Add stacklevel to warnings (#2421)

Make it easier to find out where warnings originate from.

python/sdist/amici/logging.py

@@ -175,7 +175,8 @@ def get_logger(
     elif kwargs:
         warnings.warn(
             "AMICI logger already exists, ignoring keyword "
-            "arguments to setup_logger"
+            "arguments to setup_logger",
+            stacklevel=2,
         )
 
     logger = logging.getLogger(logger_name)

python/sdist/amici/parameter_mapping.py

@@ -27,6 +27,7 @@
 warnings.warn(
     "Importing amici.parameter_mapping is deprecated. Use `amici.petab.parameter_mapping` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/petab/conditions.py

@@ -67,6 +67,7 @@ def fill_in_parameters(
             "The following problem parameters were not used: "
             + str(unused_parameters),
             RuntimeWarning,
+            stacklevel=2,
         )
 
     for edata, mapping_for_condition in zip(

python/sdist/amici/petab_import.py

@@ -13,6 +13,7 @@
 warnings.warn(
     "Importing amici.petab_import is deprecated. Use `amici.petab` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.import_helpers import (  # noqa # pylint: disable=unused-import

python/sdist/amici/petab_import_pysb.py

@@ -14,6 +14,7 @@
 warnings.warn(
     "Importing amici.petab_import_pysb is deprecated. Use `amici.petab.pysb_import` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/petab_objective.py

@@ -12,6 +12,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.simulations` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.conditions import fill_in_parameters  # noqa: F401

python/sdist/amici/petab_simulate.py

@@ -11,6 +11,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.simulator` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 from .petab.simulator import PetabSimulator  # noqa: F401

python/sdist/amici/petab_util.py

@@ -15,6 +15,7 @@
 warnings.warn(
     f"Importing {__name__} is deprecated. Use `amici.petab.util` instead.",
     DeprecationWarning,
+    stacklevel=2,
 )
 
 __all__ = [

python/sdist/amici/sbml_import.py

@@ -442,7 +442,8 @@ def sbml2amici(
             if not has_clibs:
                 warnings.warn(
                     "AMICI C++ extensions have not been built. "
-                    "Generated model code, but unable to compile."
+                    "Generated model code, but unable to compile.",
+                    stacklevel=2,
                 )
             exporter.compile_model()
 
@@ -1838,7 +1839,8 @@ def _process_event_observables(
                     f'Event observable {eo["name"]} uses `t` in '
                     "it's formula which is not the time variable. "
                     "For the time variable, please use `time` "
-                    "instead!"
+                    "instead!",
+                    stacklevel=1,
                 )
 
         # check for nesting of observables (unsupported)
@@ -2157,7 +2159,8 @@ def _get_conservation_laws_demartino(
                 "Conservation laws for non-constant species in "
                 "combination with parameterized stoichiometric "
                 "coefficients are not currently supported "
-                "and will be turned off."
+                "and will be turned off.",
+                stacklevel=1,
             )
             return []
 
@@ -2234,7 +2237,8 @@ def _get_conservation_laws_rref(
                 "Conservation laws for non-constant species in "
                 "combination with parameterized stoichiometric "
                 "coefficients are not currently supported "
-                "and will be turned off."
+                "and will be turned off.",
+                stacklevel=1,
             )
             return []
 
@@ -3048,7 +3052,8 @@ def _non_const_conservation_laws_supported(sbml_model: sbml.Model) -> bool:
         warnings.warn(
             "Conservation laws for non-constant species in "
             "models with RateRules are currently not supported "
-            "and will be turned off."
+            "and will be turned off.",
+            stacklevel=1,
         )
         return False
 
@@ -3060,7 +3065,8 @@ def _non_const_conservation_laws_supported(sbml_model: sbml.Model) -> bool:
         warnings.warn(
             "Conservation laws for non-constant species in "
             "models with Species-AssignmentRules are currently not "
-            "supported and will be turned off."
+            "supported and will be turned off.",
+            stacklevel=1,
         )
         return False
 

python/sdist/amici/swig_wrappers.py

@@ -78,7 +78,8 @@ def runAmiciSimulation(
         warnings.warn(
             "Adjoint sensitivity analysis for models with discontinuous right hand sides (events/piecewise functions) has not been thoroughly tested."
             "Sensitivities might be wrong. Tracked at https://github.com/AMICI-dev/AMICI/issues/18. "
-            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients."
+            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients.",
+            stacklevel=1,
         )
 
     with _capture_cstdout():
@@ -119,7 +120,8 @@ def runAmiciSimulations(
         warnings.warn(
             "Adjoint sensitivity analysis for models with discontinuous right hand sides (events/piecewise functions) has not been thoroughly tested. "
             "Sensitivities might be wrong. Tracked at https://github.com/AMICI-dev/AMICI/issues/18. "
-            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients."
+            "Adjoint sensitivity analysis may work if the location of the discontinuity is not parameter-dependent, but we still recommend testing accuracy of gradients.",
+            stacklevel=1,
         )
 
     with _capture_cstdout():

python/sdist/pyproject.toml

@@ -130,4 +130,5 @@ line-length = 79
 extend-include = ["*.ipynb"]
 
 [tool.ruff.lint]
+extend-select = ["B028"]
 ignore = ["E402", "F403", "F405", "E741"]