feat: updated to Biosimulators-utils 0.1.104; added pytest configurat…

…ion to ignore BioSimulators utils warnings

biosimulators_amici/__init__.py

@@ -3,7 +3,14 @@
 from ._version import __version__  # noqa: F401
 # :obj:`str`: version
 
-# 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
+
+__all__ = [
+    '__version__',
+    'get_simulator_version',
+    'exec_sed_task',
+    'exec_sedml_docs_in_combine_archive',
+]
 
 
 def get_simulator_version():

biosimulators_amici/core.py

@@ -8,6 +8,7 @@
 
 from .data_model import KISAO_ALGORITHMS_MAP, KISAO_PARAMETERS_MAP
 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
@@ -29,6 +30,11 @@
 import sys
 import tempfile
 
+# libSBML seems to need to be reloaded in some environments
+import importlib
+import libsbml  # noqa: F401
+importlib.reload(libsbml)
+
 
 __all__ = [
     'exec_sedml_docs_in_combine_archive',
@@ -43,8 +49,10 @@
 
 
 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:
@@ -56,21 +64,25 @@ 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
     """
     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=True,
+                                      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(task, variables, log=None):
@@ -132,23 +144,27 @@ def validate_sed_task(task, variables):
         :obj:`dict` of :obj:`str` to :obj:`str`: dictionary that maps each XPath to the
             value of the attribute of the object in the XML file that matches the XPath
     """
+    config = get_config()
+
     model = task.model
     sim = task.simulation
 
-    raise_errors_warnings(validation.validate_task(task),
-                          error_summary='Task `{}` is invalid.'.format(task.id))
-    raise_errors_warnings(validation.validate_model_language(task.model.language, ModelLanguage.SBML),
-                          error_summary='Language for model `{}` is not supported.'.format(model.id))
-    raise_errors_warnings(validation.validate_model_change_types(task.model.changes, ()),
-                          error_summary='Changes for model `{}` are not supported.'.format(model.id))
-    raise_errors_warnings(*validation.validate_model_changes(task.model),
-                          error_summary='Changes for model `{}` are invalid.'.format(model.id))
-    raise_errors_warnings(validation.validate_simulation_type(task.simulation, (UniformTimeCourseSimulation, )),
-                          error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
-    raise_errors_warnings(*validation.validate_simulation(task.simulation),
-                          error_summary='Simulation `{}` is invalid.'.format(sim.id))
-    raise_errors_warnings(*validation.validate_data_generator_variables(variables),
-                          error_summary='Data generator variables for task `{}` are invalid.'.format(task.id))
+    if config.VALIDATE_SEDML:
+        raise_errors_warnings(validation.validate_task(task),
+                              error_summary='Task `{}` is invalid.'.format(task.id))
+        raise_errors_warnings(validation.validate_model_language(task.model.language, ModelLanguage.SBML),
+                              error_summary='Language for model `{}` is not supported.'.format(model.id))
+        raise_errors_warnings(validation.validate_model_change_types(task.model.changes, ()),
+                              error_summary='Changes for model `{}` are not supported.'.format(model.id))
+        raise_errors_warnings(*validation.validate_model_changes(task.model),
+                              error_summary='Changes for model `{}` are invalid.'.format(model.id))
+        raise_errors_warnings(validation.validate_simulation_type(task.simulation, (UniformTimeCourseSimulation, )),
+                              error_summary='{} `{}` is not supported.'.format(sim.__class__.__name__, sim.id))
+        raise_errors_warnings(*validation.validate_simulation(task.simulation),
+                              error_summary='Simulation `{}` is invalid.'.format(sim.id))
+        raise_errors_warnings(*validation.validate_data_generator_variables(variables),
+                              error_summary='Data generator variables for task `{}` are invalid.'.format(task.id))
+
     return validation.validate_variable_xpaths(variables, task.model.source, attr='id')
 
 

pytest.ini

@@ -0,0 +1,3 @@
+[pytest]
+filterwarnings =
+    ignore::biosimulators_utils.warnings.BioSimulatorsWarning

requirements.txt

@@ -1,5 +1,5 @@
 amici >= 0.11.17
-biosimulators_utils[logging] >= 0.1.96
+biosimulators_utils[logging] >= 0.1.104
 kisao
 numpy
 sympy >= 1.7

tests/test_utils.py

@@ -1,4 +1,4 @@
-from biosimulators_amici import core as utils
+from biosimulators_amici import core
 import amici
 import os.path
 import unittest
@@ -7,15 +7,17 @@
 class UtilsTestCase(unittest.TestCase):
     def test_import_successful(self):
         model_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'biomd0000000002.xml')
-        model, sbml_model, model_name, model_dir = utils.import_model_from_sbml(
+        self.assertTrue(os.path.isfile(model_filename))
+
+        model, sbml_model, model_name, model_dir = core.import_model_from_sbml(
             model_filename, ['BLL', 'IL', 'AL'])
 
         self.assertTrue(os.path.isdir(model_dir))
         self.assertIsInstance(model, amici.amici.ModelPtr)
 
-        utils.cleanup_model(model_name, model_dir)
+        core.cleanup_model(model_name, model_dir)
         self.assertFalse(os.path.isdir(model_dir))
 
     def test_import_models_with_events(self):
         model_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297_url.xml')
-        utils.import_model_from_sbml(model_filename, [])
+        core.import_model_from_sbml(model_filename, [])