Use pathlib.Path instead of str for files

I've only recently discovered that a pathlib.Path is not just the
directory, it can also be a file.

Author: php1ic

pynch/ame_mass_parse.py

@@ -1,5 +1,6 @@
 """Extract the data from the AME mass file."""
 import logging
+import pathlib
 
 import pandas as pd
 
@@ -12,7 +13,7 @@ class AMEMassParser(AMEMassFile):
     The format is known but I don't think python can easily parse it.
     """
 
-    def __init__(self, filename: str, year: int):
+    def __init__(self, filename: pathlib.Path, year: int):
         """Set the file to read and table year."""
         self.filename = filename
         self.year = year

pynch/ame_reaction_1_parse.py

@@ -1,5 +1,6 @@
 """Extract the data from the first reaction file."""
 import logging
+import pathlib
 
 import pandas as pd
 
@@ -12,7 +13,7 @@ class AMEReactionParserOne(AMEReactionFileOne):
     The format is known but I don't think python can easily parse it.
     """
 
-    def __init__(self, filename: str, year: int):
+    def __init__(self, filename: pathlib.Path, year: int):
         """Set the file to read and table year."""
         self.filename = filename
         self.year = year

pynch/ame_reaction_2_parse.py

@@ -1,5 +1,6 @@
 """Extract the date from the second reaction file."""
 import logging
+import pathlib
 
 import pandas as pd
 
@@ -12,7 +13,7 @@ class AMEReactionParserTwo(AMEReactionFileTwo):
     The format is known but I don't think python can easily parse it.
     """
 
-    def __init__(self, filename: str, year: int):
+    def __init__(self, filename: pathlib.Path, year: int):
         """Set the file to read and table year."""
         self.filename = filename
         self.year = year

pynch/mass_table.py

@@ -27,7 +27,7 @@ def __init__(self):
         self.full_data = self._combine_all_data()
         self._do_indexing()
 
-    def _get_nubase_datafile(self, year: int) -> str:
+    def _get_nubase_datafile(self, year: int) -> pathlib.Path:
         """Use the given year to locate the nubase mass table file and return the absolute path."""
         nubase_mass = self.data_path / pathlib.Path(str(year))
         nubase_mass = nubase_mass.resolve()
@@ -38,12 +38,12 @@ def _get_nubase_datafile(self, year: int) -> str:
             nubase_mass = nubase_mass / "nubtab12.asc"
         elif year == 2016:
             nubase_mass = nubase_mass / "nubase2016.txt"
-        elif year == 2020:
+        else:  # year == 2020:
             nubase_mass = nubase_mass / "nubase_1.mas20"
 
         return nubase_mass
 
-    def _get_ame_datafiles(self, year: int) -> typing.Tuple[str, str, str]:
+    def _get_ame_datafiles(self, year: int) -> typing.Tuple[pathlib.Path, pathlib.Path, pathlib.Path]:
         """Use the given year to locate the 3 AME data file and return the absolute path."""
         data_dir = self.data_path / pathlib.Path(str(year))
         data_dir = data_dir.resolve()
@@ -60,7 +60,7 @@ def _get_ame_datafiles(self, year: int) -> typing.Tuple[str, str, str]:
             ame_mass = data_dir / "mass16.txt"
             ame_reaction_1 = data_dir / "rct1-16.txt"
             ame_reaction_2 = data_dir / "rct2-16.txt"
-        elif year == 2020:
+        else:  # year == 2020:
             ame_mass = data_dir / "mass.mas20"
             ame_reaction_1 = data_dir / "rct1.mas20"
             ame_reaction_2 = data_dir / "rct2.mas20"
@@ -107,7 +107,7 @@ def _combine_all_data(self) -> pd.DataFrame:
         df.loc[(df.Symbol == "C") & (df.A == 12), "NubaseRelativeError"] = 0.0
         df.loc[(df.Symbol == "C") & (df.A == 12), "AMERelativeError"] = 0.0
 
-        # 198Au has a typo in it's decay mode in the 2012 table. It is down as '-'
+        # 198Au has a typo in it's decay mode in the 2012 table. It is recorded as '-'
         df.loc[(df.A == 198) & (df.Z == 79) & (df.TableYear == 2012), 'Decay'] = "B-"
 
         return df

pynch/nubase_parse.py

@@ -1,5 +1,6 @@
 """Extract the data from the nubse file."""
 import logging
+import pathlib
 import re
 import typing
 
@@ -14,7 +15,7 @@ class NubaseParser(NubaseFile):
     A collection of functions to parse the weird format of the NUBASE file.
     """
 
-    def __init__(self, filename: str, year: int):
+    def __init__(self, filename: pathlib.Path, year: int):
         """Set the file to read and the table year."""
         self.filename = filename
         self.year = year