fix: correctly report lineno (#2584)

### Description

fix: #2583, #1256 and #2574

### QC
maybe #2583

* [ ] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [ ] The documentation (`docs/`) is updated to reflect the changes or
this is not necessary (e.g. if the change does neither modify the
language nor the behavior or functionalities of Snakemake).

---------

Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>

snakemake/exceptions.py

@@ -160,6 +160,12 @@ def print_exception(ex, linemaps=None):
         traceback.print_exception(type(ex), ex, ex.__traceback__)
 
 
+def update_lineno(ex: SyntaxError, linemaps):
+    if ex.filename and ex.lineno:
+        ex.lineno = linemaps[ex.filename][ex.lineno]
+        return ex
+
+
 class SourceFileError(WorkflowError):
     def __init__(self, msg):
         super().__init__(f"Error in source file definition: {msg}")
@@ -188,18 +194,18 @@ def __init__(
         snakefile -- the file the exception originates
         """
         super(RuleException, self).__init__(message)
-        self._include = set()
+        _include = set()
         if include:
             for ex in include:
-                self._include.add(ex)
-                self._include.update(ex._include)
+                _include.add(ex)
+                _include.update(ex._include)
         if rule is not None:
             if lineno is None:
                 lineno = rule.lineno
             if snakefile is None:
                 snakefile = rule.snakefile
 
-        self._include = list(self._include)
+        self._include = list(_include)
         self.rule = rule
         self.lineno = lineno
         self.filename = snakefile

snakemake/workflow.py

@@ -57,6 +57,7 @@
     UnknownRuleException,
     NoRulesException,
     WorkflowError,
+    update_lineno,
 )
 from snakemake.dag import DAG, ChangeType
 from snakemake.scheduler import JobScheduler
@@ -164,7 +165,7 @@ def __post_init__(self):
         self._linemaps = dict()
         self.rule_count = 0
         self.included = []
-        self.included_stack = []
+        self.included_stack: list[SourceFile] = []
         self._persistence: Optional[Persistence] = None
         self._dag: Optional[DAG] = None
         self._onsuccess = lambda log: None
@@ -1353,14 +1354,22 @@ def include(
         if print_compilation:
             print(code)
 
-        if isinstance(snakefile, LocalSourceFile):
+        snakefile_path_or_uri = snakefile.get_basedir().get_path_or_uri()
+        if (
+            isinstance(snakefile, LocalSourceFile)
+            and snakefile_path_or_uri not in sys.path
+        ):
             # insert the current directory into sys.path
             # this allows to import modules from the workflow directory
             sys.path.insert(0, snakefile.get_basedir().get_path_or_uri())
 
         self.linemaps[snakefile.get_path_or_uri()] = linemap
 
-        exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
+        try:
+            exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
+        except SyntaxError as e:
+            e = update_lineno(e, self.linemaps)
+            raise
 
         if not overwrite_default_target:
             self.default_target = default_target