| Age | Commit message (Collapse) | Author |
|---|
|
|
|
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.
|
|
|
|
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.
|
|
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>
|
|
--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>
|
|
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>
|
|
|
|
|
|
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>
|
|
More are on the way.
|
|
|
|
|
|
|
|
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.
|
|
|
|
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.
|
|
|
|
|
|
|
|
|
|
This has been around forever.
|
|
|
|
|
|
|
|
|
|
|
|
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
|
|
This has been around since Snakemake 3.9.0.
|
|
|
|
|
|
Closes #24.
|
|
Closes #22.
|
|
|
|
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.
|
|
|
|
|
|
|
|
|
|
wildcard_constraints was added in Snakemake v3.8.0 (feb6aee).
|
|
|
|
|
|
|
|
Closes #15.
|
|
|
|
|
|
|
|
Re: #9
|
|
This keyword was added in Snakemake version 3.5.5.
|
|
|