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="0.0.4"
+ARG VERSION="0.0.5"
 ARG SIMULATOR_VERSION=8.0
 
 # metadata
@@ -60,6 +60,11 @@ RUN apt-get update -y \
  && 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_XPP
 RUN pip install /root/Biosimulators_XPP \

biosimulators.json

@@ -26,6 +26,10 @@
  },
  "operatingSystemType": "Linux"
  },
+ "pythonApi": {
+ "package": "biosimulators-xpp",
+ "module": "biosimulators_xpp"
+ },
  "authors": [{
  "firstName": "G. Bard",
  "lastName": "Ermentrout",
@@ -36,7 +40,11 @@
  }]
  }],
  "references": {
- "identifiers": [],
+ "identifiers": [{
+ "namespace": "pypi",
+ "id": "biosimulators-xpp",
+ "url": "https://pypi.org/project/biosimulators-xpp/"
+ }],
  "citations": [{
  "title": "XPPAUT",
  "authors": "Bard Ermentrout",

biosimulators_xpp/_version.py

@@ -1 +1 @@
-__version__ = '0.0.4'
+__version__ = '0.0.5'

biosimulators_xpp/core.py

@@ -8,7 +8,7 @@
 
 from .utils import validate_variables, apply_model_changes, set_up_simulation, exec_xpp_simulation, get_results_of_sed_variables
 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.model_lang.xpp.validation import validate_model
 from biosimulators_utils.report.data_model import ReportFormat, 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=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(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 XPP doesn't support
  * Task requires an algorithm that XPP 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
@@ -121,7 +109,7 @@ def exec_sed_task(task, variables, log=None):
  apply_model_changes(xpp_sim, model.changes)
 
  # setup simulation
- exec_kisao_id = set_up_simulation(sim, xpp_sim['simulation_method'])
+ exec_kisao_id = set_up_simulation(sim, xpp_sim['simulation_method'], config=config)
 
  # run simulation
  raw_results = exec_xpp_simulation(model.source, xpp_sim)
@@ -130,8 +118,9 @@ def exec_sed_task(task, variables, log=None):
  variable_results = get_results_of_sed_variables(sim, raw_results, variables)
 
  # log action
- log.algorithm = exec_kisao_id
- log.simulator_details = xpp_sim['simulation_method']
+ if config.LOG:
+ log.algorithm = exec_kisao_id
+ log.simulator_details = xpp_sim['simulation_method']
 
  ############################
  # return the result of each variable and log

biosimulators_xpp/utils.py

@@ -7,6 +7,7 @@
 """
 
 from .data_model import KISAO_ALGORITHM_MAP
+from biosimulators_utils.config import Config # noqa: F401
 from biosimulators_utils.report.data_model import VariableResults
 from biosimulators_utils.sedml.data_model import ModelAttributeChange, UniformTimeCourseSimulation, Symbol, Variable # noqa: F401
 from biosimulators_utils.simulator.utils import get_algorithm_substitution_policy
@@ -123,12 +124,13 @@ def apply_model_changes(xpp_model, sed_changes):
  raise ValueError(msg)
 
 
-def set_up_simulation(sed_sim, xpp_sim):
+def set_up_simulation(sed_sim, xpp_sim, config=None):
  """ Apply SED simulation settings to the configuration of a XPP simulation
 
  Args:
  sed_sim (:obj:`UniformTimeCourseSimulation`): SED simulation
  xpp_sim (:obj:`dict`): XPP simulation
+ config (:obj:`Config`, optional): configuration
 
  Returns:
  :obj:`str`: KiSAO id of the algorithm to execute
@@ -138,7 +140,7 @@ def set_up_simulation(sed_sim, xpp_sim):
  xpp_sim['dt'] = str((sed_sim.output_end_time - sed_sim.output_start_time) / sed_sim.number_of_points)
  xpp_sim['njmp'] = str(1)
 
- substitution_policy = get_algorithm_substitution_policy()
+ substitution_policy = get_algorithm_substitution_policy(config=config)
  exec_kisao_id = get_preferred_substitute_algorithm_by_ids(
  sed_sim.algorithm.kisao_id, KISAO_ALGORITHM_MAP.keys(),
  substitution_policy=substitution_policy)

requirements.txt

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

tests/test_core_main.py

@@ -96,12 +96,15 @@ 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)
 
@@ -236,13 +239,16 @@ 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:
  failures.append(alg.kisao_id)