Merge branch 'main' into goodness_of_fit_fix

Author: plakrisenko

CHANGELOG.md

@@ -3,6 +3,18 @@
 
 ## 0.8 series
 
+### 0.8.2
+
+**Fixes**
+* We now support pandas>=3.0
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/471)
+* Updated to the latest PEtab v2 schema
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/470)
+* Fixed some warnings
+  (by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/475)
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.8.1...v0.8.2
+
 ### 0.8.1
 
 The only change in this release is requiring pandas<3 until we support

petab/__init__.py

@@ -26,7 +26,15 @@ def __getattr__(name):
         return importlib.import_module("petab.v1")
     if name == "v2":
         return importlib.import_module("petab.v2")
-    if name not in ("__path__", "__all__", "__wrapped__"):
+    if name not in (
+        "__path__",
+        "__all__",
+        "__wrapped__",
+        # accessed under pytest
+        "_pytestfixturefunction",
+        "__test__",
+        "__bases__",
+    ):
         warn(
             f"Accessing `petab.{name}` is deprecated and will be removed in "
             f"the next major release. Please use `petab.v1.{name}` instead.",

petab/v2/petab1to2.py

@@ -494,7 +494,7 @@ def update_prior(row):
         if new_prior_type == "log10-normal":
             warnings.warn(
                 f"Prior distribution `{new_prior_type}' for parameter "
-                f"`{row.name}' is not supported in PEtab v2. "
+                f"`{row[v1.C.PARAMETER_ID]}' is not supported in PEtab v2. "
                 "Using `log-normal` instead.",
                 # call to `petab1to2`
                 stacklevel=9,
@@ -504,7 +504,7 @@ def update_prior(row):
         if new_prior_type not in v2.C.PRIOR_DISTRIBUTIONS:
             raise NotImplementedError(
                 f"PEtab v2 does not support prior type `{new_prior_type}' "
-                f"required for parameter `{row.name}'."
+                f"required for parameter `{row[v1.C.PARAMETER_ID]}'."
             )
 
         return new_prior_type

petab/version.py

@@ -1,3 +1,3 @@
 """PEtab library version"""
 
-__version__ = "0.8.1"
+__version__ = "0.8.2"