Add warning messages for default connector params

This commit adds two warning messages:
- When a `QueueManagerConnector` is instantiated with the default value
  of 1 for the `maxConcurrentJobs` parameter;
- When an `SSHConnector` or a `QueueManagerConnector` defines at least
  one service template, but none is selected to execute a step.

This commit also substitutes the deprecated `logging.WARN` with the
preferred `logging.WARNING` constant.

streamflow/config/config.py

@@ -41,7 +41,7 @@ def __init__(self, name: str, config: MutableMapping[str, Any]) -> None:
         if not self.deplyoments:
             self.deplyoments = config.get("models", {})
             if self.deplyoments:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `models` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `deployments` instead."

streamflow/cwl/main.py

@@ -63,7 +63,7 @@ async def main(
     # Configure log level
     if args.quiet:
         # noinspection PyProtectedMember
-        cwltool.loghandler._logger.setLevel(logging.WARN)
+        cwltool.loghandler._logger.setLevel(logging.WARNING)
     # Load CWL workflow definition
     cwl_definition, loading_context = load_cwl_workflow(cwl_args[0])
     if len(cwl_args) == 2:

streamflow/cwl/runner.py

@@ -105,7 +105,7 @@ def main(args) -> int:
             print(f"StreamFlow version {VERSION}")
             return 0
         if args.quiet:
-            logger.setLevel(logging.WARN)
+            logger.setLevel(logging.WARNING)
         elif args.debug:
             logger.setLevel(logging.DEBUG)
         asyncio.run(_async_main(args))

streamflow/cwl/translator.py

@@ -1532,7 +1532,7 @@ def _translate_command_line_tool(
                     )
                 # Otherwise, throw a warning and skip the DockerRequirement conversion
                 else:
-                    if logger.isEnabledFor(logging.WARN):
+                    if logger.isEnabledFor(logging.WARNING):
                         logger.warning(
                             f"Skipping DockerRequirement conversion for step `{name_prefix}` "
                             f"when executing on `{target.deployment.name}` deployment."

streamflow/deployment/connector/container.py

@@ -122,7 +122,7 @@ def __init__(
         if cacheSize is None:
             cacheSize = resourcesCacheSize
             if cacheSize is not None:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `resourcesCacheSize` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `locationsCacheSize` instead."
@@ -133,7 +133,7 @@ def __init__(
         if cacheTTL is None:
             cacheTTL = resourcesCacheTTL
             if cacheTTL is not None:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `resourcesCacheTTL` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `locationsCacheTTL` instead."

streamflow/deployment/connector/kubernetes.py

@@ -188,7 +188,7 @@ def __init__(
         if cacheSize is None:
             cacheSize = resourcesCacheSize
             if cacheSize is not None:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `resourcesCacheSize` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `locationsCacheSize` instead."
@@ -199,7 +199,7 @@ def __init__(
         if cacheTTL is None:
             cacheTTL = resourcesCacheTTL
             if cacheTTL is not None:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `resourcesCacheTTL` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `locationsCacheTTL` instead."

streamflow/deployment/connector/queue_manager.py

@@ -340,7 +340,7 @@ def __init__(
     ) -> None:
         self._inner_ssh_connector: bool = False
         if hostname is not None:
-            if logger.isEnabledFor(logging.WARN):
+            if logger.isEnabledFor(logging.WARNING):
                 logger.warning(
                     "Inline SSH options are deprecated and will be removed in StreamFlow 0.3.0. "
                     f"Define a standalone `SSHConnector` and link the `{self.__class__.__name__}` "
@@ -374,7 +374,7 @@ def __init__(
                     with open(os.path.join(self.config_dir, service.file)) as f:
                         files_map[name] = f.read()
         if file is not None:
-            if logger.isEnabledFor(logging.WARN):
+            if logger.isEnabledFor(logging.WARNING):
                 logger.warning(
                     "The `file` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                     "Use `services` instead."
@@ -389,6 +389,12 @@ 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."
+            )
         self.pollingInterval: int = pollingInterval
         self.scheduledJobs: MutableSequence[str] = []
         self.jobsCache: cachetools.Cache = cachetools.TTLCache(
@@ -500,6 +506,13 @@ async def run(
                     )
                 )
             command = utils.encode_command(command)
+            if logger.isEnabledFor(logging.WARNING):
+                if not self.template_map.is_empty() and location.service is None:
+                    logger.warning(
+                        f"Deployment {self.deployment_name} contains some service definitions, "
+                        f"but none of them has been specified to execute job {job_name}. Execution "
+                        f"will fall back to the default template."
+                    )
             command = self.template_map.get_command(
                 command=command,
                 template=location.service,

