easylink 0.1.7__py3-none-any.whl → 0.1.9__py3-none-any.whl

easylink/step.py

@@ -54,21 +54,18 @@ class Step:
     Parameters
     ----------
     step_name
-        The name of the pipeline step in the ``PipelineSchema``.
+        The name of the pipeline step in the ``PipelineSchema``. It must also match
+        the key in the implementation metadata file to be used to run this ``Step``.
     name
-        The name of this step *node*. This can be different from the ``step_name``
-        due to the need for disambiguation during the process of unrolling loops,
-        etc. For example, if step 1 is looped multiple times, each node would
-        have a ``step_name`` of, perhaps, "step_1" but unique ``names``
-        ("step_1_loop_1", etc).
+        The name of this ``Step's`` node in its :class:`easylink.graph_components.StepGraph`.
+        This can be different from the ``step_name`` due to the need for disambiguation
+        during the process of flattening the ``Stepgraph``, e.g. unrolling loops, etc.
+        For example, if step 1 is looped multiple times, each node would have a
+        ``step_name`` of, perhaps, "step_1" but unique ``names`` ("step_1_loop_1", etc).
     input_slots
         All required :class:`InputSlots<easylink.graph_components.InputSlot>`.
     output_slots
         All required :class:`OutputSlots<easylink.graph_components.OutputSlot>`.
-    nodes
-        All sub-nodes (i.e. sub-``Steps``) of this particular ``Step`` instance.
-    edges
-        The :class:`~easylink.graph_components.EdgeParams` of this ``Step``.
     input_slot_mappings
         The :class:`InputSlotMapping<easylink.graph_components.InputSlotMapping>` of this ``Step``.
     output_slot_mappings
@@ -89,31 +86,22 @@ class Step:
         name: str | None = None,
         input_slots: Iterable[InputSlot] = (),
         output_slots: Iterable[OutputSlot] = (),
-        nodes: Iterable[Step] = (),
-        edges: Iterable[EdgeParams] = (),
         input_slot_mappings: Iterable[InputSlotMapping] = (),
         output_slot_mappings: Iterable[OutputSlotMapping] = (),
     ) -> None:
         self.step_name = step_name
-        """The name of the high-level pipeline step."""
+        """The name of the pipeline step in the ``PipelineSchema``. It must also match
+        the key in the implementation metadata file to be used to run this ``Step``."""
         self.name = name if name else step_name
-        """The name of ``Step's`` node in its :class:`~easylink.graph_components.StepGraph`. 
-        This is a more descriptive name than the ``step_name``, e.g. if "step 1" 
-        is looped multiple times. If not provided, defaults to the :attr:`step_name`."""
+        """The name of this ``Step's`` node in its :class:`easylink.graph_components.StepGraph`. 
+        This can be different from the ``step_name`` due to the need for disambiguation 
+        during the process of flattening the ``Stepgraph``, e.g. unrolling loops, etc. 
+        For example, if step 1 is looped multiple times, each node would have a 
+        ``step_name`` of, perhaps, "step_1" but unique ``names`` ("step_1_loop_1", etc)."""
         self.input_slots = {slot.name: slot for slot in input_slots}
         """A mapping of ``InputSlot`` names to their instances."""
         self.output_slots = {slot.name: slot for slot in output_slots}
         """A mapping of ``OutputSlot`` names to their instances."""
-        self.nodes = nodes
-        """All sub-nodes (i.e. sub-``Steps``) of this particular ``Step`` instance."""
-        for node in self.nodes:
-            node.set_parent_step(self)
-        self.edges = edges
-        """The :class:`~easylink.graph_components.EdgeParams` of this ``Step``."""
-        self.step_graph = self._get_step_graph(nodes, edges)
-        """The :class:`~easylink.graph_components.StepGraph` of this ``Step``, i.e.
-        the directed acyclic graph (DAG) of sub-nodes and their edges that make 
-        up this ``Step`` instance."""
         self.slot_mappings = {
             "input": list(input_slot_mappings),
             "output": list(output_slot_mappings),
@@ -164,7 +152,7 @@ class Step:
         """
         step = self
         implementation_name = (
-            self.configuration_state.pipeline_config[COMBINED_IMPLEMENTATION_KEY]
+            self.configuration_state.step_config[COMBINED_IMPLEMENTATION_KEY]
             if self.configuration_state.is_combined
             else self.configuration_state.implementation_config.name
         )
@@ -203,7 +191,8 @@ class Step:
         Parameters
         ----------
         step_config
-            The configuration of this ``Step``.
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
@@ -216,9 +205,6 @@ class Step:
 
         Notes
         -----
-        A ``Step`` can be in either a "leaf" or a "non-leaf" configuration state
-        and the validation process is different for each.
-
         If the ``Step`` does not validate (i.e. errors are found and the returned
         dictionary is non-empty), the tool will exit and the pipeline will not run.
 
