Use utf-8 encoding when writing csv files (#79)

and add a test case

Closes #77

Author: dweindl

petab/conditions.py

@@ -51,8 +51,7 @@ def write_condition_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab condition table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=True)
+    df.to_csv(filename, sep='\t', index=True)
 
 
 def create_condition_df(parameter_ids: Iterable[str],

petab/core.py

@@ -40,8 +40,7 @@ def write_simulation_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab simulation table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=False)
+    df.to_csv(filename, sep='\t', index=False)
 
 
 def get_visualization_df(visualization_file: str) -> pd.DataFrame:
@@ -70,8 +69,7 @@ def write_visualization_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab visualization table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=False)
+    df.to_csv(filename, sep='\t', index=False)
 
 
 def get_notnull_columns(df: pd.DataFrame, candidates: Iterable):

petab/measurements.py

@@ -57,8 +57,7 @@ def write_measurement_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab measurement table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=False)
+    df.to_csv(filename, sep='\t', index=False)
 
 
 def get_noise_distributions(measurement_df: pd.DataFrame) -> dict:

petab/observables.py

@@ -60,8 +60,7 @@ def write_observable_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab observable table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=True)
+    df.to_csv(filename, sep='\t', index=True)
 
 
 def get_output_parameters(

petab/parameters.py

@@ -89,8 +89,7 @@ def write_parameter_df(df: pd.DataFrame, filename: str) -> None:
         df: PEtab parameter table
         filename: Destination file name
     """
-    with open(filename, 'w') as fh:
-        df.to_csv(fh, sep='\t', index=True)
+    df.to_csv(filename, sep='\t', index=True)
 
 
 def get_optimization_parameters(parameter_df: pd.DataFrame) -> List[str]:

tests/test_parameters.py

@@ -112,7 +112,8 @@ def test_write_parameter_df():
     """Test parameters.write_parameter_df."""
     parameter_df = pd.DataFrame(data={
         PARAMETER_ID: ['par1', 'par2'],
-        PARAMETER_NAME: ['parname1', 'parname2'],
+        # Test utf8 characters
+        PARAMETER_NAME: ['ɑ', 'β'],
     }).set_index(PARAMETER_ID)
 
     with tempfile.NamedTemporaryFile(mode='w', delete=True) as fh: