biosimulators_pyneuroml package¶
- biosimulators_pyneuroml.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute the tasks specified in a SED document and generate the specified outputs
- Parameters
doc (
SedDocument
orstr
) – SED document or a path to SED-ML file which defines a SED documentworking_dir (
str
) – working directory of the SED document (path relative to which models are located)base_out_path (
str
) –path to store the outputs
CSV: directory in which to save outputs to files
{base_out_path}/{rel_out_path}/{report.id}.csv
HDF5: directory in which to save a single HDF5 file (
{base_out_path}/reports.h5
), with reports at keys{rel_out_path}/{report.id}
within the HDF5 file
rel_out_path (
str
, optional) – path relative tobase_out_path
to store the outputsapply_xml_model_changes (
bool
, optional) – ifTrue
, apply any model changes specified in the SED-ML file before callingtask_executer
.log (
SedDocumentLog
, optional) – log of the documentindent (
int
, optional) – degree to indent status messagespretty_print_modified_xml_models (
bool
, optional) – ifTrue
, pretty print modified XML modelslog_level (
StandardOutputErrorCapturerLevel
, optional) – level at which to log outputconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
ReportResults
: results of each reportSedDocumentLog
: log of the document
- Return type
tuple
- biosimulators_pyneuroml.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute a task and save its results
- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedpreprocessed_task (
dict
, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.log (
TaskLog
, optional) – log for the taskconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
VariableResults
: results of variablesTaskLog
: log- Return type
tuple
- Raises
ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded
NotImplementedError – if the task is not of a supported type or involves an unsuported feature
- biosimulators_pyneuroml.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
- Parameters
archive_filename (
str
) – path to COMBINE/OMEX archiveout_dir (
str
) –path to store the outputs of the archive
CSV: directory in which to save outputs to files
{ out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv
HDF5: directory in which to save a single HDF5 file (
{ out_dir }/reports.h5
), with reports at keys{ relative-path-to-SED-ML-file-within-archive }/{ report.id }
within the HDF5 file
simulator (
Simulator
, optional) – simulatorconfig (
Config
, optional) – BioSimulators common configuration
- Returns
SedDocumentResults
: resultsCombineArchiveLog
: log
- Return type
tuple
- biosimulators_pyneuroml.preprocess_sed_task(task, variables, config=None, simulator=Simulator.pyneuroml)[source]¶
Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of
exec_sed_task
.- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
preprocessed information about the task
- Return type
dict
Subpackages¶
Submodules¶
biosimulators_pyneuroml.core module¶
Methods for using pyNeuroML to execute SED tasks in COMBINE archives and save their outputs
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-05-28
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_pyneuroml.core.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute the tasks specified in a SED document and generate the specified outputs
- Parameters
doc (
SedDocument
orstr
) – SED document or a path to SED-ML file which defines a SED documentworking_dir (
str
) – working directory of the SED document (path relative to which models are located)base_out_path (
str
) –path to store the outputs
CSV: directory in which to save outputs to files
{base_out_path}/{rel_out_path}/{report.id}.csv
HDF5: directory in which to save a single HDF5 file (
{base_out_path}/reports.h5
), with reports at keys{rel_out_path}/{report.id}
within the HDF5 file
rel_out_path (
str
, optional) – path relative tobase_out_path
to store the outputsapply_xml_model_changes (
bool
, optional) – ifTrue
, apply any model changes specified in the SED-ML file before callingtask_executer
.log (
SedDocumentLog
, optional) – log of the documentindent (
int
, optional) – degree to indent status messagespretty_print_modified_xml_models (
bool
, optional) – ifTrue
, pretty print modified XML modelslog_level (
StandardOutputErrorCapturerLevel
, optional) – level at which to log outputconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
ReportResults
: results of each reportSedDocumentLog
: log of the document
- Return type
tuple
- biosimulators_pyneuroml.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute a task and save its results
- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedpreprocessed_task (
dict
, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.log (
TaskLog
, optional) – log for the taskconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
VariableResults
: results of variablesTaskLog
: log- Return type
tuple
- Raises
ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded
NotImplementedError – if the task is not of a supported type or involves an unsuported feature
- biosimulators_pyneuroml.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, simulator=Simulator.pyneuroml)[source]¶
Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
- Parameters
archive_filename (
str
) – path to COMBINE/OMEX archiveout_dir (
str
) –path to store the outputs of the archive
CSV: directory in which to save outputs to files
{ out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv
HDF5: directory in which to save a single HDF5 file (
{ out_dir }/reports.h5
), with reports at keys{ relative-path-to-SED-ML-file-within-archive }/{ report.id }
