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-pyneuroml

@@ -36,6 +36,11 @@ RUN mkdir -p /usr/share/man/man1/ \
     && 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_pyNeuroML
 RUN pip install /root/Biosimulators_pyNeuroML \

biosimulators-netpyne.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-pyneuroml",
+    "module": "biosimulators_pyneuroml.api.netpyne"
+  },
   "authors": [
     {
       "firstName": "Salvador",
@@ -105,7 +109,12 @@
         "namespace": "pypi",
         "id": "netpyne",
         "url": "https://pypi.org/project/netpyne"
-      }
+      },
+      {
+            "namespace": "pypi",
+            "id": "biosimulators-pyneuroml",
+            "url": "https://pypi.org/project/biosimulators-pyneuroml/"
+          }
     ],
     "citations": [
       {

biosimulators-neuron.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-pyneuroml",
+    "module": "biosimulators_pyneuroml.api.neuron"
+  },
   "authors": [
     {
       "firstName": "Michael",
@@ -89,7 +93,12 @@
         "namespace": "pypi",
         "id": "NEURON",
         "url": "https://pypi.org/project/NEURON"
-      }
+      },
+      {
+            "namespace": "pypi",
+            "id": "biosimulators-pyneuroml",
+            "url": "https://pypi.org/project/biosimulators-pyneuroml/"
+          }
     ],
     "citations": [
       {

biosimulators-pyneuroml.json

@@ -19,6 +19,10 @@
     },
     "operatingSystemType": "Linux"
   },
+  "pythonApi": {
+    "package": "biosimulators-pyneuroml",
+    "module": "biosimulators_pyneuroml.api.pyneuroml"
+  },
   "authors": [
     {
       "firstName": "Padraig",
@@ -62,7 +66,12 @@
         "namespace": "pypi",
         "id": "pyNeuroML",
         "url": "https://pypi.org/project/pyNeuroML"
-      }
+      },
+      {
+            "namespace": "pypi",
+            "id": "biosimulators-pyneuroml",
+            "url": "https://pypi.org/project/biosimulators-pyneuroml/"
+          }
     ],
     "citations": [
       {

biosimulators_pyneuroml/core.py

@@ -9,6 +9,7 @@
 from .data_model import Simulator, KISAO_ALGORITHM_MAP, SEDML_TIME_OUTPUT_COLUMN_ID, SEDML_OUTPUT_FILE_ID
 from .utils import validate_task, read_xml_file, set_sim_in_lems_xml, run_lems_xml, get_simulator_run_lems_method
 from biosimulators_utils.combine.exec import exec_sedml_docs_in_archive
+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
@@ -25,10 +26,7 @@
 
 
 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,
+                                       config=None,
                                        simulator=Simulator.pyneuroml):
     """ Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
 
@@ -41,13 +39,8 @@ 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
         simulator (:obj:`Simulator`, optional): simulator
-        raise_exceptions (:obj:`bool`, optional): whether to raise exceptions
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :obj:`tuple`:
@@ -58,21 +51,17 @@ def exec_sedml_docs_in_combine_archive(archive_filename, out_dir,
     sed_doc_executer = functools.partial(exec_sed_doc, functools.partial(exec_sed_task, simulator=simulator))
     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, simulator=Simulator.pyneuroml):
+def exec_sed_task(task, variables, log=None, config=None, simulator=Simulator.pyneuroml):
     ''' 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
        simulator (:obj:`Simulator`, optional): simulator
 
     Returns:
@@ -86,17 +75,20 @@ def exec_sed_task(task, variables, log=None, simulator=Simulator.pyneuroml):
             could not be recorded
         :obj:`NotImplementedError`: if the task is not of a supported type or involves an unsuported feature
     '''
-    log = log or TaskLog()
+    config = config or get_config()
+    if config.LOG and not log:
+        log = TaskLog()
 
     sim = task.simulation
     sim.algorithm = copy.deepcopy(sim.algorithm)
-    sim.algorithm.kisao_id = validate_task(task, variables, simulator)
+    sim.algorithm.kisao_id = validate_task(task, variables, simulator, config=config)
 
     lems_root = read_xml_file(task.model.source)
 
     set_sim_in_lems_xml(lems_root, task, variables)
     lems_results = run_lems_xml(lems_root, working_dirname=os.path.dirname(
-        task.model.source), lems_filename=task.model.source)[SEDML_OUTPUT_FILE_ID]
+        task.model.source), lems_filename=task.model.source,
+        verbose=config.VERBOSE, config=config)[SEDML_OUTPUT_FILE_ID]
 
     # transform the results to an instance of :obj:`VariableResults`
     variable_results = VariableResults()
@@ -110,15 +102,16 @@ def exec_sed_task(task, variables, log=None, simulator=Simulator.pyneuroml):
         variable_results[variable.id] = lems_result.to_numpy()[-(sim.number_of_points + 1):]
 
