Fix pandas 2.1.0 FutureWarnings (#226)

Fixes #224 and a bunch of other pandas 2.1.0 FutureWarnings.

Author: dweindl

.flake8

@@ -1,8 +1,12 @@
 [flake8]
 
 extend-ignore =
+    # whitespace before ":", conflicts with black
+    E203
     F403
     F405
+    # line too long, conflicts with black in rare cases
+    E501
 exclude =
     build,
     dist,

petab/calculate.py

@@ -83,7 +83,7 @@ def calculate_residuals_for_table(
     # create residual df as copy of measurement df, change column
     residual_df = measurement_df.copy(deep=True).rename(
         columns={MEASUREMENT: RESIDUAL})
-
+    residual_df[RESIDUAL] = residual_df[RESIDUAL].astype("float64")
     # matching columns
     compared_cols = set(MEASUREMENT_DF_COLS)
     compared_cols -= {MEASUREMENT}

petab/simplify.py

@@ -73,11 +73,11 @@ def condition_parameters_to_parameter_table(problem: Problem):
             continue
 
         series = problem.condition_df[parameter_id]
-        value = petab.to_float_if_float(series[0])
+        value = petab.to_float_if_float(series.iloc[0])
 
         # same value for all conditions and no parametric overrides (str)?
         if isinstance(value, float) and len(series.unique()) == 1:
-            replacements[parameter_id] = series[0]
+            replacements[parameter_id] = series.iloc[0]
 
     if not replacements:
         return

petab/visualize/data_overview.py

@@ -58,6 +58,8 @@ def get_data_per_observable(measurement_df: pd.DataFrame) -> pd.DataFrame:
     """
 
     my_measurements = measurement_df.copy()
+    my_measurements[PREEQUILIBRATION_CONDITION_ID] = my_measurements[PREEQUILIBRATION_CONDITION_ID].astype("object")
+
     index = [SIMULATION_CONDITION_ID]
     if PREEQUILIBRATION_CONDITION_ID in my_measurements:
         my_measurements[PREEQUILIBRATION_CONDITION_ID].fillna('', inplace=True)

petab/visualize/lint.py

@@ -124,6 +124,8 @@ def set_default(column: str, value):
         if column not in vis_df:
             vis_df[column] = value
         elif value is not None:
+            if isinstance(value, str):
+                vis_df[column] = vis_df[column].astype('object')
             vis_df[column].fillna(value, inplace=True)
 
     set_default(C.PLOT_NAME, "")

tests/test_conditions.py

@@ -26,6 +26,7 @@ def test_get_parametric_overrides():
 
     assert conditions.get_parametric_overrides(condition_df) == []
 
+    condition_df['fixedParameter1'] = condition_df['fixedParameter1'].astype("object")
     condition_df.loc[0, 'fixedParameter1'] = 'parameterId'
 
     assert conditions.get_parametric_overrides(condition_df) == ['parameterId']

tests/test_lint.py

@@ -469,7 +469,7 @@ def test_check_parameter_df():
         LOWER_BOUND: [1e-5, 1e-6, 1e-7],
         UPPER_BOUND: [1e5, 1e6, 1e7]
     }).set_index(PARAMETER_ID)
-
+    parameter_df[NOMINAL_VALUE] = parameter_df[NOMINAL_VALUE].astype("object")
     lint.check_parameter_df(df=parameter_df)
 
     # NOMINAL_VALUE empty, for non-estimated parameter

tests/test_petab.py

@@ -24,6 +24,7 @@ def condition_df_2_conditions():
         'fixedParameter1': [1.0, 2.0]
     })
     condition_df.set_index('conditionId', inplace=True)
+    condition_df.fixedParameter1 = condition_df.fixedParameter1.astype("object")
     return condition_df