Snakemake PR https://github.com/snakemake/snakemake/pull/2180/files added the localrule directive.

This directive needs to be added to the extension's keywords (I think) so that it gets highlighted correctly.

That's what it looks like at the moment:

Variables starting with the word expand, such as "expand_fields" are syntax highlighted incorrectly. The expand part is yellow and the rest white. The syntax highlighter parser thinks the beginning should be highlighted like expand in the Snakemake function call.

Just an annoyance, if I previously had syntax error(s) in my snakemake file and there's message output from those, when I've fixed them and I save the file the previous messages are still there in the output window and I'm no certain that the syntax or compile errors are gone.

• The SnakeCharm plugin for PyCharm also does suggestions for snakemake component as well as for Python component.

vscode Go to definition is not enabled

It would be great if this plugin could infer script-env dependencies from the rule files and set the Python interpreter for each Python script file accordingly. Otherwise, as it is now, Python interpreters do not match the chosen env in Snakemake.

Not sure if this is technically possible or in-scope of this plug-in. Just saying that such a feature would be great.

The rule cache keyword seems to be missing from the syntax highlighter grammar, as it doesn't seem to be highlighted properly like params, input, output, wrapper, etc.

Don't know how easy this is to do with an extension, but an annoyance of writing workflows in VS Code is the implicitly defined snakemake global variable. The type checker is not aware of this and will generate an "undefined variable" warning for each usage.

I'm using the following workaround for this:

from typing import TYPE_CHECKING

if TYPE_CHECKING:
    from snakemake.script import Snakemake
    snakemake: Snakemake
    snakemake = None  # type: ignore

But it would be really great if this could be automatically applied somehow.

Strings are highlighted as comments, especially when used as commands

rule hostname:
    output: 
        "out/{id}.txt"
    threads:
        1
    resources:
        tmpdir=".tmp"
    conda:
        'base'
    shell:
        '''
        sleep 2;echo `hostname` > {output}
        echo fdf >> {resources.tmpdir}/fdf
        
        '''

The strings in the shell, output, and conda parts are all recognized as comments and highlighted in green

Hi,

I have found, that snakemake plugin does not recognize Snakefile as smakemake file. Everything is ok for .smk files, but most content of Snakefile is underlined with red. How can I fix it?

I am using Smakemake Language v0.1.6.

Thanks,
Paweł

A lot of snakemake keywords are not highlighted.
Especially rule params like mentioned in issue #23, #18 and #14.
The following rule params are not highlighted:

• shellcmd
• name
• norun
• conda_env
• container_img
• is_containerized
• env_modules
• shadow_depth
• docstring
• notebook
• template_engine
• cache
• path_modifier
• handover
• default_target
• localrule

Besides this, also no PEP keywords are highlighted #22 and, to my knowledge, also the kewords:

• envvars
• module

It would be nice to have a script which collects all keywords.
This is maybe possible from the parser.py file.
For the rule params the ruleinfo.py scripyt would be also possible.

As explained issue #15 built-in functions like expand are not highlighted properly.
This can be fixed by integrating the snakemake rules in the MagicPython grammar.
In my fork of this repo, I could implement this by copying and modifying the whole MagicPython grammar.
Unfortunately, I did not find a way to just use the include rule key to load the MagicPython grammar and overwrite the rules that I wanted to include the sankemake rules in.

PAT for publishing the extension to visual studio market has expired:

Error: Error: {"$id":"1","customProperties":{"Descriptor":null,"IdentityDisplayName":null,"Token":null,"RequestedPermissions":0,"NamespaceId":"00000000-0000-0000-0000-000000000000"},"innerException":null,"message":"Access Denied: The Personal Access Token used has expired.","typeName":"Microsoft.VisualStudio.Services.Security.AccessCheckException, Microsoft.VisualStudio.Services.WebApi","typeKey":"AccessCheckException","errorCode":0,"eventId":3000}

Please add appropriate syntax highlighting for pepfile and pepschema.
https://snakemake.readthedocs.io/en/stable/snakefiles/configuration.html#configuring-scientific-experiments-via-peps

Thanks!

Currently shell blocks are treated as strings. Would be nice if they could have syntax highlighting for shell scripts instead. Bash is probably the most common.

rule:
	shell:
       """
       what="world"
       echo "Hello ${what}"
       """

rule:
    run: shell("echo Hello world")

retries directive keyword not syntax highlighted properly

It would be nice to have a panel in the sidebar that lists all the targets in the Snakefile so you can quickly run a target, perhaps including a [Force run] button, and an option to quickly jump to the definition.

A plain text mockup:

• all [> [!> [\
• download_data [> [!> [\
• preprocess_data [> [!> [\

using the following definitions for the symbold:

• [> Run selected rule, call snakemake {rule}
• [!> Force run selected rule, call `snakemake --force {rule}
• [\ Edit rule definition, open file and go to line

Some things that need to be considered:

• visualise modular rules
• handle multiple open folders in the current workspace
• select profile to use (per open folder)
• how and when to update the list of rules as building the list can be slow
• visualise running rules, can we allow starting multiple rules in parallel?

Finally, I don't have any experience building VS Code plugins, but I figure it should be possible.

It would be nice if this plugin worked like other language plugins and it underlined syntax or compile errors inline inside the code file, where also just like other plugins if you hovered over the underlined issue it would give you more information.