fix: various error handling improvements, fixed logging/error behavio…

…r (stdout from dryrun, stderr otherwise) (#2759)

### Description

<!--Add a description of your PR here-->

### QC
<!-- Make sure that you can tick the boxes below. -->

* [x] The PR contains a test case for the changes or the changes are
already covered by an existing test case.
* [x] 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).

snakemake/api.py

@@ -138,7 +138,7 @@ def workflow(
 
         self._check_is_in_context()
 
-        self._setup_logger(mode=workflow_settings.exec_mode)
+        self.setup_logger(mode=workflow_settings.exec_mode)
 
         self._check_default_storage_provider(storage_settings=storage_settings)
 
@@ -240,7 +240,7 @@ def print_exception(self, ex: Exception):
             linemaps = self._workflow_api._workflow_store.linemaps
         print_exception(ex, linemaps)
 
-    def _setup_logger(
+    def setup_logger(
         self,
         stdout: bool = False,
         mode: ExecMode = ExecMode.DEFAULT,
@@ -254,7 +254,7 @@ def _setup_logger(
                 debug=self.output_settings.verbose,
                 printshellcmds=self.output_settings.printshellcmds,
                 debug_dag=self.output_settings.debug_dag,
-                stdout=stdout,
+                stdout=stdout or self.output_settings.stdout,
                 mode=mode,
                 show_failed_logs=self.output_settings.show_failed_logs,
                 dryrun=dryrun,
@@ -382,11 +382,11 @@ def print_compilation(self):
     def _workflow(self):
         if self._workflow_store is None:
             workflow = self._get_workflow()
+            self._workflow_store = workflow
             workflow.include(
                 self.snakefile, overwrite_default_target=True, print_compilation=False
             )
             workflow.check()
-            self._workflow_store = workflow
         return self._workflow_store
 
     def _get_workflow(self, **kwargs):
@@ -523,7 +523,7 @@ def execute_workflow(
                 "For local execution, --shared-fs-usage has to be unrestricted."
             )
 
-        self.snakemake_api._setup_logger(
+        self.snakemake_api.setup_logger(
             stdout=executor_plugin.common_settings.dryrun_exec,
             mode=self.workflow_api.workflow_settings.exec_mode,
             dryrun=executor_plugin.common_settings.dryrun_exec,

snakemake/cli.py

@@ -1885,6 +1885,7 @@ def args_to_api(args, parser):
             show_failed_logs=args.show_failed_logs,
             log_handlers=log_handlers,
             keep_logger=False,
+            stdout=args.dryrun,
         )
     ) as snakemake_api:
         deployment_method = args.software_deployment_method

snakemake/exceptions.py

@@ -18,8 +18,10 @@ def format_error(
     msg = str(ex)
     if linemaps and snakefile and snakefile in linemaps:
         lineno = linemaps[snakefile][lineno]
-        if isinstance(ex, SyntaxError):
-            msg = ex.msg
+
+    if isinstance(ex, SyntaxError):
+        msg = ex.msg.split("(")[0]
+        msg = f"{msg}:\n{ex.text}"
 
     location = ""
     if lineno and snakefile:
@@ -157,7 +159,7 @@ def print_exception(ex, linemaps=None):
     elif isinstance(ex, KeyboardInterrupt):
         logger.info("Cancelling snakemake on user request.")
     else:
-        traceback.print_exception(type(ex), ex, ex.__traceback__)
+        logger.error(traceback.format_exeption(ex))
 
 
 def update_lineno(ex: SyntaxError, linemaps):

snakemake/report/__init__.py

@@ -271,9 +271,8 @@ def __post_init__(self, job, job_rec):
             self.conda_env = yaml.load(self._conda_env_raw, Loader=yaml.Loader)
         self.n_jobs = 1
         self.id = uuid.uuid4()
-        self._init_source()
 
-    def _init_source(self):
+    def init_source(self):
         sources, language = None, None
         if self._rule.shellcmd is not None:
             sources = [self._rule.shellcmd]
@@ -632,6 +631,7 @@ def register_file(
         rule = RuleRecord(job_rec.job, job_rec)
         if job_rec.rule not in rules:
             rules[job_rec.rule].append(rule)
+            rule.init_source()
         else:
             merged = False
             for other in rules[job_rec.rule]:
@@ -641,6 +641,7 @@ def register_file(
                     break
             if not merged:
                 rules[job_rec.rule].append(rule)
+                rule.init_source()
     # In theory there could be more than one rule with the same name kept from above.
     # For now, we just keep the first.
     rules = {rulename: items[0] for rulename, items in rules.items()}

snakemake/settings.py

@@ -340,6 +340,7 @@ class OutputSettings(SettingsBase):
     show_failed_logs: bool = False
     log_handlers: Sequence[object] = tuple()
     keep_logger: bool = False
+    stdout: bool = False
 
 
 @dataclass

snakemake/workflow.py

@@ -1395,11 +1395,7 @@ def include(
             # this allows to import modules from the workflow directory
             sys.path.insert(0, snakefile.get_basedir().get_path_or_uri())
 
-        try:
-            exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
-        except SyntaxError as e:
-            e = update_lineno(e, self.linemaps)
-            raise
+        exec(compile(code, snakefile.get_path_or_uri(), "exec"), self.globals)
 
         if not overwrite_default_target:
             self.default_target = default_target

tests/test01/Snakefile

@@ -1,4 +1,3 @@
-
 from snakemake.utils import min_version
 
 from snakemake import __version__