Merge pull request #1827 from AMICI-dev/release_0.11.31

Release 0.11.31

CHANGELOG.md

@@ -2,6 +2,13 @@
 
 ## v0.X Series
 
+### v0.11.31 (2022-07-12)
+
+Fixes:
+* Fixed `ParameterMapping.__getitem__` to either return a
+  `ParameterMappingForCondition` or a new `ParameterMapping`, but not a list
+  by @dweindl in https://github.com/AMICI-dev/AMICI/pull/1826
+
 ### v0.11.30 (2022-07-07)
 
 Features:

python/amici/parameter_mapping.py

@@ -13,7 +13,7 @@
 for usage together with PEtab, for which the whole workflow of generating
 the mapping is automatized.
 """
-
+from __future__ import annotations
 
 import numbers
 import warnings
@@ -136,8 +136,13 @@ def __init__(
     def __iter__(self):
         yield from self.parameter_mappings
 
-    def __getitem__(self, item):
-        return self.parameter_mappings[item]
+    def __getitem__(
+            self, item
+    ) -> Union[ParameterMapping, ParameterMappingForCondition]:
+        result = self.parameter_mappings[item]
+        if isinstance(result, ParameterMappingForCondition):
+            return result
+        return ParameterMapping(result)
 
     def __len__(self):
         return len(self.parameter_mappings)

python/tests/test_parameter_mapping.py

@@ -55,3 +55,6 @@ def test_parameter_mapping():
     parameter_mapping.append(par_map_for_condition)
 
     assert len(parameter_mapping) == 1
+
+    assert isinstance(parameter_mapping[0], ParameterMappingForCondition)
+    assert isinstance(parameter_mapping[:], ParameterMapping)

tests/benchmark-models/test_petab_model.py

@@ -3,8 +3,8 @@
 """
 Simulate a PEtab problem and compare results to reference values
 """
-
 import argparse
+import contextlib
 import importlib
 import logging
 import os
@@ -15,7 +15,7 @@
 from amici.logging import get_logger
 from amici.petab_objective import (simulate_petab, rdatas_to_measurement_df,
                                    LLH, RDATAS)
-from petab.visualize import plot_petab_problem
+from petab.visualize import plot_problem
 
 logger = get_logger(f"amici.{__name__}", logging.WARNING)
 
@@ -56,9 +56,7 @@ def parse_cli_args():
                         help='File to write simulation result to, in PEtab'
                         'measurement table format.')
 
-    args = parser.parse_args()
-
-    return args
+    return parser.parse_args()
 
 
 def main():
@@ -103,21 +101,17 @@ def main():
         sim_df.to_csv(index=False, sep="\t")
 
     if args.plot:
-        try:
+        with contextlib.suppress(NotImplementedError):
             # visualize fit
-            axs = plot_petab_problem(petab_problem=problem, sim_data=sim_df)
+            axs = plot_problem(petab_problem=problem, simulations_df=sim_df)
 
             # save figure
             for plot_id, ax in axs.items():
                 fig_path = os.path.join(args.model_directory,
-                                        args.model_name + "_" + plot_id
-                                        + "_vis.png")
+                                        f"{args.model_name}_{plot_id}_vis.png")
                 logger.info(f"Saving figure to {fig_path}")
                 ax.get_figure().savefig(fig_path, dpi=150)
 
-        except NotImplementedError:
-            pass
-
     if args.check:
         references_yaml = os.path.join(os.path.dirname(__file__),
                                        "benchmark_models.yaml")

version.txt

@@ -1 +1 @@
-0.11.30
+0.11.31