feat: updated to Biosimulators-utils 0.1.114: organized options, adde…

…d option to control logging; added Python package to specs; added fonts to Docker image

Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM ghcr.io/biosimulators/biosimulators_pysces/pysces_base:latest
 
-ARG VERSION=0.1.19
+ARG VERSION=0.1.20
 ARG SIMULATOR_VERSION="0.9.9"
 
 # metadata

Dockerfile-base

@@ -74,3 +74,8 @@ RUN apt-get update -y \
         gfortran \
     && apt-get autoremove -y \
     && rm -rf /var/lib/apt/lists
+
+# fonts for matplotlib
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libfreetype6 \
+    && rm -rf /var/lib/apt/lists/*

README.md

@@ -61,7 +61,7 @@ docker run \
 ```
 
 ## Documentation
-Documentation is available at https://biosimulators.github.io/Biosimulators_PySCeS/.
+Documentation is available at https://docs.biosimulators.org/Biosimulators_PySCeS/.
 
 ## License
 This package is released under the [MIT license](LICENSE).

biosimulators.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-pysces",
+    "module": "biosimulators_pysces"
+  },
   "authors": [
     {
       "firstName": "Brett",

biosimulators_pysces/_version.py

@@ -1 +1 @@
-__version__ = '0.1.19'
+__version__ = '0.1.20'

biosimulators_pysces/core.py

@@ -8,7 +8,7 @@
 
 from .data_model import KISAO_ALGORITHM_MAP
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
-from biosimulators_utils.config import get_config
+from biosimulators_utils.config import get_config, Config  # noqa: F401
 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, SedDocumentResults  # noqa: F401
@@ -34,11 +34,7 @@
 __all__ = ['exec_sedml_docs_in_combine_archive', 'exec_sed_task']
 
 
-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,
-                                       raise_exceptions=True):
+def exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None):
     """ Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
 
     Args:
@@ -50,13 +46,6 @@ 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:`tuple`:
 
@@ -66,31 +55,28 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
     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,
-                                      raise_exceptions=raise_exceptions)
+                                      config=config)
 
 
-def exec_sed_task(task, variables, log=None):
+def exec_sed_task(task, variables, log=None, config=None):
     ''' Execute a task and save its results
 
     Args:
        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
 
     Returns:
         :obj:`tuple`:
 
             :obj:`VariableResults`: results of variables
             :obj:`TaskLog`: log
     '''
-    config = get_config()
+    config = config or get_config()
 
-    log = log or TaskLog()
+    if config.LOG and not log:
+        log = TaskLog()
 
     model = task.model
     sim = task.simulation
@@ -131,7 +117,7 @@ def exec_sed_task(task, variables, log=None):
 
     # Load the algorithm specified by `simulation.algorithm.kisao_id`
     sim = task.simulation
-    algorithm_substitution_policy = get_algorithm_substitution_policy()
+    algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
     exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
         sim.algorithm.kisao_id, KISAO_ALGORITHM_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -185,7 +171,7 @@ def exec_sed_task(task, variables, log=None):
     # override algorithm choice if there are events
     if integrator['id'] == 'LSODA' and model.__events__:
         model.mode_integrator = 'CVODE'
-        substitution_policy = get_algorithm_substitution_policy()
+        substitution_policy = get_algorithm_substitution_policy(config=config)
         if (
             ALGORITHM_SUBSTITUTION_POLICY_LEVELS[substitution_policy]
             >= ALGORITHM_SUBSTITUTION_POLICY_LEVELS[AlgorithmSubstitutionPolicy.SIMILAR_VARIABLES]
@@ -260,21 +246,22 @@ def exec_sed_task(task, variables, log=None):
     os.chdir(cwd)
 
     # log action
-    log.algorithm = 'KISAO_0000019' if model.mode_integrator == 'CVODE' else 'KISAO_0000088'
-
-    arguments = {}
-    for key, val in model.__settings__.items():
-        if model.mode_integrator == 'CVODE':
-            if key.startswith('cvode_'):
-                arguments[key] = val
-        else:
-            if key.startswith('lsoda_'):
-                arguments[key] = val
+    if config.LOG:
+        log.algorithm = 'KISAO_0000019' if model.mode_integrator == 'CVODE' else 'KISAO_0000088'
+
+        arguments = {}
+        for key, val in model.__settings__.items():
+            if model.mode_integrator == 'CVODE':
+                if key.startswith('cvode_'):
+                    arguments[key] = val
+            else:
+                if key.startswith('lsoda_'):
+                    arguments[key] = val
 
-    log.simulator_details = {
-        'method': model.Simulate.__module__ + '.' + model.Simulate.__name__,
-        'arguments': arguments,
-    }
+        log.simulator_details = {
+            'method': model.Simulate.__module__ + '.' + model.Simulate.__name__,
+            'arguments': arguments,
+        }
 
     # return results and log
     return variable_results, log

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[sbml,logging] >= 0.1.104
+biosimulators_utils[sbml,logging] >= 0.1.114
 kisao
 numpy
 pysces

tests/test_core_main.py

@@ -11,6 +11,7 @@
 from biosimulators_utils.combine import data_model as combine_data_model
 from biosimulators_utils.combine.exceptions import CombineArchiveExecutionError
 from biosimulators_utils.combine.io import CombineArchiveWriter
+from biosimulators_utils.config import get_config
 from biosimulators_utils.report import data_model as report_data_model
