[patch] Replace warnings.warn with pyiron_snippets logger (#363)

pyiron_workflow/__init__.py

@@ -43,6 +43,7 @@
 from pyiron_workflow.nodes import standard as standard_nodes
 from pyiron_workflow.nodes.for_loop import for_node, for_node_factory
 from pyiron_workflow.nodes.function import Function, as_function_node, function_node
+from pyiron_workflow.logging import logger
 from pyiron_workflow.nodes.macro import Macro, as_macro_node, macro_node
 from pyiron_workflow.nodes.transform import (
     # as_dataclass_node,  # Not pickling nicely yet

pyiron_workflow/io.py

@@ -10,7 +10,6 @@
 from abc import ABC, abstractmethod
 from typing import Any
 
-from pyiron_snippets.logger import logger
 from pyiron_snippets.dotdict import DotDict
 
 from pyiron_workflow.channels import (
@@ -24,6 +23,7 @@
     AccumulatingInputSignal,
     NOT_DATA,
 )
+from pyiron_workflow.logging import logger
 from pyiron_workflow.mixin.has_interface_mixins import (
     HasChannel,
     HasLabel,

pyiron_workflow/logging.py

@@ -0,0 +1,3 @@
+from pyiron_snippets.logger import logger
+
+# For now, we use the snippets logger with absolutely zero changes

pyiron_workflow/mixin/preview.py

@@ -13,7 +13,6 @@
 from __future__ import annotations
 
 import inspect
-import warnings
 from abc import ABC, abstractmethod
 from functools import lru_cache, wraps
 from typing import (
@@ -27,6 +26,7 @@
 from pyiron_snippets.dotdict import DotDict
 
 from pyiron_workflow.channels import NOT_DATA
+from pyiron_workflow.logging import logger
 from pyiron_workflow.output_parser import ParseOutput
 
 if TYPE_CHECKING:
@@ -252,12 +252,7 @@ def _validate(cls):
             cls._validate_degeneracy()
             cls._validate_return_count()
         except OSError:
-            warnings.warn(
-                f"Could not find the source code to validate {cls.__name__} output "
-                f"labels against the number of returned values -- proceeding without "
-                f"validation",
-                OutputLabelsNotValidated,
-            )
+            logger.warn(no_output_validation_warning(cls))
 
     @classmethod
     def _validate_degeneracy(cls):
@@ -292,5 +287,8 @@ def _validate_return_count(cls):
                 )
 
 
-class OutputLabelsNotValidated(Warning):
-    pass
+def no_output_validation_warning(cls: type):
+    return (
+        f"Could not find the source code to validate {cls.__name__} output labels "
+        f"against the number of returned values -- proceeding without validation"
+    )

pyiron_workflow/mixin/semantics.py

@@ -17,8 +17,8 @@
 from typing import Optional
 
 from bidict import bidict
-from pyiron_snippets.logger import logger
 
+from pyiron_workflow.logging import logger
 from pyiron_workflow.mixin.has_interface_mixins import HasLabel, HasParent, UsesState
 
 

pyiron_workflow/mixin/storage.py

@@ -10,11 +10,11 @@
 import os
 import sys
 from typing import Optional
-import warnings
 
 import h5io
 from pyiron_snippets.files import FileObject, DirectoryObject
 
+from pyiron_workflow.logging import logger
 from pyiron_workflow.mixin.has_interface_mixins import HasLabel, HasParent
 
 
@@ -347,7 +347,7 @@ def import_ready(self) -> bool:
             module = self.__class__.__module__
             class_ = getattr(import_module(module), self.__class__.__name__)
             if module == "__main__":
-                warnings.warn(f"{self.label} is only defined in __main__")
+                logger.warning(f"{self.label} is only defined in __main__")
             return type(self) is class_
         except (ModuleNotFoundError, AttributeError):
             return False

pyiron_workflow/node.py

@@ -11,11 +11,11 @@
 from abc import ABC
 from concurrent.futures import Future
 from typing import Any, Literal, Optional, TYPE_CHECKING
-import warnings
 
 from pyiron_snippets.colors import SeabornColors
 
 from pyiron_workflow.draw import Node as GraphvizNode
+from pyiron_workflow.logging import logger
 from pyiron_workflow.mixin.has_to_dict import HasToDict
 from pyiron_workflow.mixin.injection import HasIOWithInjection
 from pyiron_workflow.mixin.run import Runnable, ReadinessError
@@ -374,7 +374,7 @@ def _after_node_setup(
                 "label to work in a new space, or give up on running after init."
             )
         elif do_load:
-            warnings.warn(
+            logger.info(
                 f"A saved file was found for the node {self.label} -- attempting to "
                 f"load it...(To delete the saved file instead, use "
                 f"`overwrite_save=True`)"
@@ -781,7 +781,7 @@ def replace_with(self, other: Node | type[Node]):
         if self.parent is not None:
             self.parent.replace_child(self, other)
         else:
-            warnings.warn(f"Could not replace_child {self.label}, as it has no parent.")
+            logger.info(f"Could not replace_child {self.label}, as it has no parent.")
 
     @property
     def storage_directory(self) -> DirectoryObject:

tests/unit/mixin/test_preview.py

@@ -4,7 +4,8 @@
 from pyiron_snippets.factory import classfactory
 
 from pyiron_workflow.channels import NOT_DATA
-from pyiron_workflow.mixin.preview import ScrapesIO, OutputLabelsNotValidated
+from pyiron_workflow.logging import logger
+from pyiron_workflow.mixin.preview import ScrapesIO, no_output_validation_warning
 
 
 class ScrapesFromDecorated(ScrapesIO):
@@ -187,9 +188,11 @@ def __source_code_not_available(x):
             ):
                 as_scraper()(f)
 
-            with self.assertWarns(
-                OutputLabelsNotValidated,
-                msg="If provided labels cannot be validated against the source code, "
-                    "a warning should be issued"
-            ):
-                as_scraper("y")(f)
+            with self.assertLogs(logger.name, level="WARNING") as log:
+                new_cls = as_scraper("y")(f)
+
+            self.assertIn(
+                f"WARNING:{logger.name}:" + no_output_validation_warning(new_cls),
+                log.output,
+                msg="Verify that the expected warning appears in the log"
+            )