Version 2021.3.661

[2021.3.661]

Released on December 7th 2021

Changed

• PyCharm 2021.3 compatibility (see #444)
• Show argument preview for int indexes completion in output[i] (see #378)
• Allocation of all top-level sections into one token and support for unknown top-level sections (see #373)

Fixed

• Resolve and completion for 'script' section (see #426)
• Only snakemake file can't end with a comment (see #365)
• SmkSectionDuplicatedArgsInspection now checks workflow top-level sections (see #407)
• All inspections warnings now can be overridden (see #423)
• Completion for .smk files in module 'snakefile' section (see #428)
• Default path "config/config.yaml" now supported (see #363)
• Access by index to input/output sections with 'multiext' function (see #278)
• Inspection: Do not show warning that rule section is unused variable if rule is defined in method (see #385)
• SOE: From UnusedLocal inspection for SnakemakeSL expression (see #380)
• Do not show syntax error for rule w/o body (see #420)

Added

• Color Settings Page (see #431)
• Inspection: highlights 'use rule' section which overrides several rules as one (see #411)
• Collecting wildcards from overridden rules in 'use' sections (see #418)
• Weak warnings for unused 'log' sections in 'use rule' (see #414)
• Weak warnings for unused 'log' sections (see #300)
• Support for 'module' and 'use' keywords (see #355)
• Inspection for improperly called functions (see #148)
• Ability for memorising new section name (see #372)
• Support for 'handover' section (see #362)
• Support for 'containerized' section (see #361)
• Inspection: Show ERROR for execution sections in 'use' section (see #408)
• Completion features related to 'use' section (see #413)
• Add reference for 'snakefile:' in module declaration (see #409)
• Initial PEPs support (see #360)

Version 2021.2.657

[2021.2.657]

Released on December 6th 2021

Changed

• Show argument preview for int indexes completion in output[i] (see #378)
• Allocation of all top-level sections into one token and support for unknown top-level sections (see #373)

Fixed

• Resolve and completion for 'script' section (see #426)
• Only snakemake file can't end with a comment (see #365)
• SmkSectionDuplicatedArgsInspection now checks workflow top-level sections (see #407)
• All inspections warnings now can be overridden (see #423)
• Completion for .smk files in module 'snakefile' section (see #428)
• Default path "config/config.yaml" now supported (see #363)
• Access by index to input/output sections with 'multiext' function (see #278)
• Inspection: Do not show warning that rule section is unused variable if rule is defined in method (see #385)
• SOE: From UnusedLocal inspection for SnakemakeSL expression (see #380)
• Do not show syntax error for rule w/o body (see #420)

Added

• Color Settings Page (see #431)
• Inspection: highlights 'use rule' section which overrides several rules as one (see #411)
• Collecting wildcards from overridden rules in 'use' sections (see #418)
• Weak warnings for unused 'log' sections in 'use rule' (see #414)
• Weak warnings for unused 'log' sections (see #300)
• Support for 'module' and 'use' keywords (see #355)
• Inspection for improperly called functions (see #148)
• Ability for memorising new section name (see #372)
• Support for 'handover' section (see #362)
• Support for 'containerized' section (see #361)
• Inspection: Show ERROR for execution sections in 'use' section (see #408)
• Completion features related to 'use' section (see #413)
• Add reference for 'snakefile:' in module declaration (see #409)
• Initial PEPs support (see #360)

Version 2021.2.424

Released on July 5th 2021

Changed

• Plugin structure changed to Developing plugins using GitHub Template (see #358)

Fixed

• Slow operations are prohibited on EDT (see #366)
• Compatibility with Snakemake 5.6.x (see #367)

Version 2021.2.1 build #2021.2.1.418

Version 2021.2.1 build #2021.2.1.418

Released on June 22th 2021

Features:

• Compatible with PyCharm 2021.1.1 - 2021.3 EAPs, DataSpell EAPs

Bundled meta-data for snakemake-wrappers (repo version: 0.75.0)

2021.2.0.414

Version 2021.2.0 build #2021.2.0.414

Released on May 3th 2021

Features:

• Compatible with PyCharm 2021.1.1 - 2021.2 EAPs, DataSpell EAPs

Version number now represents target PyCharm/DataSpell/IntelliJ platform major version for 2021.2.0.414:

• 2021.2 - intellij platform version
• .0 - plugin revision in 2021.2 version
• .414 - plugin build number

0.11.0.411

Version 0.11.0 build #0.11.0.411

Released on April 24th 2021

NB: Now Snakemake support is enabled only if Snakemake framework support is selected in

• PyCharm: Settings | Languages & Frameworks | Snakemake | Enable Snakemake Support
• IDEA: Add Snakemake facet

It is possible to use different Python Interpreters for your project and for Snakemake features.
E.g. you could have a conda environment with all packages required for scripts used in rules, but
without snakemake module itself.

