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

.github/workflows/ci.yml

@@ -168,10 +168,9 @@ jobs:
             --workdir /home/opencor/Biosimulators_OpenCOR \
             ghcr.io/biosimulators/biosimulators_opencor/opencor:latest \
             -c "
-              /home/opencor/OpenCOR/python/bin/python -m pip install pytest pytest-cov coverage; \
+              /home/opencor/OpenCOR/python/bin/python -m pip install pytest pytest-cov; \
               /home/opencor/OpenCOR/python/bin/python -m pip install -r tests/requirements.txt; \
               pythonshell -m pytest tests/ --cov=./ --cov-report=xml; \
-              /home/opencor/OpenCOR/python/bin/coverage html; \
               exit
             "
 

Dockerfile

@@ -1,5 +1,5 @@
 # VERSION
-ARG VERSION=0.0.6
+ARG VERSION=0.0.7
 ARG SIMULATOR_VERSION="2021-08-19"
 
 # Base OS
@@ -33,6 +33,11 @@ LABEL \
 ENV PYTHON="OpenCOR -c PythonShell" \
     PIP="${OPENCORDIR}/python/bin/python -m pip"
 
+# fonts for matplotlib
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libfreetype6 \
+    && rm -rf /var/lib/apt/lists/*
+
 # setup matplotlib
 RUN mkdir -p /.config/matplotlib \
     && mkdir -p /.cache/matplotlib \

biosimulators.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-opencor",
+    "module": "biosimulators_opencor"
+  },
   "authors": [
     {
       "firstName": "Alan",
@@ -56,7 +60,11 @@
     }
   ],
   "references": {
-    "identifiers": [],
+    "identifiers": [{
+            "namespace": "pypi",
+            "id": "biosimulators-opencor",
+            "url": "https://pypi.org/project/biosimulators-opencor/"
+          }],
     "citations": [
       {
         "title": "OpenCOR: a modular and interoperable approach to computational biology",

biosimulators_opencor/_version.py

@@ -1 +1 @@
-__version__ = '0.0.6'
+__version__ = '0.0.7'

biosimulators_opencor/core.py

@@ -9,6 +9,7 @@
 from .utils import (validate_simulation, load_opencor_simulation,
                     get_results_from_opencor_simulation, log_opencor_execution, get_mock_libcellml)
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
+from biosimulators_utils.config import get_config, Config  # noqa: F401
 from biosimulators_utils.log.data_model import CombineArchiveLog, TaskLog, StandardOutputErrorCapturerLevel  # noqa: F401
 from biosimulators_utils.viz.data_model import VizFormat  # noqa: F401
 from biosimulators_utils.report.data_model import ReportFormat, VariableResults, SedDocumentResults  # noqa: F401
@@ -22,11 +23,7 @@
 ]
 
 
-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:
@@ -38,12 +35,7 @@ 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`:
@@ -56,22 +48,18 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
     with mock.patch.dict('sys.modules', libcellml=get_mock_libcellml()):
         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,
                                           log_level=StandardOutputErrorCapturerLevel.python,
-                                          raise_exceptions=raise_exceptions)
+                                          config=config)
 
 
-def exec_sed_task(sed_task, sed_variables, log=None):
+def exec_sed_task(sed_task, sed_variables, log=None, config=None):
     ''' Execute a task and save its results
 
     Args:
        sed_task (:obj:`Task`): task
        sed_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`:
@@ -84,11 +72,15 @@ def exec_sed_task(sed_task, sed_variables, log=None):
             could not be recorded
         :obj:`NotImplementedError`: if the task is not of a supported type or involves an unsupported feature
     '''
+    if not config:
+        config = get_config()
+
     # initialize a log of the execution of this task
-    log = log or TaskLog()
+    if config.LOG and not log:
+        log = TaskLog()
 
     # check that a simulation (or a similar simulation) can be executed with OpenCOR
-    opencor_sed_task, opencor_variable_names = validate_simulation(sed_task, sed_variables)
+    opencor_sed_task, opencor_variable_names = validate_simulation(sed_task, sed_variables, config=config)
 
