fix: 1) improved behaviour for Unresolved reference 'snakemake' #511 …

…2) also inject snakemake in #553

CHANGELOG.md

@@ -23,6 +23,7 @@ Released on <not released>
 - Improve parser error message when rule/module is declared with name but lacks ':' (see [#515](https://github.com/JetBrains-Research/snakecharm/issues/515))
 - Support for `update` and `before_update` flags. Update inspection that warns if flag functions from `snakemake.io` is used in a wrong section, added info for all flags up to 8.23.1 version (see [#537](https://github.com/JetBrains-Research/snakecharm/issues/537))
 - Inject some modules in Snakefile file resolve scope w/o import declaration, e.g. os, sys,.. (see [#553](https://github.com/JetBrains-Research/snakecharm/issues/553)
+- Do not warn about unresolved `snakemake` variable in the python files, because they could be used as scripts/wrappers for snakemake rules.  (see [#511](https://github.com/JetBrains-Research/snakecharm/issues/511))
 
 ### Changed
 - TODO

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/SmkImplicitPySymbolsProvider.kt

@@ -126,7 +126,7 @@ class SmkImplicitPySymbolsProvider(
         ///////////////////////////////////////
         // Implicit requires: e.g. 'os', 'sys'
         val resolveContext = fromSdk(project, sdk)
-        listOf("os", "sys").forEach { moduleName ->
+        listOf("os", "sys", "snakemake").forEach { moduleName ->
             var module = resolveQualifiedName(QualifiedName.fromDottedString(moduleName), resolveContext).filterIsInstance<PyFile>().firstOrNull()
             if (module == null) {
                 module =

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/SmkTypeProvider.kt

@@ -214,7 +214,7 @@ class SmkTypeProvider : PyTypeProviderBase() {
                     pepFile?.findTopLevelClass("Project")?.getType(TypeEvalContext.codeCompletion(project, pepFile))
                 }
             }
-
+            // TODO: TYPE FOR 'snakemake' var in run section & python scripts
             else -> null
         }
     }

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/resolve/SmkImplicitPySymbolsResolveProvider.kt

@@ -1,6 +1,7 @@
 package com.jetbrains.snakecharm.codeInsight.resolve
 
 import com.intellij.psi.util.PsiTreeUtil
+import com.jetbrains.python.PythonLanguage
 import com.jetbrains.python.psi.PyQualifiedExpression
 import com.jetbrains.python.psi.resolve.PyReferenceResolveProvider
 import com.jetbrains.python.psi.resolve.RatedResolveResult
@@ -10,10 +11,12 @@ import com.jetbrains.snakecharm.codeInsight.SmkCodeInsightScope
 import com.jetbrains.snakecharm.codeInsight.SmkImplicitPySymbolsProvider
 import com.jetbrains.snakecharm.codeInsight.resolve.SmkImplicitPySymbolsResolveProviderCompanion.addSyntheticSymbols
 import com.jetbrains.snakecharm.codeInsight.resolve.SmkResolveUtil.RATE_IMPLICIT_SYMBOLS
+import com.jetbrains.snakecharm.framework.SmkSupportProjectSettings
 import com.jetbrains.snakecharm.lang.SnakemakeLanguageDialect
 import com.jetbrains.snakecharm.lang.SnakemakeNames.RUN_SECTION_VARIABLE_JOBID
 import com.jetbrains.snakecharm.lang.SnakemakeNames.RUN_SECTION_VARIABLE_RULE
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SECTION_THREADS
+import com.jetbrains.snakecharm.lang.SnakemakeNames.SMK_VARS_SNAKEMAKE
 import com.jetbrains.snakecharm.lang.SnakemakeNames.SMK_VARS_WILDCARDS
 import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpoint
 