@@ -227,14 +213,42 @@ class Step:
         all issues in one pass. In these cases, new errors may be found after the
         initial ones are handled.
         """
-        if len(self.step_graph.nodes) == 0:
-            return self._validate_leaf(step_config, combined_implementations)
-        elif self.config_key in step_config:
-            return self._validate_nonleaf(
-                step_config[self.config_key], combined_implementations, input_data_config
-            )
+        errors = {}
+        metadata = load_yaml(paths.IMPLEMENTATION_METADATA)
+        error_key = f"step {self.name}"
+        if (
+            "implementation" not in step_config
+            and COMBINED_IMPLEMENTATION_KEY not in step_config
+        ):
+            errors[error_key] = [
+                "The step configuration does not contain an 'implementation' key "
+                "or a reference to a combined implementation."
+            ]
+        elif (
+            COMBINED_IMPLEMENTATION_KEY in step_config
+            and not step_config[COMBINED_IMPLEMENTATION_KEY] in combined_implementations
+        ):
+            errors[error_key] = [
+                "The step refers to a combined implementation but "
+                f"{step_config[COMBINED_IMPLEMENTATION_KEY]} is not a valid combined "
+                "implementation."
+            ]
         else:
-            return self._validate_leaf(step_config, combined_implementations)
+            implementation_config = (
+                step_config["implementation"]
+                if "implementation" in step_config
+                else combined_implementations[step_config[COMBINED_IMPLEMENTATION_KEY]]
+            )
+            if not "name" in implementation_config:
+                errors[error_key] = [
+                    "The implementation configuration does not contain a 'name' key."
+                ]
+            elif not implementation_config["name"] in metadata:
+                errors[error_key] = [
+                    f"Implementation '{implementation_config['name']}' is not supported. "
+                    f"Supported implementations are: {list(metadata.keys())}."
+                ]
+        return errors
 
     def get_implementation_graph(self) -> ImplementationGraph:
         """Gets this ``Step's`` :class:`~easylink.graph_components.ImplementationGraph`.
@@ -276,42 +290,25 @@ class Step:
 
     def set_configuration_state(
         self,
-        parent_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ) -> None:
-        """Sets the configuration state for this ``Step``.
-
-        The so-called 'configuration state' for a given ``Step`` is backed up by
-        a :class:`ConfigurationState` class and is assigned to its :attr:`_configuration_state`
-        attribute. There are two possible ``ConfigurationStates``:
-        :class:`LeafConfigurationState` and :class:`NonLeafConfigurationState`.
-
-        This method sets the configuration state of this ``Step`` based on whether
-        or not a :attr:`config_key` is set *and exists is the ``Step's`` configuration*
-        (i.e. its portion of the user-suppled pipeline specification
-        file); any required deviation from this behavior requires special
-        handling.
+        """Sets the configuration state to 'leaf'.
 
         Parameters
         ----------
-        parent_config
-            The configuration of the parent ``Step``.
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
             The input data configuration for the entire pipeline.
         """
-        step_config = parent_config[self.name]
-        sub_config = self._get_config(step_config)
-        if self.config_key is not None and self.config_key in step_config:
-            self._configuration_state = NonLeafConfigurationState(
-                self, sub_config, combined_implementations, input_data_config
-            )
-        else:
-            self._configuration_state = LeafConfigurationState(
-                self, sub_config, combined_implementations, input_data_config
-            )
+        self._configuration_state = LeafConfigurationState(
+            self, step_config, combined_implementations, input_data_config
+        )
 
     def get_implementation_slot_mappings(self) -> dict[str, list[SlotMapping]]:
         """Gets the input and output :class:`SlotMappings<easylink.graph_components.SlotMapping>`."""
@@ -326,113 +323,6 @@ class Step:
             ],
         }
 
-    ##################
-    # Helper methods #
-    ##################
-
-    def _get_step_graph(self, nodes: list[Step], edges: list[EdgeParams]) -> StepGraph:
-        """Create a StepGraph from the nodes and edges the step was initialized with."""
-        step_graph = StepGraph()
-        for step in nodes:
-            step_graph.add_node_from_step(step)
-        for edge in edges:
-            step_graph.add_edge_from_params(edge)
-        return step_graph
-
-    def _validate_leaf(
-        self,
-        step_config: LayeredConfigTree,
-        combined_implementations: LayeredConfigTree,
-    ) -> dict[str, list[str]]:
-        """Validates a leaf ``Step``."""
-        errors = {}
-        metadata = load_yaml(paths.IMPLEMENTATION_METADATA)
-        error_key = f"step {self.name}"
-        if (
-            "implementation" not in step_config
-            and COMBINED_IMPLEMENTATION_KEY not in step_config
-        ):
-            errors[error_key] = [
-                "The step configuration does not contain an 'implementation' key or a "
-                "reference to a combined implementation."
-            ]
-        elif (
-            COMBINED_IMPLEMENTATION_KEY in step_config
-            and not step_config[COMBINED_IMPLEMENTATION_KEY] in combined_implementations
-        ):
-            errors[error_key] = [
-                f"The step refers to a combined implementation but {step_config[COMBINED_IMPLEMENTATION_KEY]} is not a "
-                f"valid combined implementation."
-            ]
-        else:
-            implementation_config = (
-                step_config["implementation"]
-                if "implementation" in step_config
-                else combined_implementations[step_config[COMBINED_IMPLEMENTATION_KEY]]
-            )
-            if not "name" in implementation_config:
-                errors[error_key] = [
-                    "The implementation configuration does not contain a 'name' key."
-                ]
-            elif not implementation_config["name"] in metadata:
-                errors[error_key] = [
-                    f"Implementation '{implementation_config['name']}' is not supported. "
-                    f"Supported implementations are: {list(metadata.keys())}."
-                ]
-        return errors
-
-    def _validate_nonleaf(
-        self,
-        step_config: LayeredConfigTree,
-        combined_implementations: LayeredConfigTree,
-        input_data_config: LayeredConfigTree,
-    ) -> dict[str, list[str]]:
-        """Validates a non-leaf ``Step``."""
-        errors = {}
-        nodes = self.step_graph.nodes
-        for node in nodes:
-            step = nodes[node]["step"]
-            if isinstance(step, IOStep):
-                continue
-            if step.name not in step_config:
-                step_errors = {f"step {step.name}": [f"The step is not configured."]}
-            else:
-                step_errors = step.validate_step(
-                    step_config[step.name], combined_implementations, input_data_config
-                )
-            if step_errors:
-                errors.update(step_errors)
-        extra_steps = set(step_config.keys()) - set(nodes)
-        for extra_step in extra_steps:
-            errors[f"step {extra_step}"] = [f"{extra_step} is not a valid step."]
-        return errors
-
-    def _get_config(self, step_config: LayeredConfigTree) -> LayeredConfigTree:
-        """Convenience method to get a ``Step's`` configuration.
-
-        Some types of ``Steps`` have a unique :attr:`config_key` (defined by the
-        user via the pipeline specification file) that is used to specify the behavior
-        of the ``Step`` (e.g. looping, parallel, etc). This method simply returns
-        the ``Step's`` sub-configuration keyed to that ``config_key`` (if it exists,
-        i.e. is not a basic ``Step``).
-
-        Parameters
-        ----------
-        step_config
-            The high-level configuration of this ``Step``.
-
-        Returns
-        -------
-            The sub-configuration of this ``Step`` keyed on the ``config_key``
-            (if it exists).
-
-        """
-        return (
-            step_config
-            if not self.config_key in step_config
-            else step_config[self.config_key]
-        )
-
 
