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="0.0.5"
+ARG VERSION="0.0.6"
 ARG SIMULATOR_VERSION=3.0.0b
 
 # metadata
@@ -27,6 +27,11 @@ LABEL \
     about.tags="BioSimulators,mathematical model,logical model,simulation,systems biology,computational biology,SBML,SED-ML,COMBINE,OMEX" \
     maintainer="BioSimulators Team <info@biosimulators.org>"
 
+# fonts for matplotlib
+RUN apt-get update -y \
+    && apt-get install -y --no-install-recommends libfreetype6 \
+    && rm -rf /var/lib/apt/lists/*
+
 # Install GINsim
 RUN apt-get update -y \
     && apt-get install -y --no-install-recommends \

biosimulators.json

@@ -17,6 +17,10 @@
         },
         "operatingSystemType": "Linux"
     },
+    "pythonApi": {
+      "package": "biosimulators-ginsim",
+      "module": "biosimulators_ginsim"
+    },
     "authors": [{
             "firstName": "Aurélien",
             "lastName": "Naldi",
@@ -104,7 +108,12 @@
                 "namespace": "biotools",
                 "id": "ginsim",
                 "url": "https://bio.tools/ginsim"
-            }
+            },
+            {
+                "namespace": "pypi",
+                "id": "biosimulators-ginsim",
+                "url": "https://pypi.org/project/biosimulators-ginsim/"
+          }
         ],
         "citations": [{
                 "title": "Logical modeling and analysis of cellular regulatory networks With GINsim 3.0",

biosimulators_ginsim/_version.py

@@ -1 +1 @@
-__version__ = '0.0.5'
+__version__ = '0.0.6'

biosimulators_ginsim/core.py

@@ -9,7 +9,7 @@
 from .utils import (validate_simulation, get_variable_target_xpath_ids,
                     read_model, set_up_simulation, exec_simulation, 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
@@ -24,11 +24,7 @@
 __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:
@@ -40,12 +36,7 @@ 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`:
@@ -56,21 +47,17 @@ 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`:
@@ -84,9 +71,10 @@ def exec_sed_task(task, variables, log=None):
           * Task requires a time course that GINsim doesn't support
           * Task requires an algorithm that GINsim doesn't support
     """
-    config = get_config()
+    config = config or get_config()
 
-    log = log or TaskLog()
+    if config.LOG and not log:
+        log = TaskLog()
 
     # validate task
     model = task.model
@@ -133,7 +121,7 @@ def exec_sed_task(task, variables, log=None):
     biolqm_model = read_model(model.source)
 
     # setup simulation
-    alg_kisao_id, method_name, method_args = set_up_simulation(sim)
+    alg_kisao_id, method_name, method_args = set_up_simulation(sim, config=config)
 
     # run simulation
     raw_results = exec_simulation(method_name, biolqm_model, method_args)
@@ -142,11 +130,12 @@ def exec_sed_task(task, variables, log=None):
     variable_results = get_variable_results(variables, model.language, target_xpath_ids, sim, raw_results)
 
     # log action
-    log.algorithm = alg_kisao_id
-    log.simulator_details = {
-        'method': method_name,
-        'arguments': method_args,
-    }
+    if config.LOG:
+        log.algorithm = alg_kisao_id
+        log.simulator_details = {
+            'method': method_name,
+            'arguments': method_args,
+        }
 
     ############################
     # return the result of each variable and log

biosimulators_ginsim/utils.py

@@ -7,6 +7,7 @@
 """
 
 from .data_model import KISAO_ALGORITHM_MAP, UpdatePolicy  # noqa: F401
+from biosimulators_utils.config import Config  # noqa: F401
 from biosimulators_utils.report.data_model import VariableResults
 from biosimulators_utils.sedml.data_model import (  # noqa: F401
     ModelLanguage, Simulation, UniformTimeCourseSimulation, Symbol)
@@ -150,11 +151,12 @@ def read_model(filename):
     return model
 
 
-def set_up_simulation(simulation):
+def set_up_simulation(simulation, config=None):
     """ Set up an analysis
 
     Args:
         simulation (:obj:`Simulation`): analysis
+        config (:obj:`Config`, optional): configuration
 
     Returns:
         :obj:`tuple`:
@@ -165,7 +167,7 @@ def set_up_simulation(simulation):
     """
     # simulation algorithm
     alg_kisao_id = simulation.algorithm.kisao_id
-    alg_substitution_policy = get_algorithm_substitution_policy()
+    alg_substitution_policy = get_algorithm_substitution_policy(config=config)
     exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
         alg_kisao_id, KISAO_ALGORITHM_MAP.keys(),
         substitution_policy=alg_substitution_policy)

requirements.txt

@@ -1,5 +1,5 @@
-biosimulators_utils[logging,sbml] >= 0.1.110
+biosimulators_utils[logging,sbml] >= 0.1.114
 ginsim >= 0.4.4
-kisao >= 2.27
+kisao >= 2.28
 lxml
 numpy

tests/test_core_main.py

@@ -177,12 +177,15 @@ 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)
 
@@ -324,12 +327,15 @@ 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)