feat: Support for Global workflow dependencies [8.0.0] syntax

Closes: #555
JetBrains-Research · Oct 22, 2024 · af1ccb1 · af1ccb1
1 parent be21e25
commit af1ccb1
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Showing 10 changed files with 47 additions and 19 deletions.
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -14,6 +14,7 @@ Released on <not released>
 - Code completion: For section keywords show 'since' version and deprecation notice in the completion list. Do not suggest already removed keywords (see [#535](https://github.com/JetBrains-Research/snakecharm/issues/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](https://github.com/JetBrains-Research/snakecharm/issues/548)
+- [8.0.0] Support for Global workflow dependencies [8.0.0] syntax (see [#555](https://github.com/JetBrains-Research/snakecharm/issues/555)
 - [8.0.0-6.8.1] Support for: 'storage', 'github', 'gitfile', 'gitlab' (see [#550](https://github.com/JetBrains-Research/snakecharm/issues/550)
 - [7.25.0] Support for localrule directive (see [#524](https://github.com/JetBrains-Research/snakecharm/issues/524)
 - [7.11] Resource scopes support (see [#510](https://github.com/JetBrains-Research/snakecharm/issues/510)

diff --git a/snakemake_api.yaml b/snakemake_api.yaml
@@ -90,6 +90,13 @@ changelog:
 
  # ---------------------------------------
   - version: "8.0.0"
+    introduced:
+      - name: "conda"
+        type: "top-level"
+        docs_url: https://snakemake.readthedocs.io/en/stable/snakefiles/deployment.html#global-workflow-dependencies
+        multiple_args_allowed: False
+        keyword_args_allowed: False
+
     removed:
       - name: "snakemake.io.dynamic"
         type: "function"

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/codeInsight/SnakemakeApi.kt b/src/main/kotlin/com/jetbrains/snakecharm/codeInsight/SnakemakeApi.kt
@@ -31,6 +31,7 @@ import com.jetbrains.snakecharm.lang.SnakemakeNames.SMK_VARS_WILDCARDS
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SMK_WITH_KEYWORD
 import com.jetbrains.snakecharm.lang.SnakemakeNames.USE_EXCLUDE_KEYWORD
 import com.jetbrains.snakecharm.lang.SnakemakeNames.USE_KEYWORD
+import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONDA_KEYWORD
 import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONFIGFILE_KEYWORD
 import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONTAINERIZED_KEYWORD
 import com.jetbrains.snakecharm.lang.SnakemakeNames.WORKFLOW_CONTAINER_KEYWORD
@@ -108,7 +109,19 @@ object SnakemakeApi {
         WORKFLOW_PEPSCHEMA_KEYWORD,
         WORKFLOW_PEPFILE_KEYWORD,
         WORKFLOW_RESOURCE_SCOPES_KEYWORD,
-        WORKFLOW_SCATTERGATHER_KEYWORD
+        WORKFLOW_SCATTERGATHER_KEYWORD,
+        WORKFLOW_CONDA_KEYWORD
+    )
+
+    // TODO Move to YAML
+    val WORKFLOW_SECTIONS_WITH_FILE_REFERENCES = setOf(
+        WORKFLOW_CONFIGFILE_KEYWORD,
+        WORKFLOW_PEPFILE_KEYWORD,
+        WORKFLOW_PEPSCHEMA_KEYWORD,
+        WORKFLOW_INCLUDE_KEYWORD,
+        WORKFLOW_REPORT_KEYWORD,
+        WORKFLOW_WORKDIR_KEYWORD,
+        WORKFLOW_CONDA_KEYWORD
     )
 
     /**

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/lang/SnakemakeNames.kt b/src/main/kotlin/com/jetbrains/snakecharm/lang/SnakemakeNames.kt
@@ -28,6 +28,7 @@ object SnakemakeNames {
     const val WORKFLOW_CONTAINERIZED_KEYWORD = "containerized"  // => 6.0.0
     const val WORKFLOW_RESOURCE_SCOPES_KEYWORD = "resource_scopes"  // => 7.11
     const val WORKFLOW_SCATTERGATHER_KEYWORD = "scattergather"  // => 7.11
+    const val WORKFLOW_CONDA_KEYWORD = "conda"  // => 8.0.0
 
     const val SUBWORKFLOW_KEYWORD = "subworkflow"
     const val SUBWORKFLOW_WORKDIR_KEYWORD = WORKFLOW_WORKDIR_KEYWORD

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/SmkFileReference.kt b/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/SmkFileReference.kt
@@ -281,7 +281,7 @@ class SmkPepschemaReference(
 
 /**
  * The path must built from directory with current snakefile
- * version 6.5.1
+ * version 6.5.1 (rule) + 8.0.0 (workfklow)
  */
 class SmkCondaEnvReference(
     element: SmkArgsSection,

diff --git a/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowArgsSectionImpl.kt b/src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/SmkWorkflowArgsSectionImpl.kt
@@ -6,6 +6,7 @@ import com.intellij.util.ArrayUtil
 import com.jetbrains.python.psi.PyElementVisitor
 import com.jetbrains.python.psi.PyStringLiteralExpression
 import com.jetbrains.python.psi.impl.PyElementImpl
+import com.jetbrains.snakecharm.codeInsight.SnakemakeApi.WORKFLOW_SECTIONS_WITH_FILE_REFERENCES
 import com.jetbrains.snakecharm.lang.SnakemakeNames
 import com.jetbrains.snakecharm.lang.parser.SmkTokenTypes
 import com.jetbrains.snakecharm.lang.psi.*
@@ -15,16 +16,6 @@ import com.jetbrains.snakecharm.lang.psi.*
  * @date 2019-02-03
  */
 class SmkWorkflowArgsSectionImpl(node: ASTNode) : PyElementImpl(node), SmkWorkflowArgsSection {
-    companion object {
-        val WORKFLOWS_WITH_FILE_REFERENCES = setOf(
-            SnakemakeNames.WORKFLOW_CONFIGFILE_KEYWORD,
-            SnakemakeNames.WORKFLOW_PEPFILE_KEYWORD,
-            SnakemakeNames.WORKFLOW_PEPSCHEMA_KEYWORD,
-            SnakemakeNames.WORKFLOW_INCLUDE_KEYWORD,
-            SnakemakeNames.WORKFLOW_REPORT_KEYWORD,
-            SnakemakeNames.WORKFLOW_WORKDIR_KEYWORD
-        )
-    }
 
