13119627889

Committed 03 Feb 2025 05:51PM UTC coverage: 95.996% (-0.5%) from 96.536%

Build # 13119627889

Build Type

Pull #555

github

Committed by

web-flow

Commit Message

Merge 05f160496 into 5ec2a2015

Pull Request Pull Request #555: Add linting

Run Details

75 of 85 new or added lines in 16 files covered. (88.24%)

1 existing line in 1 file now uncovered.

1079 of 1124 relevant lines covered (96.0%)

0.96 hits per line

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92.11

/executorlib/cache/queue_spawner.py

import os
import subprocess
from typing import Optional, Union

from pysqa import QueueAdapter

from executorlib.standalone.hdf import dump, get_queue_id
from executorlib.standalone.inputcheck import check_file_exists


def execute_with_pysqa(
    command: list,
    task_dependent_lst: Optional[list[int]] = None,
    file_name: Optional[str] = None,
    resource_dict: Optional[dict] = None,
    config_directory: Optional[str] = None,
    backend: Optional[str] = None,
    cache_directory: Optional[str] = None,
) -> Optional[int]:
    """
    Execute a command by submitting it to the queuing system

    Args:
        command (list): The command to be executed.
        task_dependent_lst (list): A list of subprocesses that the current subprocess depends on. Defaults to [].
        file_name (str): Name of the HDF5 file which contains the Python function
        resource_dict (dict): resource dictionary, which defines the resources used for the execution of the function.
                              Example resource dictionary: {
                                  cwd: None,
                              }
        config_directory (str, optional): path to the config directory.
        backend (str, optional): name of the backend used to spawn tasks.
        cache_directory (str): The directory to store the HDF5 files.

    Returns:
        int: queuing system ID
    """
    if task_dependent_lst is None:
        task_dependent_lst = []
    check_file_exists(file_name=file_name)
    queue_id = get_queue_id(file_name=file_name)
    qa = QueueAdapter(
        directory=config_directory,
        queue_type=backend,
        execute_command=_pysqa_execute_command,
    )
    if queue_id is None or qa.get_status_of_job(process_id=queue_id) is None:
        if resource_dict is None:
            resource_dict = {}
        if "cwd" in resource_dict and resource_dict["cwd"] is not None:
            cwd = resource_dict["cwd"]
        else:
            cwd = cache_directory
        submit_kwargs = {
            "command": " ".join(command),
            "dependency_list": [str(qid) for qid in task_dependent_lst],
            "working_directory": os.path.abspath(cwd),
        }
        if "cwd" in resource_dict:
            del resource_dict["cwd"]
        unsupported_keys = [
            "threads_per_core",
            "gpus_per_core",
            "openmpi_oversubscribe",
            "slurm_cmd_args",
        ]
        for k in unsupported_keys:
            if k in resource_dict:
                del resource_dict[k]
        if "job_name" not in resource_dict:
            resource_dict["job_name"] = "pysqa"
        submit_kwargs.update(resource_dict)
        queue_id = qa.submit_job(**submit_kwargs)
        dump(file_name=file_name, data_dict={"queue_id": queue_id})
    return queue_id


def _pysqa_execute_command(
    commands: str,
    working_directory: Optional[str] = None,
    split_output: bool = True,
    shell: bool = False,
    error_filename: str = "pysqa.err",
) -> Union[str, list[str]]:
    """
    A wrapper around the subprocess.check_output function. Modified from pysqa to raise an exception if the subprocess
    fails to submit the job to the queue.

    Args:
        commands (str): The command(s) to be executed on the command line
        working_directory (str, optional): The directory where the command is executed. Defaults to None.
        split_output (bool, optional): Boolean flag to split newlines in the output. Defaults to True.
        shell (bool, optional): Additional switch to convert commands to a single string. Defaults to False.
        error_filename (str, optional): In case the execution fails, the output is written to this file. Defaults to "pysqa.err".

