Refactor codebase

pysqa/__main__.py

@@ -0,0 +1,6 @@
+import sys
+from pysqa.cmd import command_line
+
+
+if __name__ == "__main__":
+    command_line(sys.argv[1:])

pysqa/queueadapter.py

@@ -2,7 +2,10 @@
 # Copyright (c) Jan Janssen
 
 import os
-from pysqa.utils.functs import read_config, set_queue_adapter
+from pysqa.utils.basic import BasisQueueAdapter
+from pysqa.ext.modular import ModularQueueAdapter
+from pysqa.ext.remote import RemoteQueueAdapter
+from pysqa.utils.config import read_config
 
 __author__ = "Jan Janssen"
 __copyright__ = "Copyright 2019, Jan Janssen"
@@ -288,3 +291,21 @@ def check_queue_parameters(
             memory_max=memory_max,
             active_queue=active_queue,
         )
+
+
+def set_queue_adapter(config, directory):
+    """
+    Initialize the queue adapter
+
+    Args:
+        config (dict): configuration for one cluster
+        directory (str): directory which contains the queue configurations
+    """
+    if config["queue_type"] in ["SGE", "TORQUE", "SLURM", "LSF", "MOAB"]:
+        return BasisQueueAdapter(config=config, directory=directory)
+    elif config["queue_type"] in ["GENT"]:
+        return ModularQueueAdapter(config=config, directory=directory)
+    elif config["queue_type"] in ["REMOTE"]:
+        return RemoteQueueAdapter(config=config, directory=directory)
+    else:
+        raise ValueError

pysqa/utils/config.py

@@ -0,0 +1,14 @@
+import yaml
+
+
+def read_config(file_name="queue.yaml"):
+    """
+
+    Args:
+        file_name (str):
+
+    Returns:
+        dict:
+    """
+    with open(file_name, "r") as f:
+        return yaml.load(f, Loader=yaml.FullLoader)

pysqa/wrapper/torque.py

@@ -2,9 +2,9 @@
 # Copyright (c) Max-Planck-Institut für Eisenforschung GmbH - Computational Materials Design (CM) Department
 # Distributed under the terms of "New BSD License", see the LICENSE file.
 
-from pysqa.wrapper.generic import SchedulerCommands
 import re
 import pandas as pd
+from pysqa.wrapper.generic import SchedulerCommands
 
 __author__ = "Jan Janssen"
 __copyright__ = (
@@ -33,7 +33,8 @@ def get_queue_status_command(self):
 
     @staticmethod
     def get_job_id_from_output(queue_submit_output):
-        # strip last line from output, leading and trailing whitespaces, and separates the queue id from the stuff after "."
+        # strip last line from output, leading and trailing whitespaces,
+        # and separates the queue id from the stuff after "."
         # Adjust if your system doesn't have output like below!
         # e.g. qsub run_queue.sh -> "12347673.gadi-pbs", the below returns 12347673
         # It must return an integer for it to not raise an exception later.
@@ -44,7 +45,8 @@ def get_job_id_from_output(queue_submit_output):
     @staticmethod
     def convert_queue_status(queue_status_output):
         # # Run the qstat -f command and capture its output
-        # output = subprocess.check_output(["qstat", "-f"]) -> output is the queue_status_output that goes into this function
+        # output = subprocess.check_output(["qstat", "-f"]) -> output is the
+        # queue_status_output that goes into this function
 
         # Split the output into lines
         lines = queue_status_output.split("\n")  # .decode().split("\n")

setup.py

@@ -36,4 +36,9 @@
                       'pyyaml==6.0',
                       'tqdm==4.65.0'],
     cmdclass=versioneer.get_cmdclass(),
+    entry_points={
+            "console_scripts": [
+                'pysqa=pysqa:main'
+            ]
+    }
     )