     override fun acceptPyVisitor(pyVisitor: PyElementVisitor) = when (pyVisitor) {
         is SmkElementVisitor -> pyVisitor.visitSmkWorkflowArgsSection(this)
@@ -58,6 +49,9 @@ class SmkWorkflowArgsSectionImpl(node: ASTNode) : PyElementImpl(node), SmkWorkfl
             SnakemakeNames.WORKFLOW_WORKDIR_KEYWORD -> SmkWorkDirReference(
                 this, textRange, strExpr, path
             )
+            SnakemakeNames.WORKFLOW_CONDA_KEYWORD -> SmkCondaEnvReference(
+                this, textRange, strExpr, path
+            )
             else -> SmkIncludeReference(
                 this, textRange, strExpr, path
             )
@@ -67,7 +61,7 @@ class SmkWorkflowArgsSectionImpl(node: ASTNode) : PyElementImpl(node), SmkWorkfl
     override fun getReference(): PsiReference? = ArrayUtil.getFirstElement(this.references)
 
     override fun getReferences(): Array<PsiReference> {
-        if (keywordName !in WORKFLOWS_WITH_FILE_REFERENCES) {
+        if (keywordName !in WORKFLOW_SECTIONS_WITH_FILE_REFERENCES) {
             return emptyArray()
         }
 

diff --git a/src/test/resources/features/completion/keywords_completion.feature b/src/test/resources/features/completion/keywords_completion.feature
@@ -27,6 +27,7 @@ Feature: Completion for snakemake keyword-like things
       | pepfile              |
       | pepschema            |
       | resource_scopes      |
+      | conda                |
 
   Scenario Outline: Complete at top-level with respect to deprecations
     Given a snakemake project

diff --git a/src/test/resources/features/completion/path_in_workflow_sections_completion.feature b/src/test/resources/features/completion/path_in_workflow_sections_completion.feature
@@ -25,6 +25,7 @@ Feature: Complete file names in workflow sections
       | report     | html      |
       | pepfile    | yaml      |
       | pepschema  | yaml      |
+      | conda      | yaml      |
 
   Scenario: Completion list for directories in 'workdir' section
     Given a snakemake project
@@ -96,7 +97,8 @@ Feature: Complete file names in workflow sections
       | configfile | yml       |
       | report     | html      |
       | pepfile    | yaml      |
-      | pepschema   | yml       |
+      | pepschema  | yml       |
+      | config     | yaml      |
 
   Scenario: Completion list in 'workdir' section when there are no appropriate directories
     Given a snakemake project

diff --git a/src/test/resources/features/refactoring/rename_path_in_workflow_sections.feature b/src/test/resources/features/refactoring/rename_path_in_workflow_sections.feature
@@ -45,6 +45,7 @@ Feature: Rename files in workflow sections
       | section    | file_type |
       | include    | smk       |
       | configfile | yaml      |
+      | conda      | yaml      |
       | configfile | yml       |
       | report     | html      |
 
@@ -63,20 +64,25 @@ Feature: Rename files in workflow sections
     """
     And reference should resolve to "Folder" directory
 
-  Scenario: Rename for directories in 'workdir' section
+  Scenario Outline: Rename for directories in 'workdir/conda' section
     Given a snakemake project
     Given a directory "Dir"
     Given I open a file "foo.smk" with text
     """
-    workdir: "Dir"
+    <section>: "Dir"
     """
     When I put the caret after Dir
     When I invoke rename with name "Folder"
     Then the file "foo.smk" should have text
     """
-    workdir: "Folder"
+    <section>: "Folder"
     """
     And reference should resolve to "Folder" directory
+    Examples:
+      | section |
+      | workdir |
+      | conda   |
+
 
   Scenario Outline: Rename in conda/scripts/etc section
     Given a snakemake project

diff --git a/src/test/resources/features/resolve/workflow_file_resolve.feature b/src/test/resources/features/resolve/workflow_file_resolve.feature
@@ -19,6 +19,7 @@ Feature: Resolve workflow file names to their corresponding files
       | report     | html      |
       | pepfile    | yaml      |
       | pepschema  | yml       |
+      | conda      | yaml      |
 
   Scenario Outline: Reference doesn't resolve to inappropriate file
     Given a snakemake project
@@ -37,7 +38,8 @@ Feature: Resolve workflow file names to their corresponding files
       | configfile | yaml      |
       | report     | html      |
       | pepfile    | yaml      |
-      | pepschema   | yml       |
+      | pepschema  | yml       |
+      | conda      | yaml      |
 
   Scenario: Reference doesn't resolve to inappropriate Directory
     Given a snakemake project
@@ -67,7 +69,8 @@ Feature: Resolve workflow file names to their corresponding files
       | configfile | yaml      |
       | report     | html      |
       | pepfile    | yaml      |
-      | pepschema   | yml       |
+      | pepschema  | yml       |
+      | conda      | yaml      |
 
   Scenario Outline: Resolve for multiple files
     Given a snakemake project