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About

SnakeCharm is a plugin for PyCharm / IntelliJ Platform IDEs which adds support for Snakemake workflows language. The plugin is developed by JetBrains Research Team, for more details see project home page.

Please report features suggestions or found bugs to project issue tracker.

Features

Features available in Snakefile and *.smk, *.rule, *.rules files:

• Python code syntax highlighting
• Snakemake specific syntax highlighting
• Limited resolve and code completion for python code
• Rules folding
• Code completion and resolve for:
  • Rules names after rules., checkpoints after checkpoints.
  • Rules sections names after rules.my_rule_name.
  • Rule sections keywords arguments, e.g. after ``rules.my_rule_name.input.`
  • Snakemake api methods like expand, temp, etc.
  • Wildcards and sections names in shell and other sections
  • Included rules files and conda environment files
• File structure view with rules
• Wildcards support (code completion, resolve, usages highligting, inspections)
• Multiple inspections inspections for possible errors in snakemake file.

Installation

If you've already configured custom file type for Snakefile or *.smk files please delete it (or change file masks to smth else). Otherwise, your custom file type will replace SnakeCharm support in snakemake files.

In PyCharm (or other IntelliJ Platfrom based IDE with Python Community Edition plugin installed) open Preferences|Plugins|Marketplace|SnakeCharm and press Install button.

At the moment the plugin is tested with:

• IDEA CI 2018.3-2019.2.x, Python Community Edition Plugin: 2018.3.183.4284.36-2019.1.191.7479.19
• PyCharm 2018.3.1-2020.2.EAP (Professional & Community Editions)

Setup Snakemake support

To enable all code insight features (e.g. code completion for directory, touch etc methods) please configure Python SDK with installed snakemake package.

https://github.com/JetBrains-Research/snakecharm/wiki#setup-snakemake-support

IntelliJ Plugins Repository

Plugin is available in IntelliJ Plugins Repository, see SnakeCharm Plugin.

EAP Updates

Early builds of coming releases are available in EAP channel. To receive this updates add EAP repository:

• Open IntelliJ IDEA / PyCharm / .. IDE setting
• In Plugins section press 'gear' icon, select Manage Plugin Repositories...
• Add repo https://plugins.jetbrains.com/plugins/eap/list using + button, press OK (Complete guide at Custom Release Channels)
• EAP builds will be visible as plugin updates

Support

Contact me at [email protected] or post issues in Issue Tracker

Development

Pull requests are welcome. It is my side project, so I appreciate your help implementing plugin desired features.

Build plugin from sources:

• Run ./gradlew buildPlugin
• Plugin bundle is located in build/distributions/snakecharm-*.zip

Install plugin from ZIP bundle:

• Open IDEA/PyCharm Preferences
• Choose Plugins section
• Press gear icon and choose Install Plugin from Disk...
• Use *.zip bundle download from Plugin Manager or built from sources

Tests: Tests are written in Gherkin:

If you get "Unimplemented substep definition" in all *.feature files, ensure:

• Not installed or disabled: Substeps IntelliJ Plugin
• Plugins installed: Cucumber Java, Gherkin

Release plugin:

• Fix version in build.gradle
• Fix since/until build versions in build.gradle
• Fix change notes in CHANGES file
• Use 'publishPlugin' task