11576835345

Committed 29 Oct 2024 03:10PM UTC coverage: 95.054% (-0.2%) from 95.228%

Build # 11576835345

Build Type

Pull #465

github

Committed by

web-flow

Commit Message

Merge 426f974c8 into b41acbaad

Pull Request Pull Request #465: Add pysqa command which raises an exception

Run Details

8 of 10 new or added lines in 1 file covered. (80.0%)

884 of 930 relevant lines covered (95.05%)

0.95 hits per line

Source File
Press 'n' to go to next uncovered line, 'b' for previous

86.96

/executorlib/standalone/cache/queue.py

import os
import subprocess
from typing import List, Optional, Union

from pysqa import QueueAdapter


def execute_with_pysqa(
    command: str,
    resource_dict: dict,
    task_dependent_lst: List[int] = [],
    config_directory: Optional[str] = None,
    backend: Optional[str] = None,
) -> 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 [].
        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.

    Returns:
        int: queuing system ID
    """
    if resource_dict is None:
        resource_dict = {"cwd": "."}
    qa = QueueAdapter(
        directory=config_directory,
        queue_type=backend,
        execute_command=_pysqa_execute_command,
    )
    submit_kwargs = {
        "command": " ".join(command),
        "dependency_list": [str(qid) for qid in task_dependent_lst],
        "working_directory": os.path.abspath(resource_dict["cwd"]),
    }
    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]
    submit_kwargs.update(resource_dict)
    return qa.submit_job(**submit_kwargs)


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

pyiron / executorlib / 11576835345

Source File Press 'n' to go to next uncovered line, 'b' for previous

Source File
Press 'n' to go to next uncovered line, 'b' for previous