Table getters: drop pre-existing table index unless it matches the PEtab format (#262)

Author: dilpath

petab/conditions.py

@@ -40,7 +40,10 @@ def get_condition_df(
     )
 
     if not isinstance(condition_file.index, pd.RangeIndex):
-        condition_file.reset_index(inplace=True)
+        condition_file.reset_index(
+            drop=condition_file.index.name != CONDITION_ID,
+            inplace=True,
+        )
 
     try:
         condition_file.set_index([CONDITION_ID], inplace=True)

petab/mapping.py

@@ -36,7 +36,10 @@ def get_mapping_df(
         )
 
     if not isinstance(mapping_file.index, pd.RangeIndex):
-        mapping_file.reset_index(inplace=True)
+        mapping_file.reset_index(
+            drop=mapping_file.index.name != PETAB_ENTITY_ID,
+            inplace=True,
+        )
 
     for col in MAPPING_DF_REQUIRED_COLS:
         if col not in mapping_file.columns:

petab/observables.py

@@ -47,7 +47,10 @@ def get_observable_df(
     )
 
     if not isinstance(observable_file.index, pd.RangeIndex):
-        observable_file.reset_index(inplace=True)
+        observable_file.reset_index(
+            drop=observable_file.index.name != OBSERVABLE_ID,
+            inplace=True,
+        )
 
     try:
         observable_file.set_index([OBSERVABLE_ID], inplace=True)

petab/parameters.py

@@ -82,7 +82,10 @@ def get_parameter_df(
     )
 
     if not isinstance(parameter_df.index, pd.RangeIndex):
-        parameter_df.reset_index(inplace=True)
+        parameter_df.reset_index(
+            drop=parameter_file.index.name != PARAMETER_ID,
+            inplace=True,
+        )
 
     try:
         parameter_df.set_index([PARAMETER_ID], inplace=True)