     # load an OpenCOR simulation
     opencor_sim = load_opencor_simulation(opencor_sed_task, sed_variables)
@@ -101,7 +93,8 @@ def exec_sed_task(sed_task, sed_variables, log=None):
     variable_results = get_results_from_opencor_simulation(opencor_sim, sed_task, sed_variables, opencor_variable_names)
 
     # log action
-    log_opencor_execution(opencor_sed_task, log)
+    if config.LOG:
+        log_opencor_execution(opencor_sed_task, log)
 
     # return results and log
     return variable_results, log

biosimulators_opencor/utils.py

@@ -7,7 +7,7 @@
 """
 
 from .data_model import KISAO_ALGORITHM_MAP
-from biosimulators_utils.config import get_config  # noqa: F401
+from biosimulators_utils.config import get_config, Config  # noqa: F401
 from biosimulators_utils.data_model import ValueType  # noqa: F401
 from biosimulators_utils.log.data_model import TaskLog  # noqa: F401
 from biosimulators_utils.report.data_model import VariableResults  # noqa: F401
@@ -44,20 +44,21 @@
 ]
 
 
-def validate_simulation(task, variables):
+def validate_simulation(task, variables, config=None):
     """ Validate that a simulation can be executed with OpenCOR
 
     Args:
         task (:obj:`Task`): request simulation task
         variables (:obj:`list` of :obj:`Variable`): variables that should be recorded
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :obj:`tuple:`:
 
             :obj:`Task`: possibly alternate task that OpenCOR should execute
             :obj:`dict`: dictionary that maps the id of each SED variable to the name that OpenCOR uses to reference it
     """
-    config = get_config()
+    config = config or get_config()
     model = task.model
     sim = task.simulation
 
@@ -102,7 +103,7 @@ def validate_simulation(task, variables):
         opencor_sim.number_of_steps = int(opencor_sim.number_of_steps)
 
     # check that OpenCOR can execute the request algorithm (or a similar one)
-    opencor_task.simulation.algorithm = get_opencor_algorithm(opencor_task.simulation.algorithm)
+    opencor_task.simulation.algorithm = get_opencor_algorithm(opencor_task.simulation.algorithm, config=config)
 
     return opencor_task, opencor_variable_names
 
@@ -163,18 +164,19 @@ def validate_variable_xpaths(sed_variables, model_filename):
     return opencor_variable_names
 
 
-def get_opencor_algorithm(requested_alg):
+def get_opencor_algorithm(requested_alg, config=None):
     """ Get a possibly alternative algorithm that OpenCOR should execute
 
     Args:
         requested_alg (:obj:`Algorithm`): requested algorithm
+        config (:obj:`Config`, optional): configuration
 
     Returns:
         :obj:`Algorithm`: possibly alternative algorithm that OpenCOR should execute
     """
     exec_alg = copy.deepcopy(requested_alg)
 
-    algorithm_substitution_policy = get_algorithm_substitution_policy()
+    algorithm_substitution_policy = get_algorithm_substitution_policy(config=config)
     exec_alg.kisao_id = get_preferred_substitute_algorithm_by_ids(
         requested_alg.kisao_id, KISAO_ALGORITHM_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)

requirements.txt

@@ -1,5 +1,5 @@
-biosimulators_utils[cellml,logging] >= 0.1.104
-kisao >= 2.23
+biosimulators_utils[cellml,logging] >= 0.1.114
+kisao >= 2.28
 lxml
 numpy
 # opencor

tests/test_core_main.py

@@ -12,6 +12,7 @@
 from biosimulators_opencor.data_model import KISAO_ALGORITHM_MAP
 from biosimulators_utils.combine import data_model as combine_data_model
 from biosimulators_utils.combine.io import CombineArchiveWriter
+from biosimulators_utils.config import get_config
 from biosimulators_utils.log.data_model import TaskLog
 from biosimulators_utils.report import data_model as report_data_model
 from biosimulators_utils.report.io import ReportReader
@@ -51,12 +52,15 @@ def test_exec_sedml_docs_in_combine_archive(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)
 
@@ -72,12 +76,15 @@ 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, '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)