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 python:3.9-slim-buster
 
-ARG VERSION="0.1.16"
+ARG VERSION="0.1.17"
 ARG SIMULATOR_VERSION="0.11.18"
 
 # metadata
@@ -38,6 +38,11 @@ RUN apt-get update -y \
     && 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/*
+
 # Copy code for command-line interface into image and install it
 COPY . /root/Biosimulators_AMICI
 RUN pip install /root/Biosimulators_AMICI \

biosimulators.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-amici",
+    "module": "biosimulators_amici"
+  },
   "authors": [
     {
       "firstName": "Fabian",

biosimulators_amici/_version.py

@@ -1 +1 @@
-__version__ = '0.1.16'
+__version__ = '0.1.17'

biosimulators_amici/core.py

@@ -8,7 +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.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  # noqa: F401
@@ -48,11 +48,7 @@
 ]
 
 
-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:
@@ -64,50 +60,44 @@ 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
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     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,
-                                      raise_exceptions=raise_exceptions)
+                                      config=None)
 
 
-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
     '''
-    log = log or TaskLog()
+    if not config:
+        config = get_config()
+    if config.LOG and not log:
+        log = TaskLog()
 
-    target_x_paths_ids = validate_sed_task(task, variables)
+    target_x_paths_ids = validate_sed_task(task, variables, config=config)
 
     # Read the model for the task
     model, sbml_model, model_name, model_dir = import_model_from_sbml(task.model.source, sorted(target_x_paths_ids.values()))
 
     # Configure task
-    solver, solver_kisao_id, solver_arguments = config_task(task, model)
+    solver, solver_kisao_id, solver_arguments = config_task(task, model, config=config)
 
     # Run simulation using default model parameters and solver options
     results = exec_task(model, solver)
@@ -121,30 +111,32 @@ def exec_sed_task(task, variables, log=None):
     cleanup_model(model_name, model_dir)
 
     # log action
-    log.algorithm = solver_kisao_id
-    arguments = solver_arguments
-    arguments['solver'] = amici.CVodeSolver.__module__ + '.' + amici.CVodeSolver.__name__
-    log.simulator_details = {
-        'method': amici.runAmiciSimulation.__module__ + '.' + amici.runAmiciSimulation.__name__,
-        'arguments': arguments,
-    }
+    if config.LOG:
+        log.algorithm = solver_kisao_id
+        arguments = solver_arguments
+        arguments['solver'] = amici.CVodeSolver.__module__ + '.' + amici.CVodeSolver.__name__
+        log.simulator_details = {
+            'method': amici.runAmiciSimulation.__module__ + '.' + amici.runAmiciSimulation.__name__,
+            'arguments': arguments,
+        }
 
     # return results and log
     return variable_results, log
 
 
-def validate_sed_task(task, variables):
+def validate_sed_task(task, variables, config=None):
     """ Validate that AMICI can support a SED task
 
     Args:
        task (:obj:`Task`): task
        variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
+       config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :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()
+    config = config or get_config()
 
     model = task.model
     sim = task.simulation
@@ -215,12 +207,13 @@ def cleanup_model(model_name, model_dir):
     shutil.rmtree(model_dir)
 
 
-def config_task(task, model):
+def config_task(task, model, config=None):
     """ Configure an AMICI model for a SED task
 
     Args:
         task (:obj:`Task`): task
         model (:obj:`amici.amici.ModelPtr`): AMICI model
+        config (:obj:`Config`): configuration
 
     Returns:
         :obj:`tuple`:
@@ -240,7 +233,7 @@ def config_task(task, model):
     model.setTimepoints(numpy.linspace(sim.output_start_time, sim.output_end_time, sim.number_of_points + 1))
 
     # Load the algorithm specified by `sim.algorithm`
-    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_ALGORITHMS_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)

requirements.txt

@@ -1,5 +1,5 @@
 amici >= 0.11.17
-biosimulators_utils[logging] >= 0.1.104
+biosimulators_utils[logging] >= 0.1.114
 kisao
 numpy
 sympy >= 1.7

tests/test_core_main.py

@@ -9,8 +9,8 @@
 from biosimulators_amici import __main__
 from biosimulators_amici import core
 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.exec import exec_sedml_docs_in_archive_with_containerized_simulator
@@ -243,7 +243,7 @@ def test_exec_sed_task_error_handling(self):
 
             # Configure task
             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.config_task(task, model)
 
             task.simulation.algorithm.kisao_id = 'KISAO_0000496'
@@ -335,13 +335,15 @@ 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)
 
@@ -507,13 +509,15 @@ def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
             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):