 class IOStep(Step):
     """A special case type of :class:`Step` used to represent incoming and outgoing data.
@@ -485,27 +375,24 @@ class IOStep(Step):
 
     def set_configuration_state(
         self,
-        parent_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ) -> None:
-        """Sets the configuration state to leaf.
-
-        An ``IOStep`` is by definition a leaf ``Step`` and so we assign that here
-        instead of relying on the default behavior of the parent class.
+        """Sets the configuration state to 'leaf'.
 
         Parameters
         ----------
-        parent_config
-            The configuration of the parent ``Step``. For ``IOSteps``, this will
-            always be the entire pipeline configuration.
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
             The input data configuration for the entire pipeline.
         """
         self._configuration_state = LeafConfigurationState(
-            self, parent_config, combined_implementations, input_data_config
+            self, step_config, combined_implementations, input_data_config
         )
 
     def get_implementation_graph(self) -> ImplementationGraph:
@@ -548,29 +435,29 @@ class InputStep(IOStep):
 
     def set_configuration_state(
         self,
-        parent_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ) -> None:
         """Sets the configuration state and updates the ``OutputSlots``.
 
-        In addition to setting ``InputStep`` to a leaf configuration state, this
+        In addition to setting ``InputStep`` to a 'leaf' configuration state, this
         method also updates the ``OutputSlots`` to include all of the dataset keys
         in the input data specification file. This allows for future use of
-        specific datasets instead of only "all" of them.
+        *specific* datasets instead of only *all* of them.
 
         Parameters
         ----------
-        parent_config
-            The configuration of the parent ``Step``. For ``IOSteps``, this will
-            always be the entire pipeline configuration.
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
             The input data configuration for the entire pipeline.
         """
         super().set_configuration_state(
-            parent_config, combined_implementations, input_data_config
+            step_config, combined_implementations, input_data_config
         )
         for input_data_key in input_data_config:
             self.output_slots[input_data_key] = OutputSlot(name=input_data_key)
@@ -601,19 +488,185 @@ class HierarchicalStep(Step):
 
     See :class:`Step` for inherited attributes.
 
-    Notes
-    -----
-    To use this feature, the sub-``Steps`` must be defined in the pipeline specification
-    file under a "substeps" key. If no "substeps" key is present, it will be  treated
-    as a single ``Step``.
+    Parameters
+    ----------
+    nodes
+        All sub-nodes (i.e. sub-``Steps``) that make up this ``HierarchicalStep``.
+    edges
+        The :class:`~easylink.graph_components.EdgeParams` of the sub-nodes.
+    step_graph
+        The :class:`~easylink.graph_components.StepGraph` i.e. the directed acyclic
+        graph (DAG) of sub-nodes and their edges that make up this ``HierarchicalStep``.
+    user_configurable
+        Whether or not the ``HierarchicalStep`` is user-configurable. It is a convenience
+        attribute to allow for back-end ``HierarchicalStep`` creation that are not
+        user-facing (i.e. they do not need to provide a 'substeps' configuration key).
 
     """
 
+    def __init__(
+        self,
+        step_name,
+        name=None,
+        input_slots=(),
+        output_slots=(),
+        nodes=(),
+        edges=(),
+        input_slot_mappings=(),
+        output_slot_mappings=(),
+        user_configurable=True,
+    ):
+        super().__init__(
+            step_name,
+            name,
+            input_slots,
+            output_slots,
+            input_slot_mappings,
+            output_slot_mappings,
+        )
+        self.nodes = nodes
+        """All sub-nodes (i.e. sub-``Steps``) that make up this ``HierarchicalStep``."""
+        for node in self.nodes:
+            node.set_parent_step(self)
+        self.edges = edges
+        """The :class:`~easylink.graph_components.EdgeParams` of the sub-nodes."""
+        self.step_graph = self._get_step_graph(nodes, edges)
+        """The :class:`~easylink.graph_components.StepGraph` i.e. the directed acyclic 
+        graph (DAG) of sub-nodes and their edges that make up this ``HierarchicalStep``."""
+        self.user_configurable = user_configurable
+        """Whether or not the ``HierarchicalStep`` is user-configurable. It is a convenience
+        attribute to allow for back-end ``HierarchicalStep`` creation that are not
+        user-facing (i.e. they do not need to provide a 'substeps' configuration key)."""
+
     @property
     def config_key(self):
         """The pipeline specification key required for a ``HierarchicalStep``."""
         return "substeps"
 
