docs: Code typos corrected

Author: Alan Christie

workflow/decoder.py

@@ -20,7 +20,7 @@
 from dataclasses import dataclass
 from typing import Any
 
-import decoder.decoder as job_defintion_decoder
+import decoder.decoder as job_definition_decoder
 import jsonschema
 import yaml
 
@@ -40,7 +40,7 @@
 
 @dataclass
 class Connector:
-    """A connection - connexts a plumbing source variable ("in_")
+    """A connection - connects a plumbing source variable ("in_")
     to destination variable ("out")."""
 
     in_: str
@@ -98,9 +98,9 @@ def get_description(definition: dict[str, Any]) -> str | None:
 
 def is_workflow_output_variable(definition: dict[str, Any], variable_name: str) -> bool:
     """True if the variable name is in the workflow variables outputs list."""
-    # We can safely pass on the workflow defitnion as its
-    # root-level 'variables' block complies with job-defintion variables.
-    return variable_name in job_defintion_decoder.get_outputs(definition)
+    # We can safely pass on the workflow definition as its
+    # root-level 'variables' block complies with job-definition variables.
+    return variable_name in job_definition_decoder.get_outputs(definition)
 
 
 def get_workflow_variable_names(definition: dict[str, Any]) -> set[str]:

workflow/workflow-schema.yaml

@@ -170,10 +170,10 @@ definitions:
         type: string
         description: A description of the step
       specification:
-        # The step Job specififcation.
+        # The step Job specification.
         # This MUST define `collection`, a 'job', and a 'version'.
         # 'variables' (a map of name and value)can also be provided.
-        # The format of this is essentially idenical to the specification
+        # The format of this is essentially identical to the specification
         # used when a Job is launched via the DM API.
         $ref: '#/definitions/step-specification'
       plumbing:

workflow/workflow_abc.py

@@ -93,26 +93,26 @@ class LaunchParameters:
     step_name: str | None = None
     # The step replication number.
     # A numeric vale expected to be in the range 0 to total_number_of_replicas - 1.
-    # If a step is laucnhed 5 times the values used when laucnhing each instance
+    # If a step is launched 5 times the values used when launching each instance
     # must be 0, 1, 2, 3, and 4.
     step_replication_number: int = 0
-    # The total number of replicas of this instance that are expected to be laucnhed.
+    # The total number of replicas of this instance that are expected to be launched.
     # This cannot be less than 1 and must be grater than any value of
     # 'step_replication_number' that will be used for the same step.
     total_number_of_replicas: int = 1
-    # A set of dependent (prior step) instance directroies that are expected to be
+    # A set of dependent (prior step) instance directories that are expected to be
     # hard-linked into the instance directory the launcher will create.
     # These are required so that the step can access the dependent step's files.
     # It is a set of instance UUIDs.
     step_dependent_instances: set[str] | None = None
     # A set of dependent project files that are expected to be hard-linked
     # into the instance directory the launcher will create.
     # These are required so that the step can access project files.
-    # It is a set project-relative filenames (or directroies).
+    # It is a set project-relative filenames (or directories).
     step_project_inputs: set[str] | None = None
     # A set of step instance files that are expected to be hard-linked
     # into the surrounding Project directory.
-    # It is a set instance-relative filenames (or directroies).
+    # It is a set instance-relative filenames (or directories).
     step_project_outputs: set[str] | None = None
     # The application ID (a custom resource name)
     # used to identify the 'type' of Instance to create.

workflow/workflow_engine.py

@@ -73,7 +73,7 @@
 from dataclasses import dataclass
 from typing import Any, Optional
 
-import decoder.decoder as job_defintion_decoder
+import decoder.decoder as job_definition_decoder
 from decoder.decoder import TextEncoding
 from google.protobuf.message import Message
 from informaticsmatters.protobuf.datamanager.pod_message_pb2 import PodMessage
@@ -134,7 +134,7 @@ def __init__(
         instance_launcher: InstanceLauncher,
         instance_link_glob: str = ".instance-*",
     ):
-        """Initialiser, given a Workflow API adapter, Instance laucnher,
+        """Initialiser, given a Workflow API adapter, Instance launcher,
         and a step (directory) link 'glob' (a convenient directory glob to
         locate the DM hard-link directories of prior instances inserted into a
         step's instance directory, typically '.instance-*')"""
@@ -326,8 +326,8 @@ def _handle_pod_message(self, msg: PodMessage) -> None:
             self._set_step_error(step_name, r_wfid, r_wfsid, exit_code, "Job failed")
             return
 
-        # If we get here the prior step completed successfullyso we
-        # mark the Step as DONE (successfully).
+        # If we get here the prior step completed successfully
+        # so we mark the Step as DONE (successfully).
         wfid = rwf_response["workflow"]["id"]
         assert wfid
         wf_response, _ = self._wapi_adapter.get_workflow(workflow_id=wfid)
@@ -358,9 +358,9 @@ def _handle_pod_message(self, msg: PodMessage) -> None:
                     # For this simple logic it is the next step.
                     next_step = wf_response["steps"][step_index + 1]
 
-                    # A mojor piece of work to accomplish is to get ourselves into a position
+                    # A major piece of work to accomplish is to get ourselves into a position
                     # that allows us to check the step command can be executed.
-                    # We do this by compiling a map of variables we belive the step needs.
+                    # We do this by compiling a map of variables we believe the step needs.
 
