Merge branch 'main' into combiner-fixes

cpg_workflows/workflow.py

@@ -639,7 +639,7 @@ def _get_action(self, target: TargetT) -> Action:
 
         if self.skipped:
             if reusable and not first_missing_path:
-                logging.info(f'{self.name}: {target} [REUSE] (stage skipped, and outputs exist)')
+                logging.debug(f'{self.name}: {target} [REUSE] (stage skipped, and outputs exist)')
                 return Action.REUSE
             if get_config()['workflow'].get('skip_sgs_with_missing_input'):
                 logging.warning(
@@ -697,13 +697,13 @@ def _is_reusable(self, expected_out: ExpectedResultT) -> tuple[bool, Path | None
                 Path | None: first missing path, if any
         """
         if self.assume_outputs_exist:
-            logging.info(f'Assuming outputs exist. Expected output is {expected_out}')
+            logging.debug(f'Assuming outputs exist. Expected output is {expected_out}')
             return True, None
 
         if not expected_out:
             # Marking is reusable. If the stage does not naturally produce any outputs,
             # it would still need to create some flag file.
-            logging.info('No expected outputs, assuming outputs exist')
+            logging.debug('No expected outputs, assuming outputs exist')
             return True, None
 
         if get_config()['workflow'].get('check_expected_outputs'):

main.py

@@ -105,7 +105,7 @@ def main(
     """
     Run a Hail Batch workflow specified as a positional command line argument [WORKFLOW]
     """
-    fmt = '%(asctime)s %(levelname)s (%(name)s %(lineno)s): %(message)s'
+    fmt = '%(asctime)s %(levelname)s (%(pathname)s %(lineno)s): %(message)s'
     coloredlogs.install(level='DEBUG' if verbose else 'INFO', fmt=fmt)
 
     if not workflow and not list_workflows: