11576479865

Committed 29 Oct 2024 02:52PM UTC coverage: 94.618% (-0.6%) from 95.228%

Build # 11576479865

Build Type

Pull #465

github

Committed by

web-flow

Commit Message

Merge cce902623 into b41acbaad

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

Run Details

3 of 9 new or added lines in 1 file covered. (33.33%)

1 existing line in 1 file now uncovered.

879 of 929 relevant lines covered (94.62%)

0.95 hits per line

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

68.18

/executorlib/standalone/cache/queue.py

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

pyiron / executorlib / 11576479865

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