+    def validate_step(
+        self,
+        step_config: LayeredConfigTree,
+        combined_implementations: LayeredConfigTree,
+        input_data_config: LayeredConfigTree,
+    ) -> dict[str, list[str]]:
+        """Validates the ``HierarchicalStep``.
+
+        Parameters
+        ----------
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
+        combined_implementations
+            The configuration for any implementations to be combined.
+        input_data_config
+            The input data configuration for the entire pipeline.
+
+        Returns
+        -------
+            A dictionary of errors, where the keys are the ``HierarchicalStep``
+            name and the values are lists of error messages associated with the
+            given ``HierarchicalStep``.
+
+        Notes
+        -----
+        A ``HierarchicalStep`` can be in either a "leaf" or a "non-leaf" configuration
+        state and the validation process is different for each.
+
+        If the ``HierarchicalStep`` does not validate (i.e. errors are found and
+        the returned dictionary is non-empty), the tool will exit and the pipeline
+        will not run.
+
+        We attempt to batch error messages as much as possible, but there may be
+        times where the configuration is so ill-formed that we are unable to handle
+        all issues in one pass. In these cases, new errors may be found after the
+        initial ones are handled.
+        """
+        if self.user_configurable:
+            if self.config_key in step_config:
+                step_config = step_config[self.config_key]
+            else:
+                # This is a leaf step
+                return super().validate_step(
+                    step_config, combined_implementations, input_data_config
+                )
+        return self._validate_step_graph(
+            step_config, combined_implementations, input_data_config
+        )
+
+    def set_configuration_state(
+        self,
+        step_config: LayeredConfigTree,
+        combined_implementations: LayeredConfigTree,
+        input_data_config: LayeredConfigTree,
+    ) -> None:
+        """Sets the configuration state.
+
+        The configuration state of a ``HierarchicalStep`` depends on (1) whether
+        or not it is :attr:`user_configurable` and (2) whether or not the
+        :attr:`config_key` exists in the pipeline specification file.
+
+        Parameters
+        ----------
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
+        combined_implementations
+            The configuration for any implementations to be combined.
+        input_data_config
+            The input data configuration for the entire pipeline.
+        """
+        if self.user_configurable:
+            if self.config_key in step_config:
+                step_config = step_config[self.config_key]
+                configuration_state_type = NonLeafConfigurationState
+            else:
+                configuration_state_type = LeafConfigurationState
+        else:
+            # Substeps must be used, so we require non-leaf here
+            configuration_state_type = NonLeafConfigurationState
+        self._configuration_state = configuration_state_type(
+            self, step_config, combined_implementations, input_data_config
+        )
+
+    ##################
+    # Helper methods #
+    ##################
+
+    def _get_step_graph(self, nodes: list[Step], edges: list[EdgeParams]) -> StepGraph:
+        """Creates a :class:`~easylink.graph_components.StepGraph` from the nodes and edges the step was initialized with."""
+        step_graph = StepGraph()
+        for step in nodes:
+            step_graph.add_node_from_step(step)
+        for edge in edges:
+            step_graph.add_edge_from_params(edge)
+        return step_graph
+
+    def _validate_step_graph(
+        self,
+        step_config: LayeredConfigTree,
+        combined_implementations: LayeredConfigTree,
+        input_data_config: LayeredConfigTree,
+    ) -> dict[str, list[str]]:
+        """Validates the nodes of a :class:`~easylink.graph_components.StepGraph`."""
+        errors = {}
+        for node in self.step_graph.nodes:
+            step = self.step_graph.nodes[node]["step"]
+            if isinstance(step, IOStep):
+                continue
+            else:
+                if step.name not in step_config:
+                    step_errors = {f"step {step.name}": ["The step is not configured."]}
+                else:
+                    step_errors = step.validate_step(
+                        step_config[step.name], combined_implementations, input_data_config
+                    )
+            if step_errors:
+                errors.update(step_errors)
+        extra_steps = set(step_config.keys()) - set(self.step_graph.nodes)
+        for extra_step in extra_steps:
+            errors[f"step {extra_step}"] = [f"{extra_step} is not a valid step."]
+        return errors
+
 
 class TemplatedStep(Step, ABC):
     """A type of :class:`Step` that may contain multiplicity.
@@ -641,8 +694,12 @@ class TemplatedStep(Step, ABC):
             template_step.input_slots.values(),
             template_step.output_slots.values(),
         )
+        self.step_graph = None
+        """The :class:`~easylink.graph_components.StepGraph` i.e. the directed acyclic 
+        graph (DAG) of sub-nodes and their edges that make up this ``TemplatedStep``."""
         self.template_step = template_step
         """The ``Step`` to be templated."""
+
         self.template_step.set_parent_step(self)
 
     @property
@@ -716,7 +773,8 @@ class TemplatedStep(Step, ABC):
         Parameters
         ----------
         step_config
-            The configuration of this ``TemplatedStep``.
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
@@ -730,7 +788,7 @@ class TemplatedStep(Step, ABC):
 
         Notes
         -----
-        If the ``Step`` does not validate (i.e. errors are found and the returned
+        If the ``TemplatedStep`` does not validate (i.e. errors are found and the returned
         dictionary is non-empty), the tool will exit and the pipeline will not run.
 
