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

@@ -14,7 +14,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.14"
+ARG VERSION="0.1.15"
 ARG SIMULATOR_VERSION="0.22.1"
 
 # metadata
@@ -41,6 +41,11 @@ LABEL \
     about.tags="constraint-based modeling,flux balance analysis,systems biology,biochemical networks,SBML,SED-ML,COMBINE,OMEX,BioSimulators" \
     maintainer="BioSimulators Team <info@biosimulators.org>"
 
+# 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_COBRApy
 RUN pip install /root/Biosimulators_COBRApy \

biosimulators.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-cobrapy",
+    "module": "biosimulators_cobrapy"
+  },
   "authors": [
     {
       "firstName": "Ali",

biosimulators_cobrapy/_version.py

@@ -1 +1 @@
-__version__ = '0.1.14'
+__version__ = '0.1.15'

biosimulators_cobrapy/core.py

@@ -10,7 +10,7 @@
 from .utils import (get_active_objective_sbml_fbc_id, set_simulation_method_arg,
                     apply_variables_to_simulation_method_args, validate_variables, get_results_of_variables)
 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 @@
 ]
 
 
-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:
@@ -50,12 +46,7 @@ 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`:
@@ -66,21 +57,17 @@ 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`:
@@ -93,9 +80,10 @@ 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
@@ -132,7 +120,7 @@ def exec_sed_task(task, variables, log=None):
     # Load the simulation method specified by ``simulation.algorithm``
     simulation = task.simulation
     algorithm_kisao_id = simulation.algorithm.kisao_id
-    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(
         simulation.algorithm.kisao_id, KISAO_ALGORITHMS_PARAMETERS_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -187,11 +175,12 @@ def exec_sed_task(task, variables, log=None):
                                                 active_objective_fbc_id, method_props, variables, solution)
 
     # log action
-    log.algorithm = exec_kisao_id
-    log.simulator_details = {
-        'method': method_props['method'].__module__ + '.' + method_props['method'].__name__,
-        'arguments': method_kw_args,
-    }
+    if config.LOG:
+        log.algorithm = exec_kisao_id
+        log.simulator_details = {
+            'method': method_props['method'].__module__ + '.' + method_props['method'].__name__,
+            'arguments': method_kw_args,
+        }
 
     # Return the results of each variable and log
     return variable_results, log

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.104
+biosimulators_utils[logging] >= 0.1.114
 cobra
 kisao
 lxml

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.exec import exec_sedml_docs_in_archive_with_containerized_simulator
@@ -211,7 +212,9 @@ def test_exec_sed_task_error_handling(self):
 
         _, archive_filename = self._build_combine_archive(algorithm=sedml_data_model.Algorithm(kisao_id='KISAO_0000448'))
         with self.assertRaisesRegex(CombineArchiveExecutionError, 'No algorithm can be substituted'):
-            core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+            if log.exception:
+                raise log.exception
 
         _, archive_filename = self._build_combine_archive(
             algorithm=sedml_data_model.Algorithm(
@@ -220,11 +223,15 @@ def test_exec_sed_task_error_handling(self):
             ))
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}):
             with self.assertRaisesRegex(CombineArchiveExecutionError, 'is not a valid'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'SIMILAR_VARIABLES'}):
             with self.assertWarnsRegex(BioSimulatorsWarning, 'Unsuported value'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         _, archive_filename = self._build_combine_archive(
             algorithm=sedml_data_model.Algorithm(
@@ -233,11 +240,15 @@ def test_exec_sed_task_error_handling(self):
             ))
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}):
             with self.assertRaisesRegex(CombineArchiveExecutionError, 'not a valid value'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'SIMILAR_VARIABLES'}):
             with self.assertWarnsRegex(BioSimulatorsWarning, 'Unsuported value'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         _, archive_filename = self._build_combine_archive(
             algorithm=sedml_data_model.Algorithm(
@@ -246,11 +257,15 @@ def test_exec_sed_task_error_handling(self):
             ))
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'NONE'}):
             with self.assertRaisesRegex(CombineArchiveExecutionError, 'does not support parameter'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         with mock.patch.dict('os.environ', {'ALGORITHM_SUBSTITUTION_POLICY': 'SIMILAR_VARIABLES'}):
             with self.assertWarnsRegex(BioSimulatorsWarning, 'does not support parameter'):
-                core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+                if log.exception:
+                    raise log.exception
 
         # no solution
         model_changes = [
@@ -262,18 +277,23 @@ def test_exec_sed_task_error_handling(self):
         ]
         _, archive_filename = self._build_combine_archive(model_changes=model_changes)
         with self.assertRaisesRegex(CombineArchiveExecutionError, 'could not be found'):
-            core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+            _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname)
+            if log.exception:
+                raise log.exception
 
     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,
-                                                ],
-                                                bundle_outputs=True,
-                                                keep_individual_outputs=True)
+
+        config = get_config()
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5]
+        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)
 
@@ -567,12 +587,15 @@ 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,
-                                                    ],
-                                                    bundle_outputs=True,
-                                                    keep_individual_outputs=True)
+
+            config = get_config()
+            config.REPORT_FORMATS = [report_data_model.ReportFormat.h5]
+            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)