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=0.1.31
+ARG VERSION=0.1.32
 ARG SIMULATOR_VERSION="1.6.2"
 
 # metadata
@@ -35,6 +35,11 @@ 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_GillesPy2
 RUN pip install /root/Biosimulators_GillesPy2 \

biosimulators.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-gillespy2",
+    "module": "biosimulators_gillespy2"
+  },
   "authors": [
     {
       "firstName": "Brian",

biosimulators_gillespy2/_version.py

@@ -1 +1 @@
-__version__ = '0.1.31'
+__version__ = '0.1.32'

biosimulators_gillespy2/core.py

@@ -9,7 +9,7 @@
 
 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
@@ -32,11 +32,7 @@
 ]
 
 
-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:
@@ -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
@@ -125,7 +113,7 @@ def exec_sed_task(task, variables, log=None):
     # Load the algorithm 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(
         algorithm_kisao_id, KISAO_ALGORITHM_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -237,11 +225,12 @@ def exec_sed_task(task, variables, log=None):
                 variable_results[variable.id] = dynamics[-(simulation.number_of_points + 1):]
 
     # log action
-    log.algorithm = exec_kisao_id
-    log.simulator_details = {
-        'method': solver.__module__ + '.' + solver.__name__,
-        'arguments': dict(**algorithm.solver_args, **algorithm_params),
-    }
+    if config.LOG:
+        log.algorithm = exec_kisao_id
+        log.simulator_details = {
+            'method': solver.__module__ + '.' + solver.__name__,
+            'arguments': dict(**algorithm.solver_args, **algorithm_params),
+        }
 
     # return results and log
     return variable_results, log

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.107
+biosimulators_utils[logging] >= 0.1.114
 gillespy2 >= 1.6.0
 kisao
 lxml # optional dependency of python_libsbml

tests/test_core_main.py

@@ -12,6 +12,7 @@
 from biosimulators_utils.archive.io import ArchiveReader
 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
@@ -249,7 +250,7 @@ def test_exec_sed_task_errors(self):
                 core.exec_sed_task(task, variables, TaskLog())
             task.model.source = os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297.edited', 'ex1', 'BIOMD0000000297.xml')
 
-            with self.assertRaisesRegex(AlgorithmCannotBeSubstitutedException, 'No algorithm can be substituted'):
+            with self.assertRaisesRegex(AlgorithmCannotBeSubstitutedException, 'Algorithms cannot be substituted'):
                 core.exec_sed_task(task, variables, TaskLog())
             task.simulation.algorithm.kisao_id = 'KISAO_0000029'
             task.simulation.algorithm.changes = [
@@ -383,13 +384,15 @@ 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,
-                                                    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)
 
@@ -440,13 +443,15 @@ 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)
 
@@ -642,14 +647,16 @@ def test_exec_sedml_docs_in_combine_archive_with_docker_image(self):
 
     def test_more_complex_archive(self):
         archive_filename = os.path.join(os.path.dirname(__file__), 'fixtures', 'BIOMD0000000297.edited.omex')
-        core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname,
-                                                report_formats=[
-                                                    report_data_model.ReportFormat.csv,
-                                                    report_data_model.ReportFormat.h5,
-                                                ],
-                                                plot_formats=[],
-                                                bundle_outputs=True,
-                                                keep_individual_outputs=True)
+
+        config = get_config()
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5, report_data_model.ReportFormat.csv]
+        config.VIZ_FORMATS = []
+        config.BUNDLE_OUTPUTS = True
+        config.KEEP_INDIVIDUAL_OUTPUTS = True
+
+        _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, self.dirname, config=config)
+        if log.exception:
+            raise log.exception
 
         self.assertEqual(set(['reports.zip', 'reports.h5', 'ex1', 'ex2']).difference(set(os.listdir(self.dirname))), set())
         self.assertEqual(set(os.listdir(os.path.join(self.dirname, 'ex1'))), set(['BIOMD0000000297.sedml']))