Create output directories in write_*

Author: dweindl

petab/v1/conditions.py

@@ -60,9 +60,11 @@ def write_condition_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab condition table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_condition_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 

petab/v1/core.py

@@ -60,8 +60,10 @@ def write_simulation_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab simulation table
-        filename: Destination file name
+        filename: Destination file name. The parent directory will be created
+            if necessary.
     """
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)
 
 

petab/v1/mapping.py

@@ -60,9 +60,11 @@ def write_mapping_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab mapping table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_mapping_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 

petab/v1/measurements.py

@@ -58,9 +58,11 @@ def write_measurement_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab measurement table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_measurement_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)
 
 

petab/v1/observables.py

@@ -67,9 +67,11 @@ def write_observable_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab observable table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_observable_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 

petab/v1/parameters.py

@@ -112,9 +112,11 @@ def write_parameter_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab parameter table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_parameter_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=True)
 
 

petab/v1/yaml.py

@@ -238,8 +238,9 @@ def write_yaml(yaml_config: dict[str, Any], filename: str | Path) -> None:
 
     Arguments:
         yaml_config: Data to write
-        filename: File to create
+        filename: File to create. Parent directories are created if necessary.
     """
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     with open(filename, "w") as outfile:
         yaml.dump(
             yaml_config, outfile, default_flow_style=False, sort_keys=False

petab/v2/experiments.py

@@ -34,7 +34,9 @@ def write_experiment_df(df: pd.DataFrame, filename: str | Path) -> None:
 
     Arguments:
         df: PEtab experiments table
-        filename: Destination file name
+        filename: Destination file name. Parent directories are created if
+            necessary.
     """
     df = get_experiment_df(df)
+    Path(filename).parent.mkdir(parents=True, exist_ok=True)
     df.to_csv(filename, sep="\t", index=False)