11749909901

Committed 08 Nov 2024 09:35PM UTC coverage: 95.011% (-0.2%) from 95.203%

Build # 11749909901

Build Type

Pull #481

github

Committed by

web-flow

Commit Message

Merge 9afcb5665 into 213202831

Pull Request Pull Request #481: Fix working directory

Run Details

2 of 7 new or added lines in 2 files covered. (28.57%)

895 of 942 relevant lines covered (95.01%)

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88.89

/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,
    cache_directory: 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.
        cache_directory (str): The directory to store the HDF5 files.

    Returns:
        int: queuing system ID
    """
    if resource_dict is None:
        resource_dict = {"cwd": cache_directory}
    elif len(resource_dict) == 0:
        resource_dict = {"cwd": cache_directory}
    elif "cwd" in resource_dict and resource_dict["cwd"] is None:
        resource_dict["cwd"] = cache_directory
    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	cache_directory: Optional[str] = None,
15	) -> int:
16	"""
17	Execute a command by submitting it to the queuing system
18
19	Args:
20	command (list): The command to be executed.
21	task_dependent_lst (list): A list of subprocesses that the current subprocess depends on. Defaults to [].
22	resource_dict (dict): resource dictionary, which defines the resources used for the execution of the function.
23	Example resource dictionary: {
24	cwd: None,
25	}
26	config_directory (str, optional): path to the config directory.
27	backend (str, optional): name of the backend used to spawn tasks.
28	cache_directory (str): The directory to store the HDF5 files.
29
30	Returns:
31	int: queuing system ID
32	"""
33	if resource_dict is None:	1✔
NEW 34	resource_dict = {"cwd": cache_directory}	×
35	elif len(resource_dict) == 0:	1✔
NEW 36	resource_dict = {"cwd": cache_directory}	×
37	elif "cwd" in resource_dict and resource_dict["cwd"] is None:	1✔
NEW 38	resource_dict["cwd"] = cache_directory	×
39	qa = QueueAdapter(	1✔
40	directory=config_directory,
41	queue_type=backend,
42	execute_command=_pysqa_execute_command,
43	)
44	submit_kwargs = {	1✔
45	"command": " ".join(command),
46	"dependency_list": [str(qid) for qid in task_dependent_lst],
47	"working_directory": os.path.abspath(resource_dict["cwd"]),
48	}
49	del resource_dict["cwd"]	1✔
50	unsupported_keys = [	1✔
51	"threads_per_core",
52	"gpus_per_core",
53	"openmpi_oversubscribe",
54	"slurm_cmd_args",
55	]
56	for k in unsupported_keys:	1✔
57	if k in resource_dict:	1✔
58	del resource_dict[k]	1✔
59	submit_kwargs.update(resource_dict)	1✔
60	return qa.submit_job(**submit_kwargs)	1✔
61
62
63	def _pysqa_execute_command(	1✔
64	commands: str,
65	working_directory: Optional[str] = None,
66	split_output: bool = True,
67	shell: bool = False,
68	error_filename: str = "pysqa.err",
69	) -> Union[str, List[str]]:
70	"""
71	A wrapper around the subprocess.check_output function. Modified from pysqa to raise an exception if the subprocess
72	fails to submit the job to the queue.
73
74	Args:
75	commands (str): The command(s) to be executed on the command line
76	working_directory (str, optional): The directory where the command is executed. Defaults to None.
77	split_output (bool, optional): Boolean flag to split newlines in the output. Defaults to True.
78	shell (bool, optional): Additional switch to convert commands to a single string. Defaults to False.
79	error_filename (str, optional): In case the execution fails, the output is written to this file. Defaults to "pysqa.err".
80
81	Returns:
82	Union[str, List[str]]: Output of the shell command either as a string or as a list of strings
83	"""
84	if shell and isinstance(commands, list):	1✔
85	commands = " ".join(commands)	1✔
86	out = subprocess.check_output(	1✔
87	commands,
88	cwd=working_directory,
89	stderr=subprocess.STDOUT,
90	universal_newlines=True,
91	shell=not isinstance(commands, list),
92	)
93	if out is not None and split_output:	1✔
94	return out.split("\n")	1✔
95	else:
96	return out	1✔

pyiron / executorlib / 11749909901

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