Features:

• Support PyCharm 2021.1 build (see #350)
• Snakemake Support Settings page (see #346)
• Support any section names syntax in rules, checkpoints, subworkflows (see #334)
• Support name: section argument syntax (see #351)
• Experimental wrappers smart features (thanks to @SimonTsirikov for help):
  • Bundled meta-data for snakemake-wrappers (repo version: 0.73.0)
  • Snakemake wrappers names resolve/completion (see #18)
  • Rule section keyword arguments completion based on wrappers info (see #18)
  • Wrapper params are taken from 'wrappers.py', 'wrappers.r', 'meta.yaml' (see #324)

Fixed:

• Inspection marks 'rules.' as unresolved in snakemake >= 6.1 (see #352)

Inspections:

• Weak warning about sections which are not recognized by SnakeCharm (see #334)

---

Enable Snakemake Support:

Wrappers names completion:

Wrappers base rules: completion for keyword arguments in rule sections:

** Quick documentation popup for wrapper:**

0.9.0.387

Version 0.9.0 build #0.9.0.387

Released on Dec 16th 2020

Special thanks to our contributors Simon Tsirikov (@SimonTsirikov) and Artem Davletov (@ArtemDavletov). Without their help this major plugin
update won't be possible.

Features:

• PyCharm 2020.3 compatibility (see #337)
• Snakemake specific formatter settings (see #338)
• envmodules parsing (see #332)
• Inspection: input, output can't be used in params sections directly (see #153)
• Inspection: Comment at the end of Snakefile is treated as syntax error (see #58)
• Inspection: envmodules directive is only allowed with shell, script, notebook, or wrapper directives (not with run) (see #340)
• Inspection: Warn about double quotation on runtime in cases like {config['foo']} for snakemake string injections (see #329)
• Inspection: Warn users if they have arguments with same value in section (see #263)
• Inspection: Comma in the end of section arg list isn't needed (see #255)
• Inspection: Warn user if rule from 'rulesorder' isn't available in current or included files (see #254)
• Inspection: Warn about string arguments split on several lines (see #259)
• Injection: Inject regexp language into wildcard_constraints section params values (see #182)
• Inspection: Correct using methods ancient, protected, directory (see #250)
• Inspection: Warn users if they have callable arguments in sections that does not expect it (see #198)
• Inspection: Warn users if they have keyword arguments in sections that does not expect it (see #196)
• Inspection: Warn about usage of rule/checkpoint/subworkflow objects as arguments instead of one of its fields (see #257)
• Action: Correct Up/Down StatementMover for rule sections (see #174)
• Action: Show folding for multiline rule sections (input, output, etc) (see #314)

Fixed:

• PluginException: Inspection #SmkAvoidTabWhitespace has no description [Plugin: SnakeCharm]
• Do not warn about 'touch' misuse in benchmark and log sections
• Completion does not suggest top-level keywords in comments (see #178)
• Suppress inspection doesn't work in some cases (see #313)
• Don't show multiline string arg, may be comma is missing for sections with single arg (see #315)
• Expected collections.iterable but got output: false positive (see #317)
• Expected type Iterable (..), git input: instead (see #319)
• Expected type Iterable (..), git input: instead (see #320)
• Workaround for: 'Shadows built-in name input' inspection on lambda parameters (see #133)
• Confusing 'Cannot check missing wildcards here.' warning (see #307)

0.8.0.214

Version 0.8.0 build #0.8.0.214

Released on July 3th 2020

Features:

• PyCharm 2020.2 builds compatibility

0.7.0.209

Version 0.7.0 build #0.7.0.209

Released on July 2th 2020

Features:

• Inspection: warn about confusing reference in localrules section (see #287)
• Inspection: Warn if mixed tabs and spaces (see #285)
• 'notebook' section parsing error (see #288)
• envvars isn't parsed properly (see #281)
• container top level and rule sections parsing (#291)
• Resolve/completion for paths in notebook section (see #289)
• Inspection: Conda environments are only allowed with shell, script, notebook,
  or wrapper directives (not with run). #290

Fixed:

• Rule not yet defined false positive for lambdas (see #286)
• Unresolved reference for 'rule' in 'run' section (see #283)
• Doesn't automatically create folding code element for "checkpoint" (see #273)
• Multiline shell commands in anonymous rules defined in loops (see #275)
• Do not warn about missing wildcards if no SmkSL injection in string (see #266)

0.6.0.165

Version 0.6.0 build #0.6.0.165

Released on April 12th 2019

Fixed:

• 2020.1 Compatibility (see #279)
• “cache:” rule section support (see #280)