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Generalized stdout *clean version* #138

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Generalized stdout *clean version* #138

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b414545
Added acceptable formats helper functions
May 9, 2023
12b92fb
added absolute imports
AlexPatrie May 10, 2023
32e1fe3
added validation
AlexPatrie May 10, 2023
1477b6a
added testing
AlexPatrie May 10, 2023
c648da9
minor adjustments
AlexPatrie May 10, 2023
46ba80a
removed shadow alias
AlexPatrie May 10, 2023
898db27
minor linting
AlexPatrie May 10, 2023
7c3b2e3
minor linting
AlexPatrie May 10, 2023
51cd112
minor linting
AlexPatrie May 10, 2023
042dda0
minor linting for
AlexPatrie May 10, 2023
04350a0
implemented config and typing
AlexPatrie May 11, 2023
e07ccfc
added docstrings
AlexPatrie May 11, 2023
ad7843b
minor changes
AlexPatrie May 11, 2023
daa48ee
implementation of commit
AlexPatrie May 11, 2023
99e36ee
Delete wip_config.py
AlexPatrie May 11, 2023
ab20f1a
linting adjustments
AlexPatrie May 11, 2023
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24 changes: 14 additions & 10 deletions biosimulators_utils/combine/exec.py
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,13 @@
:License: MIT
"""

import copy
import datetime
import glob
import os
import tempfile
import shutil
import types # noqa: F401
from ..archive.io import ArchiveWriter
from ..archive.utils import build_archive_from_paths
from ..config import get_config, Config # noqa: F401
Expand All @@ -22,13 +29,7 @@
from .utils import get_sedml_contents, get_summary_sedml_contents
from .validation import validate
from ..viz.data_model import VizFormat # noqa: F401
import copy
import datetime
import glob
import os
import tempfile
import shutil
import types # noqa: F401


__all__ = [
'exec_sedml_docs_in_archive',
Expand All @@ -38,8 +39,8 @@
def exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir, apply_xml_model_changes=False,
sed_doc_executer_supported_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
sed_doc_executer_logged_features=(Task, Report, DataSet, Plot2D, Curve, Plot3D, Surface),
log_level=StandardOutputErrorCapturerLevel.c,
config=None):
log_level: StandardOutputErrorCapturerLevel = None,
config: Config = None):
""" Execute the SED-ML files in a COMBINE/OMEX archive (execute tasks and save outputs)

Args:
Expand Down Expand Up @@ -94,7 +95,10 @@ def sed_doc_executer(doc, working_dir, base_out_path, rel_out_path=None,
* :obj:`CombineArchiveLog`: log
"""
if not config:
config = get_config()
config = get_config(easy_log=True)

if not log_level:
log_level = config.STDOUT_LEVEL

with StandardOutputErrorCapturer(relay=True, level=log_level, disabled=not config.LOG) as archive_captured:
verbose = config.VERBOSE
Expand Down