feat: update more keywords and highlighting #42
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📝 WalkthroughWalkthroughThis pull request refines and expands the handling of Snakemake syntax. It updates regex patterns to recognize additional keywords and parameters across multiple language configuration files, enhances syntax highlighting rules with new patterns and repository entries, and overhauls configuration schemas by introducing new sections and properties. One JSON configuration file is removed and replaced with an updated structure. These modifications streamline keyword recognition and improve the structured parsing of Snakemake constructs. Changes
Sequence Diagram(s)sequenceDiagram
participant User
participant Editor
participant Parser
participant Highlighter
User->>Editor: Types in a Snakemake file
Editor->>Parser: Triggers onEnterRules for input processing
Parser->>Parser: Applies expanded regex to match new keywords
Parser->>Highlighter: Identifies relevant syntax elements
Highlighter->>Editor: Applies enhanced syntax highlighting
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🧹 Nitpick comments (1)
languages/snakemake.json (1)
96-101: ExpandedbeforeTextRegex in OnEnterRules
The updated regular expression now contains a comprehensive list of Snakemake keywords and parameters, which should enhance the auto-indentation behavior when editing Snakefiles. However, note that several keywords (e.g.conda,singularity,container,containerized,wildcard_constraints, andname) are repeated. Although duplicate entries do not hinder functionality, removing them may simplify future maintenance.
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📒 Files selected for processing (7)
languages/snakemake.json(1 hunks)package.json(0 hunks)src/js/build_regex.js(0 hunks)src/js/keywords-regex.json(0 hunks)src/yaml/snakemake.snippets.yaml(0 hunks)src/yaml/snakemake.syntax.yaml(0 hunks)syntaxes/snakemake.tmLanguage.json(3 hunks)
💤 Files with no reviewable changes (5)
- package.json
- src/js/build_regex.js
- src/yaml/snakemake.syntax.yaml
- src/yaml/snakemake.snippets.yaml
- src/js/keywords-regex.json
🔇 Additional comments (21)
syntaxes/snakemake.tmLanguage.json (21)
9-17: Enhanced Quote Handling Patterns Added
The new inclusion entries for#quotessmall,#quotesmid, and#quotesbigin the main patterns array will help improve syntax highlighting for different quote styles. Please verify that the recursive inclusion of these patterns (e.g. including#quotessmallwithin itself) is intentional and does not adversely affect performance or cause unintended matches.
24-35: New Module and Rule Alias Patterns Introduced
The additions for#modules,#useruleas,#userulefromas, and#userulesfromextend the language support for module-related syntax and user-defined rule aliases. Ensure that these new patterns correctly capture the intended constructs without conflicting with existing rules.
39-56: Extended Rule & Module Parameters and Entity Inclusions
The new inclusions for#rulerunparams,#moduleparams,#classes,#object,#ruleargargs, and#ruleargsbroaden the scope of recognized Snakemake constructs. Their regex patterns appear well structured—please validate them against a representative sample of Snakefiles to confirm accurate highlighting.
65-97: Robust Repository Definition forquotessmall
The repository block for"quotessmall"is detailed with nested inclusions (e.g. for quotes and class/object patterns), which should enhance the handling of nested quote blocks. Keep an eye on potential performance issues arising from deep recursion in complex files.
98-130: Detailed Repository forquotesmid
The"quotesmid"block mirrors the structure of"quotessmall", ensuring consistent handling of mid-level quotes. Consider adding inline documentation if future maintenance reveals that the nested structure becomes challenging to manage.
131-163: Comprehensive Repository forquotesbig
The"quotesbig"repository entry is consistent with its smaller counterparts. Verify that the begin ("\\{") and end ("\\}") markers do not conflict with other JSON or code block patterns in the target files.
164-171: Expanded Configuration Keywords inconfigsSection
The regex in the"configs"section now covers a broader set of keywords (e.g.envvars,include,workdir, etc.). This expansion should improve detection of configuration blocks.
172-182: Rules Section Updated for Checkpoints and Rule Declarations
Restricting this section to detect onlycheckpointandrulekeywords is appropriate, especially if constructs likesubworkfloware now handled by the modules section.
