Update petab test suite code (#1768)

Adapt to separate sbml and pysb test suite (PEtab-dev/petab_test_suite#47)

python/amici/petab_import_pysb.py

@@ -8,16 +8,17 @@
 import logging
 import os
 from itertools import chain
-from typing import List, Dict, Union, Optional, Tuple, Iterable
+from pathlib import Path
+from typing import Dict, Iterable, List, Optional, Tuple, Union
 
 import libsbml
 import petab
 import pysb
 import sympy as sp
-from petab.C import (CONDITION_NAME, OBSERVABLE_TRANSFORMATION, LIN,
- OBSERVABLE_FORMULA, NOISE_FORMULA, FORMAT_VERSION,
- PARAMETER_FILE, SBML_FILES, CONDITION_FILES,
- MEASUREMENT_FILES, VISUALIZATION_FILES, OBSERVABLE_FILES)
+from petab.C import (CONDITION_FILES, CONDITION_NAME, FORMAT_VERSION,
+ MEASUREMENT_FILES, NOISE_FORMULA, OBSERVABLE_FILES,
+ OBSERVABLE_FORMULA, PARAMETER_FILE, SBML_FILES,
+ VISUALIZATION_FILES)
 
 from . import petab_import
 from .logging import get_logger, log_execution_time, set_log_level
@@ -194,7 +195,7 @@ def from_yaml(yaml_config: Union[Dict, str],
  """
  from petab.yaml import (load_yaml, is_composite_problem,
  assert_single_condition_and_sbml_file)
- if isinstance(yaml_config, str):
+ if isinstance(yaml_config, (str, Path)):
  path_prefix = os.path.dirname(yaml_config)
  yaml_config = load_yaml(yaml_config)
  else:
@@ -328,7 +329,7 @@ def import_model_pysb(
 
  set_log_level(logger, verbose)
 
- logger.info(f"Importing model ...")
+ logger.info("Importing model ...")
 
  observable_table = petab_problem.observable_df
  pysb_model = petab_problem.pysb_model
@@ -355,6 +356,7 @@ def import_model_pysb(
  if observable_table is None:
  observables = None
  sigmas = None
+ noise_distrs = None
  else:
  observables = [expr.name for expr in pysb_model.expressions
  if expr.name in observable_table.index]
@@ -364,7 +366,6 @@ def import_model_pysb(
  noise_distrs = petab_import.petab_noise_distributions_to_amici(
  observable_table)
 
-
  from amici.pysb_import import pysb2amici
  pysb2amici(pysb_model, model_output_dir, verbose=True,
  observables=observables,

python/tests/test_petab_simulate.py

@@ -13,7 +13,7 @@
 def petab_problem() -> petab.Problem:
  """Create a PEtab problem for use in tests."""
  test_case = '0001'
- test_case_dir = Path(petabtests.SBML_DIR) / petabtests.CASES_LIST[0]
+ test_case_dir = Path(petabtests.SBML_DIR) / test_case
  petab_yaml_path = test_case_dir / petabtests.problem_yaml_name(test_case)
  return petab.Problem.from_yaml(str(petab_yaml_path))
 

tests/petab_test_suite/conftest.py

@@ -3,7 +3,7 @@
 from typing import List
 import re
 import sys
-import petabtests
+from petabtests.core import get_cases
 
 
 def parse_selection(selection_str: str) -> List[int]:
@@ -43,22 +43,28 @@ def pytest_generate_tests(metafunc):
  # Run for all PEtab test suite cases
  if "case" in metafunc.fixturenames \
  and "model_type" in metafunc.fixturenames:
+
  # Get CLI option
  cases = metafunc.config.getoption("--petab-cases")
  if cases:
  # Run selected tests
  test_numbers = parse_selection(cases)
  else:
  # Run all tests
- test_numbers = petabtests.CASES_LIST
+ test_numbers = None
 
  if metafunc.config.getoption("--only-sbml"):
- model_types = ['sbml']
+ test_numbers = test_numbers if test_numbers else get_cases("sbml")
+ argvalues = [(case, 'sbml') for case in test_numbers]
+
  elif metafunc.config.getoption("--only-pysb"):
- model_types = ['pysb']
+ test_numbers = test_numbers if test_numbers else get_cases("pysb")
+ argvalues = [(case, 'pysb') for case in test_numbers]
  else:
- model_types = ['sbml', 'pysb']
+ argvalues = []
+ for format in ('sbml', 'pysb'):
+ test_numbers = test_numbers if test_numbers else get_cases(
+ format)
+ argvalues += [(case, format) for case in test_numbers]
 
- argvalues = [(case, model_type) for model_type in model_types
- for case in test_numbers]
  metafunc.parametrize("case,model_type", argvalues)

tests/petab_test_suite/test_petab_suite.py

@@ -3,20 +3,19 @@
 """Run PEtab test suite (https:/PEtab-dev/petab_test_suite)"""
 
 import logging
-import os
 import sys
 
 import amici
 import petab
 import petabtests
 import pytest
 from _pytest.outcomes import Skipped
+from amici import SteadyStateSensitivityMode
 from amici.gradient_check import check_derivatives as amici_check_derivatives
 from amici.logging import get_logger, set_log_level
-from amici.petab_import import import_petab_problem, PysbPetabProblem
-from amici.petab_objective import (
- simulate_petab, rdatas_to_measurement_df, create_parameterized_edatas)
-from amici import SteadyStateSensitivityMode
+from amici.petab_import import PysbPetabProblem, import_petab_problem
+from amici.petab_objective import (create_parameterized_edatas,
+ rdatas_to_measurement_df, simulate_petab)
 
 logger = get_logger(__name__, logging.DEBUG)
 set_log_level(get_logger("amici.petab_import"), logging.DEBUG)
@@ -46,17 +45,17 @@ def _test_case(case, model_type):
 
  # load
  if model_type == "sbml":
- case_dir = os.path.join(petabtests.SBML_DIR, case)
+ case_dir = petabtests.SBML_DIR / case
  # import petab problem
- yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
+ yaml_file = case_dir / petabtests.problem_yaml_name(case)
  problem = petab.Problem.from_yaml(yaml_file)
  elif model_type == "pysb":
  import pysb
  pysb.SelfExporter.cleanup()
  pysb.SelfExporter.do_export = True
- case_dir = os.path.join(petabtests.PYSB_DIR, case)
+ case_dir = petabtests.PYSB_DIR / case
  # import petab problem
- yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
+ yaml_file = case_dir / petabtests.problem_yaml_name(case)
  problem = PysbPetabProblem.from_yaml(yaml_file,
  flatten=case.startswith('0006'))
  else:
@@ -152,9 +151,10 @@ def run():
 
  n_success = 0
  n_skipped = 0
- for case in petabtests.CASES_LIST:
+ cases = petabtests.get_cases('sbml')
+ for case in cases:
  try:
- test_case(case)
+ test_case(case, 'sbml')
  n_success += 1
  except Skipped:
  n_skipped += 1
@@ -163,9 +163,9 @@ def run():
  logger.error(f"Case {case} failed.")
  logger.error(e)
 
- logger.info(f"{n_success} / {len(petabtests.CASES_LIST)} successful, "
+ logger.info(f"{n_success} / {len(cases)} successful, "
  f"{n_skipped} skipped")
- if n_success != len(petabtests.CASES_LIST):
+ if n_success != len(cases):
  sys.exit(1)