Updated for renaming 'biosimulators_utils.exec_status' to 'biosimulat…

…ors_utils.log'

Set 'VERBOSE' environment variable in Dockerfile
Added log argument to 'exec_sed_task'
Added simulation method, argument info to log

.flake8

@@ -2,4 +2,4 @@
 max-line-length = 150
 exclude =
     tests/*
-    docs/*
+    docs-src/*

Dockerfile

@@ -22,7 +22,7 @@
 
 FROM python:3.7.9-slim-buster
 
-ARG VERSION="0.1.0"
+ARG VERSION="0.1.1"
 ARG SIMULATOR_VERSION=2.5.2
 
 # metadata
@@ -74,7 +74,8 @@ ENV PATH=${PATH}:/opt/BioNetGen-${SIMULATOR_VERSION}/
 COPY . /root/Biosimulators_BioNetGen
 RUN pip install /root/Biosimulators_BioNetGen \
     && rm -rf /root/Biosimulators_BioNetGen
-ENV MPLBACKEND=PDF
+ENV VERBOSE=0 \
+    MPLBACKEND=PDF
 
 # setup entry point
 ENTRYPOINT ["bionetgen"]

biosimulators_bionetgen/_version.py

@@ -1 +1 @@
-__version__ = '0.1.0'
+__version__ = '0.1.1'

biosimulators_bionetgen/core.py

@@ -12,6 +12,7 @@
                     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.log.data_model import CombineArchiveLog, TaskLog  # noqa: F401
 from biosimulators_utils.plot.data_model import PlotFormat  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat, DataGeneratorVariableResults  # noqa: F401
 from biosimulators_utils.sedml import validation
@@ -42,25 +43,32 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
         plot_formats (:obj:`list` of :obj:`PlotFormat`, 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
+
+    Returns:
+        :obj:`CombineArchiveLog`: log
     """
     sed_doc_executer = functools.partial(exec_sed_doc, exec_sed_task)
-    exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
-                               apply_xml_model_changes=False,
-                               report_formats=report_formats,
-                               plot_formats=plot_formats,
-                               bundle_outputs=bundle_outputs,
-                               keep_individual_outputs=keep_individual_outputs)
+    return exec_sedml_docs_in_archive(sed_doc_executer, archive_filename, out_dir,
+                                      apply_xml_model_changes=False,
+                                      report_formats=report_formats,
+                                      plot_formats=plot_formats,
+                                      bundle_outputs=bundle_outputs,
+                                      keep_individual_outputs=keep_individual_outputs)
 
 
-def exec_sed_task(sed_task, variables):
+def exec_sed_task(sed_task, variables, log=None):
     """ Execute a task and save its results
 
     Args:
        sed_task (:obj:`Task`): task
        variables (:obj:`list` of :obj:`DataGeneratorVariable`): variables that should be recorded
+       log (:obj:`TaskLog`, optional): log for the task
 
     Returns:
-        :obj:`DataGeneratorVariableResults`: results of variables
+        :obj:`tuple`:
+
+            :obj:`DataGeneratorVariableResults`: results of variables
+            :obj:`TaskLog`: log
     """
     """ Validate task
 
@@ -84,7 +92,9 @@ def exec_sed_task(sed_task, variables):
         * :obj:`add_variables_to_task`
         * BioNetGen
         * :obj:`get_variables_results_from_observable_results`
-   """
+    """
+    log = log or TaskLog()
+
     validation.validate_task(sed_task)
     validation.validate_model_language(sed_task.model.language, ModelLanguage.BNGL)
     validation.validate_model_change_types(sed_task.model.changes, (ModelAttributeChange, ))
@@ -116,5 +126,11 @@ def exec_sed_task(sed_task, variables):
     for key in variable_results.keys():
         variable_results[key] = variable_results[key][-(sed_task.simulation.number_of_points + 1):]
 
-    # return the values of the variables
-    return variable_results
+    # log action
+    log.algorithm = sed_task.simulation.algorithm.kisao_id
+    log.simulator_details = {
+        'actions': bionetgen_task.actions,
+    }
+
+    # return the values of the variables and log
+    return variable_results, log

biosimulators_bionetgen/utils.py

@@ -137,7 +137,7 @@ def add_model_attribute_change_to_task(task, change):
         'function arguments and expression': function_args_expression_match,
     }
     msg = '`{}` is not a valid target. The following patterns of targets are supported:\n  - {}'.format(
-        target, '\n  - {}'.join('{}: `{}`'.format(key, target_patterns[key]) for key in sorted(target_patterns.keys())))
+        target, '\n  - '.join('{}: `{}`'.format(key, target_patterns[key]) for key in sorted(target_patterns.keys())))
     raise NotImplementedError(msg)
 
 

requirements.txt

@@ -1,2 +1,2 @@
-biosimulators_utils >= 0.1.31
+biosimulators_utils >= 0.1.32
 pandas

tests/test_core_main.py

@@ -42,7 +42,7 @@ def test_exec_sed_task(self):
         doc.models[0].source = os.path.join(os.path.dirname(__file__), 'fixtures', 'test.bngl')
 
         variables = [data_gen.variables[0] for data_gen in doc.data_generators]
-        variable_results = exec_sed_task(doc.tasks[0], variables)
+        variable_results, _ = exec_sed_task(doc.tasks[0], variables)
 
         self.assertEqual(set(variable_results.keys()), set([var.id for var in variables]))
         for var in variables:
@@ -58,7 +58,7 @@ def test_exec_sed_task_non_zero_initial_time(self):
         doc.simulations[0].initial_time = 0.1
 
         variables = [data_gen.variables[0] for data_gen in doc.data_generators]
-        variable_results = exec_sed_task(doc.tasks[0], variables)
+        variable_results, _ = exec_sed_task(doc.tasks[0], variables)
 
         self.assertEqual(set(variable_results.keys()), set([var.id for var in variables]))
         for var in variables:
@@ -166,10 +166,10 @@ def _build_sed_doc(self, algorithm=None):
             source='model_1.bngl',
             language=sedml_data_model.ModelLanguage.BNGL.value,
             changes=[
-                sedml_data_model.ModelAttributeChange('functions.gfunc.expression', '0.5*Atot^2/(10 + Atot^2)'),
-                sedml_data_model.ModelAttributeChange('functions.gfunc().expression', '0.5*Atot^2/(10 + Atot^2)'),
-                sedml_data_model.ModelAttributeChange('species.A().initialCount', '5'),
-                sedml_data_model.ModelAttributeChange('parameters.g1.value', '16.0'),
+                sedml_data_model.ModelAttributeChange(target='functions.gfunc.expression', new_value='0.5*Atot^2/(10 + Atot^2)'),
+                sedml_data_model.ModelAttributeChange(target='functions.gfunc().expression', new_value='0.5*Atot^2/(10 + Atot^2)'),
+                sedml_data_model.ModelAttributeChange(target='species.A().initialCount', new_value='5'),
+                sedml_data_model.ModelAttributeChange(target='parameters.g1.value', new_value='16.0'),
             ],
         ))
         doc.simulations.append(sedml_data_model.UniformTimeCourseSimulation(