183-193: Modules Section Implementation is Clear
The new"modules"block, which matches bothmoduleandsubworkflowkeywords, is a logical addition. Confirm that the capture groups yield the desired entity names in all cases.
194-210: User-Defined Rule Alias (useruleas) Pattern Introduced
The regex for matching patterns likeuse rule <name> as <alias>appears correct and enhances clarity when aliasing rules. Testing with edge cases is advised.
211-233: EnhanceduserulefromasPattern for Extended Aliasing
The new pattern coveringuse rule <rule> from <module> as <alias>improves the expressiveness of rule references. Verify that the capture groups are in the correct order to avoid misinterpretation.
234-250: ConciseuserulesfromPattern for Direct Rule Referencing
This pattern simplifies the syntax for references formatted asuse rule <rule> from <module>. It is succinct and appears well-targeted for its purpose.
251-258: Consistent Rule Parameters Capture Block
The"ruleparams"block leverages a comprehensive list of keywords to recognize rule parameters. No issues detected here.
259-266: New Runner Parameters Block (rulerunparams) Added
Incorporating keywords likerun,shell,script, etc., this block will help in correctly highlighting the execution stage of rules. Validate that these patterns do not accidentally overlap with other constructs.
267-274: Module Parameters Section Enhances Keyword Recognition
The"moduleparams"block now supports parameters such assnakefile,meta_wrapper, and others. The regex appears well-considered.
275-282: Accurate Class Names Recognition inclassesBlock
The matching forPathandWorkflowErroris clear and should suffice for current needs. Revisit if additional classes require highlighting later.
283-290: Effective Object Type Matching
The"object"block appropriately captures keywords likesnakemake,rules,workflow, etc. Testing against typical Snakefiles is recommended to ensure accuracy.
291-300: Robust Pattern for Rule Argument Attributes
The regex under"ruleargargs"uses dot notation effectively to capture variable attributes. This approach should be resilient for most use cases.
302-309: Concise Rule Arguments Matching
The"ruleargs"block captures the intended keywords for rule arguments succinctly.
310-317: Enhanced Built-in Functions Recognition
The updated list of functions (e.g.shell,github,gitlab, etc.) supports a more comprehensive syntax highlighting experience.
318-326: New Shell Block Captures Multi-line Shell Commands
The"shell_block"section, using triple quotes for delimiters, should robustly handle shell commands embedded in Snakefiles.
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Actionable comments posted: 0
🧹 Nitpick comments (2)
src/yaml/snakemake.language.yaml (1)
38-40: Enhanced onEnterRules Regex Pattern
The regex for the onEnterRules has been significantly expanded to include many additional keywords (e.g.workdir,configfile,pepfile, etc.). Please double-check that all added keywords trigger the intended action and that the pattern’s complexity does not impact performance.src/yaml/snakemake.syntax.yaml (1)
7-24: Expanded Patterns for Snakemake Syntax
The patterns array has been significantly expanded to include additional entries such as#quotessmall,#quotesmid,#quotesbig,#modules,#useruleas,#userulefromas,#userulesfrom,#rulerunparams, and#moduleparams. This comprehensive inclusion will improve recognition of various constructs.
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📒 Files selected for processing (5)
src/js/keywords-regex.json(1 hunks)src/keywords.yaml(1 hunks)src/yaml/snakemake.language.yaml(3 hunks)src/yaml/snakemake.syntax.yaml(3 hunks)syntaxes/snakemake.tmLanguage.json(3 hunks)
🔇 Additional comments (48)
src/yaml/snakemake.language.yaml (4)
2-2: Consistent Comment String Formatting
The change to using double quotes for thelineCommentvalue improves consistency with the rest of the file.
6-8: Brackets Configuration Updated
The brackets list now uses double quotes consistently. This promotes uniformity in string literals, and the entries are clear and correct.
11-13: AutoClosingPairs Consistency
The autoClosingPairs array now consistently uses double quotes and lists all expected bracket pairs along with additional language-specific pairs.
