feat: updating to biosimulators-utils 0.1.116

.github/workflows/ci.yml

@@ -179,7 +179,7 @@ jobs:
       - name: Run the tests
         env:
           BIONETGEN_PATH: /opt/BioNetGen/BNG2.pl
-        run: python -m pytest tests/ --cov=./ --cov-report=xml
+        run: python -m pytest tests/ --cov=./biosimulators_bionetgen/ --cov-report=xml
 
       - name: Upload the coverage report to Codecov
         uses: codecov/[email protected]

biosimulators_bionetgen/__init__.py

@@ -2,7 +2,7 @@
 # :obj:`str`: version
 
 from .config import Config
-from .core import exec_sed_task, exec_sedml_docs_in_combine_archive  # noqa: F401
+from .core import exec_sed_task, preprocess_sed_task, exec_sed_doc, exec_sedml_docs_in_combine_archive  # noqa: F401
 
 import subprocess
 
@@ -11,6 +11,8 @@
     '__version__',
     'get_simulator_version',
     'exec_sed_task',
+    'preprocess_sed_task',
+    'exec_sed_doc',
     'exec_sedml_docs_in_combine_archive',
 ]
 

biosimulators_bionetgen/core.py

@@ -13,18 +13,17 @@
 from .warnings import IgnoredBnglFileContentWarning
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
 from biosimulators_utils.config import get_config, Config  # noqa: F401
-from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog  # noqa: F401
+from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, StandardOutputErrorCapturerLevel  # noqa: F401
 from biosimulators_utils.viz.data_model import VizFormat  # 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)
-from biosimulators_utils.sedml.exec import exec_sed_doc
+from biosimulators_utils.sedml.exec import exec_sed_doc as base_exec_sed_doc
 from biosimulators_utils.utils.core import raise_errors_warnings
-import functools
 import warnings
 
-__all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_task']
+__all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_doc', 'exec_sed_task', 'preprocess_sed_task']
 
 
 def exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None):
@@ -47,20 +46,65 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None):
             * :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,
+    return exec_sedml_docs_in_archive(exec_sed_doc, archive_filename, out_dir,
                                       apply_xml_model_changes=False,
                                       config=config)
 
 
-def exec_sed_task(sed_task, variables, log=None, config=None):
+def 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):
+    """ Execute the tasks specified in a SED document and generate the specified outputs
+
+    Args:
+        doc (:obj:`SedDocument` or :obj:`str`): SED document or a path to SED-ML file which defines a SED document
+        working_dir (:obj:`str`): working directory of the SED document (path relative to which models are located)
+
+        base_out_path (:obj:`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 (:obj:`str`, optional): path relative to :obj:`base_out_path` to store the outputs
+        apply_xml_model_changes (:obj:`bool`, optional): if :obj:`True`, apply any model changes specified in the SED-ML file before
+            calling :obj:`task_executer`.
+        log (:obj:`SedDocumentLog`, optional): log of the document
+        indent (:obj:`int`, optional): degree to indent status messages
+        pretty_print_modified_xml_models (:obj:`bool`, optional): if :obj:`True`, pretty print modified XML models
+        log_level (:obj:`StandardOutputErrorCapturerLevel`, optional): level at which to log output
+        config (:obj:`Config`, optional): BioSimulators common configuration
+        simulator_config (:obj:`SimulatorConfig`, optional): tellurium configuration
+
+    Returns:
+        :obj:`tuple`:
+
+            * :obj:`ReportResults`: results of each report
+            * :obj:`SedDocumentLog`: log of the document
+    """
+    return base_exec_sed_doc(exec_sed_task, doc, working_dir, base_out_path,
+                             rel_out_path=rel_out_path,
+                             apply_xml_model_changes=apply_xml_model_changes,
+                             log=log,
+                             indent=indent,
+                             pretty_print_modified_xml_models=pretty_print_modified_xml_models,
+                             log_level=log_level,
+                             config=config)
+
+
+def exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None):
     """ Execute a task and save its results
 
