feat: updated to Biosimulators-utils 0.1.114: organized options, added option to control logging; added Python package to specs; added fonts to Docker image

Author: jonrkarr

biosimulators.json

@@ -17,6 +17,10 @@
         },
         "operatingSystemType": "Linux"
     },
+    "pythonApi": {
+      "package": "biosimulators-libsbmlsim",
+      "module": "biosimulators_libsbmlsim"
+    },
     "authors": [{
             "firstName": "Hiromu",
             "lastName": "Takizawa",
@@ -79,7 +83,11 @@
         }
     ],
     "references": {
-        "identifiers": [],
+        "identifiers": [{
+            "namespace": "pypi",
+            "id": "biosimulators-libsbmlsim",
+            "url": "https://pypi.org/project/biosimulators-libsbmlsim/"
+          }],
         "citations": [{
             "title": "LibSBMLSim: a reference implementation of fully functional SBML simulator",
             "authors": "Hiromu Takizawa, Kazushige Nakamura, Akito Tabira, Yoichi Chikahara, Tatsuhiro Matsui, Noriko Hiroi & Akira Funahashi",

biosimulators/Dockerfile

@@ -1,7 +1,7 @@
 # Base OS
 FROM python:3.9-slim-buster
 
-ARG VERSION=0.0.2
+ARG VERSION=0.0.3
 ARG SIMULATOR_VERSION=1.4.0
 ARG LIBSBML_VERSION=5.19.0
 
@@ -78,6 +78,11 @@ 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 biosimulators/ /root/biosimulators/
 RUN pip install /root/biosimulators \

biosimulators/biosimulators_libsbmlsim/_version.py

@@ -1 +1 @@
-__version__ = '0.0.2'
+__version__ = '0.0.3'

biosimulators/biosimulators_libsbmlsim/core.py

@@ -8,7 +8,7 @@
 
 from .data_model import KISAO_ALGORITHMS_MAP, get_integrator
 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
@@ -31,11 +31,7 @@
 __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:
@@ -47,12 +43,7 @@ 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`:
@@ -63,31 +54,28 @@ 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`:
 
             :obj:`VariableResults`: results of variables
             :obj:`TaskLog`: log
     '''
-    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
@@ -121,7 +109,7 @@ def exec_sed_task(task, variables, log=None):
         raise NotImplementedError(msg)
 
     # determine the simulation 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)
@@ -267,18 +255,19 @@ def exec_sed_task(task, variables, log=None):
         raise NotImplementedError(msg)
 
     # log action
-    log.algorithm = exec_kisao_id
-    log.simulator_details = {
-        'method': "simulateSBMLFromFile",
-        'arguments': {
-            'sim_time': sim.output_end_time,
-            'dt': time_step,
-            'print_interval': print_interval,
-            'print_amount': print_amount,
-            'method': integrator,
-            'use_lazy_method': use_lazy_newton_method,
-        },
-    }
+    if config.LOG:
+        log.algorithm = exec_kisao_id
+        log.simulator_details = {
+            'method': "simulateSBMLFromFile",
+            'arguments': {
+                'sim_time': sim.output_end_time,
+                'dt': time_step,
+                'print_interval': print_interval,
+                'print_amount': print_amount,
+                'method': integrator,
+                'use_lazy_method': use_lazy_newton_method,
+            },
+        }
 
     # return results and log
     return variable_results, log

biosimulators/requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[sbml,logging] >= 0.1.104
+biosimulators_utils[sbml,logging] >= 0.1.114
 # libsbmlsim
 kisao
 pandas

biosimulators/tests/test_core_main.py

@@ -11,6 +11,7 @@
 from biosimulators_libsbmlsim.data_model import KISAO_ALGORITHMS_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.sedml.data_model import (
     SedDocument, Model, ModelLanguage, UniformTimeCourseSimulation, Task, Variable, Symbol,
     Algorithm, AlgorithmParameterChange,
@@ -260,9 +261,13 @@ def test_exec_sedml_docs_in_combine_archive(self):
         CombineArchiveWriter().run(archive, archive_dirname, archive_filename)
 
         out_dir = os.path.join(self.dirname, 'results')
-        core.exec_sedml_docs_in_combine_archive(
-            archive_filename, out_dir,
-            report_formats=[report_data_model.ReportFormat.h5])
+
+        config = get_config()
+        config.REPORT_FORMATS = [report_data_model.ReportFormat.h5]
+
+        _, log = core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=config)
+        if log.exception:
+            raise log.exception
 
         results = ReportReader().run(report, out_dir, 'sim.sedml/report', format=report_data_model.ReportFormat.h5)