    Returns:
        Union[str, List[str]]: Output of the shell command either as a string or as a list of strings
    """
    if shell and isinstance(commands, list):
        commands = " ".join(commands)
    out = subprocess.check_output(
        commands,
        cwd=working_directory,
        stderr=subprocess.STDOUT,
        universal_newlines=True,
        shell=not isinstance(commands, list),
    )
    if out is not None and split_output:
        return out.split("\n")
    else:
        return out

1	import os	1✔
2	import subprocess	1✔
3	from typing import Optional, Union	1✔
4
5	from pysqa import QueueAdapter	1✔
6
7	from executorlib.standalone.hdf import dump, get_queue_id	1✔
8	from executorlib.standalone.inputcheck import check_file_exists	1✔
9
10
11	def execute_with_pysqa(	1✔
12	command: list,
13	task_dependent_lst: Optional[list[int]] = None,
14	file_name: Optional[str] = None,
15	resource_dict: Optional[dict] = None,
16	config_directory: Optional[str] = None,
17	backend: Optional[str] = None,
18	cache_directory: Optional[str] = None,
19	) -> Optional[int]:
20	"""
21	Execute a command by submitting it to the queuing system
22
23	Args:
24	command (list): The command to be executed.
25	task_dependent_lst (list): A list of subprocesses that the current subprocess depends on. Defaults to [].
26	file_name (str): Name of the HDF5 file which contains the Python function
27	resource_dict (dict): resource dictionary, which defines the resources used for the execution of the function.
28	Example resource dictionary: {
29	cwd: None,
30	}
31	config_directory (str, optional): path to the config directory.
32	backend (str, optional): name of the backend used to spawn tasks.
33	cache_directory (str): The directory to store the HDF5 files.
34
35	Returns:
36	int: queuing system ID
37	"""
38	if task_dependent_lst is None:	1✔
NEW 39	task_dependent_lst = []	×
40	check_file_exists(file_name=file_name)	1✔
41	queue_id = get_queue_id(file_name=file_name)	1✔
42	qa = QueueAdapter(	1✔
43	directory=config_directory,
44	queue_type=backend,
45	execute_command=_pysqa_execute_command,
46	)
47	if queue_id is None or qa.get_status_of_job(process_id=queue_id) is None:	1✔
48	if resource_dict is None:	1✔
49	resource_dict = {}	×
50	if "cwd" in resource_dict and resource_dict["cwd"] is not None:	1✔
51	cwd = resource_dict["cwd"]	1✔
52	else:
53	cwd = cache_directory	×
54	submit_kwargs = {	1✔
55	"command": " ".join(command),
56	"dependency_list": [str(qid) for qid in task_dependent_lst],
57	"working_directory": os.path.abspath(cwd),
58	}
59	if "cwd" in resource_dict:	1✔
60	del resource_dict["cwd"]	1✔
61	unsupported_keys = [	1✔
62	"threads_per_core",
63	"gpus_per_core",
64	"openmpi_oversubscribe",
65	"slurm_cmd_args",
66	]
67	for k in unsupported_keys:	1✔
68	if k in resource_dict:	1✔
69	del resource_dict[k]	1✔
70	if "job_name" not in resource_dict:	1✔
71	resource_dict["job_name"] = "pysqa"	1✔
72	submit_kwargs.update(resource_dict)	1✔
73	queue_id = qa.submit_job(**submit_kwargs)	1✔
74	dump(file_name=file_name, data_dict={"queue_id": queue_id})	1✔
75	return queue_id	1✔
76
77
78	def _pysqa_execute_command(	1✔
79	commands: str,
80	working_directory: Optional[str] = None,
81	split_output: bool = True,
82	shell: bool = False,
83	error_filename: str = "pysqa.err",
84	) -> Union[str, list[str]]:
85	"""
86	A wrapper around the subprocess.check_output function. Modified from pysqa to raise an exception if the subprocess
87	fails to submit the job to the queue.
88
89	Args:
90	commands (str): The command(s) to be executed on the command line
91	working_directory (str, optional): The directory where the command is executed. Defaults to None.
92	split_output (bool, optional): Boolean flag to split newlines in the output. Defaults to True.
93	shell (bool, optional): Additional switch to convert commands to a single string. Defaults to False.
94	error_filename (str, optional): In case the execution fails, the output is written to this file. Defaults to "pysqa.err".
95
96	Returns:
97	Union[str, List[str]]: Output of the shell command either as a string or as a list of strings
98	"""
99	if shell and isinstance(commands, list):	1✔
100	commands = " ".join(commands)	1✔
101	out = subprocess.check_output(	1✔
102	commands,
103	cwd=working_directory,
104	stderr=subprocess.STDOUT,
105	universal_newlines=True,
106	shell=not isinstance(commands, list),
107	)
108	if out is not None and split_output:	1✔
109	return out.split("\n")	1✔
110	else:
111	return out	1✔

pyiron / executorlib / 13119627889

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