streamflow/deployment/connector/ssh.py

@@ -283,7 +283,7 @@ def __init__(
                 with open(os.path.join(self.config_dir, service)) as f:
                     services_map[name] = f.read()
         if file is not None:
-            if logger.isEnabledFor(logging.WARN):
+            if logger.isEnabledFor(logging.WARNING):
                 logger.warning(
                     "The `file` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                     "Use `services` instead."
@@ -717,6 +717,13 @@ async def run(
             job_name=job_name,
         )
         if job_name is not None:
+            if logger.isEnabledFor(logging.WARNING):
+                if not self.template_map.is_empty() and location.service is None:
+                    logger.warning(
+                        f"Deployment {self.deployment_name} contains some service definitions, "
+                        f"but none of them has been specified to execute job {job_name}. Execution "
+                        f"will fall back to the default template."
+                    )
             command = self.template_map.get_command(
                 command=command,
                 template=location.service,

streamflow/deployment/manager.py

@@ -146,7 +146,7 @@ async def _inner_deploy(
         # If it is not a ConnectorWrapper, do nothing
         else:
             if deployment_config.wraps is not None:
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         f"The `wraps` directive has no effect on deployment {deployment_config.name}, "
                         f"as the `{deployment_config.type}` connector does not inherit from the ConnectorWrapper class."

streamflow/deployment/template.py

@@ -32,3 +32,6 @@ def get_command(
             streamflow_workdir=workdir,
             **kwargs,
         )
+
+    def is_empty(self) -> bool:
+        return len(self.templates) == 1

streamflow/deployment/utils.py

@@ -30,7 +30,7 @@ def get_binding_config(
                 target_deployment = workflow_config.deplyoments[target["deployment"]]
             else:
                 target_deployment = workflow_config.deplyoments[target["model"]]
-                if logger.isEnabledFor(logging.WARN):
+                if logger.isEnabledFor(logging.WARNING):
                     logger.warning(
                         "The `model` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                         "Use `deployment` instead."
@@ -39,7 +39,7 @@ def get_binding_config(
             if locations is None:
                 locations = target.get("resources")
                 if locations is not None:
-                    if logger.isEnabledFor(logging.WARN):
+                    if logger.isEnabledFor(logging.WARNING):
                         logger.warning(
                             "The `resources` keyword is deprecated and will be removed in StreamFlow 0.3.0. "
                             "Use `locations` instead."

streamflow/ext/plugin.py

@@ -48,7 +48,7 @@ def _register(self, name: str, cls: type, extension_point: str):
             }
         )
         if name in extension_points[extension_point]:
-            if logger.isEnabledFor(logging.WARN):
+            if logger.isEnabledFor(logging.WARNING):
                 logger.warning(
                     "{} is already installed and will be overridden by {}".format(
                         name, self.__class__.__module__ + "." + self.__class__.__name__

streamflow/main.py

@@ -260,7 +260,7 @@ def main(args):
             asyncio.run(_async_report(args))
         elif args.context == "run":
             if args.quiet:
-                logger.setLevel(logging.WARN)
+                logger.setLevel(logging.WARNING)
             elif args.debug:
                 logger.setLevel(logging.DEBUG)
             if args.color and hasattr(sys.stdout, "isatty") and sys.stdout.isatty():

streamflow/provenance/run_crate.py

@@ -570,7 +570,7 @@ async def add_file(self, file: MutableMapping[str, str]) -> None:
         dst = file.get("dst", posixpath.sep)
         dst_parent = posixpath.dirname(posixpath.normpath(dst))
         if src in self.files_map:
-            if logger.isEnabledFor(logging.WARN):
+            if logger.isEnabledFor(logging.WARNING):
                 logger.warning(f"File {src} is already present in the archive.")
         else:
             if os.path.isfile(os.path.realpath(src)):
@@ -679,7 +679,7 @@ async def add_property(self, key: str, value: str):
                     f"Token `{k}` of key `{key}` does not exist in archive manifest."
                 )
             current_obj = current_obj[k]
-        if logger.isEnabledFor(logging.WARN):
+        if logger.isEnabledFor(logging.WARNING):
             if keys[-1] in current_obj:
                 logger.warning(
                     f"Key {key} already exists in archive manifest and will be overridden."