snakecharm

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Support of format specifiers in SnakemakeSL

2

- [x] Basic parsing as valid SmkSl #214 - [ ] Syntax highlighting for format specifiers - [ ] Code completion for standard specifiers E.g. `echo {input:q}`, see https://snakemake.readthedocs.io/en/stable/snakefiles/rules.html

iromeo

Implicit Includes support

2

Code insight support for case ``` # foo.smk rule foo: output: "foo.out" ``` ``` # boo.smk rule boo: input: rules.foo.output output: "out" ``` ``` # Snakefile include "foo.smk" include "boo.smk"...

iromeo

rule foo: output: "file.txt" input: "input.txt" shell: "echo hello" rule boo: input: ... If the entire file is indented with tabs but a rule section, e.g. `output`, is indented with...

sharkovadarya

``` from snakemake.utils import validate configfile: "config.yaml" validate(config, schema="schemas/config.schema.yaml") cells = pd.read_csv(config["cells"], sep="\t").set_index("id", drop=False) validate(cells, schema="schemas/cells.schema.yaml") rule foo: input: "boo" ``` Scheme is a *.yaml file relative to this file

iromeo

`snakemake` script run creates a `.snakemake` directory in the working directory. There can be a `shadow` directory in `.snakemake`, which contains symlinks to files in the current workdir; this results...

sharkovadarya

Wildcards code insight

1

Sometimes user expects that he is using already defined variable or rule section, but get error like: wildcard `threads` cannot be defined from input/output error. E.g. in: ``` rule: threads:...

iromeo

Given a file: ``` workdir: "Dir" include: "Dir/foo.smk" ``` Renaming directory _Dir_ to _Folder_ will result in ``` workdir: "Folder" include: "Dir/foo.smk" ``` But the desired result is: ``` workdir:...

nikita-nazarov

Debugger for snakemake files

2

At the moment PyCharm debugger doesn't allow to place breakpoints into snakefiles and debug it's pure python code at toplevel and in rule sections. Also debugger doesn't stop on breakpoints...

iromeo

We could provide basic completion (and hide unresolve ref warning) even if Python SDK with snakecharm not configured. Not sure that all users will use proper SDK. Probably completion could...

iromeo

Completion false positives for snakemake.io, etc.

1

Current completion implementation adds all top-level methods from `snakemake.io` to autocompletion, although `snakemake` imports only some of methods, e.g. See ``` # ~/anaconda/envs/snakemake/lib/python3.6/site-packages/snakemake/workflow.py from snakemake.io import protected, temp, temporary, ancient,...

iromeo