25-27: SurroundingPairs Updated
The surroundingPairs section has been updated to use consistent double quotes. This makes the configuration clearer and easier to maintain.src/js/keywords-regex.json (1)
1-12: Comprehensive Update of Keyword Regex Configuration
The JSON object now includes expanded properties such as"modules","rulerunparams","moduleparams","classes","objects", and"ruleargs". These updates align with the changes in other syntax and configuration files, improving the structured parsing of Snakemake constructs. Please verify these regex patterns capture all intended keywords as expected.src/yaml/snakemake.syntax.yaml (16)
27-67: Enhanced Repository Patterns for Quotes and Configuration
The repository section now defines detailed patterns forquotessmall,quotesmid, andquotesbig, and also includes references to#classes,#object, and rule argument patterns. Double-check that the recursive includes do not incur performance issues on large files.
68-75: Configs Syntax Pattern Validation
The regex under theconfigssection effectively uses the{{configs}}placeholder to capture a wide range of configuration keywords. Ensure that the substitution happens correctly at runtime.
76-86: Rules Pattern Update
The rules pattern correctly captures a leading keyword (eithercheckpointorrule) and optionally a rule name before the colon. This implementation is clear and maintainable.
87-97: Modules Pattern Addition
The new modules pattern for capturingmoduleandsubworkflowkeywords (optionally with a following name) is a good extension for improved syntax recognition.
98-109: Useruleas Pattern Refinement
The pattern for matching constructs like “use rule … as … with” is detailed and clearly defines capture groups for each keyword segment. Verify this pattern against real-world usage cases.
110-121: Userulesfromas Pattern Confirmation
This regex covers the case of importing rules with aliasing (including wildcards), and it appears robust.
122-131: Userulesfrom Pattern Validation
This simpler pattern for “use rule … from …” is straightforward and correctly captures the expected groups.
132-140: Rule Parameters Pattern
The use of the{{ruleparams}}placeholder in the regex for rule parameters is clear and adequately captures the increased set of keywords.
141-149: Rulerunparams Pattern Addition
The new regex for runtime parameters (rulerunparams) is well integrated and uses an intuitive capture structure.
150-157: Moduleparams Pattern Addition
The module-specific parameters now have their own regex pattern, ensuring consistency with the overall design.
158-162: Classes Pattern Definition
The classes pattern, which captures keywords like those defined in{{classes}}, is concise and effective for highlighting class names.
163-167: Objects Pattern Definition
The objects pattern correctly targets workflow objects based on the{{objects}}list, ensuring proper syntax highlighting.
168-173: Rule Argument Accessor Pattern
The pattern to capture object properties within rule arguments (e.g.x.y) is implemented clearly and should aid in detailed highlighting.
174-178: Rule Arguments Pattern Simplicity
The standalone rule arguments pattern is straightforward and effective at matching the expected tokens.
179-183: Functions Pattern Update
The functions regex now supports a larger set of built-in functions and uses a negative lookahead to avoid matching assignments. This is a strong improvement over previous versions.
184-189: Shell Block Pattern for Multi-line Commands
The newshell_blocksection clearly defines boundaries for shell commands using triple double-quotes. Please verify that the pattern handles various indentation levels and line break scenarios in actual Snakefiles.src/keywords.yaml (10)
1-24: Updated Configs List in Keywords
The configs list has been revised to include new entries such asworkdir,configfile,pepfile,pepschema,report,ruleorder, and many others. This expanded list will improve the parser’s ability to recognize all relevant configuration keywords.
25-28: Rules Section Remains Stable
The rules section still only includescheckpointandrule, which is appropriate given the current design.
29-32: New Modules Section
The addition of a modules section listingmoduleandsubworkflowis a valuable extension that aligns with the updated configuration schema.
33-67: Expanded Rule Parameters List
The ruleparams section now includes an expanded set of keywords (e.g.threads,log,message,shadow, etc.), which enhances the expressiveness of the syntax. Make sure these changes are reflected in the corresponding regex patterns used elsewhere.
68-76: New Rulerunparams Section
Introducing therulerunparamssection with values likerun,shell,script,notebook, and others provides clear categorization of runtime parameters.
