feat: Inject some modules in Snakefile file resolve scope w/o import …

…declaration, e.g. os, sys,..

Closes #553

CHANGELOG.md

@@ -22,6 +22,7 @@ Released on <not released>
 ### Fixed
 - 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)
 
 ### Changed
 - TODO

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

@@ -19,6 +19,7 @@ import com.intellij.openapi.vfs.VirtualFile
 import com.intellij.psi.PsiElement
 import com.intellij.psi.impl.source.resolve.ResolveCache
 import com.intellij.psi.util.QualifiedName
+import com.intellij.util.PlatformIcons
 import com.intellij.util.SlowOperations
 import com.jetbrains.python.extensions.inherits
 import com.jetbrains.python.packaging.PyPackage
@@ -122,6 +123,49 @@ class SmkImplicitPySymbolsProvider(
         val elementsCache = ArrayList<ImplicitPySymbol>()
         val syntheticElementsCache = ArrayList<Pair<SmkCodeInsightScope, LookupElement>>()
 
+        ///////////////////////////////////////
+        // Implicit requires: e.g. 'os', 'sys'
+        val resolveContext = fromSdk(project, sdk)
+        listOf("os", "sys").forEach { moduleName ->
+            var module = resolveQualifiedName(QualifiedName.fromDottedString(moduleName), resolveContext).filterIsInstance<PyFile>().firstOrNull()
+            if (module == null) {
+                module =
+                    resolveQualifiedName(QualifiedName.fromDottedString("${moduleName}.__init__"), resolveContext).filterIsInstance<PyFile>()
+                        .firstOrNull()
+            }
+            if (module != null) {
+                usedFiles.add(module.virtualFile)
+
+                syntheticElementsCache.add(
+                    SmkCodeInsightScope.TOP_LEVEL to SmkCompletionUtil.createPrioritizedLookupElement(
+                        moduleName,
+                        module,
+                        icon = PlatformIcons.VARIABLE_ICON,
+                        typeText = moduleName,
+                        priority = SmkCompletionUtil.WORKFLOW_GLOBALS_PRIORITY
+                    )
+                )
+            }
+        }
+        // Add 'Path' from pathlib
+        listOf("pathlib.Path").forEach() { fqn ->
+            val qualifiedName = QualifiedName.fromDottedString(fqn)
+            val pyClass = resolveTopLevelMember(qualifiedName, resolveContext) as? PyClass
+            if (pyClass != null) {
+                usedFiles.add(pyClass.containingFile.virtualFile)
+
+                syntheticElementsCache.add(
+                    SmkCodeInsightScope.TOP_LEVEL to SmkCompletionUtil.createPrioritizedLookupElement(
+                        qualifiedName.lastComponent.toString(),
+                        pyClass,
+                        icon = PlatformIcons.CLASS_ICON,
+                        typeText = fqn,
+                        priority = SmkCompletionUtil.WORKFLOW_GLOBALS_PRIORITY
+                    )
+                )
+            }
+        }
+
         ///////////////////////////////////////
         // E.g. rules, config, ... defined in Workflow code as global variables
 
@@ -485,6 +529,7 @@ class SmkImplicitPySymbolsProvider(
         classFQN.forEach { fqn ->
             val pyElement = resolveTopLevelMember(QualifiedName.fromDottedString(fqn), resolveContext)
             if (pyElement is PyClass) {
+                usedFiles.add(pyElement.containingFile.virtualFile)
                 processor(pyElement)
             }
         }

src/test/kotlin/features/glue/CompletionResolveSteps.kt

@@ -134,7 +134,7 @@ class CompletionResolveSteps {
         }
     }
 
-    @Then("^reference should resolve to \"(.+)\" in \"(.+)\"$")
+    @Then("^reference should resolve to \"(.+|[SKIP])\" in \"(.+)\"$")
     fun referenceShouldResolveToIn(targetPrefix: String, file: String) {
         DumbService.getInstance(SnakemakeWorld.fixture().project).waitForSmartMode()
         ApplicationManager.getApplication().runReadAction {
@@ -180,19 +180,21 @@ class CompletionResolveSteps {
         )
         assertEquals(file, actualSubString, msg)
 
-        assertTrue(
-            targetPrefix.length <= result.textLength,
-            "Expected result prefix <$targetPrefix> is longer than element <${result.text}>\n$msg"
-        )
+        if (targetPrefix != "[SKIP]") {
+            assertTrue(
+                targetPrefix.length <= result.textLength,
+                "Expected result prefix <$targetPrefix> is longer than element <${result.text}>\n$msg"
+            )
 
-        val elementText = TextRange.from(result.textOffset, targetPrefix.length).substring(result.containingFile.text)
+            val elementText =
+                TextRange.from(result.textOffset, targetPrefix.length).substring(result.containingFile.text)
 //        val elementText = TextRange.from(0, targetPrefix.length).substring(result.text)
-        assertEquals(targetPrefix, elementText, msg)
-
-        val text =
-            TextRange.from(injectionStartOffset + result.textOffset, context.length).substring(containingFile.text)
-        assertEquals(context, text, msg)
+            assertEquals(targetPrefix, elementText, msg)
 
+            val text =
+                TextRange.from(injectionStartOffset + result.textOffset, context.length).substring(containingFile.text)
+            assertEquals(context, text, msg)
+        }
     }
 
     @Then("^reference in injection should multi resolve to name, file in same order$")

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

@@ -35,6 +35,19 @@ Feature: Completion in python part of snakemake file
       | gitlab        |
       | gitfile       |
 
+  Scenario: Complete imported python modules/classes at top-level
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+    """
+    foo = 1;
+    """
+    When I put the caret after foo = 1;
+    And I invoke autocompletion popup
+    Then completion list should contain:
+      | os   |
+      | sys  |
+      | Path |
+
   Scenario: Complete at top-level (GTE 6.1)
     Given a snakemake:6.1 project
     Given I open a file "foo.smk" with text

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

@@ -81,6 +81,21 @@ Feature: Resolve implicitly imported python names
       | snakemake        | pe  | pep             | __init__      | project.py   |
       | snakemake        | pe  | pep.config      | __init__      | project.py   |
 
+  Scenario Outline: Resolve implicit python modules/classes at top-level
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+    """
+    <text>
+    """
+    When I put the caret at <ptn>
+    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     |
+
   Scenario: Resolve at top-level: shell()
     Given a snakemake project
     Given I open a file "foo.smk" with text