         We attempt to batch error messages as much as possible, but there may be
@@ -739,6 +797,7 @@ class TemplatedStep(Step, ABC):
         initial ones are handled.
         """
         if not self.config_key in step_config:
+            # This is a leaf step
             return self.template_step.validate_step(
                 step_config, combined_implementations, input_data_config
             )
@@ -770,51 +829,32 @@ class TemplatedStep(Step, ABC):
                 ]
             parallel_errors.update(
                 self.template_step.validate_step(
-                    parallel_config, combined_implementations, input_data_config
+                    LayeredConfigTree(parallel_config),
+                    combined_implementations,
+                    input_data_config,
                 )
             )
             if parallel_errors:
                 errors[f"step {self.name}"][f"{self.node_prefix}_{i+1}"] = parallel_errors
         return errors
 
-    def _get_config(self, step_config: LayeredConfigTree) -> LayeredConfigTree:
-        """Convenience method to get the ``TemplatedStep's`` configuration.
-
-        ``TemplatedSteps`` may include multiplicity. In such cases, their configurations
-        must be modified to include the expanded ``Steps``.
-
-        Parameters
-        ----------
-        step_config
-            The high-level configuration of this ``TemplatedStep``.
-
-        Returns
-        -------
-            The expanded sub-configuration of this ``TemplatedStep`` based on the
-            :attr:`Step.config_key` and expanded to include all looped or parallelized
-            sub-``Steps``).
-        """
-        if self.config_key in step_config:
-            expanded_step_config = LayeredConfigTree()
-            for i, sub_config in enumerate(step_config[self.config_key]):
-                expanded_step_config.update(
-                    {f"{self.name}_{self.node_prefix}_{i+1}": sub_config}
-                )
-            return expanded_step_config
-        return step_config
-
     def set_configuration_state(
         self,
-        parent_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ):
-        """Sets the configuration state and updates the :class:`SlotMappings<easylink.graph_components.SlotMapping>`.
+        """Sets the configuration state to 'non-leaf'.
+
+        In addition to setting the configuration state, this also updates the
+        :class:`~easylink.graph_components.StepGraph` and
+        :class:`SlotMappings<easylink.graph_components.SlotMapping>`.
 
         Parameters
         ----------
-        parent_config
-            The configuration of the parent ``Step``.
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
@@ -828,7 +868,6 @@ class TemplatedStep(Step, ABC):
         :class:`~easylink.implementation.Implementation`, i.e. the one with a
         :class:`LeafConfigurationState`.
         """
-        step_config = parent_config[self.name]
         if self.config_key not in step_config:
             # Special handle the step_graph update
             self.step_graph = StepGraph()
@@ -857,6 +896,36 @@ class TemplatedStep(Step, ABC):
             self, expanded_config, combined_implementations, input_data_config
         )
 
+    ##################
+    # Helper Methods #
+    ##################
+
+    def _get_config(self, step_config: LayeredConfigTree) -> LayeredConfigTree:
+        """Convenience method to get the ``TemplatedStep's`` configuration.
+
+        ``TemplatedSteps`` may include multiplicity. In such cases, their configurations
+        must be modified to include the expanded ``Steps``.
+
+        Parameters
+        ----------
+        step_config
+            The high-level configuration of this ``TemplatedStep``.
+
+        Returns
+        -------
+            The expanded sub-configuration of this ``TemplatedStep`` based on the
+            :attr:`Step.config_key` and expanded to include all looped or parallelized
+            sub-``Steps``).
+        """
+        if self.config_key in step_config:
+            expanded_step_config = LayeredConfigTree()
+            for i, sub_config in enumerate(step_config[self.config_key]):
+                expanded_step_config.update(
+                    {f"{self.name}_{self.node_prefix}_{i+1}": sub_config}
+                )
+            return expanded_step_config
+        return step_config
+
     def _duplicate_template_step(self) -> Step:
         """Makes a duplicate of the template ``Step``.
 
@@ -1069,17 +1138,25 @@ class EmbarrassinglyParallelStep(Step):
 
     An ``EmbarrassinglyParallelStep`` is different than a :class:`ParallelStep`
     in that it is not configured by the user to be run in parallel - it completely
-    happens on the back end for performance reasons. As such, note that it inherits
-    from :class:`Step` instead of :class:`TemplatedStep`.
+    happens on the back end for performance reasons.
+
+    See :class:`Step` for inherited attributes.
+
+    Parameters
+    ----------
+    step
+        The ``Step`` to be run in an embarrassingly parallel manner. To run multiple
+        steps in parallel, use a :class:`HierarchicalStep`.
+
     """
 
     def __init__(
         self,
-        step_name: str,
-        input_slots: Iterable[InputSlot],
-        output_slots: Iterable[OutputSlot],
+        step: Step,
     ) -> None:
-        super().__init__(step_name, input_slots=input_slots, output_slots=output_slots)
+        super().__init__(
+            step.step_name, step.name, step.input_slots.values(), step.output_slots.values()
+        )
         self._validate()
 
     def _validate(self) -> None:
@@ -1124,10 +1201,7 @@ class EmbarrassinglyParallelStep(Step):
 
 
 class ChoiceStep(Step):
-    """A type of :class:`Step` that allows for choosing between multiple paths.
-
-    A ``ChoiceStep`` allows a user to select a single path from a set of possible
-    paths.
+    """A type of :class:`Step` that allows for choosing from a set of options.
 
     See :class:`Step` for inherited attributes.
 
