From c9d01e0af5e31fd646817a54b2fa726e6f508d7c Mon Sep 17 00:00:00 2001
From: Steve Bachmeier <sbachmei@uw.edu>
Date: Tue, 7 Jan 2025 08:47:56 -0800
Subject: [PATCH] various other pr fixes

---
 src/easylink/graph_components.py        | 15 ++++++++-----
 src/easylink/implementation.py          | 28 ++++++++++++-------------
 src/easylink/utilities/general_utils.py |  4 ----
 3 files changed, 24 insertions(+), 23 deletions(-)

diff --git a/src/easylink/graph_components.py b/src/easylink/graph_components.py
index b933f74e..a525e8d1 100644
--- a/src/easylink/graph_components.py
+++ b/src/easylink/graph_components.py
@@ -179,11 +179,16 @@ class ImplementationGraph(nx.MultiDiGraph):
 
     Notes
     -----
-    Unlike a :class:`StepGraph`, an ImplementationGraph is a low-level abstraction;
-    it represents the actual implementations of each :class:`~easylink.step.Step`
-    in the pipeline.
-
-    The highest level ImplementationGraph is the that of the entire :class:`~easylink.pipeline_graph.PipelineGraph`.
+    An ImplementationGraph is a low-level abstraction; it represents the _actual
+    implementations_ of each :class:`~easylink.step.Step` in the pipeline. This
+    is in contrast to a :class:`StepGraph`, which can be an intricate nested structure
+    due to the various complex and self-similar :class:`~easylink.step.Step` instances
+    (which represent abstract operations such as "loop this step N times"). An
+    ImplementationGraph the flattened and concrete graph of
+    :class:`Implementations<easylink.implementation.Implementation>` to run.
+
+    The highest level ImplementationGraph is the that of the entire
+    :class:`~easylink.pipeline_graph.PipelineGraph`.
 
     See Also
     --------
diff --git a/src/easylink/implementation.py b/src/easylink/implementation.py
index 276cbee9..ece45fed 100644
--- a/src/easylink/implementation.py
+++ b/src/easylink/implementation.py
@@ -75,14 +75,16 @@ def validate(self) -> list[str]:
 
         Returns
         -------
-            A list of logs containing any validation errors.
+            A list of logs containing any validation errors. Each item in the list
+            is a distinct message about a particular validation error (e.g. if a
+            required container does not exist).
 
         Notes
         -----
         This is intended to be run from :meth:`easylink.pipeline.Pipeline._validate`.
         """
         logs = []
-        logs = self._validate_expected_step(logs)
+        logs = self._validate_expected_steps(logs)
         logs = self._validate_container_exists(logs)
         return logs
 
@@ -95,11 +97,12 @@ def _load_metadata(self) -> dict[str, str]:
         metadata = load_yaml(paths.IMPLEMENTATION_METADATA)
         return metadata[self.name]
 
-    def _validate_expected_step(self, logs: list[str]) -> list[str]:
+    def _validate_expected_steps(self, logs: list[str]) -> list[str]:
         """Validates that the Implementation is responsible for the correct steps."""
         if not set(self.schema_steps) == set(self.metadata_steps):
             logs.append(
-                f"Pipeline configuration nodes {self.schema_steps} do not match metadata steps {self.metadata_steps}."
+                f"Pipeline configuration nodes {self.schema_steps} do not match "
+                f"metadata steps {self.metadata_steps}."
             )
         return logs
 
@@ -133,7 +136,13 @@ def outputs(self) -> dict[str, list[str]]:
 
 
 class NullImplementation:
-    """A representation of a :class:`~easylink.step.Step` that does not have an :class:`Implementation`.
+    """An object with a partial :class:`Implementation` interface that represents that no container needs to run.
+
+    The primary use case for this class is when adding an :class:`~easylink.step.IOStep` -
+    which does not have a corresponding :class:`Implementation` - to an
+    :class:`~easylink.graph_components.ImplementationGraph` since adding any new
+    node requires an object with :class:`~easylink.graph_components.InputSlot`
+    and :class:`~easylink.graph_components.OutputSlot` names.
 
     Parameters
     ----------
@@ -143,15 +152,6 @@ class NullImplementation:
         The :class:`InputSlots<easylink.graph_components.InputSlot>` for this NullImplementation.
     output_slots
         The :class:`OutputSlots<easylink.graph_components.OutputSlot>` for this NullImplementation.
-
-    Notes
-    -----
-    The primary use case for this class is when adding an :class:`~easylink.step.IOStep` -
-    which does not have a corresponding :class:`Implementation` - to an
-    :class:`~easylink.graph_components.ImplementationGraph`. Adding a new node
-    requires an ``implementation`` attribute with :class:`~easylink.graph_components.InputSlot`
-    and :class:`~easylink.graph_components.OutputSlot` names.
-
     """
 
     def __init__(
diff --git a/src/easylink/utilities/general_utils.py b/src/easylink/utilities/general_utils.py
index a5806b57..f5c033f2 100644
--- a/src/easylink/utilities/general_utils.py
+++ b/src/easylink/utilities/general_utils.py
@@ -93,10 +93,6 @@ def exit_with_validation_error(error_msg: dict) -> None:
     YAML format and terminates the program execution with a non-zero exit code
     (indicating an error).
 
-    This function logs the provided validation error messages using a structured
-    YAML format and terminates the program execution with a non-zero exit code
-    (indicating an error).
-
     Parameters
     ----------
     error_msg