     Args:
-       sed_task (:obj:`Task`): task
-       variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
-       log (:obj:`TaskLog`, optional): log for the task
-       config (:obj:`Config`, optional): BioSimulators common configuration
+        task (:obj:`Task`): SED task
+        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
+        preprocessed_task (:obj:`object`, 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 (:obj:`TaskLog`, optional): log for the task
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :obj:`tuple`:
@@ -95,54 +139,57 @@ def exec_sed_task(sed_task, variables, log=None, config=None):
     if config.LOG and not log:
         log = TaskLog()
 
+    if preprocessed_task is None:
+        preprocessed_task = preprocess_sed_task(task, variables, config=config)
+
     if config.VALIDATE_SEDML:
         raise_errors_warnings(
-            validation.validate_task(sed_task),
-            error_summary='Task `{}` is invalid.'.format(sed_task.id))
+            validation.validate_task(task),
+            error_summary='Task `{}` is invalid.'.format(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))
+            validation.validate_model_language(task.model.language, ModelLanguage.BNGL),
+            error_summary='Language for model `{}` is not supported.'.format(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))
+            validation.validate_model_change_types(task.model.changes, (ModelAttributeChange, )),
+            error_summary='Changes for model `{}` are not supported.'.format(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))
+            *validation.validate_model_changes(task.model),
+            error_summary='Changes for model `{}` are invalid.'.format(task.model.id))
         raise_errors_warnings(
-            validation.validate_simulation_type(sed_task.simulation, (UniformTimeCourseSimulation, )),
+            validation.validate_simulation_type(task.simulation, (UniformTimeCourseSimulation, )),
             error_summary='{} `{}` is not supported.'.format(
-                sed_task.simulation.__class__.__name__,
-                sed_task.simulation.id))
+                task.simulation.__class__.__name__,
+                task.simulation.id))
         raise_errors_warnings(
-            *validation.validate_simulation(sed_task.simulation),
-            error_summary='Simulation `{}` is invalid.'.format(sed_task.simulation.id))
+            *validation.validate_simulation(task.simulation),
+            error_summary='Simulation `{}` is invalid.'.format(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))
+            error_summary='Data generator variables for task `{}` are invalid.'.format(task.id))
 
     # read the model from the BNGL file
-    bionetgen_task = read_task(sed_task.model.source)
+    bionetgen_task = read_task(task.model.source)
     if bionetgen_task.actions:
         warnings.warn('Actions in the BNGL file were ignored.', IgnoredBnglFileContentWarning)
         bionetgen_task.actions = []
 
     # validate and apply the model attribute changes to the BioNetGen task
-    for change in sed_task.model.changes:
+    for change in task.model.changes:
         add_model_attribute_change_to_task(bionetgen_task, change)
 
     # add observables for the variables to the BioNetGen model
     add_variables_to_model(bionetgen_task.model, variables)
 
     # apply the SED algorithm and its parameters to the BioNetGen task
-    alg_kisao_id = add_simulation_to_task(bionetgen_task, sed_task.simulation)
+    alg_kisao_id = add_simulation_to_task(bionetgen_task, task.simulation)
 
     # execute the task
     observable_results = exec_bionetgen_task(bionetgen_task)
 
     # get predicted values of the variables
     variable_results = get_variables_results_from_observable_results(observable_results, variables)
     for key in variable_results.keys():
-        variable_results[key] = variable_results[key][-(sed_task.simulation.number_of_points + 1):]
+        variable_results[key] = variable_results[key][-(task.simulation.number_of_points + 1):]
 
     # log action
     if config.LOG:
@@ -153,3 +200,21 @@ def exec_sed_task(sed_task, variables, log=None, config=None):
 
     # return the values of the variables and log
     return variable_results, log
+
+
+def preprocess_sed_task(task, variables, config=None):
+    """ Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding
+    repeatedly initializing tasks on repeated calls of :obj:`exec_sed_task`.
+
+    Args:
+        task (:obj:`Task`): task
+        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
+        preprocessed_task (:obj:`PreprocessedTask`, 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.
+        config (:obj:`Config`, optional): BioSimulators common configuration
+
+    Returns:
+        :obj:`object`: preprocessed information about the task
+    """
+    pass

requirements.txt

@@ -1,3 +1,3 @@
-biosimulators_utils[bngl,logging] >= 0.1.114
+biosimulators_utils[bngl,logging] >= 0.1.116
 kisao
 pandas