feat: update more keywords and highlighting (#42)

* feat: update more keywords and highlighting

* try my best to make params colored in function calls

* fix: drop duplicates

* feat: update upstream yaml as debugger do

Author: Hocnonsense

languages/snakemake.json

@@ -94,7 +94,7 @@
   ],
   "onEnterRules": [
     {
-      "beforeText": "\\s*(?:(?:rule|subworkflow|checkpoint|async|class|def|elif|except|for|if|while|with)\\s.*|(?:input|output|params|priority|shadow|group|log|benchmark|message|threads|resources|version|run|shell|script|cwl|container|shellcmd|name|norun|conda_env|container_img|containerized|is_containerized|env_modules|shadow_depth|docstring|notebook|template_engine|cache|path_modifier|handover|default_target|localrule|pepfile|pepschema|conda|singularity|wildcard_constraints|wrapper|else|finally|try))\\s*:\\s*(?:#.*)?$",
+      "beforeText": "\\s*(?:(?:checkpoint|rule|module|subworkflow|async|class|def|elif|except|for|if|while|with)\\s.*|(?:envvars|include|workdir|configfile|pepfile|pepschema|report|ruleorder|localrules|onsuccess|onerror|onstart|wildcard_constraints|singularity|container|containerized|conda|scattergather|inputflags|outputflags|storage|resource_scopes|name|input|output|params|threads|resources|retries|priority|log|message|benchmark|envmodules|shadow|group|cache|handover|default_target|localrule|version|run|shell|script|notebook|wrapper|template_engine|cwl|snakefile|meta_wrapper|config|skip_validation|replace_prefix|prefix|else|finally|try))\\s*:\\s*(?:#.*)?$",
       "action": {
         "indent": "indent"
       }

src/js/keywords-regex.json

@@ -1,6 +1,12 @@
 {
-    "configs": "configfile|envvars|module|scattergather|include|localrules|onerror|onstart|onsuccess|ruleorder|snakefile|workdir|container|containerized|pepfile|pepschema",
-    "rules": "checkpoint|rule|subworkflow",
-    "ruleparams": "benchmark|conda|cwl|container|pepfile|pepschema|shellcmd|name|norun|conda_env|container_img|is_containerized|env_modules|shadow_depth|docstring|notebook|template_engine|cache|path_modifier|handover|default_target|localrule|group|input|log|message|notebook|output|params|priority|resources|run|script|shadow|shell|singularity|threads|version|wildcard_constraints|wrapper|default_target|handover|container|containerized|retries",
-    "functions": "ancient|directory|expand|pipe|protected|report|temp|touch|unpack"
-}
+    "configs": "envvars|include|workdir|configfile|pepfile|pepschema|report|ruleorder|localrules|onsuccess|onerror|onstart|wildcard_constraints|singularity|container|containerized|conda|scattergather|inputflags|outputflags|storage|resource_scopes",
+    "rules": "checkpoint|rule",
+    "modules": "module|subworkflow",
+    "ruleparams": "name|input|output|params|threads|resources|retries|priority|log|message|benchmark|conda|singularity|container|containerized|envmodules|wildcard_constraints|shadow|group|cache|handover|default_target|localrule|version|container_img|is_containerized|shellcmd|norun|conda_env|env_modules|shadow_depth|docstring|path_modifier",
+    "rulerunparams": "run|shell|script|notebook|wrapper|template_engine|cwl",
+    "moduleparams": "name|snakefile|meta_wrapper|config|skip_validation|replace_prefix|prefix",
+    "classes": "Path|WorkflowError",
+    "objects": "snakemake|rules|workflow|checkpoints|storage|access|scatter|gather",
+    "ruleargs": "input|output|params|wildcards|threads|resources|log|config",
+    "functions": "shell|github|gitlab|gitfile|from_queue|protected|temp|temporary|ancient|directory|expand|glob_wildcards|flag|touch|unpack|local|pipe|service|repeat|report|multiext|ensure|update|before_update|lookup|evaluate|branch|collect|exists|subpath|parse_input|extract_checksum|flatten"
+}

src/keywords.yaml

@@ -1,81 +1,143 @@
 configs:
-  - configfile
+  - envvars
   - include
+  - workdir
+  - configfile
+  - pepfile
+  - pepschema
+  - report
+  - ruleorder
   - localrules
+  - onsuccess
   - onerror
   - onstart
-  - onsuccess
-  - ruleorder
-  - scattergather
-  - snakefile
-  - workdir
-  - envvars
-  - module
+  - wildcard_constraints
+  - singularity
+  - container
   - containerized
-  - pepfile
-  - pepschema
+  - conda
+  - scattergather
+  - inputflags
+  - outputflags
+  - storage
+  - resource_scopes
 