within the HDF5 file
simulator (
Simulator
, optional) – simulatorconfig (
Config
, optional) – BioSimulators common configuration
- Returns
SedDocumentResults
: resultsCombineArchiveLog
: log
- Return type
tuple
- biosimulators_pyneuroml.core.preprocess_sed_task(task, variables, config=None, simulator=Simulator.pyneuroml)[source]¶
Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of
exec_sed_task
.- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedconfig (
Config
, optional) – BioSimulators common configurationsimulator (
Simulator
, optional) – simulator
- Returns
preprocessed information about the task
- Return type
dict
biosimulators_pyneuroml.data_model module¶
Data model for pyNeuroML algorithms and their parameters
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-06-02
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- class biosimulators_pyneuroml.data_model.RunLemsOptions(paths_to_include=None, num_processors=None, max_memory=None, skip_run=False, no_gui=True, load_saved_data=False, reload_events=False, plot=False, show_plot_already=False, exec_in_dir='.', verbose=False, exit_on_fail=False, cleanup=True, only_generate_scripts=False, compile_mods=True, realtime_output=False)[source]¶
Bases:
object
Options for running a LEMS file
biosimulators_pyneuroml.utils module¶
Utilities for pyNeuroML
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-06-02
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_pyneuroml.utils.get_available_memory()[source]¶
Get the amount of memory available
- Returns
amount of memory available in bytes
- Return type
int
- biosimulators_pyneuroml.utils.get_available_processors()[source]¶
Get the amount of processors available
- Returns
amount of processors available
- Return type
int
- biosimulators_pyneuroml.utils.get_run_lems_options(num_processors=None, max_memory=None, verbose=False)[source]¶
Get options for running a LEMS document
- Parameters
num_processors (
int
, optional) – number of processors to use (only used with NetPyNe)max_memory (
int
, optional) – maximum memory to use in bytesverbose (
bool
, optional) – whether to display extra information about simulation runs
- Returns
options
- Return type
RunLemsOptions
- biosimulators_pyneuroml.utils.get_simulator_run_lems_method(simulator)[source]¶
Get the LEMS run method for a simulator
- Parameters
simulator (
Simulator
) – simulator to run the LEMS document- Returns
run LEMS method
- Return type
types.FunctionType
- biosimulators_pyneuroml.utils.read_lems_output_files_configuration(xml_root)[source]¶
Read the configuration of the output files of a LEMS document
- Parameters
xml_root (
lxml.etree._Element
) – LEMS document- Returns
configuration of the output files of a LEMS document
- Return type
list
ofdict
- biosimulators_pyneuroml.utils.read_xml_file(filename, remove_blank_text=True)[source]¶
Read an XML file
- Parameters
filename (
str
) – path to an XML fileremove_blank_text (
bool
, optional) – whether to remove formatting so that the file could be exported pretty-printed
- Returns
root element for the XML file
- Return type
lxml.etree._Element
- biosimulators_pyneuroml.utils.run_lems_xml(lems_xml_root, working_dirname='.', lems_filename=None, simulator=Simulator.pyneuroml, num_processors=None, max_memory=None, verbose=False, config=None)[source]¶
Run a LEMS document with a simulator
- Parameters
lems_xml_root (
lxml.etree._Element
) – LEMS documentworking_dirname (
str
, optional) – working directory for the LEMS documentlems_filename (
str
, optional) – path to file for the LEMS documentsimulator (
Simulator
, optional) – simulator to run the LEMS documentnum_processors (
int
, optional) – number of processors to use (only used with NetPyNe)max_memory (
int
, optional) – maximum memory to use in bytesverbose (
bool
, optional) – whether to display extra information about simulation runsconfig (
Config
, optional) – BioSimulators common configuration
- Returns
- dictionary that maps the id of each output file
to a Pandas data frame with its value
- Return type
dict
ofstr
=>pandas.DataFrame
- biosimulators_pyneuroml.utils.set_sim_in_lems_xml(simulation_xml, task, variables, simulator=Simulator.pyneuroml)[source]¶
Set the simulation in a LEMS document
- Parameters
simulation_xml (
lxml.etree._Element
) – LEMS simulationtask (
Task
) – taskvariables (
list
ofVariable
) – variables to recordsimulator (
Simulator
, optional) – simulator to run the LEMS document
- biosimulators_pyneuroml.utils.validate_lems_document(lems_xml_root)[source]¶
Validate LEMS document
- Parameters
lems_xml_root (
lxml.etree._Element
) – LEMS document
- biosimulators_pyneuroml.utils.validate_task(task, variables, simulator, config=None)[source]¶
Validate a task
- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variablessimulator (
Simulator
) – simulatorconfig (
Config
, optional) – BioSimulators common configuration
- Returns
KiSAO id for a possibly alternative simulation algorithm
- Return type
str
- biosimulators_pyneuroml.utils.write_lems_output_files_configuration(xml_root, output_file_configs)[source]¶
Read the configuration of the output files of a LEMS document
- Parameters
xml_root (
lxml.etree._Element
) – LEMS documentoutput_file_configs (
list
ofdict
) – configuration of the output files of a LEMS document
- biosimulators_pyneuroml.utils.write_xml_file(root, filename, pretty_print=True)[source]¶
Write an XML file
- Parameters
root (
lxml.etree._Element
) – root element for the XML filefilename (
str
) – path to an XML filepretty_print (
bool
, optional) – whether to pretty-print the file (required for NeuroML)