77-85: New Moduleparams Section
Themoduleparamssection is now defined to capture module-specific parameters. This ensures that settings likesnakefileandmeta_wrapperare singled out for proper handling.
86-89: Classes Definition Update
The new classes list (Path,WorkflowError) improves clarity for class-based constructs in Snakemake and is consistent with changes across the project.
90-99: Enhanced Objects List
The objects section now covers a broader set of workflow-related terms such assnakemake,rules,workflow, etc., which will support more precise syntax highlighting.
100-109: Rule Arguments Definition
The ruleargs section is clear and well-organized, listing necessary elements likeinput,output,params, etc., and supporting proper parsing of rule-related properties.
110-144: Expanded Functions List
The functions section now includes many additional entries such asgithub,gitlab,gitfile,from_queue,glob_wildcards, and more. This significantly improves the coverage of built-in functions and utilities in Snakemake.syntaxes/snakemake.tmLanguage.json (17)
9-63: Enhanced Patterns Array in tmLanguage JSON
The main patterns array now includes additional entries for advanced constructs (e.g.#quotessmall,#quotesmid,#quotesbig,#modules,#useruleas,#userulefromas,#userulesfrom,#rulerunparams,#moduleparams,#classes,#object,#ruleargargs, and#ruleargs). This expansion offers granular control over syntax highlighting and is consistent with other configuration updates.
64-163: Detailed Repository Entries for Quotes and Classes
The repository section now clearly defines nested patterns forquotessmall,quotesmid, andquotesbig, including multiple levels of includes (e.g. references to#classes,#object, etc.). Please verify that the nested structure does not negatively impact editor performance for large files.
164-171: Updated Configs Regex in Repository
Theconfigsrepository entry now uses an expanded regex that captures an extended list of configuration keywords. Make sure the regex remains readable and maintainable as changes continue.
172-182: Rules Regex in Repository
The rules entry regex correctly captures the leading whitespace, the keyword (eithercheckpointorrule), and an optional rule name. This is a clear and concise implementation.
183-193: Modules Regex Update
The addition of the modules regex for capturingmoduleandsubworkflowkeywords is effective and consistent with the changes in the YAML configuration.
194-213: Useruleas Repository Entry Check
The regex for theuseruleasentry, which matches the “use rule … as … with” construct, is detailed and well segmented. Testing with real examples is recommended.
214-236: Userulesfromas Repository Entry
The repository entry foruserulesfromaseffectively captures the more complex pattern of importing rules with aliasing and wildcards.
237-253: Userulesfrom Repository Entry
This simpler pattern for “use rule … from …” is straightforward and correctly implemented.
254-261: Ruleparams Repository Regex
The ruleparams regex entry now accommodates a comprehensive list of keywords. Ensure that this list remains in sync with the definitions in the YAML configuration.
262-269: Rulerunparams Repository Regex
The new rulerunparams entry accurately captures runtime parameters. Its structure is consistent with the YAML changes.
270-277: Moduleparams Repository Regex
The moduleparams repository entry is correctly implemented to capture module-specific parameters.
278-285: Classes Regex in Repository
The regex forclassesneatly matches the provided keywords (e.g.PathandWorkflowError) and uses a negative lookahead to avoid assignment conflicts.
286-293: Objects Repository Regex
The objects regex captures the intended workflow-related terms and is consistent with the overall design.
294-304: Ruleargargs Repository Regex
The pattern for capturing property access within rule arguments (e.g.input.foo) is implemented clearly and will aid in granular highlighting.
305-312: Ruleargs Repository Regex
This regex matches rule arguments without dot notation in a straightforward manner. No issues detected.
313-320: Functions Repository Regex Update
The updated functions regex includes a broader set of built-in function names and uses a negative lookahead to avoid misclassification. This is a solid improvement.
321-329: Shell Block Repository Regex
The shell_block entry clearly defines a start and end for multi-line shell command blocks using triple double-quotes. Please test with various indentation and formatting scenarios to ensure robustness.
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This will allow snakefile more colorful in vscode
However, when things exists in function calls, it will just lost it's color...
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