updating to biosimulators-utils 0.1.95

Author: jonrkarr

Dockerfile

@@ -22,7 +22,7 @@
 
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.10"
+ARG VERSION="0.1.11"
 ARG SIMULATOR_VERSION=2.6.0
 
 # metadata

biosimulators_bionetgen/_version.py

@@ -1 +1 @@
-__version__ = '0.1.10'
+__version__ = '0.1.11'

requirements.txt

@@ -1,3 +1,3 @@
-biosimulators_utils[bngl,logging] >= 0.1.83
+biosimulators_utils[bngl,logging] >= 0.1.95
 kisao
 pandas

tests/test_core_main.py

@@ -132,15 +132,13 @@ def _build_combine_archive(self, algorithm=None):
         sim_filename = os.path.join(archive_dirname, 'sim_1.sedml')
         SedmlSimulationWriter().run(doc, sim_filename)
 
-        updated = datetime.datetime(2020, 1, 2, 1, 2, 3, tzinfo=dateutil.tz.tzutc())
         archive = combine_data_model.CombineArchive(
             contents=[
                 combine_data_model.CombineArchiveContent(
-                    'model_1.bngl', combine_data_model.CombineArchiveContentFormat.BNGL.value, updated=updated),
+                    'model_1.bngl', combine_data_model.CombineArchiveContentFormat.BNGL.value),
                 combine_data_model.CombineArchiveContent(
-                    'sim_1.sedml', combine_data_model.CombineArchiveContentFormat.SED_ML.value, updated=updated),
+                    'sim_1.sedml', combine_data_model.CombineArchiveContentFormat.SED_ML.value),
             ],
-            updated=updated,
         )
         archive_filename = os.path.join(self.dirname,
                                         'archive.omex' if algorithm is None else 'archive-{}.omex'.format(algorithm.kisao_id))

tests/test_utils.py

@@ -259,7 +259,8 @@ def test_get_parameters_variables_for_simulation(self):
             os.path.join(fixtures_dirname, 'test.bngl'),
             os.path.join(fixtures_dirname, 'LR_comp_resolved.bngl'),
         ]:
-            changes, variables = get_parameters_variables_for_simulation(model_filename, None, None, None)
+            changes, sim, variables = get_parameters_variables_for_simulation(
+                model_filename, None, UniformTimeCourseSimulation, None)
 
             task = read_task(model_filename)
             task.actions = []
@@ -272,7 +273,8 @@ def test_get_parameters_variables_for_simulation(self):
             model_filename_2 = os.path.join(self.dirname, 'task.bngl')
             write_task(task, model_filename_2)
 
-            changes_2, variables_2 = get_parameters_variables_for_simulation(model_filename_2, None, None, None)
+            changes_2, sim, variables_2 = get_parameters_variables_for_simulation(
+                model_filename_2, None, UniformTimeCourseSimulation, None)
             for change, change_2 in zip(changes, changes_2):
                 self.assertTrue(change_2.is_equal(change))
             for variable, variable_2 in zip(variables, variables_2):