 rules:
   - checkpoint
   - rule
+
+modules:
+  - module
   - subworkflow
 
 ruleparams:
-  - benchmark
-  - conda
-  - container
-  - cwl
-  - group
+  - name
   - input
-  - log
-  - message
-  - notebook
   - output
   - params
-  - priority
+  - threads
   - resources
   - retries
-  - run
-  - script
-  - shadow
-  - shell
+  - priority
+  - log
+  - message
+  - benchmark
+  - conda
   - singularity
-  - threads
-  - version
-  - wildcard_constraints
-  - wrapper
-  - default_target
-  - pepfile
-  - pepschema
-  - template_engine
-  - handover
   - container
   - containerized
+  - envmodules
+  - wildcard_constraints
+  - shadow
+  - group
+  - cache
+  - handover
+  - default_target
+  - localrule
+  - version
+  - container_img
+  - is_containerized
   - shellcmd
-  - name
   - norun
   - conda_env
-  - container_img
-  - is_containerized
   - env_modules
   - shadow_depth
   - docstring
-  - notebook
-  - template_engine
-  - cache
   - path_modifier
-  - handover
-  - default_target
-  - localrule
+
+rulerunparams:
+  - run
+  - shell
+  - script
+  - notebook
+  - wrapper
   - template_engine
+  - cwl
+
+moduleparams:
+  - name
+  - snakefile
+  - meta_wrapper
+  - config
+  - skip_validation
+  - replace_prefix
+  - prefix
+
+classes:
+  - Path
+  - WorkflowError
+
+objects:
+  - snakemake
+  - rules
+  - workflow
+  - checkpoints
+  - storage
+  - access
+  - scatter
+  - gather
+
+ruleargs:
+  - input
+  - output
+  - params
+  - wildcards
+  - threads
+  - resources
+  - log
+  - config
 
 functions:
+  - shell
+  - github
+  - gitlab
+  - gitfile
+  - from_queue
+  - protected
+  - temp
+  - temporary
   - ancient
   - directory
   - expand
-  - pipe
-  - protected
-  - temp
+  - glob_wildcards
+  - flag
   - touch
   - unpack
+  - local
+  - pipe
+  - service
+  - repeat
   - report
+  - multiext
+  - ensure
+  - update
+  - before_update
+  - lookup
+  - evaluate
+  - branch
+  - collect
+  - exists
+  - subpath
+  - parse_input
+  - extract_checksum
+  - flatten

src/yaml/snakemake.language.yaml

@@ -1,16 +1,16 @@
 comments:
-  lineComment: '#'
+  lineComment: "#"
   blockComment: ['"""', '"""']
 
 brackets:
-  - ['{', '}']
-  - ['[', ']']
-  - ['(', ')']
+  - ["{", "}"]
+  - ["[", "]"]
+  - ["(", ")"]
 
 autoClosingPairs:
-  - ['{', '}']
-  - ['[', ']']
-  - ['(', ')']
+  - ["{", "}"]
+  - ["[", "]"]
+  - ["(", ")"]
   - ['"""', '"""']
   - ['"', '"']
   - ['r"', '"']
@@ -22,9 +22,9 @@ autoClosingPairs:
   - ["b'", "'"]
 
 surroundingPairs:
-  - ['{', '}']
-  - ['[', ']']
-  - ['(', ')']
+  - ["{", "}"]
+  - ["[", "]"]
+  - ["(", ")"]
   - ['"', '"']
   - ["'", "'"]
 
@@ -36,9 +36,7 @@ surroundingPairs:
 #   decreaseIndentPattern: ^\s*(?:else|finally|(?:elif|except)\b.*)\s*:\s*(#.*)?$
 
 onEnterRules:
-  - beforeText: >-
-    \s*(?:(?:rule|subworkflow|checkpoint|async|class|def|elif|except|for|if|while|with)\s.*|(?:input|output|params|priority|shadow|group|log|benchmark|message|threads|resources|version|run|shell|script|cwl|conda|singularity|pepfile|pepschema|container|shellcmd|name|norun|conda_env|container_img|containerized|is_containerized|env_modules|shadow_depth|docstring|notebook|template_engine|cache|path_modifier|handover|default_target|localrule|wildcard_constraints|wrapper|else|finally|try))\s*:\s*(?:#.*)?$
+  - beforeText: \s*(?:(?:checkpoint|rule|module|subworkflow|async|class|def|elif|except|for|if|while|with)\s.*|(?:envvars|include|workdir|configfile|pepfile|pepschema|report|ruleorder|localrules|onsuccess|onerror|onstart|wildcard_constraints|singularity|container|containerized|conda|scattergather|inputflags|outputflags|storage|resource_scopes|name|input|output|params|threads|resources|retries|priority|log|message|benchmark|envmodules|shadow|group|cache|handover|default_target|localrule|version|run|shell|script|notebook|wrapper|template_engine|cwl|snakefile|meta_wrapper|config|skip_validation|replace_prefix|prefix|else|finally|try))\s*:\s*(?:#.*)?$
 
     action:
-
       indent: indent