                     # If the step about to be launched is based on a prior step
                     # that generates multiple outputs (files) then we have to
@@ -459,7 +459,7 @@ def _prepare_step(
         # whose origin is of type 'files'.
 
         our_job_definition: dict[str, Any] = self._get_step_job(step=step_definition)
-        our_inputs: dict[str, Any] = job_defintion_decoder.get_inputs(
+        our_inputs: dict[str, Any] = job_definition_decoder.get_inputs(
             our_job_definition
         )
         # get all our step connections that relate to prior steps.
@@ -470,10 +470,10 @@ def _prepare_step(
 
         we_are_a_combiner: bool = False
 
-        # What step might we be comnining?
-        # It'll remain None afdter the next block if we're not combining.
+        # What step might we be combining?
+        # It'll remain None after the next block if we're not combining.
         step_name_being_combined: str | None = None
-        # If we are a combiner, what is the varaible (identifying a set of files)
+        # If we are a combiner, what is the variable (identifying a set of files)
         # that is bing combined? There can only be one.
         combiner_input_variable: str | None = None
         for p_step_name, connections in plumbing_of_prior_steps.items():
@@ -502,7 +502,7 @@ def _prepare_step(
             assert num_step_recplicas_being_combined > 0
             assert "status" in response
 
-            # Assume all the dependent prior step instnaces are done
+            # Assume all the dependent prior step instances are done
             # and undo our assumption if not...
             all_step_instances_done: bool = True
 
@@ -539,7 +539,7 @@ def _prepare_step(
                     error_msg=f"Prior instance of step '{step_name_being_combined}' has failed",
                 )
 
-        # We're not a cmbiner or we are
+        # We're not a combiner or we are
         # (and all the dependent instances have completed successfully).
         # We can now compile a set of variables for it.
 
@@ -563,9 +563,9 @@ def _prepare_step(
         #
         # The decoder gives us a list of 'Connectors' that are a par of variable
         # names representing "in" (workflow) and "out" (step) variable names.
-        # "in" variables are worklfow variables, and "out" variables
-        # are expected Stewp (Job) variables. We use these connections to
-        # take workflow variables and puth them in our variables map.
+        # "in" variables are workflow variables, and "out" variables
+        # are expected Step (Job) variables. We use these connections to
+        # take workflow variables and put them in our variables map.
         for connector in get_step_workflow_variable_connections(
             step_definition=step_definition
         ):
@@ -607,13 +607,13 @@ def _prepare_step(
 
         # The step's prime variables are now set.
 
-        # Before we return these to the claler do we have enough
+        # Before we return these to the caller do we have enough
         # to satisfy the step Job's command? It's a simple check -
         # we give the step's Job command and our prime variables
-        # to the Job decoder - it wil tell us if an inportnat
+        # to the Job decoder - it wil tell us if an important
         # variable is missing....
         job: dict[str, Any] = self._get_step_job(step=step_definition)
-        message, success = job_defintion_decoder.decode(
+        message, success = job_definition_decoder.decode(
             job["command"], prime_variables, "command", TextEncoding.JINJA2_3_0
         )
         if not success:
@@ -628,7 +628,7 @@ def _prepare_step(
         # We need to set the number of step replicas to run.
         #
         # If we're not a combiner and a variable in our "plumbing" refers to a variable
-        # of type "files" in a prior step then we are expected to run multipe times
+        # of type "files" in a prior step then we are expected to run multiple times
         # (even if just once). The number of times we're expected to run is dictated
         # by the number of values (files) in the "files" variable.
         #
@@ -650,7 +650,7 @@ def _prepare_step(
                 wf_step: dict[str, Any] = get_step(wf, p_step_name)
                 assert wf_step
                 job_definition: dict[str, Any] = self._get_step_job(step=wf_step)
-                jd_outputs: dict[str, Any] = job_defintion_decoder.get_outputs(
+                jd_outputs: dict[str, Any] = job_definition_decoder.get_outputs(
                     job_definition
                 )
                 for connector in connections:
@@ -712,7 +712,7 @@ def _launch(
         step_definition: dict[str, Any],
         step_preparation_response: StepPreparationResponse,
     ) -> None:
-        """Given a runningWorkflow record, a step defitnion (from the Workflow),
+        """Given a runningWorkflow record, a step definition (from the Workflow),
         and the step's variables (in a preparation object) this method launches
         one or more instances of the given step."""
         step_name: str = step_definition["name"]