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="0.0.2"
+ARG VERSION="0.0.3"
 ARG SIMULATOR_VERSION=0.1.2
 
 # metadata

biosimulators.json

@@ -46,6 +46,10 @@
  },
  "operatingSystemType": "Linux"
  },
+ "pythonApi": {
+ "package": "biosimulators-masspy",
+ "module": "biosimulators_masspy"
+ },
  "authors": [{
  "firstName": "Zachary",
  "lastName": "Haiman",
@@ -81,7 +85,16 @@
  }
  ],
  "references": {
- "identifiers": [],
+ "identifiers": [{
+ "namespace": "pypi",
+ "id": "masspy",
+ "url": "https://pypi.org/project/masspy/"
+ },
+ {
+ "namespace": "pypi",
+ "id": "biosimulators-masspy",
+ "url": "https://pypi.org/project/biosimulators-masspy/"
+ }],
  "citations": [{
  "title": "MASSpy: Building, simulating, and visualizing dynamic biological models in Python using mass action kinetics",
  "authors": "Zachary B. Haiman, Daniel C. Zielinski, Yuko Koike, James T. Yurkovich & Bernhard O. Palsson",

biosimulators_masspy/_version.py

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

biosimulators_masspy/core.py

@@ -8,7 +8,7 @@
 
 from .data_model import KISAO_ALGORITHM_MAP
 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.report.data_model import ReportFormat, VariableResults, SedDocumentResults # noqa: F401
 from biosimulators_utils.sedml import validation
@@ -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`:
@@ -90,9 +77,10 @@ def exec_sed_task(task, variables, log=None):
  * Task requires a time course that MASSpy doesn't support
  * Task requires an algorithm that MASSpy 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
@@ -198,7 +186,7 @@ def exec_sed_task(task, variables, log=None):
  time = (sim.initial_time, sim.output_end_time, number_of_points)
 
  # configure 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_ALGORITHM_MAP.keys(),
  substitution_policy=algorithm_substitution_policy)
@@ -207,7 +195,6 @@ def exec_sed_task(task, variables, log=None):
  mass_sim.roadrunner.setIntegrator(alg_props['id'])
 
  # configure parameters of the simulation algorithm
- # TODO: handle substituted algorithm
  if exec_kisao_id == sim.algorithm.kisao_id:
  for change in sim.algorithm.changes:
  param_props = alg_props['parameters'].get(change.kisao_id, None)
@@ -287,13 +274,14 @@ def exec_sed_task(task, variables, log=None):
  variable_results[variable.id] = rxn_fluxes[sbml_id[2:]][-(sim.number_of_points + 1):]
 
  # log action
- log.algorithm = exec_kisao_id
+ if config.LOG:
+ log.algorithm = exec_kisao_id
 
- log.simulator_details = {}
- log.simulator_details['integrator'] = mass_sim.integrator.getName()
- for i_param in range(mass_sim.integrator.getNumParams()):
- param_name = mass_sim.integrator.getParamName(i_param)
- log.simulator_details[param_name] = getattr(mass_sim.integrator, param_name)
+  log.simulator_details = {}
+  log.simulator_details['integrator'] = mass_sim.integrator.getName()
+  for i_param in range(mass_sim.integrator.getNumParams()):
+  param_name = mass_sim.integrator.getParamName(i_param)
+  log.simulator_details[param_name] = getattr(mass_sim.integrator, param_name)
 
  ############################
  # return the result of each variable and log

requirements.txt

@@ -1,4 +1,4 @@
-biosimulators_utils[logging] >= 0.1.105
-kisao >= 2.26
+biosimulators_utils[logging] >= 0.1.114
+kisao >= 2.28
 masspy >= 0.1.2
 numpy

tests/test_core_main.py

@@ -366,12 +366,15 @@ 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)
 
@@ -486,13 +489,16 @@ 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)
+
+ config = get_config()
+ config.REPORT_FORMATS = [report_data_model.ReportFormat.h5]
+ config.BUNDLE_OUTPUTS = True
+ config.KEEP_INDIVIDUAL_OUTPUTS = True
+
  try:
- 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)
+ _, 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)
  except CombineArchiveExecutionError as exception:
  if 'Simulation failed' in str(exception):