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

@@ -22,7 +22,7 @@
 
 FROM python:3.9-slim-buster
 
-ARG VERSION="0.1.11"
+ARG VERSION="0.1.12"
 ARG SIMULATOR_VERSION=2.6.0
 
 # metadata
@@ -70,6 +70,11 @@ RUN apt-get update -y \
     && rm -rf /var/lib/apt/lists/*
 ENV PATH=${PATH}:/opt/BioNetGen-${SIMULATOR_VERSION}/
 
+# fonts for matplotlib
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libfreetype6 \
+    && rm -rf /var/lib/apt/lists/*
+
 # install BioSimulators-compliant command-line interface to BioNetGen
 COPY . /root/Biosimulators_BioNetGen
 RUN pip install /root/Biosimulators_BioNetGen \

biosimulators.json

@@ -17,6 +17,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-bionetgen",
+    "module": "biosimulators_bionetgen"
+  },
   "authors": [{
       "firstName": "Ali",
       "middleName": "Sinan",
@@ -91,7 +95,13 @@
     }
   ],
   "references": {
-    "identifiers": [{
+    "identifiers": [
+      {
+            "namespace": "pypi",
+            "id": "bionetgen",
+            "url": "https://pypi.org/project/bionetgen/"
+          },
+      {
         "namespace": "pypi",
         "id": "biosimulators-bionetgen",
         "url": "https://pypi.org/project/biosimulators-bionetgen/"
@@ -434,7 +444,7 @@
 
       "modelingFrameworks": [{
         "namespace": "SBO",
-        "id": "SBO_0000295"
+        "id": "SBO_0000680"
       }],
       "modelFormats": [{
         "namespace": "EDAM",

biosimulators_bionetgen/_version.py

@@ -1 +1 @@
-__version__ = '0.1.11'
+__version__ = '0.1.12'

biosimulators_bionetgen/core.py

@@ -12,7 +12,7 @@
                     get_variables_results_from_observable_results, add_variables_to_model)
 from .warnings import IgnoredBnglFileContentWarning
 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
@@ -27,11 +27,7 @@
 __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:
@@ -43,12 +39,7 @@ 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`:
@@ -59,21 +50,17 @@ 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=False,
-                                      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(sed_task, variables, log=None):
+def exec_sed_task(sed_task, variables, log=None, config=None):
     """ Execute a task and save its results
 
     Args:
        sed_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`:
@@ -104,8 +91,9 @@ def exec_sed_task(sed_task, variables, log=None):
         * BioNetGen
         * :obj:`get_variables_results_from_observable_results`
     """
-    config = get_config()
-    log = log or TaskLog()
+    config = config or get_config()
+    if config.LOG and not log:
+        log = TaskLog()
 
     if config.VALIDATE_SEDML:
         raise_errors_warnings(
@@ -157,10 +145,11 @@ def exec_sed_task(sed_task, variables, log=None):
         variable_results[key] = variable_results[key][-(sed_task.simulation.number_of_points + 1):]
 
     # log action
-    log.algorithm = alg_kisao_id
-    log.simulator_details = {
-        'actions': bionetgen_task.actions,
-    }
+    if config.LOG:
+        log.algorithm = alg_kisao_id
+        log.simulator_details = {
+            'actions': bionetgen_task.actions,
+        }
 
     # return the values of the variables and log
     return variable_results, log

biosimulators_bionetgen/utils.py

@@ -6,9 +6,10 @@
 :License: MIT
 """
 
-from .config import Config
+from .config import Config as SimulatorConfig
 from .data_model import Model, ModelBlock, Task, KISAO_SIMULATION_METHOD_ARGUMENTS_MAP  # noqa: F401
 from .io import write_task, read_simulation_results
+from biosimulators_utils.config import Config  # noqa: F401
 from biosimulators_utils.report.data_model import VariableResults
 from biosimulators_utils.sedml.data_model import (ModelAttributeChange, Variable,  # noqa: F401
                                                   Symbol, UniformTimeCourseSimulation)
@@ -197,12 +198,13 @@ def add_variables_to_model(model, variables):
         raise NotImplementedError(msg)
 
 
-def add_simulation_to_task(task, simulation):
+def add_simulation_to_task(task, simulation, config=None):
     """ Add a SED simulation to a BioNetGen task
 
     Args:
         task (:obj:`Task`): BioNetGen task
         simulation (:obj:`UniformTimeCourseSimulation`): SED simulation
+        config (:obj:`Config`, optional): configuration
 
     Raises:
         :obj:`NotImplementedError`: if BioNetGen doesn't support the request algorithm or
@@ -227,7 +229,7 @@ def add_simulation_to_task(task, simulation):
 
     simulate_args['n_steps'] = int(n_steps)
 
-    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_SIMULATION_METHOD_ARGUMENTS_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -298,7 +300,7 @@ def exec_bionetgen_task(task):
     write_task(task, task_filename)
 
     # execute the task
-    bionetgen_path = Config().bionetgen_path
+    bionetgen_path = SimulatorConfig().bionetgen_path
     try:
         subprocess.check_call([bionetgen_path, task_filename, '--outdir', temp_dirname])
     except Exception:

requirements.txt

@@ -1,3 +1,3 @@
-biosimulators_utils[bngl,logging] >= 0.1.104
+biosimulators_utils[bngl,logging] >= 0.1.114
 kisao
 pandas

tests/test_core_main.py

@@ -11,6 +11,7 @@
 from biosimulators_bionetgen.core import exec_sed_task, exec_sedml_docs_in_combine_archive
 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.report import data_model as report_data_model
 from biosimulators_utils.report.io import ReportReader
 from biosimulators_utils.sedml import data_model as sedml_data_model
@@ -72,13 +73,15 @@ def test_exec_sedml_docs_in_combine_archive(self):
         doc, archive_filename = self._build_combine_archive()
 
         out_dir = os.path.join(self.dirname, 'out')
-        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)
 
@@ -87,13 +90,15 @@ 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)
-            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 test_exec_with_cli(self):