-05-17Bump versionv0.5.0Kyle Meyer
2016-05-11Define function for add-log-current-defun-functionKyle Meyer
2016-05-11Define defun navigation commandsKyle Meyer
2016-05-03mode: Add ".rules" as a file suffixKyle Meyer
Closes #15.
2016-05-03NEWS: Mention snakemake-mode-setup-mmmKyle Meyer
2016-04-19Add snakemake-graph-this-file commandKyle Meyer
2016-04-18Bump versionv0.4.0Kyle Meyer
2016-04-17Add snakemake-graph commandKyle Meyer
Re: #9
2016-04-16Add wrapper keywordKyle Meyer
This keyword was added in Snakemake version 3.5.5.
2016-04-16Support anonymous rule blocksKyle Meyer
2016-03-12mode: Add ".snakefile" as a file suffixKyle Meyer
https://groups.google.com/d/msg/snakemake/segLE-RlV_s/nQCTxH_TJwAJ
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