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

@@ -41,6 +41,11 @@ LABEL \
     about.tags="kinetic modeling,dynamical simulation,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators" \
     maintainer="BioSimulators Team <[email protected]>"
 
+# 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_COPASI
 RUN pip install /root/Biosimulators_COPASI \

biosimulators.json

@@ -1245,7 +1245,7 @@
       "modelingFrameworks": [
         {
           "namespace": "SBO",
-          "id": "SBO_0000295"
+          "id": "SBO_0000690"
         }
       ],
       "modelFormats": [
@@ -1481,7 +1481,7 @@
       "modelingFrameworks": [
         {
           "namespace": "SBO",
-          "id": "SBO_0000295"
+          "id": "SBO_0000690"
         }
       ],
       "modelFormats": [
@@ -1768,7 +1768,7 @@
       "modelingFrameworks": [
         {
           "namespace": "SBO",
-          "id": "SBO_0000295"
+          "id": "SBO_0000690"
         }
       ],
       "modelFormats": [
@@ -1989,7 +1989,7 @@
       "modelingFrameworks": [
         {
           "namespace": "SBO",
-          "id": "SBO_0000293"
+          "id": "SBO_0000676"
         }
       ],
       "modelFormats": [

biosimulators_copasi/core.py

@@ -8,7 +8,7 @@
 """
 
 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
@@ -32,11 +32,7 @@
 __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:
@@ -48,12 +44,7 @@ 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:`tuple`:
@@ -64,21 +55,17 @@ 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`:
@@ -91,9 +78,10 @@ def exec_sed_task(task, variables, log=None):
             could not be recorded
         :obj:`NotImplementedError`: if the task is not of a supported type or involves an unsuported feature
     '''
-    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
@@ -129,7 +117,7 @@ def exec_sed_task(task, variables, log=None):
 
     # determine the algorithm to execute
     alg_kisao_id = sim.algorithm.kisao_id
-    exec_alg_kisao_id, alg_copasi_id = get_algorithm_id(alg_kisao_id, events=copasi_model.getNumEvents() >= 1)
+    exec_alg_kisao_id, alg_copasi_id = get_algorithm_id(alg_kisao_id, events=copasi_model.getNumEvents() >= 1, config=config)
 
     # initialize COPASI task
     copasi_task = copasi_data_model.getTask('Time-Course')
@@ -142,7 +130,7 @@ def exec_sed_task(task, variables, log=None):
 
     # Apply the algorithm parameter changes specified by `simulation.algorithm_parameter_changes`
     method_parameters = {}
-    algorithm_substitution_policy = get_algorithm_substitution_policy()
+    algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
     if exec_alg_kisao_id == alg_kisao_id:
         for change in sim.algorithm.changes:
             try:
@@ -288,12 +276,13 @@ def exec_sed_task(task, variables, log=None):
             ))
 
     # log action
-    log.algorithm = exec_alg_kisao_id
-    log.simulator_details = {
-        'methodName': KISAO_ALGORITHMS_MAP[exec_alg_kisao_id]['id'],
-        'methodCode': alg_copasi_id,
-        'parameters': method_parameters,
-    }
+    if config.LOG:
+        log.algorithm = exec_alg_kisao_id
+        log.simulator_details = {
+            'methodName': KISAO_ALGORITHMS_MAP[exec_alg_kisao_id]['id'],
+            'methodCode': alg_copasi_id,
+            'parameters': method_parameters,
+        }
 
     # return results and log
     return variable_results, log

biosimulators_copasi/utils.py

@@ -7,6 +7,7 @@
 """
 
 from .data_model import KISAO_ALGORITHMS_MAP, KISAO_PARAMETERS_MAP, Units
+from biosimulators_utils.config import Config  # noqa: F401
 from biosimulators_utils.data_model import ValueType
 from biosimulators_utils.simulator.utils import get_algorithm_substitution_policy
 from biosimulators_utils.utils.core import validate_str_value, parse_value
@@ -23,13 +24,14 @@
 ]
 
 
-def get_algorithm_id(kisao_id, events=False):
+def get_algorithm_id(kisao_id, events=False, config=None):
     """ Get the COPASI id for an algorithm
 
     Args:
         kisao_id (:obj:`str`): KiSAO algorithm id
         events (:obj:`bool`, optional): whether an algorithm that supports
             events is needed
+        config (:obj:`Config`, optional): configuration
 
     Returns:
         :obj:`tuple`:
@@ -43,7 +45,7 @@ def get_algorithm_id(kisao_id, events=False):
         if not events or props['supports_events']
     ]
 
-    substitution_policy = get_algorithm_substitution_policy()
+    substitution_policy = get_algorithm_substitution_policy(config=config)
     try:
         exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
             kisao_id, possible_alg_kisao_ids,

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging,sbml] >= 0.1.104
+biosimulators_utils[logging,sbml] >= 0.1.114
 kisao
 numpy
 python_copasi >= 4.33.246

tests/test_core_main.py

@@ -14,6 +14,7 @@
 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.exec import exec_sedml_docs_in_archive_with_containerized_simulator
@@ -454,27 +455,36 @@ def test_exec_sed_task_copasi_error_handling(self):
         _, log = exec_sed_task(task, variables)
         self.assertEqual(log.algorithm, 'KISAO_0000304')
 
+        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
+
         with self.assertRaises(CombineArchiveExecutionError):
             with mock.patch.object(COPASI.CCopasiTask, 'processRaw', return_value=False):
-                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 = 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(self):
         doc, archive_filename = self._build_combine_archive()
 
         out_dir = os.path.join(self.dirname, 'out')
-        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 = 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)
 
@@ -487,14 +497,19 @@ def test_exec_sedml_docs_in_combine_archive_with_continuous_model_all_algorithms
                                                                 var_targets=[None, 'A', 'C', 'DA'])
 
             out_dir = os.path.join(self.dirname, alg.kisao_id)
+
+            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
+
             try:
-                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 = 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)
             except CombineArchiveExecutionError:
                 errored_algs.append(alg.kisao_id)
@@ -518,13 +533,18 @@ def test_exec_sedml_docs_in_combine_archive_with_stochastic_model_all_algorithms
                                                                 var_targets=[None, 'Mdm2', 'p53', 'Mdm2_p53'])
 
             out_dir = os.path.join(self.dirname, alg.kisao_id)
-            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 = 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 _build_combine_archive(self, algorithm=None, orig_model_filename='model.xml', var_targets=[None, 'A', 'C', 'DA']):
@@ -691,12 +711,17 @@ def _assert_combine_archive_outputs(self, doc, out_dir):
     def test_exec_sedml_docs_in_combine_archive_real_example(self):
         archive_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint.omex')
         out_dir = os.path.join(self.dirname, 'out')
-        exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
-                                           report_formats=[
-                                               report_data_model.ReportFormat.h5,
-                                           ],
-                                           bundle_outputs=True,
-                                           keep_individual_outputs=False)
+
+        config = get_config()
+        config.REPORT_FORMATS = [
+            report_data_model.ReportFormat.h5,
+        ]
+        config.BUNDLE_OUTPUTS = True
+        config.KEEP_INDIVIDUAL_OUTPUTS = False
+
+        _, log = exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+        if log.exception:
+            raise log.exception
 
         report = sedml_data_model.Report(
             data_sets=[