Fix flake8 warnings

Two files each have one line that's too long but they are for a string
and variable name so will leave for the moment.

Author: php1ic

.flake8

@@ -1,4 +1,7 @@
 [flake8]
+ignore =
+    # I'm not always in an imperative mood
+    D401
 exclude = tests,.git,__pycache__
 max-line-length = 120
 count = True

app.py

@@ -1,8 +1,12 @@
+"""dsfds."""
 import dash
+from dash.dependencies import Input, Output
+
+import dash_bootstrap_components as dbc
+
 import dash_core_components as dcc
+
 import dash_html_components as html
-import dash_bootstrap_components as dbc
-from dash.dependencies import Input, Output
 
 import plotly.express as px
 
@@ -34,7 +38,7 @@
     ],
 )
 def update_graph(y_var, x_value, year):
-
+    """The actions to do when the selected data is changed."""
     df_f = df.loc[table_years[year]][["Symbol", "Decay", "A", "Z", "N", y_var]]
     df_ff = df_f.loc[(df_f["A"] == x_value)]
 
@@ -75,19 +79,19 @@ def update_graph(y_var, x_value, year):
 
     title = html.H2(f"A = {x_value}")
 
-    minA = df_f["A"].min()
-    maxA = df_f["A"].max()
+    min_a = df_f["A"].min()
+    max_a = df_f["A"].max()
 
-    marksA = {i: f"{i}" for i in range(20, maxA, 20)}
+    marks_a = {i: f"{i}" for i in range(20, max_a, 20)}
 
     return (
         title,
         a_fig,
         z_fig.update_traces(mode="lines+markers"),
         n_fig.update_traces(mode="lines+markers"),
-        minA,
-        maxA,
-        marksA,
+        min_a,
+        max_a,
+        marks_a,
     )
 
 
@@ -144,8 +148,7 @@ def update_graph(y_var, x_value, year):
 
 
 def main():
-    """
-    """
+    """For testing."""
 
     # df = MassData().full_data
     # print(df)

pynch/__init__.py

@@ -0,0 +1 @@
+"""May not actually be needed."""

pynch/ame_mass_file.py

@@ -1,13 +1,12 @@
+"""Storage for variable line positions."""
 from pynch.parse import Parse
 
 
 class AMEMassFile(Parse):
-    """Easy access to where the variables are in the AME mass file
-
-    The AME mass file
-    """
+    """Easy access to where the variables are in the AME mass file."""
 
     def __init__(self):
+        """Setup up the values."""
         super(AMEMassFile, self).__init__()
         self.START_A = 16
         self.END_A = 19

pynch/ame_mass_parse.py

@@ -1,24 +1,24 @@
+"""Extract the data from the AME mass file."""
 import pandas as pd
 
 from pynch.ame_mass_file import AMEMassFile
 
 
 class AMEMassParser(AMEMassFile):
-    """Parse the AME mass file
+    """Parse the AME mass file.
 
     The format is known but I don't think python can easily parse it.
     """
 
     def __init__(self, filename: str, year: int):
+        """Set the file to read and table year."""
         super().__init__()
         self.filename = filename
         self.year = year
         print(f"Reading {self.filename} from {self.year}")
 
     def _read_line(self, line: str) -> dict:
-        """
-        Read a line from the file
-        """
+        """Read a line from the file."""
         if line.find("#") != -1:
             line = line.replace("#", " ")
 
@@ -43,9 +43,7 @@ def _read_line(self, line: str) -> dict:
         return data
 
     def read_file(self) -> pd.DataFrame:
-        """
-        Read the file
-        """
+        """Read the file."""
         with open(self.filename, "r") as f:
             lines = [line.rstrip() for line in f]
 

pynch/ame_reaction_1_file.py

@@ -1,14 +1,13 @@
+"""Storage for the variable line positions."""
 from pynch.parse import Parse
 
 
-class AMEReactionFile_1(Parse):
-    """Easy access to where the variables are in the first AME reaction file
-
-    The AME first reaction file
-    """
+class AMEReactionFileOne(Parse):
+    """Easy access to where the variables are in the first AME reaction file."""
 
