feat: updated to BioSimulators-utils 0.1.104

Author: jonrkarr

biosimulators_bionetgen/__init__.py

@@ -2,12 +2,17 @@
 # :obj:`str`: version
 
 from .config import Config
-from .core import exec_sedml_docs_in_combine_archive  # noqa: F401
+from .core import exec_sed_task, exec_sedml_docs_in_combine_archive  # noqa: F401
 
 import subprocess
 
 
-__all = ['__version__', 'get_simulator_version']
+__all = [
+    '__version__',
+    'get_simulator_version',
+    'exec_sed_task',
+    'exec_sedml_docs_in_combine_archive',
+]
 
 
 def get_simulator_version():

biosimulators_bionetgen/core.py

@@ -12,9 +12,10 @@
                     get_variables_results_from_observable_results, add_variables_to_model)
 from .warnings import IgnoredBnglFileContentWarning
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
+from biosimulators_utils.config import get_config
 from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog  # noqa: F401
 from biosimulators_utils.viz.data_model import VizFormat  # noqa: F401
-from biosimulators_utils.report.data_model import ReportFormat, VariableResults  # noqa: F401
+from biosimulators_utils.report.data_model import ReportFormat, VariableResults, SedDocumentResults  # noqa: F401
 from biosimulators_utils.sedml import validation
 from biosimulators_utils.sedml.data_model import (Task, ModelLanguage, ModelAttributeChange,  # noqa: F401
                                                   UniformTimeCourseSimulation, Variable)
@@ -27,8 +28,10 @@
 
 
 def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
+                                       return_results=False,
                                        report_formats=None, plot_formats=None,
-                                       bundle_outputs=None, keep_individual_outputs=None):
+                                       bundle_outputs=None, keep_individual_outputs=None,
+                                       raise_exceptions=True):
     """ Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
 
     Args:
@@ -40,21 +43,28 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
             * 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
 
+        return_results (:obj:`bool`, optional): whether to return the result of each output of each SED-ML file
         report_formats (:obj:`list` of :obj:`ReportFormat`, optional): report format (e.g., csv or h5)
         plot_formats (:obj:`list` of :obj:`VizFormat`, optional): report format (e.g., pdf)
         bundle_outputs (:obj:`bool`, optional): if :obj:`True`, bundle outputs into archives for reports and plots
         keep_individual_outputs (:obj:`bool`, optional): if :obj:`True`, keep individual output files
+        raise_exceptions (:obj:`bool`, optional): whether to raise exceptions
 
     Returns:
-        :obj:`CombineArchiveLog`: log
+        :obj:`tuple`:
+
+            * :obj:`SedDocumentResults`: results
+            * :obj:`CombineArchiveLog`: log
     """
     sed_doc_executer = functools.partial(exec_sed_doc, exec_sed_task)
     return exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
                                       apply_xml_model_changes=False,
+                                      return_results=return_results,
                                       report_formats=report_formats,
                                       plot_formats=plot_formats,
                                       bundle_outputs=bundle_outputs,
-                                      keep_individual_outputs=keep_individual_outputs)
+                                      keep_individual_outputs=keep_individual_outputs,
+                                      raise_exceptions=raise_exceptions)
 
 
 def exec_sed_task(sed_task, variables, log=None):
@@ -94,22 +104,33 @@ def exec_sed_task(sed_task, variables, log=None):
         * BioNetGen
         * :obj:`get_variables_results_from_observable_results`
     """
+    config = get_config()
     log = log or TaskLog()
 
-    raise_errors_warnings(validation.validate_task(sed_task),
-                          error_summary='Task `{}` is invalid.'.format(sed_task.id))
-    raise_errors_warnings(validation.validate_model_language(sed_task.model.language, ModelLanguage.BNGL),
-                          error_summary='Language for model `{}` is not supported.'.format(sed_task.model.id))
-    raise_errors_warnings(validation.validate_model_change_types(sed_task.model.changes, (ModelAttributeChange, )),
-                          error_summary='Changes for model `{}` are not supported.'.format(sed_task.model.id))
-    raise_errors_warnings(*validation.validate_model_changes(sed_task.model),
-                          error_summary='Changes for model `{}` are invalid.'.format(sed_task.model.id))
-    raise_errors_warnings(validation.validate_simulation_type(sed_task.simulation, (UniformTimeCourseSimulation, )),
-                          error_summary='{} `{}` is not supported.'.format(sed_task.simulation.__class__.__name__, sed_task.simulation.id))
-    raise_errors_warnings(*validation.validate_simulation(sed_task.simulation),
-                          error_summary='Simulation `{}` is invalid.'.format(sed_task.simulation.id))
-    raise_errors_warnings(*validation.validate_data_generator_variables(variables),
-                          error_summary='Data generator variables for task `{}` are invalid.'.format(sed_task.id))
+    if config.VALIDATE_SEDML:
+        raise_errors_warnings(
+            validation.validate_task(sed_task),
+            error_summary='Task `{}` is invalid.'.format(sed_task.id))
+        raise_errors_warnings(
+            validation.validate_model_language(sed_task.model.language, ModelLanguage.BNGL),
+            error_summary='Language for model `{}` is not supported.'.format(sed_task.model.id))
+        raise_errors_warnings(
+            validation.validate_model_change_types(sed_task.model.changes, (ModelAttributeChange, )),
+            error_summary='Changes for model `{}` are not supported.'.format(sed_task.model.id))
+        raise_errors_warnings(
+            *validation.validate_model_changes(sed_task.model),
+            error_summary='Changes for model `{}` are invalid.'.format(sed_task.model.id))
+        raise_errors_warnings(
+            validation.validate_simulation_type(sed_task.simulation, (UniformTimeCourseSimulation, )),
+            error_summary='{} `{}` is not supported.'.format(
+                sed_task.simulation.__class__.__name__,
+                sed_task.simulation.id))
+        raise_errors_warnings(
+            *validation.validate_simulation(sed_task.simulation),
+            error_summary='Simulation `{}` is invalid.'.format(sed_task.simulation.id))
+        raise_errors_warnings(
+            *validation.validate_data_generator_variables(variables),
+            error_summary='Data generator variables for task `{}` are invalid.'.format(sed_task.id))
 
     # read the model from the BNGL file
     bionetgen_task = read_task(sed_task.model.source)

requirements.txt

@@ -1,3 +1,3 @@
-biosimulators_utils[bngl,logging] >= 0.1.96
+biosimulators_utils[bngl,logging] >= 0.1.104
 kisao
 pandas