Add stacklevel to warnings

Make it easier to find out where warnings originate from.
dweindl · May 2, 2024 · 265fe3b · 265fe3b
1 parent 6b05ddd
commit 265fe3b
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Showing 9 changed files with 11 additions and 2 deletions.
diff --git a/python/sdist/amici/logging.py b/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)

diff --git a/python/sdist/amici/parameter_mapping.py b/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__ = [

diff --git a/python/sdist/amici/petab/conditions.py b/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(

diff --git a/python/sdist/amici/petab_import.py b/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

diff --git a/python/sdist/amici/petab_import_pysb.py b/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__ = [

diff --git a/python/sdist/amici/petab_objective.py b/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

diff --git a/python/sdist/amici/petab_simulate.py b/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

diff --git a/python/sdist/amici/petab_util.py b/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__ = [

diff --git a/python/sdist/amici/sbml_import.py b/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()