Roman Chernyatchik

On DS startup DataSpell 2021.3 Snapshot Build #PD-213.223, built on June 21, 2021 Non-Bundled Plugins: SnakeCharm (2021.2.1.418) ``` java.lang.Throwable: Slow operations are prohibited on EDT. See SlowOperations.assertSlowOperationsAreAllowed javadoc. at com.intellij.openapi.diagnostic.Logger.error(Logger.java:182)...

Methods from another *.smk files highlighted as unresolved

2

Make accessible methods defined in the *.smk files. On runtime everything will be merged to the same file E.g. ``` # rules/common.smk def foo(): pass # rules/foo.smk a = foo()...

Before ``` rule foo: input: pass ``` should be ``` rule foo: input: pass ``` but is ``` rule foo: input: foo pass ```

PyCharm type checker False positive here 

AttributeError: 'Checkpoint' object has no attribute 'output'

1

Checkpoint type differs from Rule type: `checkpoints.A.output.mydir` leads to `AttributeError: 'Checkpoint' object has no attribute 'output'`, should be `checkpoints.A.get(**wildcards).output.mydir` Code example: ``` import os from snakemake import shell shell.prefix('set -vexu...

Code indentation fix in rules

19

Code indentation fix in rules for new line after: * rule name declaration * rule parameter name

Resolve/completion for `config` attrs

1

E.g. `config[genome]` where `genome` is defined in `configfile` or in cmdline using `--config` argument. Warn only about first usage and consider defined downstream. ``` rule download_fa: output: directory("fa") shell: 'rsync...

Fetch correct wildcards if arg value in rule is link to other section or section arg

1

Fetch correct wildcards if arg value in rule is link to other section or section arg. Support required for inspection checking undeclards wildcards and for completion/resolve ``` rule foo1: output:...

May be caused: 1) set custom interpreter in snakemake settings (not project one) 2) updated the interpreter using terminal snakemake version 3) resolve/completion issues for interpreter sdk methods Vers: 0.10.0.SNAPSHOT...