Python: Only track modules that are imported

python/ql/src/semmle/python/Module.qll

@@ -201,6 +201,20 @@ private string moduleNameFromBase(Container file) {
   file instanceof File and result = file.getStem()
 }
 
+/**
+ * Holds if `file` may be transitively imported from a file that may serve as the entry point of
+ * the execution.
+ */
+private predicate transitively_imported_from_entry_point(File file) {
+  file.getExtension().matches("%py%") and
+  exists(File importer |
+    importer.getParent() = file.getParent() and
+    exists(ImportExpr i | i.getLocation().getFile() = importer and i.getName() = file.getStem())
+  |
+    importer.maybeExecutedDirectly() or transitively_imported_from_entry_point(importer)
+  )
+}
+
 string moduleNameFromFile(Container file) {
   exists(string basename |
     basename = moduleNameFromBase(file) and
@@ -208,9 +222,10 @@ string moduleNameFromFile(Container file) {
   |
     result = moduleNameFromFile(file.getParent()) + "." + basename
     or
-    // If execution can start in the folder containing this module, then we will assume `file` can
-    // be imported as an absolute import, and hence return `basename` as a possible name.
-    file.getParent().(Folder).mayContainEntryPoint() and result = basename
+    // If `file` is a transitive import of a file that's executed directly, we allow references
+    // to it by its `basename`.
+    transitively_imported_from_entry_point(file) and
+    result = basename
   )
   or
   isPotentialSourcePackage(file) and