Merge branch 'main' into develop

Author: dweindl

CHANGELOG.md

@@ -2,6 +2,19 @@
 
 ## 0.2 series
 
+### 0.2.4
+
+* Made figure sizes for visualization functions customizable via `petab.visualize.plotting.DEFAULT_FIGSIZE`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/222
+* Fixed Handling missing `nominalValue` in `Problem.get_x_nominal`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/223
+* Fixed pandas 2.1.0 `FutureWarnings`
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/226
+* Added pre-commit-config, ran black, isort, ...
+  by @dweindl in https://github.com/PEtab-dev/libpetab-python/pull/225
+
+**Full Changelog**: https://github.com/PEtab-dev/libpetab-python/compare/v0.2.3...v0.2.4
+
 ### 0.2.3
 
 * Fixed validation failures in case of missing optional fields in visualization tables

doc/conf.py

@@ -20,7 +20,7 @@
 # -- Project information -----------------------------------------------------
 
 project = "libpetab-python"
-copyright = "2018, the PEtab developers"
+copyright = "2018-2023, the PEtab developers"
 author = "PEtab developers"
 
 # The full version, including alpha/beta/rc tags

petab/core.py

@@ -70,15 +70,25 @@ def write_simulation_df(df: pd.DataFrame, filename: Union[str, Path]) -> None:
     df.to_csv(filename, sep="\t", index=False)
 
 
-def get_visualization_df(visualization_file: Union[str, Path]) -> pd.DataFrame:
+def get_visualization_df(
+        visualization_file: Union[str, Path, pd.DataFrame, None]
+) -> Union[pd.DataFrame, None]:
     """Read PEtab visualization table
 
     Arguments:
-        visualization_file: URL or filename of PEtab visualization table
+        visualization_file:
+            URL or filename of PEtab visualization table to read from,
+            or a DataFrame or None that will be returned as is.
 
     Returns:
         Visualization DataFrame
     """
+    if visualization_file is None:
+        return None
+
+    if isinstance(visualization_file, pd.DataFrame):
+        return visualization_file
+
     try:
         types = {PLOT_NAME: str}
         vis_spec = pd.read_csv(

petab/version.py

@@ -1,2 +1,2 @@
 """PEtab library version"""
-__version__ = "0.2.3"
+__version__ = "0.2.4"