docs: Make docstring compatible with pydocstyle

reana_job_controller/compute4punch_job_manager.py

@@ -4,6 +4,8 @@
 # REANA is free software; you can redistribute it and/or modify it
 # under the terms of the MIT License; see LICENSE file for more details.
 
+"""Compute4PUNCH Job Manager."""
+
 import base64
 import logging
 import os
@@ -26,7 +28,7 @@
 
 
 class Compute4PUNCHJobManager(JobManager):
-    """Compute4PUNCH Job Manager"""
+    """Compute4PUNCH Job Manager."""
 
     C4P_WORKSPACE_PATH = ""
     """Absolute path on the Compute4PUNCH head node used for submission"""
@@ -169,6 +171,13 @@ def get_logs(cls, backend_job_id: str, **kwargs) -> str:
     def get_outputs(cls, c4p_connection, src, dest) -> None:
         """
         Transfer job outputs from Compute4PUNCH to local REANA workspace.
+
+        :param c4p_connection: SSH connection to Compute4PUNCH
+        :type c4p_connection: SSHClient
+        :param src: Source directory
+        :type src: str
+        :param dest: Destination directory
+        :type dest: str
         """
         sftp_client = c4p_connection.ssh_client.open_sftp()
         sftp_client.chdir(src)
@@ -191,9 +200,7 @@ def stop(self, backend_job_id: str) -> None:
 
     @property
     def c4p_home_path(self) -> str:
-        """
-        Determine and return the Compute4PUNCH home directory on Compute4PUNCH
-        """
+        """Determine and return the Compute4PUNCH home directory on Compute4PUNCH."""
         if not self.C4P_HOME_PATH:
             # Since the JobMonitor entirely rely on class variables to get corresponding
             # paths on Compute4PUNCH, the class variable C4P_HOME_PATH needs to be
@@ -205,9 +212,7 @@ def c4p_home_path(self) -> str:
 
     @property
     def c4p_abs_workspace_path(self) -> str:
-        """
-        Determine and return the absolute Compute4PUNCH workspace path
-        """
+        """Determine and return the absolute Compute4PUNCH workspace path."""
         if not self.C4P_WORKSPACE_PATH:
             # Since the JobMonitor entirely rely on class variables to get corresponding
             # paths on Compute4PUNCH, the class variable C4P_WORKSPACE_PATH needs to be
@@ -219,15 +224,11 @@ def c4p_abs_workspace_path(self) -> str:
 
     @property
     def c4p_rel_workspace_path(self) -> str:
-        """
-        Determine and return the relative Compute4PUNCH workspace path
-        """
+        """Determine and return the relative Compute4PUNCH workspace path."""
         return os.path.join("reana/workflows", self.workflow_uuid)
 
     def _create_c4p_job_description(self) -> None:
-        """
-        Create job description for Compute4PUNCH
-        """
+        """Create job description for Compute4PUNCH."""
         job_inputs = ",".join(self._get_inputs())
         job_outputs = "."  # download everything from remote job
         job_description_template = [
@@ -257,9 +258,7 @@ def _create_c4p_job_description(self) -> None:
         )
 
     def _create_c4p_job_execution_script(self) -> None:
-        """
-        Create job execution script for Compute4PUNCH
-        """
+        """Create job execution script for Compute4PUNCH."""
         # The workflow workspace does not exist on Compute4PUNCH,
         # therefore replace it with CONDOR_JOB_IWD
         self.cmd = self.cmd.replace(self.workflow_workspace, "$_CONDOR_JOB_IWD")
@@ -274,9 +273,7 @@ def _create_c4p_job_execution_script(self) -> None:
         )
 
     def _create_c4p_workspace_environment(self) -> None:
-        """
-        Create workspace environment for REANA @ Compute4PUNCH
-        """
+        """Create workspace environment for REANA @ Compute4PUNCH."""
         self.c4p_connection.exec_command(f"mkdir -p {self.c4p_abs_workspace_path}")
         self.c4p_connection.exec_command(
             os.path.join(
@@ -331,9 +328,7 @@ def _encode_cmd(cmd: str) -> str:
         return f"echo {encoded_cmd} | base64 -d | bash"
 
     def _get_inputs(self) -> Iterable:
-        """
-        Collect all input files in the local REANA workspace.
-        """
+        """Collect all input files in the local REANA workspace."""
         skipped_input_files = (".job.ad", ".machine.ad", ".chirp.config")
         return filter(
             lambda x: x not in skipped_input_files,
@@ -343,9 +338,7 @@ def _get_inputs(self) -> Iterable:
         )
 
     def _upload_job_inputs(self) -> None:
-        """
-        Upload job inputs to Compute4PUNCH
-        """
+        """Upload job inputs to Compute4PUNCH."""
         sftp_client = self.c4p_connection.ssh_client.open_sftp()
         sftp_client.chdir(self.c4p_rel_workspace_path)
 

reana_job_controller/job_monitor.py

@@ -576,6 +576,13 @@ def watch_jobs(self, job_db, app=None):
 
 
 def query_c4p_jobs(*backend_job_ids: str, ssh_client: SSHClient):
+    """
+    Query status information of backend jobs on Compute4PUNCH.
+
+    :param backend_job_ids: List of job ids to query on Compute4PUNCH
+    :type backend_job_ids: str
+    :param ssh_client: SSH client used to communicate with Compute4PUNCH
+    """
     attributes = ("JobStatus", "ClusterId", "ProcId", "ExitCode", "HoldReasonCode")
     attributes_string = " ".join(attributes)
 
@@ -607,6 +614,18 @@ def query_c4p_jobs(*backend_job_ids: str, ssh_client: SSHClient):
 def filter_jobs_to_watch(
     id, job_db, compute_backend, statuses_to_skip=("finished", "failed", "stopped")
 ):
+    """
+    Filter jobs to watch for job completion.
+
+    :param id: REANA job id
+    :type id: str
+    :param job_db: REANA job database
+    :type job_db: JOB_DB
+    :param compute_backend: REANA compute backend used
+    :type compute_backend: str
+    :param statuses_to_skip: REANA job statuses to skip
+    :type statuses_to_skip: tuple[str]
+    """
     return job_db[id]["compute_backend"] == compute_backend and not (
         job_db[id]["deleted"] or job_db[id]["status"] in statuses_to_skip
     )

reana_job_controller/utils.py

@@ -82,7 +82,7 @@ def csv_parser(
     skip_trailing_space: bool = False,
 ):
     """
-    Parses CSV formatted input
+    Parse CSV formatted input.
 
     :param input_csv: CSV formatted input
     :type input_csv: str
@@ -116,6 +116,15 @@ def csv_parser(
 
 
 def motley_cue_auth_strategy_factory(hostname):
+    """
+    Paramiko auth strategy factory that provides oauth based ssh token authentication.
+
+    This auth strategy has been developed against the motley cue implementation of
+    oauth based ssh token authentication on the server side.
+
+    :param hostname: hostname of the ssh node
+    :type hostname: str
+    """
     # Using a factory to avoid a general dependency on libmytoken, paramiko and pyjwt
     from libmytoken import get_access_token_from_jwt_mytoken
     from paramiko.auth_strategy import AuthSource