@@ -22,6 +25,20 @@ class SmkImplicitPySymbolsResolveProvider : PyReferenceResolveProvider {
         element: PyQualifiedExpression,
         context: TypeEvalContext,
     ): List<RatedResolveResult> {
+        if (!SmkSupportProjectSettings.getInstance(element.project).snakemakeSupportEnabled) {
+            return emptyList()
+        }
+
+        if (context.origin?.language == PythonLanguage.getInstance()) {
+            // only ignore `snakemake`
+            @Suppress("UnstableApiUsage") val referencedName = element.referencedName
+
+            val items = mutableListOf<RatedResolveResult>()
+            if (referencedName == SMK_VARS_SNAKEMAKE) {
+                items.add(RatedResolveResult(RATE_IMPLICIT_SYMBOLS, null))
+            }
+            return items
+        }
         if (SnakemakeLanguageDialect.isInsideSmkFile(context.origin)) {
 
             val contextScope = SmkCodeInsightScope[element]

src/main/kotlin/com/jetbrains/snakecharm/lang/SnakemakeNames.kt

@@ -79,6 +79,7 @@ object SnakemakeNames {
     const val UNPACK_FUNCTION = "unpack"
 
     // TODO: move to YAML api
+    const val SMK_VARS_SNAKEMAKE = "snakemake"
     const val SMK_VARS_WORKFLOW = "workflow"
     const val SMK_VARS_CONFIG = "config"
     const val SMK_VARS_CLUSTER_ONFIG = "cluster_config" // TODO seems removed in 8.x

src/test/resources/features/completion/implicit_py_symbols_completion.feature

@@ -44,9 +44,10 @@ Feature: Completion in python part of snakemake file
     When I put the caret after foo = 1;
     And I invoke autocompletion popup
     Then completion list should contain:
-      | os   |
-      | sys  |
-      | Path |
+      | os        |
+      | sys       |
+      | snakemake |
+      | Path      |
 
   Scenario: Complete at top-level (GTE 6.1)
     Given a snakemake:6.1 project

src/test/resources/features/resolve/implicit_py_symbols_resolve.feature

@@ -91,10 +91,11 @@ Feature: Resolve implicitly imported python names
     Then reference should resolve to "<symbol_name>" in "<file>"
 
     Examples:
-      | ptn | text | symbol_name | file            |
-      | os  | os   | [SKIP]      | os/__init__.pyi |
-      | sy  | sys  | [SKIP]      | sys.py          |
-      | Pat | Path | Path        | pathlib.pyi     |
+      | ptn | text      | symbol_name | file                  |
+      | os  | os        | [SKIP]      | os/__init__.pyi       |
+      | sy  | sys       | [SKIP]      | sys.py                |
+      | sn  | snakemake | [SKIP]      | snakemake/__init__.py |
+      | Pat | Path      | Path        | pathlib.pyi           |
 
   Scenario: Resolve at top-level: shell()
     Given a snakemake project
@@ -422,3 +423,19 @@ Feature: Resolve implicitly imported python names
       | rule       | input   | checkpoints |
       | rule       | input   | config      |
       | checkpoint | input   | rules       |
+
+  Scenario: Warn about unresolved snakemake variable in run section, behaviour differs from scripts
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+     """
+     rule a:
+         run:
+             # this becomes too much and should be migrated into a script directive
+             path = snakemake.input[0]
+     """
+    And PyUnresolvedReferencesInspection inspection is enabled
+    Then I expect inspection warning on <input> with message
+      """
+      Cannot find reference 'input' in '__init__.py'
+      """
+    When I check highlighting warnings

src/test/resources/features/resolve/py_code_resolve.feature

@@ -8,3 +8,14 @@ Feature: Resolve in python part of snakemake file
     """
     When I put the caret at repr
     Then reference should resolve to "repr" in "builtins.pyi"
+
+
+  Scenario: Do not warn about unresolved snakemake variable in python scripts and wrappers
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+     """
+     assert snakemake.input.get("sort", "missing") == "missing"
+     """
+    And PyUnresolvedReferencesInspection inspection is enabled
+    Then I expect no inspection errors
+    When I check highlighting errors