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 ghcr.io/biosimulators/biosimulators_boolnet/boolnet_base:latest
 
-ARG VERSION="0.1.14"
+ARG VERSION="0.1.15"
 ARG SIMULATOR_VERSION=2.1.5
 
 # metadata

Dockerfile-base

@@ -47,3 +47,8 @@ RUN apt-get update -y \
         libxml2-dev \
     && 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/*

biosimulators.json

@@ -17,6 +17,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-boolnet",
+    "module": "biosimulators_boolnet"
+  },
   "authors": [{
       "firstName": "Christoph",
       "middleName": null,

biosimulators_boolnet/_version.py

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

biosimulators_boolnet/core.py

@@ -10,7 +10,7 @@
 from .utils import (validate_time_course, validate_data_generator_variables, get_variable_target_x_path_keys,
                     get_boolnet, set_simulation_method_arg, get_variable_results)
 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
@@ -30,11 +30,7 @@
 __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:
@@ -46,12 +42,7 @@ 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`:
@@ -62,21 +53,17 @@ 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`:
@@ -90,8 +77,9 @@ def exec_sed_task(task, variables, log=None):
           * Task requires a time course that BoolNet doesn't support
           * Task requires an algorithm that BoolNet doesn't support
     """
-    config = get_config()
-    log = log or TaskLog()
+    config = config or get_config()
+    if config.LOG and not log:
+        log = TaskLog()
 
     # validate task
     model = task.model
@@ -138,7 +126,7 @@ def exec_sed_task(task, variables, log=None):
 
     # Load the algorithm specified by :obj:`task.simulation.algorithm.kisao_id`
     alg_kisao_id = sim.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(
         alg_kisao_id, KISAO_METHOD_ARGUMENTS_MAP.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -186,12 +174,13 @@ def exec_sed_task(task, variables, log=None):
         variable_results[variable.id] = variable_results[variable.id][-(int(sim.number_of_points) + 1):]
 
     # log action
-    log.algorithm = exec_kisao_id
-    log.simulator_details = {
-        'method': 'BoolNet::generateTimeSeries',
-        'arguments': simulation_method_args,
-    }
-    simulation_method_args['type'] = alg['type']
+    if config.LOG:
+        log.algorithm = exec_kisao_id
+        log.simulator_details = {
+            'method': 'BoolNet::generateTimeSeries',
+            'arguments': simulation_method_args,
+        }
+        simulation_method_args['type'] = alg['type']
 
     # return the result of each variable and log
     return variable_results, log

requirements.txt

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

tests/test_core_main.py

@@ -160,12 +160,15 @@ 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)
 
@@ -296,12 +299,15 @@ def test_exec_sedml_docs_in_combine_archive_with_all_algorithms(self):
         for alg in gen_algorithms_from_specs(self.SPECIFICATIONS_FILENAME).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)