     # log action
-    log.algorithm = sim.algorithm.kisao_id
-    log.simulator_details = {
-        'method': 'pyneuroml.pynml.' + get_simulator_run_lems_method(simulator).__name__,
-        'lemsSimulation': {
-            'length': '{}s'.format(sim.output_end_time),
-            'step': '{}s'.format((sim.output_end_time - sim.output_start_time) / sim.number_of_steps),
-            'method': KISAO_ALGORITHM_MAP[sim.algorithm.kisao_id]['id'],
-        },
-    }
+    if config.LOG:
+        log.algorithm = sim.algorithm.kisao_id
+        log.simulator_details = {
+            'method': 'pyneuroml.pynml.' + get_simulator_run_lems_method(simulator).__name__,
+            'lemsSimulation': {
+                'length': '{}s'.format(sim.output_end_time),
+                'step': '{}s'.format((sim.output_end_time - sim.output_start_time) / sim.number_of_steps),
+                'method': KISAO_ALGORITHM_MAP[sim.algorithm.kisao_id]['id'],
+            },
+        }
 
     # return results and log
     return variable_results, log

biosimulators_pyneuroml/utils.py

@@ -37,18 +37,19 @@
 ]
 
 
-def validate_task(task, variables, simulator):
+def validate_task(task, variables, simulator, config=None):
     """ Validate a task
 
     Args:
         task (:obj:`Task`): task
         variables (:obj:`list` of :obj:`Variable`): variables
         simulator (:obj:`Simulator`): simulator
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :obj:`str`: KiSAO id for a possibly alternative simulation algorithm
     """
-    config = get_config()
+    config = config or get_config()
 
     model = task.model
     sim = task.simulation
@@ -90,7 +91,7 @@ def validate_task(task, variables, simulator):
     simulator_kisao_alg_map = {kisao_id: alg_props for kisao_id,
                                alg_props in KISAO_ALGORITHM_MAP.items() if simulator in alg_props['simulators']}
 
-    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, simulator_kisao_alg_map.keys(),
         substitution_policy=algorithm_substitution_policy)
@@ -159,7 +160,8 @@ def set_sim_in_lems_xml(lems_xml_root, task, variables):
 
 
 def run_lems_xml(lems_xml_root, working_dirname='.', lems_filename=None,
-                 simulator=Simulator.pyneuroml, num_processors=None, max_memory=None, verbose=None):
+                 simulator=Simulator.pyneuroml, num_processors=None, max_memory=None, verbose=False,
+                 config=None):
     """Run a LEMS document with a simulator
 
     Args:
@@ -170,11 +172,13 @@ def run_lems_xml(lems_xml_root, working_dirname='.', lems_filename=None,
         num_processors (:obj:`int`, optional): number of processors to use (only used with NetPyNe)
         max_memory (:obj:`int`, optional): maximum memory to use in bytes
         verbose (:obj:`bool`, optional): whether to display extra information about simulation runs
+        config (:obj:`Config`, optional): BioSimulators common configuration
 
     Returns:
         :obj:`dict` of :obj:`str` => :obj:`pandas.DataFrame`: dictionary that maps the id of each output file
             to a Pandas data frame with its value
     """
+    config = config or get_config()
     run_lems_method = get_simulator_run_lems_method(simulator)
     options = get_run_lems_options(num_processors=num_processors, max_memory=max_memory, verbose=verbose)
 
@@ -194,16 +198,17 @@ def run_lems_xml(lems_xml_root, working_dirname='.', lems_filename=None,
 
     results_dirname = tempfile.mkdtemp()
     options.exec_in_dir = results_dirname
-    with StandardOutputErrorCapturer(relay=options.verbose) as captured:
+    with StandardOutputErrorCapturer(relay=options.verbose, disabled=not config.LOG) as captured:
         result = run_lems_method(temp_filename, **options.to_kw_args(simulator))
         if not result:
             os.remove(temp_filename)
             shutil.rmtree(results_dirname)
 
-            msg = '`{}` was not able to execute {}:\n\n  {}'.format(
+            msg = '`{}` was not able to execute {}'.format(
                 simulator.value,
-                '`{}`'.format(lems_filename) if lems_filename else 'the LEMS document',
-                captured.get_text().replace('\n', '\n  '))
+                '`{}`'.format(lems_filename) if lems_filename else 'the LEMS document')
+            if config.LOG:
+                msg += '\n\n  ' + captured.get_text().replace('\n', '\n  ')
             raise RuntimeError(msg)
 
     # read results
@@ -242,7 +247,7 @@ def get_simulator_run_lems_method(simulator):
         raise NotImplementedError('`{}` is not a supported simulator.'.format(simulator))
 
 
-def get_run_lems_options(num_processors=None, max_memory=None, verbose=None):
+def get_run_lems_options(num_processors=None, max_memory=None, verbose=False):
     """ Get options for running a LEMS document
 
     Args:
@@ -259,9 +264,6 @@ def get_run_lems_options(num_processors=None, max_memory=None, verbose=None):
     if max_memory is None:
         max_memory = get_available_memory() - 100 * 1000000
 
-    if verbose is None:
-        verbose = get_config().VERBOSE
-
     options = RunLemsOptions(num_processors=num_processors, max_memory=max_memory, verbose=verbose)
 
     return options

requirements.txt

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

tests/test_core_main.py

@@ -10,6 +10,7 @@
 from biosimulators_pyneuroml.data_model import Simulator, SIMULATOR_ENABLED, KISAO_ALGORITHM_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.log.data_model import TaskLog
 from biosimulators_utils.report import data_model as report_data_model
 from biosimulators_utils.report.io import ReportReader
@@ -74,12 +75,15 @@ 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,
-                                                ],
-                                                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)
 
@@ -91,12 +95,15 @@ 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, '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)