     def __init__(self):
-        super(AMEReactionFile_1, self).__init__()
+        """Setup the values that locate the variable."""
+        super(AMEReactionFileOne, self).__init__()
         self.START_R1_A = 1
         self.END_R1_A = 4
         self.START_R1_Z = 8

pynch/ame_reaction_1_parse.py

@@ -1,24 +1,24 @@
+"""Extract the data from the first reaction file."""
 import pandas as pd
 
-from pynch.ame_reaction_1_file import AMEReactionFile_1
+from pynch.ame_reaction_1_file import AMEReactionFileOne
 
 
-class AMEReactionParser_1(AMEReactionFile_1):
-    """ Parse the first AME reaction file
+class AMEReactionParserOne(AMEReactionFileOne):
+    """Parse the first AME reaction file.
 
     The format is known but I don't think python can easily parse it.
     """
 
     def __init__(self, filename: str, year: int):
+        """Set the file to read and table year."""
         super().__init__()
         self.filename = filename
         self.year = year
         print(f"Reading {self.filename} from {self.year}")
 
     def _read_line(self, line: str) -> dict:
-        """
-        Read a line from the file
-        """
+        """Read a line from the file."""
         # Don't use a '#' as an experimental marker in this file
         # but still need to remove it
         if line.find("#") != -1:
@@ -51,9 +51,7 @@ def _read_line(self, line: str) -> dict:
         return data
 
     def read_file(self) -> pd.DataFrame:
-        """
-        Read the file
-        """
+        """Read the file."""
         with open(self.filename, "r") as f:
             lines = [line.rstrip() for line in f]
 

pynch/ame_reaction_2_file.py

@@ -1,14 +1,13 @@
+"""Storage for the variable line positions."""
 from pynch.parse import Parse
 
 
-class AMEReactionFile_2(Parse):
-    """Easy access to where the variables are in the second AME reaction file
-
-    The second AME reaction file
-    """
+class AMEReactionFileTwo(Parse):
+    """Easy access to where the variables are in the second AME reaction file."""
 
     def __init__(self):
-        super(AMEReactionFile_2, self).__init__()
+        """Setup the values that locate the variables."""
+        super(AMEReactionFileTwo, self).__init__()
         self.START_R2_A = 1
         self.END_R2_A = 4
         self.START_R2_Z = 8

pynch/ame_reaction_2_parse.py

@@ -1,24 +1,24 @@
+"""Extract the date from the second reaction file."""
 import pandas as pd
 
-from pynch.ame_reaction_2_file import AMEReactionFile_2
+from pynch.ame_reaction_2_file import AMEReactionFileTwo
 
 
-class AMEReactionParser_2(AMEReactionFile_2):
-    """Parse the second AME reaction file
+class AMEReactionParserTwo(AMEReactionFileTwo):
+    """Parse the second AME reaction file.
 
     The format is known but I don't think python can easily parse it.
     """
 
     def __init__(self, filename: str, year: int):
+        """Set the file to read and table year."""
         super().__init__()
         self.filename = filename
         self.year = year
         print(f"Reading {self.filename} from {self.year}")
 
     def _read_line(self, line: str) -> dict:
-        """
-        Read a line from the file
-        """
+        """Read a line from the file."""
         # Don't use a '#' as an experimental marker in this file
         # but still need to remove it
         if line.find("#") != -1:
@@ -51,9 +51,7 @@ def _read_line(self, line: str) -> dict:
         return data
 
     def read_file(self) -> pd.DataFrame:
-        """
-        Read the file
-        """
+        """Read the file."""
         with open(self.filename, "r") as f:
             lines = [line.rstrip() for line in f]
 

pynch/mass_table.py

@@ -1,20 +1,23 @@
-import pandas as pd
+"""Functionality to parse all data file into a single object."""
 import pathlib
 import typing
 
-from pynch.nubase_parse import NubaseParser
+import pandas as pd
+
 from pynch.ame_mass_parse import AMEMassParser
-from pynch.ame_reaction_1_parse import AMEReactionParser_1
-from pynch.ame_reaction_2_parse import AMEReactionParser_2
+from pynch.ame_reaction_1_parse import AMEReactionParserOne
+from pynch.ame_reaction_2_parse import AMEReactionParserTwo
+from pynch.nubase_parse import NubaseParser
 
 
 class MassTable:
-    """Storage class for all of the mass data
+    """Storage class for all of the mass data.
 
