[TYPING](ALL): Fix typing errors

biobb_dna/backbone/bipopulations.py

@@ -2,6 +2,7 @@
 """Module containing the BIPopulations class and the command line interface."""
 
 import argparse
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -183,7 +184,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -233,7 +234,7 @@ def bipopulations(
         input_epsilC_path: str, input_epsilW_path: str,
         input_zetaC_path: str, input_zetaW_path: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`BIPopulations <dna.backbone.bipopulations.BIPopulations>` class and
     execute the: meth: `launch() <dna.backbone.bipopulations.BIPopulations.launch>` method. """
 

biobb_dna/backbone/canonicalag.py

@@ -2,6 +2,7 @@
 """Module containing the CanonicalAG class and the command line interface."""
 
 import argparse
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -185,7 +186,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -241,7 +242,7 @@ def canonicalag(
         input_alphaC_path: str, input_alphaW_path: str,
         input_gammaC_path: str, input_gammaW_path: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`CanonicalAG <dna.backbone.canonicalag.CanonicalAG>` class and
     execute the: meth: `launch() <dna.backbone.canonicalag.CanonicalAG.launch>` method. """
 

biobb_dna/backbone/puckering.py

@@ -2,6 +2,7 @@
 """Module containing the Puckering class and the command line interface."""
 
 import argparse
+from typing import Optional
 
 import matplotlib.pyplot as plt
 import pandas as pd
@@ -183,7 +184,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -235,7 +236,7 @@ def fix_angles(self, dataset):
 def puckering(
         input_phaseC_path: str, input_phaseW_path: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Puckering <dna.backbone.puckering.Puckering>` class and
     execute the: meth: `launch() <dna.backbone.puckering.Puckering.launch>` method. """
 

biobb_dna/curvesplus/biobb_canal.py

@@ -4,6 +4,7 @@
 import os
 import zipfile
 import argparse
+from typing import Optional
 from pathlib import Path
 
 from biobb_common.generic.biobb_object import BiobbObject
@@ -185,7 +186,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -197,8 +198,8 @@ def launch(self) -> int:
 def biobb_canal(
         input_cda_file: str,
         output_zip_path: str,
-        input_lis_file: str = None,
-        properties: dict = None,
+        input_lis_file: Optional[str] = None,
+        properties: Optional[dict] = None,
         **kwargs) -> int:
     """Create :class:`Canal <biobb_dna.curvesplus.biobb_canal.Canal>` class and
     execute the :meth:`launch() <biobb_dna.curvesplus.biobb_canal.Canal.launch>` method."""

biobb_dna/curvesplus/biobb_canion.py

@@ -4,6 +4,7 @@
 import os
 import zipfile
 import argparse
+from typing import Optional
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -196,7 +197,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -207,7 +208,7 @@ def launch(self) -> int:
 
 def biobb_canion(
         input_cdi_path: str, input_afr_path: str, input_avg_struc_path: str,
-        output_zip_path: str = None, properties: dict = None, **kwargs) -> int:
+        output_zip_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Canion <biobb_dna.curvesplus.biobb_canion.Canion>` class and
     execute the :meth:`launch() <biobb_dna.curvesplus.biobb_canion.Canion.launch>` method."""
 

biobb_dna/curvesplus/biobb_curves.py

@@ -4,6 +4,7 @@
 import os
 import zipfile
 import argparse
+from typing import Optional
 import shutil
 from pathlib import Path
 from biobb_common.generic.biobb_object import BiobbObject
@@ -243,7 +244,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -254,8 +255,8 @@ def launch(self) -> int:
 
 def biobb_curves(
         input_struc_path: str, output_lis_path: str, output_cda_path: str,
-        input_top_path: str = None, output_zip_path: str = None,
-        properties: dict = None, **kwargs) -> int:
+        input_top_path: Optional[str] = None, output_zip_path: Optional[str] = None,
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`Curves <biobb_dna.curvesplus.biobb_curves.Curves>` class and
     execute the :meth:`launch() <biobb_dna.curvesplus.biobb_curves.Curves.launch>` method."""
 

biobb_dna/curvesplus/canal_unzip.py

@@ -5,6 +5,7 @@
 import zipfile
 import shutil
 import argparse
+from typing import Optional
 
 from biobb_common.generic.biobb_object import BiobbObject
 from biobb_common.configuration import settings
@@ -171,7 +172,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -183,8 +184,8 @@ def launch(self) -> int:
 def canal_unzip(
         input_zip_file: str,
         output_path: str,
-        output_list_path: str = None,
-        properties: dict = None,
+        output_list_path: Optional[str] = None,
+        properties: Optional[dict] = None,
         **kwargs) -> int:
     """Create :class:`CanalUnzip <biobb_dna.curvesplus.canal_unzip.CanalUnzip>` class and
     execute the :meth:`launch() <biobb_dna.curvesplus.canal_unzip.CanalUnzip.launch>` method."""

biobb_dna/dna/dna_averages.py

@@ -2,6 +2,7 @@
 
 """Module containing the HelParAverages class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
 
 import matplotlib.pyplot as plt
@@ -205,7 +206,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -216,7 +217,7 @@ def launch(self) -> int:
 
 def dna_averages(
         input_ser_path: str, output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParAverages <dna.dna_averages.HelParAverages>` class and
     execute the :meth:`launch() <dna.dna_averages.HelParAverages.launch>` method."""
 