@@ -1141,7 +1215,7 @@ class ChoiceStep(Step):
         All required :class:`OutputSlots<easylink.graph_components.OutputSlot>`.
     choices
         A dictionary of choices, where the keys are the names/types of choices and
-        the values are dictionaries containing that type's nodes, edges, and
+        the values are dictionaries containing that type's ``Step`` and related
         :class:`SlotMappings<easylink.graph_components.SlotMapping>`.
 
     Notes
@@ -1150,6 +1224,13 @@ class ChoiceStep(Step):
     :attr:`Step.config_key` in the pipeline specification file. Instead, the pipeline
     configuration must contain a 'type' key that specifies which option to choose.
 
+    The :attr:`choices` dictionary must contain the choice type names as the outer
+    keys. The values of each of these types is then another dictionary containing
+    'step', 'input_slot_mappings', and 'output_slot_mappings' keys with their
+    corresponding values.
+
+    Each choice type must specify a *single* ``Step`` and its associated ``SlotMappings``.
+    Any choice paths that require multiple sub-steps should specify a :class:`HierarchicalStep`.
     """
 
     def __init__(
@@ -1157,9 +1238,7 @@ class ChoiceStep(Step):
         step_name: str,
         input_slots: Iterable[InputSlot],
         output_slots: Iterable[OutputSlot],
-        choices: dict[
-            str, dict[str, list[Step | EdgeParams | InputSlotMapping | OutputSlotMapping]]
-        ],
+        choices: dict[str, dict[str, Step | SlotMapping]],
     ) -> None:
         super().__init__(
             step_name,
@@ -1182,7 +1261,8 @@ class ChoiceStep(Step):
         Parameters
         ----------
         step_config
-            The configuration of this ``ChoiceStep``.
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
@@ -1195,8 +1275,6 @@ class ChoiceStep(Step):
 
         Notes
         -----
-        A ``ChoiceStep`` by definition must be set with a :class:`NonLeafConfigurationState`.
-
         If the ``Step`` does not validate (i.e. errors are found and the returned
         dictionary is non-empty), the tool will exit and the pipeline will not run.
 
@@ -1205,16 +1283,9 @@ class ChoiceStep(Step):
         all issues in one pass. In these cases, new errors may be found after the
         initial ones are handled.
 
-        We update the :class:`easylink.graph_components.StepGraph` and ``SlotMappings``
-        in :meth:`validate_step` (as opposed to in :meth:`set_configuration_state`
-        as is done in :class:`TemplatedStep`) because :meth:`validate_step` is called
-        prior to :meth:`set_configuration_state`, but the validations itself actually
-        requires the updated ``StepGraph`` and ``SlotMappings``.
-
         We do not attempt to validate the subgraph here if the 'type' key is unable
         to be validated.
         """
-
         chosen_type = step_config.get("type")
         # Handle problems with the 'type' key
         if not chosen_type:
@@ -1222,104 +1293,64 @@ class ChoiceStep(Step):
         if chosen_type not in self.choices:
             return {
                 f"step {self.name}": [
-                    f"'{step_config['type']}' is not a supported 'type'. Valid choices are: {list(self.choices)}."
+                    f"'{step_config.type}' is not a supported 'type'. Valid choices are: {list(self.choices)}."
                 ]
             }
-        # Handle type-subgraph inconsistencies
-        subgraph = self.choices[chosen_type]
+
+        chosen_step = self.choices[chosen_type]["step"]
         chosen_step_config = LayeredConfigTree(
             {key: value for key, value in step_config.items() if key != "type"}
         )
-        allowable_steps = [node.name for node in subgraph["nodes"]]
-        if set(allowable_steps) != set(chosen_step_config):
+        if chosen_step.name not in chosen_step_config:
             return {
                 f"step {self.name}": [
-                    f"Invalid configuration for '{chosen_type}' type. Valid steps are {allowable_steps}."
+                    f"'{chosen_step.name}' is not configured. Confirm you have specified "
+                    f"the correct steps for the '{chosen_type}' type."
                 ]
             }
-
-        # HACK: Update the step graph and mappings here because we need them for validation
-        self.step_graph = self._update_step_graph(subgraph)
-        self.slot_mappings = self._update_slot_mappings(subgraph)
         # NOTE: A ChoiceStep is by definition non-leaf step
-        return self._validate_nonleaf(
-            chosen_step_config, combined_implementations, input_data_config
+        return chosen_step.validate_step(
+            chosen_step_config[chosen_step.name], combined_implementations, input_data_config
         )
 
     def set_configuration_state(
         self,
-        parent_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ):
-        """Sets the configuration state for a ``ChoiceStep``.
+        """Sets the configuration state to 'non-leaf'.
+
+        In addition to setting the configuration state, this also updates the
+        :class:`~easylink.graph_components.StepGraph` and
+        :class:`SlotMappings<easylink.graph_components.SlotMapping>`.
 
