snakecharm

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'prefix:' keyword support for modules

1

'prefix:' directive support for modules Introduced in 6.13.0 (2021-12-21): > allow prefix definition in module statements ([#1310](https://www.github.com/snakemake/snakemake/issues/1310)) ([29e6540](https://www.github.com/snakemake/snakemake/commit/29e6540aac95b08b5e386a8478bd2013334e5954)) Related documentation: * https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html * https://snakemake.readthedocs.io/en/stable/snakefiles/modularization.html?highlight=module

iromeo

E.g. check `min_version` declaration and warn if not supported, e.g. `template_enginge` introduced only in 7.0.0 ``` from snakemake.utils import min_version min_version("6.0") configfile: "config.yaml" ``` * https://snakemake.readthedocs.io/en/stable/snakefiles/writing_snakefiles.html?highlight=min_version#depend-on-a-minimum-snakemake-version

iromeo

Possible future improvements: - *.jinja2 file type is supported by PyCharm Professional, some inspection which highlights/resolves/completes related rule params, input, and output section arguments could be useful - Specific YTE...

iromeo

E.g. 1) add navigation gutter for conda sections or multi-resolve 2) rename files with conda env See * https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html?highlight=pin.txt#freezing-environments-to-exactly-pinned-packages * https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html?highlight=pin.txt#providing-post-deployment-scripts Introduced in: [6.15.1](https://www.github.com/snakemake/snakemake/compare/v6.15.0...v6.15.1) (2022-01-31) Bug Fixes * [6.14.0](https://www.github.com/snakemake/snakemake/compare/v6.13.1...v6.14.0) (2022-01-26)...

iromeo

Features/#462 gutter icons module case

2

New index was implemented, so issues #462 and #463 were resolved

dakochik

It is worth disabling default unresolved reference inspection, and replacing it with custom inspection.  Related to #433

dakochik

Resolve and completion should works for such methods as `.get()`, `.items()` and the other dictionary methods 

dakochik

In in the following project: ``` + - - projectDirectory | + - - keys.yml | + - - smk | + - - Snakefile ``` If we run `Snakefile`...

dakochik

This code results in runtime error: ``` CreateRuleException in line 16 of /Users/romeo/work/snakecharm/snakemaek_examples/untitled10/rule_001_use_check/rule_001.smk: The name m_001_new is already used by another rule File "/Users/romeo/work/snakecharm/snakemaek_examples/untitled10/rule_001_use_check/rule_001.smk", line 16, in ``` ``` use...

iromeo

E.g. get runtime error: ``` RuleException in line 3 of /Users/romeo/work/snakecharm/snakemaek_examples/untitled10/rule_001_use_check/template_module_001.smk: 'Params' object has no attribute 'p' ``` for ``` import os print(os.cpu_count()) module m_001: snakefile: "template_module_001.smk" config: dict(key="foo") use...

iromeo