biobb_dna/dna/dna_bimodality.py

@@ -4,6 +4,7 @@
 import os
 import zipfile
 import argparse
+from typing import Optional
 from pathlib import Path
 
 import pandas as pd
@@ -231,7 +232,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -293,7 +294,7 @@ def helguero_theorem(self, mean1, mean2, var1, var2):
 
 def dna_bimodality(
         input_csv_file, output_csv_path, output_jpg_path,
-        input_zip_file: str = None, properties: dict = None, **kwargs) -> int:
+        input_zip_file: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParBimodality <dna.dna_bimodality.HelParBimodality>` class and
     execute the :meth:`launch() <dna.dna_bimodality.HelParBimodality.launch>` method."""
 

biobb_dna/dna/dna_timeseries.py

@@ -2,6 +2,7 @@
 
 """Module containing the HelParTimeSeries class and the command line interface."""
 import argparse
+from typing import Optional
 import zipfile
 import re
 from pathlib import Path
@@ -263,7 +264,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -274,7 +275,7 @@ def launch(self) -> int:
 
 def dna_timeseries(
         input_ser_path: str, output_zip_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParTimeSeries <dna.dna_timeseries.HelParTimeSeries>` class and
     execute the :meth:`launch() <dna.dna_timeseries.HelParTimeSeries.launch>` method."""
 

biobb_dna/dna/dna_timeseries_unzip.py

@@ -5,6 +5,7 @@
 import zipfile
 import shutil
 import argparse
+from typing import Optional
 
 from biobb_dna.utils import constants
 from biobb_common.generic.biobb_object import BiobbObject
@@ -173,7 +174,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -186,8 +187,8 @@ def dna_timeseries_unzip(
         input_zip_file: str,
         output_path_csv: str,
         output_path_jpg: str,
-        output_list_path: str = None,
-        properties: dict = None,
+        output_list_path: Optional[str] = None,
+        properties: Optional[dict] = None,
         **kwargs) -> int:
     """Create :class:`DnaTimeseriesUnzip <biobb_dna.dna.dna_timeseries_unzip.DnaTimeseriesUnzip>` class and
     execute the :meth:`launch() <biobb_dna.dna.dna_timeseries_unzip.DnaTimeseriesUnzip.launch>` method."""

biobb_dna/interbp_correlations/interbpcorr.py

@@ -2,6 +2,7 @@
 
 """Module containing the InterBasePairCorrelation class and the command line interface."""
 import argparse
+from typing import Optional
 from itertools import product
 
 import numpy as np
@@ -233,7 +234,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
+            self.stage_io_dict.get("unique_dir", ""),
         ])
         self.remove_tmp_files()
 
@@ -270,7 +271,7 @@ def interbpcorr(
         input_filename_rise: str, input_filename_tilt: str,
         input_filename_roll: str, input_filename_twist: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParCorrelation <correlations.interbpcorr.InterBasePairCorrelation>` class and
     execute the :meth:`launch() <correlations.interbpcorr.InterBasePairCorrelation.launch>` method."""
 

biobb_dna/interbp_correlations/interhpcorr.py

@@ -2,6 +2,7 @@
 
 """Module containing the InterHelParCorrelation class and the command line interface."""
 import argparse
+from typing import Optional
 
 import pandas as pd
 import numpy as np
@@ -232,7 +233,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir"),
+            self.stage_io_dict.get("unique_dir", ""),
         ])
         self.remove_tmp_files()
 
@@ -280,7 +281,7 @@ def interhpcorr(
         input_filename_rise: str, input_filename_tilt: str,
         input_filename_roll: str, input_filename_twist: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`InterHelParCorrelation <interbp_correlations.interhpcorr.InterHelParCorrelation>` class and
     execute the :meth:`launch() <interbp_correlations.interhpcorr.InterHelParCorrelation.launch>` method."""
 

biobb_dna/interbp_correlations/interseqcorr.py

@@ -2,6 +2,7 @@
 
 """Module containing the InterSequenceCorrelation class and the command line interface."""
 import argparse
+from typing import Optional
 from pathlib import Path
 
 import numpy as np
@@ -177,7 +178,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -199,7 +200,7 @@ def circular(x1, x2):
 def interseqcorr(
         input_ser_path: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParCorrelation <interbp_correlations.interseqcorr.InterSequenceCorrelation>` class and
     execute the :meth:`launch() <interbp_correlations.interseqcorr.InterSequenceCorrelation.launch>` method."""
 

biobb_dna/intrabp_correlations/intrabpcorr.py

@@ -2,6 +2,7 @@
 
 """Module containing the IntraBasePairCorrelation class and the command line interface."""
 import argparse
+from typing import Optional
 from itertools import product
 
 import numpy as np
@@ -233,7 +234,7 @@ def launch(self) -> int:
 
         # Remove temporary file(s)
         self.tmp_files.extend([
-            self.stage_io_dict.get("unique_dir")
+            self.stage_io_dict.get("unique_dir", "")
         ])
         self.remove_tmp_files()
 
@@ -270,7 +271,7 @@ def intrabpcorr(
         input_filename_stagger: str, input_filename_buckle: str,
         input_filename_propel: str, input_filename_opening: str,
         output_csv_path: str, output_jpg_path: str,
-        properties: dict = None, **kwargs) -> int:
+        properties: Optional[dict] = None, **kwargs) -> int:
     """Create :class:`HelParCorrelation <intrabp_correlations.intrabpcorr.IntraBasePairCorrelation>` class and
     execute the :meth:`launch() <intrabp_correlations.intrabpcorr.IntraBasePairCorrelation.launch>` method."""