Version 2024.2.2

Released on 24 October 2024

NB: Please configure/ensure the desired snakemake language level in the plugin settings, by default, it will be 8.24.0 in this release. Language level setting is required to show Snakemake API that is deprecated in the desired Snakemake version or not yet available. See example screenshots in #508

Features

• Inspection: Warn about deprecated or not yet available features based on snakemake language level (see #508
• Move snakemake API addition/removal info from JAR into extra/snakemake_api.yaml in plugin directory
• Inspection: Warn if snakemake section type or API function isn't supported in the current snakemake project based on a snakemake version (see #500
• Code completion: For section keywords show 'since' version and deprecation notice in the completion list. Do not suggest already removed keywords (see #535
• Set default project Snakemake language level in Snakemake support settings to 8.24.0
• [8.3.0] Support for: lookup, evaluate, branch, collect, exists (see #548
• [8.0.0] Support for Global workflow dependencies [8.0.0] syntax (see #555
• [8.0.0-6.8.1] Support for: 'storage', 'github', 'gitfile', 'gitlab' (see #550
• [7.25.0] Support for localrule directive (see #524
• [7.11] Resource scopes support (see #510

Fixed

• Improve parser error message when rule/module is declared with name but lacks ':' (see #515)
• Support for update and before_update flags. Update inspection that warns if flag functions from snakemake.io is used in a wrong section, added info for all flags up to 8.23.1 version (see #537)
• Inject some modules in Snakefile file resolve scope w/o import declaration, e.g. os, sys,.. (see #553
• Do not warn about unresolved snakemake variable in the python files, because they could be used as scripts/wrappers for snakemake rules. (see #511)
• Undeclared section threads warning should not be shown here (see #539

Version 2024.2.1

Released on 9 October 2024

Fixed

• Compatibility with PyCharm 2024.2-2024.3 EAPs (see #532)
• Improve the parser error message when rule/module is declared with name but lacks ':' (see #515)
• For some wrappers the documentation popup shows the wrong description (e.g. bio/bwa/mem-samblaster for bio/bwa/mem)
• Bundled snakemake wrappers list updated to v4.6.0
• Use SDK chooser w/o mange sdks button on the Snakemake Language Frameworks Settings page. The previous version used legacy API that doesn't manage SDKs correctly.
• Exceptions: EA-655, EA-220, EA-100, EA-40

Changed

• Switch plugin build scripts to intellij-gradle-plugin 2.1.0 API version (required for 2024.2+ PyCharm)
• Move cached wrappers info out of plugin JAR file to ../extra directory

Version 2024.1.1

Released on 20 April 2024

Fixed

• Compatibility with PyCharm 2024.1
• Bundled snakemake wrappers list updated to v3.8.0
• Completion for wrapper names rarely works (see #517)

Version 2023.3.1

Released on 6 Dec 2023 (EAP on 3 Nov 2023)

Fixed

• Compatibility with PyCharm 2023.3 (see #507)

Changed:

• Bundled snakemake wrappers list updated to v2.9.1

Version 2023.2.1

Released on 27 Jul 2023

Fixed

• Compatibility with PyCharm 2023.2

Changed:

• Bundled snakemake wrappers list updated to v2.2.1

Version 2023.1.1

Released on 9 April 2023

Fixed

• Compatibility with PyCharm 2023.1 (see #505)
• Exception: "Access is allowed from write thread only" creating project in dumb mode (see #506)
• Make Snakecharm trusted plugins, even though it is provided not by JetBrains but by JetBrains Research (see #503)
• Empty What's New section fixed

Changed:

• Bundled snakemake wrappers list updated to v1.25.0
• Plugin versioning changed, now minor version is not CI build, just manual counter

Version 2022.3.771

Released on December 7th 2022

Fixed

• Compatibility with PyCharm 2022.3 #501 (see #501)

Changed:

• Bundles snakemake wrappers list updated to v1.20.0

Version 2022.2.761

Released on August 5th 2022

Fixed

• Compatibility with PyCharm 2022.2
• Ignore whitespaces that could occur after as in use block
• Bundled wrappers repo updated to v1.7.1

Added:

• [7.10.0] Support conda environment definitions to be passed as function pointers, similar to input, params, and resources #494 (see #494)
• [7.9.0] Syntax supprt for exclude keyword in use rules (see #495, #496)
• [ 7.0.0] template_engine: basic support (see #497)
  • Do not highlight template_engine as unrecognized section
  • Inspections:
    • Only one argument expected after template_engine
    • Keywords arguments not supported after template_engine
    • Do not warn about unused log section if rule with template_engine
    • template_engine is execution section, so could not be with run/shell/notebook/script
    • template_engine should be last in the rule
    • Completion for "yte", "jinja2" in template_engine string argument
    • Inspection that warns when template= keyword argument is required in section with template_engine

Version 2022.1.749

Released on June 15th 2022

Fixed

• "Snakemake support is disabled. Not all features are available" is show in non Snakemake context (see #491)
• Do not show error for conda env that looks like already existing env (see #493)

Added:

• "default_target:" directive support (see #473)
• "retries:" directive support (see #490)
• "ensure:" directive support (see #489)

Version 2022.1.743

[2022.1.743], [2021.3.744]

Released on May 4th 2022

Changed:

• Bundles snakemake wrappers list updated to v1.3.2
• [2022.1.743] Plugin for PyCharm 2022.x (see #487)
• [2021.3.744] Plugin for PyCharm 2021.3

Fixed

• Resolve/completion for checkpoints after rules keyword (see #262)
• Quick fix for unused log file inspection (see #452)
• Resolve for rule names in use rule section (see #455)
• Multiple args inspection in workdir case (see #140)
• localrules and ruleorder now take into account use rule (see #448)
• Keyword arguments highlighting (see #454)
• Resolve for rules keyword if snakemake version less than 6.1 (see #359)
• Plugin Logo Updated (see #449)
• Snakemake file type icon updated
• 'copy-minimal' shadow section missing in completion (see #467)

Added

• Inspection: warns that that all docstrings except the first one will be ignored (see #341)
• Quick fix for unresolved files (conda, configfile. etc.) (see #277)
• Gutter icons for rule inheritance (see #429)
• Warning: Snakemake support is disabled (see #109)