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Changed log level of Capturer Object #67

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merged 3 commits into from
May 8, 2023
+15 −3
Merged

Changed log level of Capturer Object #67

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0be700c
changed standard output errror capturer level to python
AlexPatrie May 7, 2023
52ab854
Added catch block for macOS
AlexPatrie May 7, 2023
68a807d
implemented try block for darwin
AlexPatrie May 8, 2023
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18 changes: 15 additions & 3 deletions biosimulators_copasi/core.py
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Original file line number Diff line number Diff line change
Expand Up @@ -31,10 +31,20 @@
import numpy
import os
import tempfile
import platform


__all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_doc', 'exec_sed_task', 'preprocess_sed_task']


CURRENT_PLATFORM = platform.system()
try:
assert CURRENT_PLATFORM == "Darwin"
DEFAULT_STDOUT_LEVEL = StandardOutputErrorCapturerLevel.python
except AssertionError as e:
DEFAULT_STDOUT_LEVEL = StandardOutputErrorCapturerLevel.c


def exec_sedml_docs_in_combine_archive(archive_filename: str, out_dir: str, config: Optional[Config] = None,
fix_copasi_generated_combine_archive: Optional[bool] = None) -> Tuple[SedDocumentResults, CombineArchiveLog]:
""" Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
Expand Down Expand Up @@ -79,7 +89,7 @@ def exec_sedml_docs_in_combine_archive(archive_filename: str, out_dir: str, conf
def exec_sed_doc(doc: Union[SedDocument, str], working_dir: str, base_out_path: str, rel_out_path: Optional[str] = None,
apply_xml_model_changes: bool = True, log: Optional[SedDocumentLog] = None,
indent: int = 0, pretty_print_modified_xml_models: bool = False,
log_level: Optional[Union[StandardOutputErrorCapturerLevel, str]] = StandardOutputErrorCapturerLevel.c,
log_level: Optional[StandardOutputErrorCapturerLevel]=DEFAULT_STDOUT_LEVEL,
config: Optional[Config] = None) -> Tuple[ReportResults, SedDocumentLog]:
""" Execute the tasks specified in a SED document and generate the specified outputs

Expand Down Expand Up @@ -190,8 +200,10 @@ def exec_sed_task(task: Task, variables: List[Variable], preprocessed_task: Opti
else: # noqa python:S3776
step_number = (
sim.number_of_points
* (sim.output_end_time - sim.initial_time)
/ (sim.output_end_time - sim.output_start_time)
* (
(sim.output_end_time - sim.initial_time)
/ (sim.output_end_time - sim.output_start_time)
)
)
if step_number != math.floor(step_number):
raise NotImplementedError('Time course must specify an integer number of time points')
Expand Down