 from biosimulators_utils.report.io import ReportReader
 from biosimulators_utils.simulator.exceptions import AlgorithmDoesNotSupportModelFeatureException
@@ -160,7 +161,7 @@ def test_exec_sed_task_error_handling(self):
             task.model.source = os.path.join(os.path.dirname(__file__), 'fixtures', 'biomd0000000002.xml')
 
             task.simulation.algorithm.kisao_id = 'KISAO_0000448'
-            with self.assertRaisesRegex(AlgorithmCannotBeSubstitutedException, 'No algorithm can be substituted'):
+            with self.assertRaisesRegex(AlgorithmCannotBeSubstitutedException, 'Algorithms cannot be substituted'):
                 core.exec_sed_task(task, variables)
             task.simulation.algorithm.kisao_id = 'KISAO_0000088'
 
@@ -237,13 +238,15 @@ def test_exec_sedml_docs_in_combine_archive_successfully(self):
         doc, archive_filename = self._build_combine_archive()
 
         out_dir = os.path.join(self.dirname, 'out')
-        core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
-                                                report_formats=[
-                                                    report_data_model.ReportFormat.h5,
-                                                    report_data_model.ReportFormat.csv,
-                                                ],
-                                                bundle_outputs=True,
-                                                keep_individual_outputs=True)
+
+        config = get_config()
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
+        config.BUNDLE_OUTPUTS = True
+        config.KEEP_INDIVIDUAL_OUTPUTS = True
+
+        _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+        if log.exception:
+            raise log.exception
 
         self._assert_combine_archive_outputs(doc, out_dir)
 
@@ -409,6 +412,11 @@ def test_algorithm_substitution(self):
 
         out_dir = self.dirname
 
+        config = get_config()
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
+        config.BUNDLE_OUTPUTS = True
+        config.KEEP_INDIVIDUAL_OUTPUTS = True
+
         # NONE
         env = {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}
 
@@ -422,13 +430,9 @@ def pysces_model(filename):
         with mock.patch.dict(os.environ, env):
             with mock.patch('pysces.model', side_effect=pysces_model):
                 with self.assertRaises(CombineArchiveExecutionError):
-                    core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
-                                                            report_formats=[
-                                                                report_data_model.ReportFormat.h5,
-                                                                report_data_model.ReportFormat.csv,
-                                                            ],
-                                                            bundle_outputs=True,
-                                                            keep_individual_outputs=True)
+                    _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+                    if log.exception:
+                        raise log.exception
 
         # SAME FRAMEWORK
         env = {'ALGORITHM_SUBSTITUTION_POLICY': 'SIMILAR_VARIABLES'}
@@ -437,26 +441,24 @@ def pysces_model(filename):
                 with mock.patch.object(pysces.PyscesModel.PysMod, 'Simulate', side_effect=Exception('Stop')):
                     with self.assertRaisesRegex(CombineArchiveExecutionError, 'Stop$'):
                         with self.assertWarns(AlgorithmSubstitutedWarning):
-                            core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
-                                                                    report_formats=[
-                                                                        report_data_model.ReportFormat.h5,
-                                                                        report_data_model.ReportFormat.csv,
-                                                                    ],
-                                                                    bundle_outputs=True,
-                                                                    keep_individual_outputs=True)
+                            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+                            if log.exception:
+                                raise log.exception
 
     def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
         for alg in gen_algorithms_from_specs(os.path.join(os.path.dirname(__file__), '..', 'biosimulators.json')).values():
             doc, archive_filename = self._build_combine_archive(algorithm=alg)
 
             out_dir = os.path.join(self.dirname, alg.kisao_id)
-            core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
-                                                    report_formats=[
-                                                        report_data_model.ReportFormat.h5,
-                                                        report_data_model.ReportFormat.csv,
-                                                    ],
-                                                    bundle_outputs=True,
-                                                    keep_individual_outputs=True)
+
+            config = get_config()
+            config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
+            config.BUNDLE_OUTPUTS = True
+            config.KEEP_INDIVIDUAL_OUTPUTS = True
+
+            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+            if log.exception:
+                raise log.exception
             self._assert_combine_archive_outputs(doc, out_dir)
 
     def test_raw_cli(self):