         Parameters
         ----------
-        parent_config
-            The configuration of the parent ``Step``.
+        step_config
+            The internal configuration of this ``Step``, i.e. it should not include
+            the ``Step's`` name.
         combined_implementations
             The configuration for any implementations to be combined.
         input_data_config
             The input data configuration for the entire pipeline.
-
-        Notes
-        -----
-        We update the :class:`easylink.graph_components.StepGraph` and ``SlotMappings``
-        in :meth:`validate_step` (as opposed to in :meth:`set_configuration_state`
-        as is done in :class:`TemplatedStep`) because :meth:`validate_step` is called
-        prior to :meth:`set_configuration_state`, but the validations itself actually
-        requires the updated ``StepGraph`` and ``SlotMappings``.
         """
+        choice = self.choices[step_config["type"]]
+        self.step_graph = StepGraph()
+        self.step_graph.add_node_from_step(choice["step"])
+        self.slot_mappings = {
+            "input": choice["input_slot_mappings"],
+            "output": choice["output_slot_mappings"],
+        }
 
-        chosen_parent_config = LayeredConfigTree(
-            {key: value for key, value in parent_config[self.name].items() if key != "type"}
+        chosen_step_config = LayeredConfigTree(
+            {key: value for key, value in step_config.items() if key != "type"}
         )
-        # ChoiceSteps by definition cannot be in a LeafConfigurationState.
+        # ChoiceSteps by definition are in a NonLeafConfigurationState
         self._configuration_state = NonLeafConfigurationState(
-            self, chosen_parent_config, combined_implementations, input_data_config
+            self, chosen_step_config, combined_implementations, input_data_config
         )
 
-    @staticmethod
-    def _update_step_graph(subgraph: dict[str, Any]) -> StepGraph:
-        """Updates the :class:`~easylink.graph_components.StepGraph` with the choice.
-
-        Parameters
-        ----------
-        subgraph
-            Subgraph parameters (nodes, edges, and slot mappings) for the chosen type.
-
-        Returns
-        -------
-            The updated ``StepGraph`` for the chosen type.
-        """
-        nodes = subgraph["nodes"]
-        edges = subgraph["edges"]
-
-        graph = StepGraph()
-        for node in nodes:
-            graph.add_node_from_step(node)
-        for edge in edges:
-            graph.add_edge_from_params(edge)
-        return graph
-
-    @staticmethod
-    def _update_slot_mappings(subgraph: dict[str, Any]) -> dict[str, list[SlotMapping]]:
-        """Updates the :class:`SlotMappings<easylink.graph_components.SlotMapping>` to the choice type.
-
-        Parameters
-        ----------
-        sub_graph
-            Subgraph parameters (nodes, edges, and slot mappings) for the chosen type.
-
-        Returns
-        -------
-            Updated ``SlotMappings`` that match the choice type.
-        """
-        input_mappings = subgraph["input_slot_mappings"]
-        output_mappings = subgraph["output_slot_mappings"]
-        return {"input": input_mappings, "output": output_mappings}
-
 
 class ConfigurationState(ABC):
     """A given :class:`Step's<Step>` configuration state.
@@ -1334,8 +1365,9 @@ class ConfigurationState(ABC):
     ----------
     step
         The ``Step`` this ``ConfigurationState`` is tied to.
-    pipeline_config
-        The relevant configuration for the ``Step`` we are setting the state for.
+    step_config
+        The internal configuration of this ``Step`` we are setting the state
+        for; it should not include the ``Step's`` name.
     combined_implementations
         The configuration for any implementations to be combined.
     input_data_config
@@ -1346,14 +1378,15 @@ class ConfigurationState(ABC):
     def __init__(
         self,
         step: Step,
-        pipeline_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ):
         self._step = step
         """The ``Step`` this ``ConfigurationState`` is tied to."""
-        self.pipeline_config = pipeline_config
-        """The relevant configuration for the ``Step`` we are setting the state for."""
+        self.step_config = step_config
+        """The internal configuration of this ``Step`` we are setting the state 
+        for; it should not include the ``Step's`` name."""
         self.combined_implementations = combined_implementations
         """The relevant configuration if the ``Step's`` ``Implementation``
         has been requested to be combined with that of a different ``Step``."""
@@ -1394,15 +1427,15 @@ class LeafConfigurationState(ConfigurationState):
     @property
     def is_combined(self) -> bool:
         """Whether or not this ``Step`` is combined with another ``Step``."""
-        return True if COMBINED_IMPLEMENTATION_KEY in self.pipeline_config else False
+        return COMBINED_IMPLEMENTATION_KEY in self.step_config
 
     @property
     def implementation_config(self) -> LayeredConfigTree:
         """The ``Step's`` specific ``Implementation`` configuration."""
         return (
-            self.combined_implementations[self.pipeline_config[COMBINED_IMPLEMENTATION_KEY]]
+            self.combined_implementations[self.step_config[COMBINED_IMPLEMENTATION_KEY]]
             if self.is_combined
-            else self.pipeline_config["implementation"]
+            else self.step_config.implementation
         )
 
