Merge pull request #609 from ICB-DCM/develop

Release 0.12.11

Author: yannikschaelte

CHANGELOG.rst

@@ -8,6 +8,16 @@ Release Notes
 ...........
 
 
+0.12.11 (2023-07-06)
+--------------------
+
+Fixes (#608)
+
+* Fix petab test suite (different name resolution)
+* Fix LocalTransition (pandas -> numpy argument)
+* Fix sklearn intersphinx
+
+
 0.12.10 (2023-05-09)
 --------------------
 

doc/conf.py

@@ -71,6 +71,7 @@
     'pandas': ('https://pandas.pydata.org/pandas-docs/dev', None),
     'petab': ('https://petab.readthedocs.io/en/stable/', None),
     'amici': ('https://amici.readthedocs.io/en/latest/', None),
+    "sklearn": ("https://scikit-learn.org/stable/", None),
 }
 
 

pyabc/transition/local_transition.py

@@ -84,8 +84,8 @@ def fit(self, X, w):
             raise NotEnoughParticles("Fitting not possible.")
         self.X_arr = X.values
 
-        ctree = cKDTree(X)
-        _, indices = ctree.query(X, k=min(self.k + 1, X.shape[0]))
+        ctree = cKDTree(self.X_arr)
+        _, indices = ctree.query(self.X_arr, k=min(self.k + 1, X.shape[0]))
 
         covs, inv_covs, dets = list(
             zip(*[self._cov_and_inv(n, indices) for n in range(X.shape[0])])

pyabc/version.py

@@ -1 +1 @@
-__version__ = '0.12.10'
+__version__ = '0.12.11'

setup.cfg

@@ -93,9 +93,9 @@ copasi =
 ot =
     pot >= 0.7.0
 petab =
-    petab >= 0.1.18
+    petab >= 0.2.0
 amici =
-    amici >= 0.11.19
+    amici >= 0.18.0
 yaml2sbml =
     yaml2sbml >= 0.2.1
 migrate =

test/petab/test_petab_suite.py

@@ -1,7 +1,6 @@
 """Execute petab test suite."""
 
 import logging
-import os
 import sys
 
 import petabtests
@@ -22,8 +21,11 @@
 logging.basicConfig(level=logging.INFO)
 logger = logging.getLogger(__name__)
 
+MODEL_TYPE = "sbml"
+PETAB_VERSION = "v1.0.0"
 
-@pytest.fixture(params=petabtests.CASES_LIST)
+
+@pytest.fixture(params=petabtests.get_cases(MODEL_TYPE, version=PETAB_VERSION))
 def case(request):
     """A single test case."""
     return request.param
@@ -63,11 +65,10 @@ def _execute_case(case):
     case = petabtests.test_id_str(case)
     logger.info(f"Case {case}")
 
-    # case folder
-    case_dir = os.path.join(petabtests.CASES_DIR, case)
-
     # load solution
-    solution = petabtests.load_solution(case, format='sbml')
+    solution = petabtests.load_solution(
+        case, format=MODEL_TYPE, version=PETAB_VERSION
+    )
     gt_chi2 = solution[petabtests.CHI2]
     gt_llh = solution[petabtests.LLH]
     gt_simulation_dfs = solution[petabtests.SIMULATION_DFS]
@@ -79,16 +80,23 @@ def _execute_case(case):
     output_folder = f'amici_models/model_{case}'
 
     # import petab problem
-    yaml_file = os.path.join(case_dir, petabtests.problem_yaml_name(case))
+    case_dir = petabtests.get_case_dir(case, MODEL_TYPE, PETAB_VERSION)
+    yaml_file = case_dir / petabtests.problem_yaml_name(case)
 
     # create problem
     petab_problem = petab.Problem.from_yaml(yaml_file)
 
     # compile amici
     if output_folder not in sys.path:
         sys.path.insert(0, output_folder)
+
+    # use distinct model IDs for each test case since we cannot import different
+    # models with the same name in a single python session
+    model_name = f"petab_{MODEL_TYPE}_test_case_{case}_{PETAB_VERSION.replace('.', '_')}"
+
     amici_model = amici.petab_import.import_petab_problem(
         petab_problem=petab_problem,
+        model_name=model_name,
         model_output_dir=output_folder,
         generate_sensitivity_code=False,
     )