Fixed typo errors (#326)

This commit fixes several issues:
- Fixes several typos in the code
- Removes the unused `step` parameter in the `_get_timeout`
  method
- Renames the `inputs` parameter in the `_persist_token`
  method to `input_token_ids`
- Improves the command format in the logs when the
  color feature is enabled

streamflow/cwl/command.py

@@ -334,7 +334,7 @@ async def _save_additional_params(
             },
         }
 
-    def _get_timeout(self, job: Job, step: Step) -> int | None:
+    def _get_timeout(self, job: Job) -> int | None:
         timeout = 0
         if isinstance(self.time_limit, int):
             timeout = self.time_limit
@@ -355,7 +355,7 @@ def _get_timeout(self, job: Job, step: Step) -> int | None:
             )
         if timeout and timeout < 0:
             raise WorkflowDefinitionException(
-                f"Invalid time limit for step {step.name}: {timeout}. Time limit should be >= 0."
+                f"Invalid time limit for step {self.step.name}: {timeout}. Time limit should be >= 0."
             )
         elif timeout == 0:
             return None
@@ -824,7 +824,7 @@ async def execute(self, job: Job) -> CWLCommandOutput:
             else stdout
         )
         # Get timeout
-        timeout = self._get_timeout(job=job, step=self.step)
+        timeout = self._get_timeout(job=job)
         # Execute remote command
         start_time = time.time_ns()
         result, exit_code = await connector.run(

streamflow/deployment/connector/kubernetes.py

@@ -215,7 +215,7 @@ def __init__(
     def _configure_incluster_namespace(self):
         if self.namespace is None:
             if not os.path.isfile(SERVICE_NAMESPACE_FILENAME):
-                raise ConfigException("Service namespace file does not exists.")
+                raise ConfigException("Service namespace file does not exist.")
 
             with open(SERVICE_NAMESPACE_FILENAME) as f:
                 self.namespace = f.read()

streamflow/deployment/connector/queue_manager.py

@@ -389,12 +389,13 @@ def __init__(
                 template_map=files_map,
             )
         self.maxConcurrentJobs: int = maxConcurrentJobs
-        if logger.isEnabledFor(logging.WARNING):
-            logger.warning(
-                "The `maxConcurrentJobs` parameter is set to the default value 1, which prevents "
-                "multiple jobs to be concurrently submitted to the queue manager. Consider raising "
-                "this value to improve performance."
-            )
+        if self.maxConcurrentJobs == 1:
+            if logger.isEnabledFor(logging.WARNING):
+                logger.warning(
+                    "The `maxConcurrentJobs` parameter is set to the default value 1, which prevents "
+                    "multiple jobs to be concurrently submitted to the queue manager. Consider raising "
+                    "this value to improve performance."
+                )
         self.pollingInterval: int = pollingInterval
         self.scheduledJobs: MutableSequence[str] = []
         self.jobsCache: cachetools.Cache = cachetools.TTLCache(

streamflow/deployment/connector/schemas/kubernetes.json

@@ -8,7 +8,7 @@
       "items": {
         "type": "string"
       },
-      "description": "A list of yaml file to deploy. Files will be deployed in direct order and undeplyoed in reverse order"
+      "description": "A list of yaml file to deploy. Files will be deployed in direct order and undeployed in reverse order"
     },
     "debug": {
       "type": "boolean",

streamflow/deployment/connector/schemas/ssh.json

@@ -29,7 +29,7 @@
             "string",
             "null"
           ],
-          "description": "Path to the SSH key needed to connect with Slurm environment"
+          "description": "Path to the SSH key needed to connect with the environment"
         },
         "sshKeyPassphraseFile": {
           "type": [
@@ -133,7 +133,7 @@
     },
     "sshKey": {
       "type": "string",
-      "description": "Path to the SSH key needed to connect with Slurm environment"
+      "description": "Path to the SSH key needed to connect with the environment"
     },
     "sshKeyPassphraseFile": {
       "type": "string",

streamflow/log_handler.py

@@ -89,7 +89,7 @@ def filter(self, record):
 
     def highlight(self, msg):
         msg = str(msg)
-        msg_tok = msg.split()
+        msg_tok = msg.split(" ")
         for pattern, category in self.patterns.items():
             if msg_tok[0] == pattern:
                 if category == 0:

streamflow/parser.py

@@ -127,7 +127,7 @@ def __call__(self, _parser, namespace, values, option_string=None):
     "--all",
     "-a",
     action="store_true",
-    help="If true, include all executions of the selected worwflow. "
+    help="If true, include all executions of the selected workflow. "
     "If false, include just the last one. (default: false)",
 )
 prov_parser.add_argument(
@@ -168,7 +168,7 @@ def __call__(self, _parser, namespace, values, option_string=None):
     "--all",
     "-a",
     action="store_true",
-    help="If true, include all executions of the selected worwflow. "
+    help="If true, include all executions of the selected workflow. "
     "If false, include just the last one. (default: false)",
 )
 report_parser.add_argument(

streamflow/workflow/step.py

@@ -514,10 +514,10 @@ async def run(self):
                             )
                             # Propagate the connector in the output port
                             self.get_output_port().put(
-                                await self.persist_token(
+                                await self._persist_token(
                                     token=Token(value=self.deployment_config.name),
                                     port=self.get_output_port(),
-                                    inputs=_get_token_ids(inputs.values()),
+                                    input_token_ids=_get_token_ids(inputs.values()),
                                 )
                             )
             else: