Adding snakemake to language (#11858)

* feat: snakemake language

* feat: snakemake syntax highlighting

* doc: xtask docgen - snakemake

* Addressed feedback: removed redundant grammar

* fixed indentation

* removed has-ancestor predicate

---------

Co-authored-by: “SebastianDall” <“semoda@bio.auu.dk”>

book/src/generated/lang-support.md

@@ -186,6 +186,7 @@
 | smali | ✓ |  | ✓ |  |
 | smithy | ✓ |  |  | `cs` |
 | sml | ✓ |  |  |  |
+| snakemake | ✓ |  | ✓ | `pylsp` |
 | solidity | ✓ | ✓ |  | `solc` |
 | spicedb | ✓ |  |  |  |
 | sql | ✓ | ✓ |  |  |

languages.toml

@@ -3835,3 +3835,17 @@ language-servers = ["circom-lsp"]
 [[grammar]]
 name   = "circom"
 source = { git = "https://github.com/Decurity/tree-sitter-circom", rev = "02150524228b1e6afef96949f2d6b7cc0aaf999e" }
+
+[[language]]
+name = "snakemake"
+scope = "source.snakemake"
+roots = ["Snakefile", "config.yaml", "environment.yaml", "workflow/"]
+file-types = ["smk", "Snakefile"]
+comment-tokens = ["#", "##"]
+indent = { tab-width = 2, unit = "  " }
+language-servers = ["pylsp" ]
+
+
+[[grammar]]
+name = "snakemake"
+source = { git = "https://github.com/osthomas/tree-sitter-snakemake", rev = "e909815acdbe37e69440261ebb1091ed52e1dec6" }

runtime/queries/snakemake/LICENSE

@@ -0,0 +1,20 @@
+Copyright (c) 2016 Max Brunsfeld
+Copyright (c) 2023 Oliver Thomas
+
+Permission is hereby granted, free of charge, to any person obtaining a copy of
+this software and associated documentation files (the "Software"), to deal in
+the Software without restriction, including without limitation the rights to
+use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies
+of the Software, and to permit persons to whom the Software is furnished to do
+so, subject to the following conditions:
+
+The above copyright notice and this permission notice shall be included in all
+copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+SOFTWARE.

runtime/queries/snakemake/folds.scm

@@ -0,0 +1,8 @@
+; inherits: python
+
+[
+  (rule_definition)
+  (rule_inheritance)
+  (module_definition)
+  (checkpoint_definition)
+] @fold

runtime/queries/snakemake/highlights.scm

@@ -0,0 +1,76 @@
+; inherits: python
+
+; Compound directives
+[
+  "rule"
+  "checkpoint"
+  "module"
+] @keyword
+
+; Top level directives (eg. configfile, include)
+(module
+  (directive
+    name: _ @keyword))
+
+; Subordinate directives (eg. input, output)
+((_)
+  body: (_
+    (directive
+      name: _ @label)))
+
+; rule/module/checkpoint names
+(rule_definition
+  name: (identifier) @type)
+
+(module_definition
+  name: (identifier) @type)
+
+(checkpoint_definition
+  name: (identifier) @type)
+
+; Rule imports
+(rule_import
+  "use" @keyword.import
+  "rule" @keyword.import
+  "from" @keyword.import
+  "exclude"? @keyword.import
+  "as"? @keyword.import
+  "with"? @keyword.import)
+
+; Rule inheritance
+(rule_inheritance
+  "use" @keyword
+  "rule" @keyword
+  "with" @keyword)
+
+; Wildcard names
+(wildcard (identifier) @variable)
+(wildcard (flag) @variable.parameter.builtin)
+
+; builtin variables
+((identifier) @variable.builtin
+  (#any-of? @variable.builtin "checkpoints" "config" "gather" "rules" "scatter" "workflow"))
+
+; References to directive labels in wildcard interpolations
+; the #any-of? queries are moved above the #has-ancestor? queries to
+; short-circuit the potentially expensive tree traversal, if possible
+; see:
+; https://github.com/nvim-treesitter/nvim-treesitter/pull/4302#issuecomment-1685789790
+; directive labels in wildcard context
+((wildcard
+  (identifier) @label)
+  (#any-of? @label "input" "log" "output" "params" "resources" "threads" "wildcards"))
+
+((wildcard
+  (attribute
+    object: (identifier) @label))
+  (#any-of? @label "input" "log" "output" "params" "resources" "threads" "wildcards"))
+
+((wildcard
+  (subscript
+    value: (identifier) @label))
+  (#any-of? @label "input" "log" "output" "params" "resources" "threads" "wildcards"))
+
+; directive labels in block context (eg. within 'run:')
+((identifier) @label
+  (#any-of? @label "input" "log" "output" "params" "resources" "threads" "wildcards"))

runtime/queries/snakemake/indents.scm

@@ -0,0 +1,27 @@
+; inherits: python
+
+
+[
+  (rule_definition)
+  (checkpoint_definition)
+  (rule_inheritance)
+  (module_definition)
+] @indent
+
+[
+  (rule_definition)
+  (checkpoint_definition)
+  (rule_inheritance)
+  (module_definition)
+] @extend
+
+
+(directive) @indent
+(directive) @extend
+
+(rule_import
+  "with"
+  ":") @indent
+(rule_import
+  "with"
+  ":") @extend

runtime/queries/snakemake/injections.scm

@@ -0,0 +1,5 @@
+; inherits: python
+
+(wildcard
+  (constraint) @injection.content
+  (#set! injection.language "regex"))

runtime/queries/snakemake/locals.scm

@@ -0,0 +1 @@
+; inherits: python