-    Internally there are separate dataframes for the NUBASE and AME data
+    Internally there are separate dataframes for the NUBASE and AME data as well as a combined one for all data
     """
 
     def __init__(self):
+        """Do all of the work at construction."""
         # Assume this file is some/path/pynch/pynch/mass_table.py
         self.data_path = pathlib.Path(__file__) / ".." / ".." / "data"
         self.existing_years = [2003, 2012, 2016]
@@ -24,9 +27,7 @@ def __init__(self):
         self._do_indexing()
 
     def _get_nubase_datafile(self, year: int) -> str:
-        """
-        Use the given year to locate the nubase mass table file and return the absolute 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()
 
@@ -40,9 +41,7 @@ def _get_nubase_datafile(self, year: int) -> str:
         return nubase_mass
 
     def _get_ame_datafiles(self, year: int) -> typing.Tuple[str, str, str]:
-        """
-        Use the given year to locate the 3 AME data file and return the absolute 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()
 
@@ -62,40 +61,32 @@ def _get_ame_datafiles(self, year: int) -> typing.Tuple[str, str, str]:
         return ame_mass, ame_reaction_1, ame_reaction_2
 
     def _validate_year(self, year: int) -> None:
-        """
-        Point the appropriate variables at the required data files for the table year
-        """
+        """Point the appropriate variables at the required data files for the table year."""
         if year not in self.existing_years:
             print(f"WARNING: {year} not a valid table year, using {self.existing_years[-1]}")
             year = self.existing_years[-1]
 
         return year
 
     def _parse_nubase_data(self, year: int) -> pd.DataFrame:
-        """
-        Get the nubase for the given year as a pandas.DataFrame.
-        """
+        """Get the nubase for the given year as a pandas.DataFrame."""
         year = self._validate_year(year)
         return NubaseParser(self._get_nubase_datafile(year), year).read_file()
 
     def _parse_ame_data(self, year: int) -> pd.DataFrame:
-        """
-        Combine all the AME files from the given year into a pandas.DataFrame.
-        """
+        """Combine all the AME files from the given year into a pandas.DataFrame."""
         year = self._validate_year(year)
         ame_mass, ame_reaction_1, ame_reaction_2 = self._get_ame_datafiles(year)
 
         ame_mass_df = AMEMassParser(ame_mass, year).read_file()
 
         # Merge all 3 of the AME files/data frames into one
         common_columns = ['A', 'Z', 'N', 'TableYear', 'Symbol']
-        temp_df = ame_mass_df.merge(AMEReactionParser_1(ame_reaction_1, year).read_file(), on=common_columns)
-        return temp_df.merge(AMEReactionParser_2(ame_reaction_2, year).read_file(), on=common_columns)
+        temp_df = ame_mass_df.merge(AMEReactionParserOne(ame_reaction_1, year).read_file(), on=common_columns)
+        return temp_df.merge(AMEReactionParserTwo(ame_reaction_2, year).read_file(), on=common_columns)
 
     def _combine_all_data(self) -> pd.DataFrame:
-        """
-        Combine all NUBASE and AME data into a single pandas DataFrame
-        """
+        """Combine all NUBASE and AME data into a single pandas DataFrame."""
         common_columns = ['A', 'Z', 'N', 'TableYear', 'Symbol']
         return self.nubase.merge(self.ame, on=common_columns)
 

pynch/nubase_file.py

@@ -1,8 +1,9 @@
+"""Storage for the variable line positions."""
 from pynch.parse import Parse
 
 
 class NubaseFile(Parse):
-    """Easy access to where variables are in the NUBASE file
+    """Easy access to where variables are in the NUBASE file.
 
     The NUBASE data file is formatted by location in the line, values exist
     between 2 specific columns in the line. Store the start and end locations
@@ -11,6 +12,7 @@ class NubaseFile(Parse):
     """
 
     def __init__(self):
+        """Setup the values that locate the variable."""
         super(NubaseFile, self).__init__()
         self.START_A = 0
         self.END_A = 3