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2023-12-10snakemake-mode-setup-mmm: Tweak symbol quotingKyle Meyer
2023-12-10snakemake-mode-setup-mmm: Fix condition for warningKyle Meyer
snakemake-mode-setup-mmm should give this warning when mmm-global-mode is nil, but it does the opposite.
2023-04-17add localrule to field namesNathan J Dwarshuis
This new keyword was added in snakemake 7.25.0 Message-Id: <871qki2w9t.fsf@yavin4.ch>
2023-04-17ci: Add Emacs 28.2Kyle Meyer
2023-04-17ci: Update for compat upstream changeKyle Meyer
2023-04-17transient: Specify arglistKyle Meyer
As of 5337e5e (transient-define-{*}: Error if ARGLIST is missing, 2023-01-20), Transient throws an error.
2022-08-20ci, make: Include compat for TransientKyle Meyer
Transient requires compat as of 5ae3c40 (Depend on compat package from GNU Elpa, 2022-04-22).
2022-08-20ci: Fix typo in step nameKyle Meyer
2022-08-20make: Drop CURL variableKyle Meyer
This is unused since c657cfa (ci: Switch to GitHub Actions, 2022-02-21).
2022-02-22make: Add target to create tar signature for cgitKyle Meyer
This command is modified from an example in the "Signatures" section of cgitrc(5).
2022-02-22Release 2.0.0v2.0.0Kyle Meyer
2022-02-22make: Drop transient from the load pathKyle Meyer
This is no longer needed following the switch from Magit Popup to Transient.
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
2022-02-22snakemake-rx-constituents: Drop deprecated sm-funcKyle Meyer
This was marked as deprecated in v1.1.0, and it's unlikely that anyone ever relied on it.
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>
2022-02-21Drop cl-lib from Package-Requires headerKyle Meyer
cl-lib was added in the Emacs 24.3 release, so cl-lib no longer needed to be specified when ca4d60d (Change Emacs requirement for Emacs 24 to Emacs 24.5, 2018-08-16) changed (emacs "24") to (emacs "24.5").
2022-02-21transient: Use --cores=all by defaultKyle Meyer
--cores has been a mandatory argument since v5.11. Set the default to something that can actually build targets. Message-Id: <20220222030207.204401-4-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>
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.
2022-02-21ci: Switch to GitHub ActionsKyle Meyer
After GitHub Actions were available, this repository kept using Travis because it worked well enough, especially given this package is very much in maintenance mode. However, going forward it'd be nice to use purcell/setup-emacs action to test various Emacs versions. Don't bother testing against Emacs 24 because the next release will bump the minimum Emacs version to at least 25.1. While touching this setup, drop the Makefile target for downloading dependencies and instead just expect dependencies to be one level up from the snakemake-mode checkout.
2022-02-21make: Load autoload.el before calling update-directory-autoloadsKyle Meyer
--eval uses lexical scoping as of Emacs 27. Load autoload.el to evaluate (defvar generated-autoload-file ...) and get dynamic scope. See Emacs's bug#39823.
2020-12-24mode: Add "name" to the list of field keysKyle Meyer
2020-11-08Release 1.8.0v1.8.0Kyle Meyer
2020-11-01docs: Update stale Snakemake linksKyle 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>
2020-11-01travis: Turn off emails about successful runsKyle Meyer
2020-11-01travis: Bump Python version to 3.7Kyle Meyer
The Travis builds have started to fail because Snakemake now requires at least Python 3.7.
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
2020-04-16README: Revise contributing sectionKyle Meyer
2020-04-16issue_template.md: Tweak wordingKyle Meyer
2020-04-16issue_template.md: ReflowKyle Meyer
I went with the long lines because that will be rendered more nicely by GitHub. But this is shown in the text field so it doesn't matter.
2020-04-13Merge branch 'readme-updates'Kyle Meyer
2020-04-13README: Add a contributing sectionKyle Meyer
2020-04-13README: Rewrite as a plain text fileKyle Meyer
2020-04-13Rename READMEKyle Meyer
2020-04-13README: Update Snakemake linkKyle Meyer
2020-04-13Add COPYING fileKyle Meyer
I shouldn't rely on the license notice at the top of the files.
2020-04-13Redirect those opening issues/PRs on GitHubKyle Meyer
2020-04-13Update links for repo's new homeKyle Meyer
2020-02-22Release 1.7.0v1.7.0Kyle Meyer
2020-02-21Merge branch 'emacs27-font-lock'Kyle 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.
2020-02-21font-lock: Pull python-font-lock-keywords into snakemake'sKyle Meyer
This will make it easier to work around a change to python-font-lock-keywords in Emacs 27.
2020-02-21mode: Retain non-keyword parts of inherited font-lock-defaultsKyle Meyer
snakemake-font-lock-keywords is extended with python-font-lock-keywords, but the non-keyword bits that python.el defines for font-lock-defaults are discarded. Keep those too because python.el sets a value for font-lock-syntactic-face-function.
2020-02-21mode: Add "multiext" to list of built-insKyle Meyer
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