     def get_implementation_graph(self) -> ImplementationGraph:
@@ -1416,31 +1449,30 @@ class LeafConfigurationState(ConfigurationState):
         -------
             The ``ImplementationGraph`` related to this ``Step``.
         """
-
+        step = self._step
         implementation_graph = ImplementationGraph()
-        implementation_node_name = self._step.implementation_node_name
         if self.is_combined:
-            if isinstance(self._step, EmbarrassinglyParallelStep):
+            if isinstance(step, EmbarrassinglyParallelStep):
                 raise NotImplementedError(
                     "Combining implementations with embarrassingly parallel steps "
                     "is not yet supported."
                 )
             implementation = PartialImplementation(
-                combined_name=self.pipeline_config[COMBINED_IMPLEMENTATION_KEY],
-                schema_step=self._step.step_name,
-                input_slots=self._step.input_slots.values(),
-                output_slots=self._step.output_slots.values(),
+                combined_name=self.step_config[COMBINED_IMPLEMENTATION_KEY],
+                schema_step=step.step_name,
+                input_slots=step.input_slots.values(),
+                output_slots=step.output_slots.values(),
             )
         else:
             implementation = Implementation(
-                schema_steps=[self._step.step_name],
+                schema_steps=[step.step_name],
                 implementation_config=self.implementation_config,
-                input_slots=self._step.input_slots.values(),
-                output_slots=self._step.output_slots.values(),
-                is_embarrassingly_parallel=isinstance(self._step, EmbarrassinglyParallelStep),
+                input_slots=step.input_slots.values(),
+                output_slots=step.output_slots.values(),
+                is_embarrassingly_parallel=isinstance(step, EmbarrassinglyParallelStep),
             )
         implementation_graph.add_node_from_implementation(
-            implementation_node_name,
+            step.implementation_node_name,
             implementation=implementation,
         )
         return implementation_graph
@@ -1481,10 +1513,10 @@ class LeafConfigurationState(ConfigurationState):
             for mapping in mappings:
                 # FIXME [MIC-5771]: Fix ParallelSteps
                 if (
-                    "input_data_file" in self.pipeline_config
+                    "input_data_file" in self.step_config
                     and edge.source_node == "pipeline_graph_input_data"
                 ):
-                    edge.output_slot = self.pipeline_config["input_data_file"]
+                    edge.output_slot = self.step_config["input_data_file"]
                 imp_edge = mapping.remap_edge(edge)
                 implementation_edges.append(imp_edge)
         else:
@@ -1506,8 +1538,10 @@ class NonLeafConfigurationState(ConfigurationState):
     ----------
     step
         The ``Step`` this ``ConfigurationState`` is tied to.
-    pipeline_config
-        The relevant configuration for the ``Step`` we are setting the state for.
+    step_config
+        The internal configuration of this ``Step`` we are setting the state
+        for; it should not include the ``Step's`` name (though it must include
+        the sub-step names).
     combined_implementations
         The configuration for any implementations to be combined.
     input_data_config
@@ -1538,16 +1572,17 @@ class NonLeafConfigurationState(ConfigurationState):
     def __init__(
         self,
         step: Step,
-        pipeline_config: LayeredConfigTree,
+        step_config: LayeredConfigTree,
         combined_implementations: LayeredConfigTree,
         input_data_config: LayeredConfigTree,
     ):
-        super().__init__(step, pipeline_config, combined_implementations, input_data_config)
+        super().__init__(step, step_config, combined_implementations, input_data_config)
         if not step.step_graph:
             raise ValueError(
                 "NonLeafConfigurationState requires a subgraph upon which to operate, "
                 f"but Step {step.name} has no step graph."
             )
+        self._nodes = step.step_graph.nodes
         self._configure_subgraph_steps()
 
     def get_implementation_graph(self) -> ImplementationGraph:
@@ -1578,8 +1613,8 @@ class NonLeafConfigurationState(ConfigurationState):
 
     def add_nodes(self, implementation_graph: ImplementationGraph) -> None:
         """Adds nodes for each ``Step`` to the ``ImplementationGraph``."""
-        for node in self._step.step_graph.nodes:
-            step = self._step.step_graph.nodes[node]["step"]
+        for node in self._nodes:
+            step = self._nodes[node]["step"]
             implementation_graph.update(step.get_implementation_graph())
 
     def add_edges(self, implementation_graph: ImplementationGraph) -> None:
@@ -1587,8 +1622,8 @@ class NonLeafConfigurationState(ConfigurationState):
         for source, target, edge_attrs in self._step.step_graph.edges(data=True):
             all_edges = []
             edge = EdgeParams.from_graph_edge(source, target, edge_attrs)
-            parent_source_step = self._step.step_graph.nodes[source]["step"]
-            parent_target_step = self._step.step_graph.nodes[target]["step"]
+            parent_source_step = self._nodes[source]["step"]
+            parent_target_step = self._nodes[target]["step"]
 
             source_edges = parent_source_step.get_implementation_edges(edge)
             for source_edge in source_edges:
@@ -1624,7 +1659,7 @@ class NonLeafConfigurationState(ConfigurationState):
             ]
             for mapping in mappings:
                 new_edge = mapping.remap_edge(edge)
-                new_step = self._step.step_graph.nodes[mapping.child_node]["step"]
+                new_step = self._nodes[mapping.child_node]["step"]
                 imp_edges = new_step.get_implementation_edges(new_edge)
                 implementation_edges.extend(imp_edges)
         elif edge.target_node == self._step.name:
@@ -1635,7 +1670,7 @@ class NonLeafConfigurationState(ConfigurationState):
             ]
             for mapping in mappings:
                 new_edge = mapping.remap_edge(edge)
-                new_step = self._step.step_graph.nodes[mapping.child_node]["step"]
+                new_step = self._nodes[mapping.child_node]["step"]
                 imp_edges = new_step.get_implementation_edges(new_edge)
                 implementation_edges.extend(imp_edges)
         else:
@@ -1650,9 +1685,12 @@ class NonLeafConfigurationState(ConfigurationState):
         This method recursively traverses the ``StepGraph`` and sets the configuration
         state for each ``Step`` until reaching all leaf nodes.
         """
-        nodes = self._step.step_graph.nodes
-        for node in nodes:
-            step = nodes[node]["step"]
+        for node in self._nodes:
+            step = self._nodes[node]["step"]
+            # IOStep names never appear in configuration
+            step_config = (
+                self.step_config if isinstance(step, IOStep) else self.step_config[step.name]
+            )
             step.set_configuration_state(
-                self.pipeline_config, self.combined_implementations, self.input_data_config
+                step_config, self.combined_implementations, self.input_data_config
             )